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Schadt C, Martin S, Carrell A, Fortner A, Hopp D, Jacobson D, Klingeman D, Kristy B, Phillips J, Piatkowski B, Miller MA, Smith M, Patil S, Flynn M, Canon S, Clum A, Mungall CJ, Pennacchio C, Bowen B, Louie K, Northen T, Eloe-Fadrosh EA, Mayes MA, Muchero W, Weston DJ, Mitchell J, Doktycz M. An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments. Sci Data 2024; 11:339. [PMID: 38580669 PMCID: PMC10997577 DOI: 10.1038/s41597-024-03069-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/13/2024] [Indexed: 04/07/2024] Open
Abstract
Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.
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Affiliation(s)
- Christopher Schadt
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
| | - Alyssa Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Allison Fortner
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dan Hopp
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dan Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dawn Klingeman
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Brandon Kristy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jana Phillips
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Division of Computational Biology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Mark A Miller
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Montana Smith
- Pacific Northwest National Laboratory, Richland, WA, 99354, USA
| | - Sujay Patil
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mark Flynn
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Shane Canon
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Alicia Clum
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christopher J Mungall
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Christa Pennacchio
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Benjamin Bowen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine Louie
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Trent Northen
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Melanie A Mayes
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Julie Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mitchel Doktycz
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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2
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Wang Y, Mao J, Brelsford CM, Ricciuto DM, Yuan F, Shi X, Rastogi D, Mayes MM, Kao SC, Warren JM, Griffiths NA, Cheng X, Weston DJ, Zhou Y, Gu L, Thornton PE. Thermal, water, and land cover factors led to contrasting urban and rural vegetation resilience to extreme hot months. PNAS Nexus 2024; 3:pgae147. [PMID: 38638834 PMCID: PMC11026108 DOI: 10.1093/pnasnexus/pgae147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Accepted: 03/28/2024] [Indexed: 04/20/2024]
Abstract
With continuing global warming and urbanization, it is increasingly important to understand the resilience of urban vegetation to extreme high temperatures, but few studies have examined urban vegetation at large scale or both concurrent and delayed responses. In this study, we performed an urban-rural comparison using the Enhanced Vegetation Index and months that exceed the historical 90th percentile in mean temperature (referred to as "hot months") across 85 major cities in the contiguous United States. We found that hot months initially enhanced vegetation greenness but could cause a decline afterwards, especially for persistent (≥4 months) and intense (≥+2 °C) episodes in summer. The urban responses were more positive than rural in the western United States or in winter, but more negative during spring-autumn in the eastern United States. The east-west difference can be attributed to the higher optimal growth temperatures and lower water stress levels of the western urban vegetation than the rural. The urban responses also had smaller magnitudes than the rural responses, especially in deciduous forest biomes, and least in evergreen forest biomes. Within each biome, analysis at 1 km pixel level showed that impervious fraction and vegetation cover, local urban heat island intensity, and water stress were the key drivers of urban-rural differences. These findings advance our understanding of how prolonged exposure to warm extremes, particularly within urban environments, affects vegetation greenness and vitality. Urban planners and ecosystem managers should prioritize the long and intense events and the key drivers in fostering urban vegetation resilience to heat waves.
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Affiliation(s)
- Yaoping Wang
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jiafu Mao
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Christa M Brelsford
- Geospatial Science and Human Security Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
- Analytics, Intelligence and Technology Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA
| | - Daniel M Ricciuto
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Fengming Yuan
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xiaoying Shi
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Deeksha Rastogi
- Computational Science and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Melanie M Mayes
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Shih-Chieh Kao
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Jeffrey M Warren
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Natalie A Griffiths
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Xinghua Cheng
- Department of Natural Resources and the Environment, University of Connecticut, Storrs, CT 06269, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Yuyu Zhou
- Department of Geography, The University of Hong Kong, Hong Kong, 999077, China
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
| | - Peter E Thornton
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37830, USA
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3
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Yang X, Liu Y, Yuan G, Weston DJ, Tuskan GA. Engineering Crassulacean Acid Metabolism in C 3 and C 4 Plants. Cold Spring Harb Perspect Biol 2024; 16:a041674. [PMID: 38052496 PMCID: PMC10982706 DOI: 10.1101/cshperspect.a041674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Carbon dioxide (CO2) is a major greenhouse gas contributing to changing climatic conditions, which is a grand challenge affecting the security of food, energy, and environment. Photosynthesis plays the central role in plant-based CO2 reduction. Plants performing CAM (crassulacean acid metabolism) photosynthesis have a much higher water use efficiency than those performing C3 or C4 photosynthesis. Therefore, there is a great potential for engineering CAM in C3 or C4 crops to enhance food/biomass production and carbon sequestration on arid, semiarid, abandoned, or marginal lands. Recent progresses in CAM plant genomics and evolution research, along with new advances in plant biotechnology, have provided a solid foundation for bioengineering to convert C3/C4 plants into CAM plants. Here, we first discuss the potential strategies for CAM engineering based on our current understanding of CAM evolution. Then we describe the technical approaches for engineering CAM in C3 and C4 plants, with a focus on an iterative four-step pipeline: (1) designing gene modules, (2) building the gene modules and transforming them into target plants, (3) testing the engineered plants through an integration of molecular biology, biochemistry, metabolism, and physiological approaches, and (4) learning to inform the next round of CAM engineering. Finally, we discuss the challenges and future opportunities for fully realizing the potential of CAM engineering.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Guoliang Yuan
- Chemical and Biological Process Development Group, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Kilner CL, Carrell AA, Wieczynski DJ, Votzke S, DeWitt K, Yammine A, Shaw J, Pelletier DA, Weston DJ, Gibert JP. Temperature and CO 2 interactively drive shifts in the compositional and functional structure of peatland protist communities. Glob Chang Biol 2024; 30:e17203. [PMID: 38433341 DOI: 10.1111/gcb.17203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 01/20/2024] [Accepted: 01/26/2024] [Indexed: 03/05/2024]
Abstract
Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2 jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria and fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, and metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2 with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2 and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2 levels could alter the structure and function of peatland microbial food webs-a fragile ecosystem that stores upwards of 25% of all terrestrial carbon and is increasingly threatened by human exploitation.
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Affiliation(s)
- Christopher L Kilner
- Department of Biology, Duke University, Durham, North Carolina, USA
- Bird Conservancy of the Rockies, Fort Collins, Colorado, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | | | - Samantha Votzke
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Katrina DeWitt
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Andrea Yammine
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Jonathan Shaw
- Department of Biology, Duke University, Durham, North Carolina, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, North Carolina, USA
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5
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Piatkowski B, Weston DJ, Aguero B, Duffy A, Imwattana K, Healey AL, Schmutz J, Shaw AJ. Divergent selection and climate adaptation fuel genomic differentiation between sister species of Sphagnum (peat moss). Ann Bot 2023; 132:499-512. [PMID: 37478307 PMCID: PMC10666999 DOI: 10.1093/aob/mcad104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 07/24/2023] [Indexed: 07/23/2023]
Abstract
BACKGROUND AND AIMS New plant species can evolve through the reinforcement of reproductive isolation via local adaptation along habitat gradients. Peat mosses (Sphagnaceae) are an emerging model system for the study of evolutionary genomics and have well-documented niche differentiation among species. Recent molecular studies have demonstrated that the globally distributed species Sphagnum magellanicum is a complex of morphologically cryptic lineages that are phylogenetically and ecologically distinct. Here, we describe the architecture of genomic differentiation between two sister species in this complex known from eastern North America: the northern S. diabolicum and the largely southern S. magniae. METHODS We sampled plant populations from across a latitudinal gradient in eastern North America and performed whole genome and restriction-site associated DNA sequencing. These sequencing data were then analyzed computationally. KEY RESULTS Using sliding-window population genetic analyses we find that differentiation is concentrated within 'islands' of the genome spanning up to 400 kb that are characterized by elevated genetic divergence, suppressed recombination, reduced nucleotide diversity and increased rates of non-synonymous substitution. Sequence variants that are significantly associated with genetic structure and bioclimatic variables occur within genes that have functional enrichment for biological processes including abiotic stress response, photoperiodism and hormone-mediated signalling. Demographic modelling demonstrates that these two species diverged no more than 225 000 generations ago with secondary contact occurring where their ranges overlap. CONCLUSIONS We suggest that this heterogeneity of genomic differentiation is a result of linked selection and reflects the role of local adaptation to contrasting climatic zones in driving speciation. This research provides insight into the process of speciation in a group of ecologically important plants and strengthens our predictive understanding of how plant populations will respond as Earth's climate rapidly changes.
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Affiliation(s)
- Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, USA
| | - Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, USA
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6
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Sreedasyam A, Plott C, Hossain MS, Lovell J, Grimwood J, Jenkins J, Daum C, Barry K, Carlson J, Shu S, Phillips J, Amirebrahimi M, Zane M, Wang M, Goodstein D, Haas F, Hiss M, Perroud PF, Jawdy S, Yang Y, Hu R, Johnson J, Kropat J, Gallaher S, Lipzen A, Shakirov E, Weng X, Torres-Jerez I, Weers B, Conde D, Pappas M, Liu L, Muchlinski A, Jiang H, Shyu C, Huang P, Sebastian J, Laiben C, Medlin A, Carey S, Carrell A, Chen JG, Perales M, Swaminathan K, Allona I, Grattapaglia D, Cooper E, Tholl D, Vogel J, Weston DJ, Yang X, Brutnell T, Kellogg E, Baxter I, Udvardi M, Tang Y, Mockler T, Juenger T, Mullet J, Rensing S, Tuskan G, Merchant S, Stacey G, Schmutz J. JGI Plant Gene Atlas: an updateable transcriptome resource to improve functional gene descriptions across the plant kingdom. Nucleic Acids Res 2023; 51:8383-8401. [PMID: 37526283 PMCID: PMC10484672 DOI: 10.1093/nar/gkad616] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 06/21/2023] [Accepted: 07/11/2023] [Indexed: 08/02/2023] Open
Abstract
Gene functional descriptions offer a crucial line of evidence for candidate genes underlying trait variation. Conversely, plant responses to environmental cues represent important resources to decipher gene function and subsequently provide molecular targets for plant improvement through gene editing. However, biological roles of large proportions of genes across the plant phylogeny are poorly annotated. Here we describe the Joint Genome Institute (JGI) Plant Gene Atlas, an updateable data resource consisting of transcript abundance assays spanning 18 diverse species. To integrate across these diverse genotypes, we analyzed expression profiles, built gene clusters that exhibited tissue/condition specific expression, and tested for transcriptional response to environmental queues. We discovered extensive phylogenetically constrained and condition-specific expression profiles for genes without any previously documented functional annotation. Such conserved expression patterns and tightly co-expressed gene clusters let us assign expression derived additional biological information to 64 495 genes with otherwise unknown functions. The ever-expanding Gene Atlas resource is available at JGI Plant Gene Atlas (https://plantgeneatlas.jgi.doe.gov) and Phytozome (https://phytozome.jgi.doe.gov/), providing bulk access to data and user-specified queries of gene sets. Combined, these web interfaces let users access differentially expressed genes, track orthologs across the Gene Atlas plants, graphically represent co-expressed genes, and visualize gene ontology and pathway enrichments.
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Affiliation(s)
| | | | - Md Shakhawat Hossain
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - John T Lovell
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry W Jenkins
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Christopher Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kerrie Barry
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Joseph Carlson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shengqiang Shu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeremy Phillips
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mojgan Amirebrahimi
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Matthew Zane
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mei Wang
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David Goodstein
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Fabian B Haas
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Manuel Hiss
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Pierre-François Perroud
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Sara S Jawdy
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Yongil Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Rongbin Hu
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jenifer Johnson
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Janette Kropat
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Sean D Gallaher
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Anna Lipzen
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eugene V Shakirov
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - Xiaoyu Weng
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | | | - Brock Weers
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Daniel Conde
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
| | - Marilia R Pappas
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | - Lifeng Liu
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Andrew Muchlinski
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - Hui Jiang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Christine Shyu
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Pu Huang
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jose Sebastian
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Carol Laiben
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa Medlin
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Sankalpi Carey
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mariano Perales
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | | | - Isabel Allona
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Madrid, Spain
- Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Madrid, Spain
| | - Dario Grattapaglia
- Laboratório de Genética Vegetal, EMBRAPA Recursos Genéticos e Biotecnologia, EPQB Final W5 Norte, Brasília, Brazil
| | | | - Dorothea Tholl
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, USA
| | - John P Vogel
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaohan Yang
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | | | - Ivan Baxter
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | | | - Todd C Mockler
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas at Austin, Austin, TX, USA
| | - John Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, USA
| | - Stefan A Rensing
- Plant Cell Biology, Faculty of Biology, University of Marburg, Karl-von-Frisch-Str, Marburg, Germany
| | - Gerald A Tuskan
- Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Sabeeha S Merchant
- Department of Chemistry and Biochemistry and Institute for Genomics and Proteomics, University of California, Los Angeles, CA, USA
| | - Gary Stacey
- Division of Plant Science and Technology, C.S. Bond Life Science Center, University of Missouri, Columbia, MO, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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7
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Norby RJ, Baxter T, Živković T, Weston DJ. Shading contributes to Sphagnum decline in response to warming. Ecol Evol 2023; 13:e10542. [PMID: 37732286 PMCID: PMC10507575 DOI: 10.1002/ece3.10542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 08/28/2023] [Accepted: 09/06/2023] [Indexed: 09/22/2023] Open
Abstract
Experimental warming of an ombrotrophic bog in northern Minnesota has caused a rapid decline in the productivity and areal cover of Sphagnum mosses, affecting whole-ecosystem carbon balance and biogeochemistry. Direct effects of elevated temperature and the attendant drying are most likely the primary cause of the effects on Sphagnum, but there may also be responses to the increased shading from shrubs, which increased with increasing temperature. To evaluate the independent effects of reduction in light availability and deposition of shrub litter on Sphagnum productivity, small plots with shrubs removed were laid out adjacent to the warming experiment on hummocks and hollows in three blocks and with five levels of shading. Four plots were covered with neutral density shade cloth to simulate shading from shrubs of 30%-90% reduction in light; one plot was left open. Growth of Sphagnum angustifolium/fallax and S. divinum declined linearly with increasing shade in hollows, but there was no response to shade on hummocks, where higher irradiance in the open plots may have been inhibitory. Shading caused etiolation of Sphagnum-they were thin and spindly under the deepest shade. A dense mat of shrub litter, corresponding to the amount of shrub litter produced in response to warming, did not inhibit Sphagnum growth or cause increases in potentially toxic base cations. CO2 exchange and chlorophyll-a fluorescence of S. angustifolium/fallax from the 30% and 90% shade cloth plots were measured in the laboratory. Light response curves indicate that maximal light saturated photosynthesis was 42% greater for S. angustifolium/fallax grown under 30% shade cloth relative to plants grown under 90% shade cloth. The response of Sphagnum growth in response to increasing shade is consistent with the hypothesis that increased shade resulting from shrub expansion in response to experimental warming contributed to reduced Sphagnum growth.
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Affiliation(s)
- Richard J Norby
- Environmental Sciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee USA
| | - Taylor Baxter
- Department of Ecology and Evolutionary Biology University of Tennessee Knoxville Tennessee USA
| | - Tatjana Živković
- Department of Biology Dalhousie University Halifax Nova Scotia Canada
- Biological Sciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
| | - David J Weston
- Biological Sciences Division Oak Ridge National Laboratory Oak Ridge Tennessee USA
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8
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Davidson RB, Coletti M, Gao M, Piatkowski B, Sreedasyam A, Quadir F, Weston DJ, Schmutz J, Cheng J, Skolnick J, Parks JM, Sedova A. Predicted structural proteome of Sphagnum divinum and proteome-scale annotation. Bioinformatics 2023; 39:btad511. [PMID: 37589594 PMCID: PMC10463551 DOI: 10.1093/bioinformatics/btad511] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/16/2023] [Indexed: 08/18/2023] Open
Abstract
MOTIVATION Sphagnum-dominated peatlands store a substantial amount of terrestrial carbon. The genus is undersampled and under-studied. No experimental crystal structure from any Sphagnum species exists in the Protein Data Bank and fewer than 200 Sphagnum-related genes have structural models available in the AlphaFold Protein Structure Database. Tools and resources are needed to help bridge these gaps, and to enable the analysis of other structural proteomes now made possible by accurate structure prediction. RESULTS We present the predicted structural proteome (25 134 primary transcripts) of Sphagnum divinum computed using AlphaFold, structural alignment results of all high-confidence models against an annotated nonredundant crystallographic database of over 90,000 structures, a structure-based classification of putative Enzyme Commission (EC) numbers across this proteome, and the computational method to perform this proteome-scale structure-based annotation. AVAILABILITY AND IMPLEMENTATION All data and code are available in public repositories, detailed at https://github.com/BSDExabio/SAFA. The structural models of the S. divinum proteome have been deposited in the ModelArchive repository at https://modelarchive.org/doi/10.5452/ma-ornl-sphdiv.
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Affiliation(s)
- Russell B Davidson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Mark Coletti
- Computer Science and Mathematics Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Mu Gao
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
| | - Farhan Quadir
- Electrical Engineering and Computer Science, University of Missouri, Columbia, MS 65211, United States
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, United States
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - Jianlin Cheng
- Electrical Engineering and Computer Science, University of Missouri, Columbia, MS 65211, United States
| | - Jeffrey Skolnick
- Center for the Study of Systems Biology, School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, United States
| | - Jerry M Parks
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
| | - Ada Sedova
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830, United States
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9
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Lee JH, Burdick LH, Piatkowski B, Carrell AA, Doktycz MJ, Pelletier DA, Weston DJ. A rapid assay for assessing bacterial effects on Arabidopsis thermotolerance. Plant Methods 2023; 19:63. [PMID: 37386471 DOI: 10.1186/s13007-023-01022-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 05/01/2023] [Indexed: 07/01/2023]
Abstract
BACKGROUND The role of beneficial microbes in mitigating plant abiotic stress has received considerable attention. However, the lack of a reproducible and relatively high-throughput screen for microbial contributions to plant thermotolerance has greatly limited progress in this area, this slows the discovery of novel beneficial isolates and the processes by which they operate. RESULTS We designed a rapid phenotyping method to assess the effects of bacteria on plant host thermotolerance. After testing multiple growth conditions, a hydroponic system was selected and used to optimize an Arabidopsis heat shock regime and phenotypic evaluation. Arabidopsis seedlings germinated on a PTFE mesh disc were floated onto a 6-well plate containing liquid MS media, then subjected to heat shock at 45 °C for various duration. To characterize phenotype, plants were harvested after four days of recovery to measure chlorophyll content. The method was extended to include bacterial isolates and to quantify bacterial contributions to host plant thermotolerance. As an exemplar, the method was used to screen 25 strains of the plant growth promoting Variovorax spp. for enhanced plant thermotolerance. A follow-up study demonstrated the reproducibility of this assay and led to the discovery of a novel beneficial interaction. CONCLUSIONS This method enables rapid screening of individual bacterial strains for beneficial effects on host plant thermotolerance. The throughput and reproducibility of the system is ideal for testing many genetic variants of Arabidopsis and bacterial strains.
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Affiliation(s)
- Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA
| | - Leah H Burdick
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA.
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, 1 Bethel Valley Rd Bldg. 1507, Rm. 214, Oak Ridge, TN, 37831, USA.
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10
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Petro C, Carrell AA, Wilson RM, Duchesneau K, Noble-Kuchera S, Song T, Iversen CM, Childs J, Schwaner G, Chanton JP, Norby RJ, Hanson PJ, Glass JB, Weston DJ, Kostka JE. Climate drivers alter nitrogen availability in surface peat and decouple N 2 fixation from CH 4 oxidation in the Sphagnum moss microbiome. Glob Chang Biol 2023; 29:3159-3176. [PMID: 36999440 DOI: 10.1111/gcb.16651] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Accepted: 12/20/2022] [Indexed: 05/03/2023]
Abstract
Peat mosses (Sphagnum spp.) are keystone species in boreal peatlands, where they dominate net primary productivity and facilitate the accumulation of carbon in thick peat deposits. Sphagnum mosses harbor a diverse assemblage of microbial partners, including N2 -fixing (diazotrophic) and CH4 -oxidizing (methanotrophic) taxa that support ecosystem function by regulating transformations of carbon and nitrogen. Here, we investigate the response of the Sphagnum phytobiome (plant + constituent microbiome + environment) to a gradient of experimental warming (+0°C to +9°C) and elevated CO2 (+500 ppm) in an ombrotrophic peatland in northern Minnesota (USA). By tracking changes in carbon (CH4 , CO2 ) and nitrogen (NH4 -N) cycling from the belowground environment up to Sphagnum and its associated microbiome, we identified a series of cascading impacts to the Sphagnum phytobiome triggered by warming and elevated CO2 . Under ambient CO2 , warming increased plant-available NH4 -N in surface peat, excess N accumulated in Sphagnum tissue, and N2 fixation activity decreased. Elevated CO2 offset the effects of warming, disrupting the accumulation of N in peat and Sphagnum tissue. Methane concentrations in porewater increased with warming irrespective of CO2 treatment, resulting in a ~10× rise in methanotrophic activity within Sphagnum from the +9°C enclosures. Warming's divergent impacts on diazotrophy and methanotrophy caused these processes to become decoupled at warmer temperatures, as evidenced by declining rates of methane-induced N2 fixation and significant losses of keystone microbial taxa. In addition to changes in the Sphagnum microbiome, we observed ~94% mortality of Sphagnum between the +0°C and +9°C treatments, possibly due to the interactive effects of warming on N-availability and competition from vascular plant species. Collectively, these results highlight the vulnerability of the Sphagnum phytobiome to rising temperatures and atmospheric CO2 concentrations, with significant implications for carbon and nitrogen cycling in boreal peatlands.
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Affiliation(s)
- Caitlin Petro
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Rachel M Wilson
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Katherine Duchesneau
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Sekou Noble-Kuchera
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Tianze Song
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Colleen M Iversen
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joanne Childs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Geoff Schwaner
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jeffrey P Chanton
- Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, Florida, USA
| | - Richard J Norby
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Department of Ecology & Evolutionary Biology, University of Tennessee, Knoxville, Tennessee, USA
| | - Paul J Hanson
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jennifer B Glass
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Joel E Kostka
- Center for Microbial Dynamics and Infection, School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
- School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, Georgia, USA
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11
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Porada P, Bader MY, Berdugo MB, Colesie C, Ellis CJ, Giordani P, Herzschuh U, Ma Y, Launiainen S, Nascimbene J, Petersen I, Raggio Quílez J, Rodríguez-Caballero E, Rousk K, Sancho LG, Scheidegger C, Seitz S, Van Stan JT, Veste M, Weber B, Weston DJ. A research agenda for nonvascular photoautotrophs under climate change. New Phytol 2023; 237:1495-1504. [PMID: 36511294 DOI: 10.1111/nph.18631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Nonvascular photoautotrophs (NVP), including bryophytes, lichens, terrestrial algae, and cyanobacteria, are increasingly recognized as being essential to ecosystem functioning in many regions of the world. Current research suggests that climate change may pose a substantial threat to NVP, but the extent to which this will affect the associated ecosystem functions and services is highly uncertain. Here, we propose a research agenda to address this urgent question, focusing on physiological and ecological processes that link NVP to ecosystem functions while also taking into account the substantial taxonomic diversity across multiple ecosystem types. Accordingly, we developed a new categorization scheme, based on microclimatic gradients, which simplifies the high physiological and morphological diversity of NVP and world-wide distribution with respect to several broad habitat types. We found that habitat-specific ecosystem functions of NVP will likely be substantially affected by climate change, and more quantitative process understanding is required on: (1) potential for acclimation; (2) response to elevated CO2 ; (3) role of the microbiome; and (4) feedback to (micro)climate. We suggest an integrative approach of innovative, multimethod laboratory and field experiments and ecophysiological modelling, for which sustained scientific collaboration on NVP research will be essential.
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Affiliation(s)
- Philipp Porada
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Maaike Y Bader
- Ecological Plant Geography, University of Marburg, Deutschhausstr. 10, 35032, Marburg, Germany
| | - Monica B Berdugo
- Ecological Plant Geography, University of Marburg, Deutschhausstr. 10, 35032, Marburg, Germany
| | - Claudia Colesie
- School of Geosciences, University of Edinburgh, Edinburgh, EH9 3JW, UK
| | | | | | - Ulrike Herzschuh
- Polar Terrestrial Environmental Systems, Alfred Wegener Institute, Telegrafenberg A45, 14473, Potsdam, Germany
| | - Yunyao Ma
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - Samuli Launiainen
- Ecosystems and Modeling, Natural Resources Institute Finland (Luke), Latokartanonkaari 9, 00790, Helsinki, Finland
| | - Juri Nascimbene
- BIOME Lab, Department of Biological, Geological and Environmental Sciences, Alma Mater Studiorum University of Bologna, 40126, Bologna, Italy
| | - Imke Petersen
- Ecological Modelling, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
| | - José Raggio Quílez
- Department of Pharmacology, Pharmacognosy and Botany, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | | | - Kathrin Rousk
- Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, København, Denmark
| | - Leopoldo G Sancho
- Department of Pharmacology, Pharmacognosy and Botany, Universidad Complutense de Madrid, E-28040, Madrid, Spain
| | - Christoph Scheidegger
- Biodiversity and Conservation Biology, Eidg. Forschungsanstalt WSL, Zürcherstr. 111, 8903, Birmensdorf, Switzerland
| | - Steffen Seitz
- Soil Science and Geomorphology, University of Tübingen, Rümelinstr. 19-23, 72070, Tübingen, Germany
| | - John T Van Stan
- Department of Biological, Geological, and Environmental Sciences, Cleveland State University, 2121 Euclid Ave., Cleveland, OH, 44115, USA
| | - Maik Veste
- Institute of Environmental Sciences, Brandenburgische Technische Universität Cottbus-Senftenberg, Konrad-Wachsmann-Allee 6, 03046, Cottbus, Germany
| | - Bettina Weber
- Division of Plant Sciences, Institute for Biology, University of Graz, Holteigasse 6, A-8010, Graz, Austria
- Multiphase Chemistry Department, Max Planck Institute for Chemistry, Hahn-Meitner-Weg 1, 55128, Mainz, Germany
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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12
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Wieczynski DJ, Yoshimura KM, Denison ER, Geisen S, DeBruyn JM, Shaw AJ, Weston DJ, Pelletier DA, Wilhelm SW, Gibert JP. Viral infections likely mediate microbial controls on ecosystem responses to global warming. FEMS Microbiol Ecol 2023; 99:7057867. [PMID: 36828391 DOI: 10.1093/femsec/fiad016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 12/05/2022] [Accepted: 02/22/2023] [Indexed: 02/26/2023] Open
Abstract
Climate change is affecting how energy and matter flow through ecosystems, thereby altering global carbon and nutrient cycles. Microorganisms play a fundamental role in carbon and nutrient cycling and are thus an integral link between ecosystems and climate. Here, we highlight a major black box hindering our ability to anticipate ecosystem climate responses: viral infections within complex microbial food webs. We show how understanding and predicting ecosystem responses to warming could be challenging-if not impossible-without accounting for the direct and indirect effects of viral infections on different microbes (bacteria, archaea, fungi, protists) that together perform diverse ecosystem functions. Importantly, understanding how rising temperatures associated with climate change influence viruses and virus-host dynamics is crucial to this task, yet is severely understudied. In this perspective, we (i) synthesize existing knowledge about virus-microbe-temperature interactions and (ii) identify important gaps to guide future investigations regarding how climate change might alter microbial food web effects on ecosystem functioning. To provide real-world context, we consider how these processes may operate in peatlands-globally significant carbon sinks that are threatened by climate change. We stress that understanding how warming affects biogeochemical cycles in any ecosystem hinges on disentangling complex interactions and temperature responses within microbial food webs.
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Affiliation(s)
| | - Kristin M Yoshimura
- Department of Microbiology, The University of Tennessee, Knoxville, United States
| | - Elizabeth R Denison
- Department of Microbiology, The University of Tennessee, Knoxville, United States
| | - Stefan Geisen
- Netherlands Institute of Ecology, 6708 PB Wageningen, Netherlands
| | - Jennifer M DeBruyn
- Department of Biosystems Engineering and Soil Science, The University of Tennessee, Knoxville, United States
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, United States
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, United States
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, United States
| | - Steven W Wilhelm
- Department of Microbiology, The University of Tennessee, Knoxville, United States
| | - Jean P Gibert
- Department of Biology, Duke University, Durham, NC, 27708, United States
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13
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Healey AL, Piatkowski B, Lovell JT, Sreedasyam A, Carey SB, Mamidi S, Shu S, Plott C, Jenkins J, Lawrence T, Aguero B, Carrell AA, Nieto-Lugilde M, Talag J, Duffy A, Jawdy S, Carter KR, Boston LB, Jones T, Jaramillo-Chico J, Harkess A, Barry K, Keymanesh K, Bauer D, Grimwood J, Gunter L, Schmutz J, Weston DJ, Shaw AJ. Newly identified sex chromosomes in the Sphagnum (peat moss) genome alter carbon sequestration and ecosystem dynamics. Nat Plants 2023; 9:238-254. [PMID: 36747050 PMCID: PMC9946827 DOI: 10.1038/s41477-022-01333-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 12/13/2022] [Indexed: 06/18/2023]
Abstract
Peatlands are crucial sinks for atmospheric carbon but are critically threatened due to warming climates. Sphagnum (peat moss) species are keystone members of peatland communities where they actively engineer hyperacidic conditions, which improves their competitive advantage and accelerates ecosystem-level carbon sequestration. To dissect the molecular and physiological sources of this unique biology, we generated chromosome-scale genomes of two Sphagnum species: S. divinum and S. angustifolium. Sphagnum genomes show no gene colinearity with any other reference genome to date, demonstrating that Sphagnum represents an unsampled lineage of land plant evolution. The genomes also revealed an average recombination rate an order of magnitude higher than vascular land plants and short putative U/V sex chromosomes. These newly described sex chromosomes interact with autosomal loci that significantly impact growth across diverse pH conditions. This discovery demonstrates that the ability of Sphagnum to sequester carbon in acidic peat bogs is mediated by interactions between sex, autosomes and environment.
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Affiliation(s)
- Adam L Healey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA.
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - John T Lovell
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Avinash Sreedasyam
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Sarah B Carey
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Sujan Mamidi
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Shengqiang Shu
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Chris Plott
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Jerry Jenkins
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Travis Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Jayson Talag
- Arizona Genomics Institute, University of Arizona, Tucson, AZ, USA
| | - Aaron Duffy
- Department of Biology, Duke University, Durham, NC, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kelsey R Carter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Earth and Environmental Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Lori-Beth Boston
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Teresa Jones
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | - Alex Harkess
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Crop, Soil, and Environmental Sciences, Auburn University, Auburn, AL, USA
| | - Kerrie Barry
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Keykhosrow Keymanesh
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Diane Bauer
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Lee Gunter
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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14
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Shaw AJ, Piatkowski B, Duffy AM, Aguero B, Imwattana K, Nieto-Lugilde M, Healey A, Weston DJ, Patel MN, Schmutz J, Grimwood J, Yavitt JB, Hassel K, Stenøien HK, Flatberg KI, Bickford CP, Hicks KA. Phylogenomic structure and speciation in an emerging model: the Sphagnum magellanicum complex (Bryophyta). New Phytol 2022; 236:1497-1511. [PMID: 35971292 DOI: 10.1111/nph.18429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Sphagnum magellanicum is one of two Sphagnum species for which a reference-quality genome exists to facilitate research in ecological genomics. Phylogenetic and comparative genomic analyses were conducted based on resequencing data from 48 samples and RADseq analyses based on 187 samples. We report herein that there are four clades/species within the S. magellanicum complex in eastern North America and that the reference genome belongs to Sphagnum divinum. The species exhibit tens of thousands (RADseq) to millions (resequencing) of fixed nucleotide differences. Two species, however, referred to informally as S. diabolicum and S. magni because they have not been formally described, are differentiated by only 100 (RADseq) to 1000 (resequencing) of differences. Introgression among species in the complex is demonstrated using D-statistics and f4 ratios. One ecologically important functional trait, tissue decomposability, which underlies peat (carbon) accumulation, does not differ between segregates in the S. magellanicum complex, although previous research showed that many closely related Sphagnum species have evolved differences in decomposability/carbon sequestration. Phylogenetic resolution and more accurate species delimitation in the S. magellanicum complex substantially increase the value of this group for studying the early evolutionary stages of climate adaptation and ecological evolution more broadly.
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Affiliation(s)
- A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Bryan Piatkowski
- Biosciences Division, Oak Ridge, National Laboratory, Oak Ridge, TN, 37831, USA
| | - Aaron M Duffy
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Blanka Aguero
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | | | - Adam Healey
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
| | - David J Weston
- Biosciences Division, Oak Ridge, National Laboratory, Oak Ridge, TN, 37831, USA
| | - Megan N Patel
- Biosciences Division, Oak Ridge, National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Lawrence Berkeley, National Laboratory, Berkeley, CA, 94720, USA
| | - Jane Grimwood
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
| | - Joseph B Yavitt
- Department of Natural Resources, Cornell University, Ithaca, NY, 14853, USA
| | - Kristian Hassel
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | - Kjell-Ivar Flatberg
- NTNU University Museum, Norwegian University of Science and Technology, Trondheim, NO-7491, Norway
| | | | - Karen A Hicks
- Department of Biology, Kenyon College, Gambier, OH, 43022, USA
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15
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Blumstein M, Sala A, Weston DJ, Holbrook NM, Hopkins R. Plant carbohydrate storage: intra- and inter-specific trade-offs reveal a major life history trait. New Phytol 2022; 235:2211-2222. [PMID: 35524463 DOI: 10.1111/nph.18213] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/24/2022] [Indexed: 06/14/2023]
Abstract
Trade-offs among carbon sinks constrain how trees physiologically, ecologically, and evolutionarily respond to their environments. These trade-offs typically fall along a productive growth to conservative, bet-hedging continuum. How nonstructural carbohydrates (NSCs) stored in living tree cells (known as carbon stores) fit in this trade-off framework is not well understood. We examined relationships between growth and storage using both within species genetic variation from a common garden, and across species phenotypic variation from a global database. We demonstrate that storage is actively accumulated, as part of a conservative, bet-hedging life history strategy. Storage accumulates at the expense of growth both within and across species. Within the species Populus trichocarpa, genetic trade-offs show that for each additional unit of wood area growth (in cm2 yr-1 ) that genotypes invest in, they lose 1.2 to 1.7 units (mg g-1 NSC) of storage. Across species, for each additional unit of area growth (in cm2 yr-1 ), trees, on average, reduce their storage by 9.5% in stems and 10.4% in roots. Our findings impact our understanding of basic plant biology, fit storage into a widely used growth-survival trade-off spectrum describing life history strategy, and challenges the assumptions of passive storage made in ecosystem models today.
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Affiliation(s)
- Meghan Blumstein
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA, 02138, USA
- Civil and Environmental Engineering, Massachusetts Institute of Technology, 15 Vassar St, Cambridge, MA, 02139, USA
| | - Anna Sala
- Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Noel Michelle Holbrook
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA, 02138, USA
| | - Robin Hopkins
- Department of Organismic and Evolutionary Biology, Harvard University, 26 Oxford St, Cambridge, MA, 02138, USA
- The Arnold Arboretum, 1300 Centre St, Boston, MA, 02130, USA
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16
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Carrell AA, Lawrence TJ, Cabugao KGM, Carper DL, Pelletier DA, Lee JH, Jawdy SS, Grimwood J, Schmutz J, Hanson PJ, Shaw AJ, Weston DJ. Habitat-adapted microbial communities mediate Sphagnum peatmoss resilience to warming. New Phytol 2022; 234:2111-2125. [PMID: 35266150 PMCID: PMC9310625 DOI: 10.1111/nph.18072] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 02/21/2022] [Indexed: 05/19/2023]
Abstract
Sphagnum peatmosses are fundamental members of peatland ecosystems, where they contribute to the uptake and long-term storage of atmospheric carbon. Warming threatens Sphagnum mosses and is known to alter the composition of their associated microbiome. Here, we use a microbiome transfer approach to test if microbiome thermal origin influences host plant thermotolerance. We leveraged an experimental whole-ecosystem warming study to collect field-grown Sphagnum, mechanically separate the associated microbiome and then transfer onto germ-free laboratory Sphagnum for temperature experiments. Host and microbiome dynamics were assessed with growth analysis, Chla fluorescence imaging, metagenomics, metatranscriptomics and 16S rDNA profiling. Microbiomes originating from warming field conditions imparted enhanced thermotolerance and growth recovery at elevated temperatures. Metagenome and metatranscriptome analyses revealed that warming altered microbial community structure in a manner that induced the plant heat shock response, especially the HSP70 family and jasmonic acid production. The heat shock response was induced even without warming treatment in the laboratory, suggesting that the warm-microbiome isolated from the field provided the host plant with thermal preconditioning. Our results demonstrate that microbes, which respond rapidly to temperature alterations, can play key roles in host plant growth response to rapidly changing environments.
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Affiliation(s)
- Alyssa A. Carrell
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Travis J. Lawrence
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Kristine Grace M. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee1502 Cumberland Ave.KnoxvilleTN37996USA
| | - Dana L. Carper
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Dale A. Pelletier
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jun Hyung Lee
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Sara S. Jawdy
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | - Jane Grimwood
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology601 Genome WayHuntsvilleAL35806USA
- Department of Energy Joint Genome InstituteLawrence Berkeley National Lab1 Cyclotron Rd.BerkeleyCA94720USA
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
| | | | - David J. Weston
- Biosciences DivisionOak Ridge National Laboratory1 Bethel Valley RdOak RidgeTN37831USA
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17
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Yuan G, Lu H, Weston DJ, Jawdy S, Tschaplinski TJ, Tuskan GA, Yang X. Reporter genes confer new-to-nature ornamental traits in plants. Hortic Res 2022; 9:uhac077. [PMID: 35669710 PMCID: PMC9160727 DOI: 10.1093/hr/uhac077] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 03/17/2022] [Indexed: 05/14/2023]
Abstract
This manuscript has been authored by UT-Battelle, LLC under Contract No. DE-AC05-00OR22725 with the U.S. Department of Energy. The United States Government retains and the publisher, by accepting the article for publication, acknowledges that the United States Government retains a non-exclusive, paid-up, irrevocable, worldwide license to publish or reproduce the published form of this manuscript, or allow others to do so, for United States Government purposes. The Department of Energy will provide public access to these results of federally sponsored research in accordance with the DOE Public Access Plan (http://energy.gov/downloads/doe-public-access-plan).
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author: ;
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Corresponding author: ;
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18
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Yang X, Liu D, Lu H, Weston DJ, Chen JG, Muchero W, Martin S, Liu Y, Hassan MM, Yuan G, Kalluri UC, Tschaplinski TJ, Mitchell JC, Wullschleger SD, Tuskan GA. Biological Parts for Plant Biodesign to Enhance Land-Based Carbon Dioxide Removal. Biodes Res 2021; 2021:9798714. [PMID: 37849951 PMCID: PMC10521660 DOI: 10.34133/2021/9798714] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/07/2021] [Indexed: 10/19/2023] Open
Abstract
A grand challenge facing society is climate change caused mainly by rising CO2 concentration in Earth's atmosphere. Terrestrial plants are linchpins in global carbon cycling, with a unique capability of capturing CO2 via photosynthesis and translocating captured carbon to stems, roots, and soils for long-term storage. However, many researchers postulate that existing land plants cannot meet the ambitious requirement for CO2 removal to mitigate climate change in the future due to low photosynthetic efficiency, limited carbon allocation for long-term storage, and low suitability for the bioeconomy. To address these limitations, there is an urgent need for genetic improvement of existing plants or construction of novel plant systems through biosystems design (or biodesign). Here, we summarize validated biological parts (e.g., protein-encoding genes and noncoding RNAs) for biological engineering of carbon dioxide removal (CDR) traits in terrestrial plants to accelerate land-based decarbonization in bioenergy plantations and agricultural settings and promote a vibrant bioeconomy. Specifically, we first summarize the framework of plant-based CDR (e.g., CO2 capture, translocation, storage, and conversion to value-added products). Then, we highlight some representative biological parts, with experimental evidence, in this framework. Finally, we discuss challenges and strategies for the identification and curation of biological parts for CDR engineering in plants.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics, and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Haiwei Lu
- Department of Academic Education, Central Community College-Hastings, Hastings, NE 68902USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yang Liu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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19
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Hogan JA, Baraloto C, Ficken C, Clark MD, Weston DJ, Warren JM. The physiological acclimation and growth response of Populus trichocarpa to warming. Physiol Plant 2021; 173:1008-1029. [PMID: 34272872 DOI: 10.1111/ppl.13498] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Revised: 06/16/2021] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
Plant metabolic acclimation to thermal stress remains underrepresented in current global climate models. Gaps exist in our understanding of how metabolic processes (i.e., photosynthesis, respiration) acclimate over time and how aboveground versus belowground acclimation differs. We measured the thermal acclimation of Populus trichocarpa, comparing aboveground versus belowground physiology over time. Ninety genetically identical ramets were propagated in mesocosms that separated root and microbial components. After establishment at 25°C for 6 weeks, 60 clones were warmed +4 or +8°C and monitored for 10 weeks, measuring photosynthesis (A), leaf respiration (R), soil respiration (Rs ), root plus soil respiration (Rs+r ), and root respiration (Rr ). We observed thermal acclimation in both A and R, with rates initially increasing, then declining as the thermal photosynthetic optimum (Topt ) and the temperature-sensitivity (Q10 ) of respiration adjusted to warmer conditions. Photosynthetic acclimation was constructive, based on an increase in both Topt and peak A. Belowground, Rs+r decreased linearly with warming, while Rs rates declined abruptly, then remained constant with additional warming. Plant biomass was greatest at +4°C, with 30% allocated belowground. Rates of mass-based Rr were similar among treatments; however, root nitrogen declined at +8°C leading to less mass nitrogen-based Rr in that treatment. The Q10 -temperature relationship of Rr was affected by warming, leading to differing values among treatments. Aboveground acclimation exceeded belowground acclimation, and plant nitrogen-use mediated the acclimatory response. Results suggest that moderate climate warming (+4°C) may lead to acclimation and increased plant biomass production but increases in production could be limited with severe warming (+8°C).
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Affiliation(s)
- J Aaron Hogan
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, Florida, USA
- Division of Environmental Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher Baraloto
- Department of Biological Sciences, Institute of Environment, Florida International University, Miami, Florida, USA
| | - Cari Ficken
- Department of Geology, University at Buffalo, Buffalo, New York, USA
| | - Miranda D Clark
- Division of Biosciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - David J Weston
- Division of Biosciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jeffrey M Warren
- Division of Environmental Science, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
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20
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Lawrence TJ, Carper DL, Spangler MK, Carrell AA, Rush TA, Minter SJ, Weston DJ, Labbé JL. amPEPpy 1.0: a portable and accurate antimicrobial peptide prediction tool. Bioinformatics 2021; 37:2058-2060. [PMID: 33135060 DOI: 10.1093/bioinformatics/btaa917] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 10/07/2020] [Accepted: 10/16/2020] [Indexed: 01/16/2023] Open
Abstract
SUMMARY Antimicrobial peptides (AMPs) are promising alternative antimicrobial agents. Currently, however, portable, user-friendly and efficient methods for predicting AMP sequences from genome-scale data are not readily available. Here we present amPEPpy, an open-source, multi-threaded command-line application for predicting AMP sequences using a random forest classifier. AVAILABILITY AND IMPLEMENTATION amPEPpy is implemented in Python 3 and is freely available through GitHub (https://github.com/tlawrence3/amPEPpy). SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Margaret K Spangler
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Tomás A Rush
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jessy L Labbé
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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21
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Salmon VG, Brice DJ, Bridgham S, Childs J, Graham J, Griffiths NA, Hofmockel K, Iversen CM, Jicha TM, Kolka RK, Kostka JE, Malhotra A, Norby RJ, Phillips JR, Ricciuto D, Schadt CW, Sebestyen SD, Shi X, Walker AP, Warren JM, Weston DJ, Yang X, Hanson PJ. Nitrogen and phosphorus cycling in an ombrotrophic peatland: a benchmark for assessing change. Plant Soil 2021; 466:649-674. [PMID: 36267144 PMCID: PMC9580354 DOI: 10.1007/s11104-021-05065-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 06/23/2021] [Indexed: 06/16/2023]
Abstract
AIMS Slow decomposition and isolation from groundwater mean that ombrotrophic peatlands store a large amount of soil carbon (C) but have low availability of nitrogen (N) and phosphorus (P). To better understand the role these limiting nutrients play in determining the C balance of peatland ecosystems, we compile comprehensive N and P budgets for a forested bog in northern Minnesota, USA. METHODS N and P within plants, soils, and water are quantified based on field measurements. The resulting empirical dataset are then compared to modern-day, site-level simulations from the peatland land surface version of the Energy Exascale Earth System Model (ELM-SPRUCE). RESULTS Our results reveal N is accumulating in the ecosystem at 0.2 ± 0.1 g N m-2 year-1 but annual P inputs to this ecosystem are balanced by losses. Biomass stoichiometry indicates that plant functional types differ in N versus P limitation, with trees exhibiting a stronger N limitation than ericaceous shrubs or Sphagnum moss. High biomass and productivity of Sphagnum results in the moss layer storing and cycling a large proportion of plant N and P. Comparing our empirically-derived nutrient budgets to ELM-SPRUCE shows the model captures N cycling within dominant plant functional types well. CONCLUSIONS The nutrient budgets and stoichiometry presented serve as a baseline for quantifying the nutrient cycling response of peatland ecosystems to both observed and simulated climate change. Our analysis improves our understanding of N and P dynamics within nutrient-limited peatlands and represents a crucial step toward improving C-cycle projections into the twenty-first century.
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Affiliation(s)
- Verity G Salmon
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Deanne J Brice
- Climate Change Science Institute and Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Scott Bridgham
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA
| | - Joanne Childs
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jake Graham
- Department of Geosciences, Boise State University, Boise, ID, USA
| | - Natalie A Griffiths
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kirsten Hofmockel
- Earth and Biological Sciences Directorate Molecular, Science Laboratory, Pacific Northwest National, Laboratory, Richland, WA, USA
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA, USA
| | - Colleen M Iversen
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Terri M Jicha
- US Environmental Protection Agency, Office of Research and Development, National Health and Environmental Effects Laboratory, Mid-Continent Ecology Division, Center for Computational Toxicology and Exposure, Great, Lakes Toxicology and Ecology Division, Duluth, MN, USA
| | - Randy K Kolka
- USDA Forest Service Northern Research Station, Grand Rapids, MN, USA
| | - Joel E Kostka
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Avni Malhotra
- Department of Earth System Science, Stanford University, Stanford, CA, USA
| | - Richard J Norby
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Ecology and Evolutionary Biology, University of Tennessee, Knoxville, TN, USA
| | - Jana R Phillips
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Daniel Ricciuto
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Christopher W Schadt
- Climate Change Science Institute and Biosciences, Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | | | - Xiaoying Shi
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Anthony P Walker
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Jeffrey M Warren
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - David J Weston
- Climate Change Science Institute and Biosciences, Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Xiaojuan Yang
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Paul J Hanson
- Climate Change Science Institute and Environmental, Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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22
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Meleshko O, Martin MD, Korneliussen TS, Schröck C, Lamkowski P, Schmutz J, Healey A, Piatkowski BT, Shaw AJ, Weston DJ, Flatberg KI, Szövényi P, Hassel K, Stenøien HK. Extensive Genome-Wide Phylogenetic Discordance Is Due to Incomplete Lineage Sorting and Not Ongoing Introgression in a Rapidly Radiated Bryophyte Genus. Mol Biol Evol 2021; 38:2750-2766. [PMID: 33681996 PMCID: PMC8233498 DOI: 10.1093/molbev/msab063] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The relative importance of introgression for diversification has long been a highly disputed topic in speciation research and remains an open question despite the great attention it has received over the past decade. Gene flow leaves traces in the genome similar to those created by incomplete lineage sorting (ILS), and identification and quantification of gene flow in the presence of ILS is challenging and requires knowledge about the true phylogenetic relationship among the species. We use whole nuclear, plastid, and organellar genomes from 12 species in the rapidly radiated, ecologically diverse, actively hybridizing genus of peatmoss (Sphagnum) to reconstruct the species phylogeny and quantify introgression using a suite of phylogenomic methods. We found extensive phylogenetic discordance among nuclear and organellar phylogenies, as well as across the nuclear genome and the nodes in the species tree, best explained by extensive ILS following the rapid radiation of the genus rather than by postspeciation introgression. Our analyses support the idea of ancient introgression among the ancestral lineages followed by ILS, whereas recent gene flow among the species is highly restricted despite widespread interspecific hybridization known in the group. Our results contribute to phylogenomic understanding of how speciation proceeds in rapidly radiated, actively hybridizing species groups, and demonstrate that employing a combination of diverse phylogenomic methods can facilitate untangling complex phylogenetic patterns created by ILS and introgression.
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Affiliation(s)
- Olena Meleshko
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Michael D Martin
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | | | | | - Paul Lamkowski
- Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
| | - Jeremy Schmutz
- United States Department of Energy, Joint Genome Institute, Berkeley, CA, USA.,HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | - Adam Healey
- HudsonAlpha Institute for Biotechnology, Huntsville, AL, USA
| | | | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.,Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Kjell Ivar Flatberg
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany & Zurich-Basel Plant Science Center, University of Zurich, Zurich, Switzerland
| | - Kristian Hassel
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
| | - Hans K Stenøien
- Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology, Trondheim, Norway
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23
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Cabugao KG, Yaffar D, Stenson N, Childs J, Phillips J, Mayes MA, Yang X, Weston DJ, Norby RJ. Bringing function to structure: Root-soil interactions shaping phosphatase activity throughout a soil profile in Puerto Rico. Ecol Evol 2021; 11:1150-1164. [PMID: 33598120 PMCID: PMC7863403 DOI: 10.1002/ece3.7036] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/22/2020] [Accepted: 10/28/2020] [Indexed: 01/16/2023] Open
Abstract
Large areas of highly productive tropical forests occur on weathered soils with low concentrations of available phosphorus (P). In such forests, root and microbial production of acid phosphatase enzymes capable of mineralizing organic phosphorus is considered vital to increasing available P for plant uptake.We measured both root and soil phosphatase throughout depth and alongside a variety of root and soil factors to better understand the potential of roots and soil biota to increase P availability and to constrain estimates of the biochemical mineralization within ecosystem models.We measured soil phosphatase down to 1 m, root phosphatase to 30 cm, and collected data on fine-root mass density, specific root length, soil P, bulk density, and soil texture using soil cores in four tropical forests within the Luquillo Experimental Forest in Puerto Rico.We found that soil phosphatase decreased with soil depth, but not root phosphatase. Furthermore, when both soil and root phosphatase were expressed per soil volume, soil phosphatase was 100-fold higher that root phosphatase.Both root and soil factors influenced soil and root phosphatase. Soil phosphatase increased with fine-root mass density and organic P, which together explained over 50% of the variation in soil phosphatase. Over 80% of the variation in root phosphatase per unit root mass was attributed to specific root length (positive correlation) and available (resin) P (negative correlation). Synthesis: Fine-root traits and soil P data are necessary to understand and represent soil and root phosphatase activity throughout the soil column and across sites with different soil conditions and tree species. These findings can be used to parameterize or benchmark estimates of biochemical mineralization in ecosystem models that contain fine-root biomass and soil P distributions throughout depth.
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Affiliation(s)
- Kristine Grace Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee KnoxvilleKnoxvilleTNUSA
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Daniela Yaffar
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
- Ecology and Evolutionary BiologyUniversity of Tennessee KnoxvilleKnoxvilleTNUSA
| | - Nathan Stenson
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Joanne Childs
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Jana Phillips
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Melanie A. Mayes
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - Xiaojuan Yang
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
| | - David J. Weston
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTNUSA
| | - Richard J. Norby
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of Tennessee KnoxvilleKnoxvilleTNUSA
- Environmental Sciences Division and Climate Change Science InstituteOak Ridge National LaboratoryOak RidgeTNUSA
- Ecology and Evolutionary BiologyUniversity of Tennessee KnoxvilleKnoxvilleTNUSA
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24
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Yang X, Medford JI, Markel K, Shih PM, De Paoli HC, Trinh CT, McCormick AJ, Ployet R, Hussey SG, Myburg AA, Jensen PE, Hassan MM, Zhang J, Muchero W, Kalluri UC, Yin H, Zhuo R, Abraham PE, Chen JG, Weston DJ, Yang Y, Liu D, Li Y, Labbe J, Yang B, Lee JH, Cottingham RW, Martin S, Lu M, Tschaplinski TJ, Yuan G, Lu H, Ranjan P, Mitchell JC, Wullschleger SD, Tuskan GA. Plant Biosystems Design Research Roadmap 1.0. Biodes Res 2020; 2020:8051764. [PMID: 37849899 PMCID: PMC10521729 DOI: 10.34133/2020/8051764] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2020] [Accepted: 10/30/2020] [Indexed: 10/19/2023] Open
Abstract
Human life intimately depends on plants for food, biomaterials, health, energy, and a sustainable environment. Various plants have been genetically improved mostly through breeding, along with limited modification via genetic engineering, yet they are still not able to meet the ever-increasing needs, in terms of both quantity and quality, resulting from the rapid increase in world population and expected standards of living. A step change that may address these challenges would be to expand the potential of plants using biosystems design approaches. This represents a shift in plant science research from relatively simple trial-and-error approaches to innovative strategies based on predictive models of biological systems. Plant biosystems design seeks to accelerate plant genetic improvement using genome editing and genetic circuit engineering or create novel plant systems through de novo synthesis of plant genomes. From this perspective, we present a comprehensive roadmap of plant biosystems design covering theories, principles, and technical methods, along with potential applications in basic and applied plant biology research. We highlight current challenges, future opportunities, and research priorities, along with a framework for international collaboration, towards rapid advancement of this emerging interdisciplinary area of research. Finally, we discuss the importance of social responsibility in utilizing plant biosystems design and suggest strategies for improving public perception, trust, and acceptance.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - June I. Medford
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Henrique C. De Paoli
- Department of Biodesign, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Cong T. Trinh
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN 37996, USA
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Raphael Ployet
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Steven G. Hussey
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Alexander A. Myburg
- Department of Biochemistry, Genetics and Microbiology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Rolighedsvej 26, DK-1858, Frederiksberg, Copenhagen, Denmark
| | - Md Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin Zhang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Udaya C. Kalluri
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Hengfu Yin
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Renying Zhuo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, Zhejiang 311400, China
| | - Paul E. Abraham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Yinong Yang
- Department of Plant Pathology and Environmental Microbiology and the Huck Institute of the Life Sciences, The Pennsylvania State University, University Park, PA 16802, USA
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Yi Li
- Department of Plant Science and Landscape Architecture, University of Connecticut, Storrs, CT 06269, USA
| | - Jessy Labbe
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Bing Yang
- Division of Plant Sciences, Bond Life Sciences Center, University of Missouri, Columbia, MO, USA
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Jun Hyung Lee
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | | | - Stanton Martin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Mengzhu Lu
- State Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Julie C. Mitchell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Stan D. Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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Yuan G, Hassan MM, Liu D, Lim SD, Yim WC, Cushman JC, Markel K, Shih PM, Lu H, Weston DJ, Chen JG, Tschaplinski TJ, Tuskan GA, Yang X. Biosystems Design to Accelerate C 3-to-CAM Progression. Biodes Res 2020; 2020:3686791. [PMID: 37849902 PMCID: PMC10521703 DOI: 10.34133/2020/3686791] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 08/21/2020] [Indexed: 10/19/2023] Open
Abstract
Global demand for food and bioenergy production has increased rapidly, while the area of arable land has been declining for decades due to damage caused by erosion, pollution, sea level rise, urban development, soil salinization, and water scarcity driven by global climate change. In order to overcome this conflict, there is an urgent need to adapt conventional agriculture to water-limited and hotter conditions with plant crop systems that display higher water-use efficiency (WUE). Crassulacean acid metabolism (CAM) species have substantially higher WUE than species performing C3 or C4 photosynthesis. CAM plants are derived from C3 photosynthesis ancestors. However, it is extremely unlikely that the C3 or C4 crop plants would evolve rapidly into CAM photosynthesis without human intervention. Currently, there is growing interest in improving WUE through transferring CAM into C3 crops. However, engineering a major metabolic plant pathway, like CAM, is challenging and requires a comprehensive deep understanding of the enzymatic reactions and regulatory networks in both C3 and CAM photosynthesis, as well as overcoming physiometabolic limitations such as diurnal stomatal regulation. Recent advances in CAM evolutionary genomics research, genome editing, and synthetic biology have increased the likelihood of successful acceleration of C3-to-CAM progression. Here, we first summarize the systems biology-level understanding of the molecular processes in the CAM pathway. Then, we review the principles of CAM engineering in an evolutionary context. Lastly, we discuss the technical approaches to accelerate the C3-to-CAM transition in plants using synthetic biology toolboxes.
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Affiliation(s)
- Guoliang Yuan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Md. Mahmudul Hassan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- Department of Genetics and Plant Breeding, Patuakhali Science and Technology University, Dumki, Patuakhali 8602, Bangladesh
| | - Degao Liu
- Department of Genetics, Cell Biology and Development, Center for Precision Plant Genomics, and Center for Genome Engineering, University of Minnesota, Saint Paul, MN 55108, USA
| | - Sung Don Lim
- Department of Applied Plant Sciences, Kangwon National University, Chuncheon 24341, Republic of Korea
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - John C. Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, Reno, NV, USA
| | - Kasey Markel
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
| | - Patrick M. Shih
- Department of Plant Biology, University of California, Davis, Davis, CA, USA
- Feedstocks Division, Joint BioEnergy Institute, Emeryville, CA, USA
| | - Haiwei Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Timothy J. Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
- The Center for Bioenergy Innovation, Oak Ridge National Laboratory, Oak Ridge, TN 37831, USA
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26
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Oke TA, Turetsky MR, Weston DJ, Shaw JA. Tradeoffs between phenotypic plasticity and local adaptation influence the ecophysiology of the moss, Sphagnum magellanicum. Oecologia 2020; 193:867-877. [PMID: 32809053 DOI: 10.1007/s00442-020-04735-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Accepted: 08/13/2020] [Indexed: 11/28/2022]
Abstract
Bryophytes are a diverse plant group and are functionally different from vascular plants. Yet, their peculiarities are rarely considered in the theoretical frameworks for plants. Currently, we lack information about the magnitude and the importance of intraspecific variability in the ecophysiology of bryophytes and how these might translate to local adaptation-a prerequisite for adaptive evolution. Capitalizing on two ecologically distinct (hummock and hollow) phenotypes of Sphagnum magellanicum, we explored the magnitude and pattern of intraspecific variability in this species and asked whether the environmental-mediated changes in shoot and physiological traits are due to phenotypic plasticity or local adaptation. Size, pigmentation, and habitat type that distinguished the phenotypes in the field did not influence the trait responses under a transplant and factorial experiment. In addition, the magnitude and pattern of trait variability (e.g., branch, stem and capitulum mass) changed with the treatments, which suggest that trait responses were due largely to phenotypic plasticity. The trait responses also suggest that the ecophysiological needs for mosses to grow in clumps, where they maintain a uniform growth may have an overriding effect over the potential for a fixed adaptive response to environmental heterogeneity, which would constrain local adaptation. We conclude that extending the trait-based framework to mosses or making comparisons between mosses and vascular plants under any theoretical framework would only be meaningful to the extent that growth form and dispersal strategies are considered.
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Affiliation(s)
- Tobi A Oke
- Marine Science Institute, The University of Texas Austin, Port Aransas, TX, USA.
| | - Merritt R Turetsky
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, CO, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
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27
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Piatkowski BT, Imwattana K, Tripp EA, Weston DJ, Healey A, Schmutz J, Shaw AJ. Phylogenomics reveals convergent evolution of red-violet coloration in land plants and the origins of the anthocyanin biosynthetic pathway. Mol Phylogenet Evol 2020; 151:106904. [PMID: 32645485 DOI: 10.1016/j.ympev.2020.106904] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 06/23/2020] [Accepted: 07/01/2020] [Indexed: 11/17/2022]
Abstract
The flavonoids, one of the largest classes of plant secondary metabolites, are found in lineages that span the land plant phylogeny and play important roles in stress responses and as pigments. Perhaps the most well-studied flavonoids are the anthocyanins that have human health benefits and help plants attract pollinators, regulate hormone production, and confer resistance to abiotic and biotic stresses. The canonical biochemical pathway responsible for the production of these pigments is well-characterized for flowering plants yet its conservation across deep divergences in land plants remains debated and poorly understood. Many early land plants such as mosses, liverworts, and ferns produce flavonoid pigments, but their biosynthetic origins and homologies to the anthocyanin pathway remain uncertain. We conducted phylogenetic analyses using full genome sequences representing nearly all major green plant lineages to reconstruct the evolutionary history of the anthocyanin biosynthetic pathway then test the hypothesis that genes in this pathway are present in early land plants. We found that the entire pathway was not intact until the most recent common ancestor of seed plants and that orthologs of many downstream enzymes are absent from seedless plants including mosses, liverworts, and ferns. Our results also highlight the utility of phylogenetic inference, as compared to pairwise sequence similarity, in orthology assessment within large gene families that have complex duplication-loss histories. We suggest that the production of red-violet flavonoid pigments widespread in seedless plants, including the 3-deoxyanthocyanins, requires the activity of novel, as-yet discovered enzymes, and represents convergent evolution of red-violet coloration across land plants.
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Affiliation(s)
- Bryan T Piatkowski
- Department of Biology, Duke University, Durham, NC 27708, United States.
| | - Karn Imwattana
- Department of Biology, Duke University, Durham, NC 27708, United States
| | - Erin A Tripp
- Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309, United States
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States; Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Adam Healey
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806, United States
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL 35806, United States; Department of Energy Joint Genome Institute, Berkeley, CA 94720, United States
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC 27708, United States
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28
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Carper DL, Lawrence TJ, Carrell AA, Pelletier DA, Weston DJ. DISCo-microbe: design of an identifiable synthetic community of microbes. PeerJ 2020; 8:e8534. [PMID: 32149021 PMCID: PMC7049465 DOI: 10.7717/peerj.8534] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Microbiomes are extremely important for their host organisms, providing many vital functions and extending their hosts' phenotypes. Natural studies of host-associated microbiomes can be difficult to interpret due to the high complexity of microbial communities, which hinders our ability to track and identify individual members along with the many factors that structure or perturb those communities. For this reason, researchers have turned to synthetic or constructed communities in which the identities of all members are known. However, due to the lack of tracking methods and the difficulty of creating a more diverse and identifiable community that can be distinguished through next-generation sequencing, most such in vivo studies have used only a few strains. RESULTS To address this issue, we developed DISCo-microbe, a program for the design of an identifiable synthetic community of microbes for use in in vivo experimentation. The program is composed of two modules; (1) create, which allows the user to generate a highly diverse community list from an input DNA sequence alignment using a custom nucleotide distance algorithm, and (2) subsample, which subsamples the community list to either represent a number of grouping variables, including taxonomic proportions, or to reach a user-specified maximum number of community members. As an example, we demonstrate the generation of a synthetic microbial community that can be distinguished through amplicon sequencing. The synthetic microbial community in this example consisted of 2,122 members from a starting DNA sequence alignment of 10,000 16S rRNA sequences from the Ribosomal Database Project. We generated simulated Illumina sequencing data from the constructed community and demonstrate that DISCo-microbe is capable of designing diverse communities with members distinguishable by amplicon sequencing. Using the simulated data we were able to recover sequences from between 97-100% of community members using two different post-processing workflows. Furthermore, 97-99% of sequences were assigned to a community member with zero sequences being misidentified. We then subsampled the community list using taxonomic proportions to mimic a natural plant host-associated microbiome, ultimately yielding a diverse community of 784 members. CONCLUSIONS DISCo-microbe can create a highly diverse community list of microbes that can be distinguished through 16S rRNA gene sequencing, and has the ability to subsample (i.e., design) the community for the desired number of members and taxonomic proportions. Although developed for bacteria, the program allows for any alignment input from any taxonomic group, making it broadly applicable. The software and data are freely available from GitHub (https://github.com/dlcarper/DISCo-microbe) and Python Package Index (PYPI).
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Affiliation(s)
- Dana L. Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Travis J. Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee—Knoxville, Knoxville, TN, United States of America
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States of America
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29
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Henning JA, Weston DJ, Pelletier DA, Timm CM, Jawdy SS, Classen AT. Relatively rare root endophytic bacteria drive plant resource allocation patterns and tissue nutrient concentration in unpredictable ways. Am J Bot 2019; 106:1423-1434. [PMID: 31657872 DOI: 10.1002/ajb2.1373] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Accepted: 09/06/2019] [Indexed: 05/12/2023]
Abstract
PREMISE Plant endophytic bacterial strains can influence plant traits such as leaf area and root length. Yet, the influence of more complex bacterial communities in regulating overall plant phenotype is less explored. Here, in two complementary experiments, we tested whether we can predict plant phenotype response to changes in microbial community composition. METHODS In the first study, we inoculated a single genotype of Populus deltoides with individual root endophytic bacteria and measured plant phenotype. Next, data from this single inoculation were used to predict phenotypic traits after mixed three-strain community inoculations, which we tested in the second experiment. RESULTS By itself, each bacterial endophyte significantly but weakly altered plant phenotype relative to noninoculated plants. In a mixture, bacterial strain Burkholderia BT03, constituted at least 98% of community relative abundance. Yet, plant resource allocation and tissue nutrient concentrations were disproportionately influenced by Pseudomonas sp. GM17, GM30, and GM41. We found a 10% increase in leaf mass fraction and an 11% decrease in root mass fraction when replacing Pseudomonas GM17 with GM41 in communities containing both Pseudomonas GM30 and Burkholderia BT03. CONCLUSIONS Our results indicate that interactions among endophytic bacteria may drive plant phenotype over the contribution of each strain individually. Additionally, we have shown that low-abundance strains contribute to plant phenotype challenging the assumption that the dominant strains will drive plant function.
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Affiliation(s)
- Jeremiah A Henning
- Ecology & Evolutionary Biology, University of Tennessee, 569 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996, USA
- Ecology, Evolution, and Behavior, University of Minnesota, 140 Gortner Avenue, St. Paul, MN, 55108, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Biosciences, Johns Hopkins University Applied Physics Laboratory, 11100 Johns Hopkins Road, Laurel, MD, 20723, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Aimée T Classen
- Ecology & Evolutionary Biology, University of Tennessee, 569 Dabney Hall, 1416 Circle Drive, Knoxville, TN, 37996, USA
- The Rubenstein School of Environment & Natural Resources, University of Vermont, Burlington, VT, 05405, USA
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30
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Carrell AA, Kolton M, Glass JB, Pelletier DA, Warren MJ, Kostka JE, Iversen CM, Hanson PJ, Weston DJ. Experimental warming alters the community composition, diversity, and N 2 fixation activity of peat moss (Sphagnum fallax) microbiomes. Glob Chang Biol 2019; 25:2993-3004. [PMID: 31148286 PMCID: PMC6852288 DOI: 10.1111/gcb.14715] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 05/17/2019] [Accepted: 05/24/2019] [Indexed: 05/19/2023]
Abstract
Sphagnum-dominated peatlands comprise a globally important pool of soil carbon (C) and are vulnerable to climate change. While peat mosses of the genus Sphagnum are known to harbor diverse microbial communities that mediate C and nitrogen (N) cycling in peatlands, the effects of climate change on Sphagnum microbiome composition and functioning are largely unknown. We investigated the impacts of experimental whole-ecosystem warming on the Sphagnum moss microbiome, focusing on N2 fixing microorganisms (diazotrophs). To characterize the microbiome response to warming, we performed next-generation sequencing of small subunit (SSU) rRNA and nitrogenase (nifH) gene amplicons and quantified rates of N2 fixation activity in Sphagnum fallax individuals sampled from experimental enclosures over 2 years in a northern Minnesota, USA bog. The taxonomic diversity of overall microbial communities and diazotroph communities, as well as N2 fixation rates, decreased with warming (p < 0.05). Following warming, diazotrophs shifted from a mixed community of Nostocales (Cyanobacteria) and Rhizobiales (Alphaproteobacteria) to predominance of Nostocales. Microbiome community composition differed between years, with some diazotroph populations persisting while others declined in relative abundance in warmed plots in the second year. Our results demonstrate that warming substantially alters the community composition, diversity, and N2 fixation activity of peat moss microbiomes, which may ultimately impact host fitness, ecosystem productivity, and C storage potential in peatlands.
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Affiliation(s)
- Alyssa A. Carrell
- Bredesen Center for Interdisciplinary Research and Graduate EducationUniversity of TennesseeKnoxvilleTennessee
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
| | - Max Kolton
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
| | - Jennifer B. Glass
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | | | - Melissa J. Warren
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
- Present address:
CH2MAtlantaGeorgia30328USA
| | - Joel E. Kostka
- School of BiologyGeorgia Institute of TechnologyAtlantaGeorgia
- School of Earth and Atmospheric SciencesGeorgia Institute of TechnologyAtlantaGeorgia
| | - Colleen M. Iversen
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - Paul J. Hanson
- Environmental Sciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
| | - David J. Weston
- Biosciences DivisionOak Ridge National LaboratoryOak RidgeTennessee
- Climate Change Science Institute, Oak Ridge National LaboratoryOak RidgeTennessee
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31
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Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X. Correction to: Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics 2019; 20:279. [PMID: 30971209 PMCID: PMC6456932 DOI: 10.1186/s12864-019-5663-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 04/01/2019] [Indexed: 11/28/2022] Open
Affiliation(s)
- Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Present address: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou, 311400, Zhejiang, China
| | - Hao-Bo Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Wachira
- Department of Biology, Morgan State University, Baltimore, MD, 21251, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hong Guo
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Present address: Illumina, Inc., San Diego, CA, 92122, USA
| | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Nagy G, Veličković D, Chu RK, Carrell AA, Weston DJ, Ibrahim YM, Anderton CR, Smith RD. Towards resolving the spatial metabolome with unambiguous molecular annotations in complex biological systems by coupling mass spectrometry imaging with structures for lossless ion manipulations. Chem Commun (Camb) 2019; 55:306-309. [PMID: 30534702 PMCID: PMC6537888 DOI: 10.1039/c8cc07482h] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
We demonstrate the coupling of liquid extraction surface analysis (LESA) to structures for lossless ion manipulations in conjunction with serpentine ultralong path with extending routing (SLIM SUPER) ion mobility-mass spectrometry (IM-MS) for the unambiguous annotation of important isomeric glycoforms in carbon-fixing communities.
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Affiliation(s)
- Gabe Nagy
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA.
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33
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Arkin AP, Cottingham RW, Henry CS, Harris NL, Stevens RL, Maslov S, Dehal P, Ware D, Perez F, Canon S, Sneddon MW, Henderson ML, Riehl WJ, Murphy-Olson D, Chan SY, Kamimura RT, Kumari S, Drake MM, Brettin TS, Glass EM, Chivian D, Gunter D, Weston DJ, Allen BH, Baumohl J, Best AA, Bowen B, Brenner SE, Bun CC, Chandonia JM, Chia JM, Colasanti R, Conrad N, Davis JJ, Davison BH, DeJongh M, Devoid S, Dietrich E, Dubchak I, Edirisinghe JN, Fang G, Faria JP, Frybarger PM, Gerlach W, Gerstein M, Greiner A, Gurtowski J, Haun HL, He F, Jain R, Joachimiak MP, Keegan KP, Kondo S, Kumar V, Land ML, Meyer F, Mills M, Novichkov PS, Oh T, Olsen GJ, Olson R, Parrello B, Pasternak S, Pearson E, Poon SS, Price GA, Ramakrishnan S, Ranjan P, Ronald PC, Schatz MC, Seaver SMD, Shukla M, Sutormin RA, Syed MH, Thomason J, Tintle NL, Wang D, Xia F, Yoo H, Yoo S, Yu D. KBase: The United States Department of Energy Systems Biology Knowledgebase. Nat Biotechnol 2018; 36:566-569. [PMID: 29979655 PMCID: PMC6870991 DOI: 10.1038/nbt.4163] [Citation(s) in RCA: 684] [Impact Index Per Article: 114.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Adam P Arkin
- Department of Bioengineering, University of California, Berkeley, California, USA.,Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Robert W Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Christopher S Henry
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Nomi L Harris
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Rick L Stevens
- Computer Science Department and Computation Institute, University of Chicago, Chicago, Illinois, USA.,Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Sergei Maslov
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Paramvir Dehal
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Doreen Ware
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Fernando Perez
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Berkeley Institute for Data Science, University of California, Berkeley, California, USA.,Department of Statistics, University of California, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Shane Canon
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael W Sneddon
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Matthew L Henderson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - William J Riehl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Murphy-Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Stephen Y Chan
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Roy T Kamimura
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sunita Kumari
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Meghan M Drake
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Thomas S Brettin
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Elizabeth M Glass
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Dylan Chivian
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Dan Gunter
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Benjamin H Allen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Jason Baumohl
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Aaron A Best
- Department of Biology, Hope College, Holland, Michigan, USA
| | - Ben Bowen
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Steven E Brenner
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Christopher C Bun
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - John-Marc Chandonia
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jer-Ming Chia
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Ric Colasanti
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Neal Conrad
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - James J Davis
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Brian H Davison
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Matthew DeJongh
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Scott Devoid
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Emily Dietrich
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Inna Dubchak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Janaka N Edirisinghe
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA.,Computation Institute, University of Chicago, Chicago, Illinois, USA
| | - Gang Fang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - José P Faria
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Paul M Frybarger
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Wolfgang Gerlach
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Mark Gerstein
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA
| | - Annette Greiner
- National Energy Research Scientific Computing Center, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - James Gurtowski
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Holly L Haun
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Fei He
- Biology Department, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Rashmi Jain
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Marcin P Joachimiak
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Kevin P Keegan
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinnosuke Kondo
- Department of Computer Science, Hope College, Holland, Michigan, USA
| | - Vivek Kumar
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Miriam L Land
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Folker Meyer
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Marissa Mills
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA
| | - Pavel S Novichkov
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Taeyun Oh
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Gary J Olsen
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Robert Olson
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Bruce Parrello
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shiran Pasternak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Erik Pearson
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sarah S Poon
- Computational Research Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Gavin A Price
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Srividya Ramakrishnan
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Plant Sciences, University of Tennessee, Knoxville, Tennessee, USA
| | - Pamela C Ronald
- Department of Plant Pathology and Genome Center, University of California, Davis, Davis, California, USA.,Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Michael C Schatz
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Samuel M D Seaver
- Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, Illinois, USA
| | - Maulik Shukla
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Roman A Sutormin
- Environmental Genomics and Systems Biology Division, E.O. Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Mustafa H Syed
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - James Thomason
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA
| | - Nathan L Tintle
- Department of Mathematics, Hope College, Holland, Michigan, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Daifeng Wang
- Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
| | - Fangfang Xia
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Hyunseung Yoo
- Computing, Environment, and Life Sciences Directorate, Argonne National Laboratory, Argonne, Illinois, USA
| | - Shinjae Yoo
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA
| | - Dantong Yu
- Computer Science and Math, Computer Science Initiative, Brookhaven National Laboratory, Upton, New York, USA.,Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA (S.M.); Department of Statistics, University of California, Berkeley, California, USA (F.P.); New York University Shanghai Campus, Pudong, Shanghai, China (G.F.); Department of Plant Pathology, Kansas State University, Manhattan, Kansas, USA (F.H.); Insilicogen. Inc., Giheung-gu, Yongin-si, Gyeonggi-do, Korea (T.O.); Department of Computer Science, Johns Hopkins University, Baltimore, Maryland, USA (S.R., M.C.S.); Memorial Sloan Kettering Cancer Center, New York, New York, USA (M.H.S.); Dordt College, Sioux Center, Iowa, USA (N.L.T.); Department of Biomedical Informatics, Stony Brook University, Stony Brook, New York, USA (D.W.); Martin Tuchman School of Management, New Jersey Institute of Technology, Newark, New Jersey, USA (D.Y.)
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34
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Yin H, Guo HB, Weston DJ, Borland AM, Ranjan P, Abraham PE, Jawdy SS, Wachira J, Tuskan GA, Tschaplinski TJ, Wullschleger SD, Guo H, Hettich RL, Gross SM, Wang Z, Visel A, Yang X. Diel rewiring and positive selection of ancient plant proteins enabled evolution of CAM photosynthesis in Agave. BMC Genomics 2018; 19:588. [PMID: 30081833 PMCID: PMC6090859 DOI: 10.1186/s12864-018-4964-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 07/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Crassulacean acid metabolism (CAM) enhances plant water-use efficiency through an inverse day/night pattern of stomatal closure/opening that facilitates nocturnal CO2 uptake. CAM has evolved independently in over 35 plant lineages, accounting for ~ 6% of all higher plants. Agave species are highly heat- and drought-tolerant, and have been domesticated as model CAM crops for beverage, fiber, and biofuel production in semi-arid and arid regions. However, the genomic basis of evolutionary innovation of CAM in genus Agave is largely unknown. Results Using an approach that integrated genomics, gene co-expression networks, comparative genomics and protein structure analyses, we investigated the molecular evolution of CAM as exemplified in Agave. Comparative genomics analyses among C3, C4 and CAM species revealed that core metabolic components required for CAM have ancient genomic origins traceable to non-vascular plants while regulatory proteins required for diel re-programming of metabolism have a more recent origin shared among C3, C4 and CAM species. We showed that accelerated evolution of key functional domains in proteins responsible for primary metabolism and signaling, together with a diel re-programming of the transcription of genes involved in carbon fixation, carbohydrate processing, redox homeostasis, and circadian control is required for the evolution of CAM in Agave. Furthermore, we highlighted the potential candidates contributing to the adaptation of CAM functional modules. Conclusions This work provides evidence of adaptive evolution of CAM related pathways. We showed that the core metabolic components required for CAM are shared by non-vascular plants, but regulatory proteins involved in re-reprogramming of carbon fixation and metabolite transportation appeared more recently. We propose that the accelerated evolution of key proteins together with a diel re-programming of gene expression were required for CAM evolution from C3 ancestors in Agave. Electronic supplementary material The online version of this article (10.1186/s12864-018-4964-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Present address: Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Zhejiang, 311400, Hangzhou, China
| | - Hao-Bo Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Paul E Abraham
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Sara S Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - James Wachira
- Department of Biology, Morgan State University, Baltimore, MD, 21251, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Timothy J Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Hong Guo
- Department of Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Robert L Hettich
- DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.,Chemical Sciences Division, Oak Ridge National Laboratory, 37831, Oak Ridge, TN, USA
| | - Stephen M Gross
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,Present address: Illumina, Inc., San Diego, CA, 92122, USA
| | - Zhong Wang
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Axel Visel
- DOE Joint Genome Institute, Walnut Creek, CA, 94598, USA.,School of Natural Sciences, University of California, Merced, CA, 95343, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA. .,DOE-Center for Bioenergy Innovation (CBI), Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA.
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Weston DJ, Turetsky MR, Johnson MG, Granath G, Lindo Z, Belyea LR, Rice SK, Hanson DT, Engelhardt KAM, Schmutz J, Dorrepaal E, Euskirchen ES, Stenøien HK, Szövényi P, Jackson M, Piatkowski BT, Muchero W, Norby RJ, Kostka JE, Glass JB, Rydin H, Limpens J, Tuittila ES, Ullrich KK, Carrell A, Benscoter BW, Chen JG, Oke TA, Nilsson MB, Ranjan P, Jacobson D, Lilleskov EA, Clymo RS, Shaw AJ. The Sphagnome Project: enabling ecological and evolutionary insights through a genus-level sequencing project. New Phytol 2018; 217:16-25. [PMID: 29076547 DOI: 10.1111/nph.14860] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Considerable progress has been made in ecological and evolutionary genetics with studies demonstrating how genes underlying plant and microbial traits can influence adaptation and even 'extend' to influence community structure and ecosystem level processes. Progress in this area is limited to model systems with deep genetic and genomic resources that often have negligible ecological impact or interest. Thus, important linkages between genetic adaptations and their consequences at organismal and ecological scales are often lacking. Here we introduce the Sphagnome Project, which incorporates genomics into a long-running history of Sphagnum research that has documented unparalleled contributions to peatland ecology, carbon sequestration, biogeochemistry, microbiome research, niche construction, and ecosystem engineering. The Sphagnome Project encompasses a genus-level sequencing effort that represents a new type of model system driven not only by genetic tractability, but by ecologically relevant questions and hypotheses.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Merritt R Turetsky
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Matthew G Johnson
- Department of Biological Sciences, Texas Tech University, Lubbock, TX, 79414, USA
| | - Gustaf Granath
- Department of Ecology, Swedish University of Agricultural Sciences, Box 7044, SE-750 07, Uppsala, Sweden
| | - Zoë Lindo
- Department of Biology, The University of Western Ontario, London, ON, N6A 5B7, Canada
| | - Lisa R Belyea
- School of Geography, Queen Mary University of London, London, E1 4NS, UK
| | - Steven K Rice
- Department of Biological Sciences, Union College, Schenectady, NY, 12308, USA
| | - David T Hanson
- Department of Biology, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Katharina A M Engelhardt
- Appalachian Lab, University of Maryland Center of Environmental Science, Frostburg, MD, 21532, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
| | - Ellen Dorrepaal
- Climate Impacts Research Center, Department of Ecology and Environmental Science, Umeå University, 98107, Abisko, Sweden
| | | | - Hans K Stenøien
- NTNU University Museum, Norwegian University of Science and Technology, NO-7491, Trondheim, Norway
| | - Péter Szövényi
- Department of Systematic and Evolutionary Botany, University of Zurich, 8008, Zurich, Switzerland
| | | | | | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Richard J Norby
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Jennifer B Glass
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Håkan Rydin
- Department of Ecology and Genetics, Uppsala University, Norbyvägen 18D, SE-75236, Uppsala, Sweden
| | - Juul Limpens
- Plant Ecology and Nature Conservation Group, Department of Environmental Sciences, Wageningen University, Droevendaalse steeg 3a, NL-6708 PD, Wageningen, the Netherlands
| | - Eeva-Stiina Tuittila
- Peatland and Soil Ecology Group, School of Forest Sciences, University of Eastern Finland, Joensuu, Finland
| | | | - Alyssa Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Brian W Benscoter
- Department of Biological Sciences, Florida Atlantic University, Davie, FL, 33314, USA
| | - Jin-Gui Chen
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Tobi A Oke
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Mats B Nilsson
- Department of Forest Ecology and Management, Swedish University of Agricultural Sciences, Skogsmarksgränd, SE-901 83, Umeå, Sweden
| | - Priya Ranjan
- Department of Plant Sciences, University of Tennessee, 2431 Joe Johnson Drive, Knoxville, TN, 37996-4561, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Erik A Lilleskov
- US Forest Service, Northern Research Station, 410 MacInnes Dr., Houghton, MI, 49931, USA
| | - R S Clymo
- School of Biological & Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
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Veličković D, Chu RK, Carrell AA, Thomas M, Paša-Tolić L, Weston DJ, Anderton CR. Multimodal MSI in Conjunction with Broad Coverage Spatially Resolved MS 2 Increases Confidence in Both Molecular Identification and Localization. Anal Chem 2017; 90:702-707. [PMID: 29210566 DOI: 10.1021/acs.analchem.7b04319] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
One critical aspect of mass spectrometry imaging (MSI) is the need to confidently identify detected analytes. While orthogonal tandem MS (e.g., LC-MS2) experiments from sample extracts can assist in annotating ions, the spatial information about these molecules is lost. Accordingly, this could cause mislead conclusions, especially in cases where isobaric species exhibit different distributions within a sample. In this Technical Note, we employed a multimodal imaging approach, using matrix assisted laser desorption/ionization (MALDI)-MSI and liquid extraction surface analysis (LESA)-MS2I, to confidently annotate and localize a broad range of metabolites involved in a tripartite symbiosis system of moss, cyanobacteria, and fungus. We found that the combination of these two imaging modalities generated very congruent ion images, providing the link between highly accurate structural information onfered by LESA and high spatial resolution attainable by MALDI. These results demonstrate how this combined methodology could be very useful in differentiating metabolite routes in complex systems.
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Affiliation(s)
| | | | - Alyssa A Carrell
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
| | | | | | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37830, United States
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Cabugao KG, Timm CM, Carrell AA, Childs J, Lu TYS, Pelletier DA, Weston DJ, Norby RJ. Root and Rhizosphere Bacterial Phosphatase Activity Varies with Tree Species and Soil Phosphorus Availability in Puerto Rico Tropical Forest. Front Plant Sci 2017; 8:1834. [PMID: 29163572 PMCID: PMC5670114 DOI: 10.3389/fpls.2017.01834] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 10/10/2017] [Indexed: 05/29/2023]
Abstract
Tropical forests generally occur on highly weathered soils that, in combination with the immobility of phosphorus (P), often result in soils lacking orthophosphate, the form of P most easily metabolized by plants and microbes. In these soils, mineralization of organic P can be the major source for orthophosphate. Both plants and microbes encode for phosphatases capable of mineralizing a range of organic P compounds. However, the activity of these enzymes depends on several edaphic factors including P availability, tree species, and microbial communities. Thus, phosphatase activity in both roots and the root microbial community constitute an important role in P mineralization and P nutrient dynamics that are not well studied in tropical forests. To relate phosphatase activity of roots and bacteria in tropical forests, we measured phosphatase activity in roots and bacterial isolates as well as bacterial community composition from the rhizosphere. Three forests in the Luquillo Mountains of Puerto Rico were selected to represent a range of soil P availability as measured using the resin P method. Within each site, a minimum of three tree species were chosen to sample. Root and bacterial phosphatase activity were both measured using a colorimetric assay with para-nitrophenyl phosphate as a substrate for the phosphomonoesterase enzyme. Both root and bacterial phosphatase were chiefly influenced by tree species. Though tree species was the only significant factor in root phosphatase activity, there was a negative trend between soil P availability and phosphatase activity in linear regressions of average root phosphatase and resin P. Permutational multivariate analysis of variance of bacterial community composition based on 16S amplicon sequencing indicated that bacterial composition was strongly controlled by soil P availability (p-value < 0.05). These results indicate that although root and bacterial phosphatase activity were influenced by tree species; bacterial community composition was chiefly influenced by P availability. Although the sample size is limited given the tremendous diversity of tropical forests, our study indicates the importance of roots and bacterial function to understanding phosphatase activity. Future work will broaden the diversity of tree species and microbial members sampled to provide insight into P mineralization and model representation of tropical forests.
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Affiliation(s)
- Kristine G. Cabugao
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, United States
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Collin M. Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Alyssa A. Carrell
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Joanne Childs
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Tse-Yuan S. Lu
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David J. Weston
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Richard J. Norby
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, United States
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Norby RJ, Gu L, Haworth IC, Jensen AM, Turner BL, Walker AP, Warren JM, Weston DJ, Xu C, Winter K. Informing models through empirical relationships between foliar phosphorus, nitrogen and photosynthesis across diverse woody species in tropical forests of Panama. New Phytol 2017; 215:1425-1437. [PMID: 27870067 DOI: 10.1111/nph.14319] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 09/24/2016] [Indexed: 06/06/2023]
Abstract
Our objective was to analyze and summarize data describing photosynthetic parameters and foliar nutrient concentrations from tropical forests in Panama to inform model representation of phosphorus (P) limitation of tropical forest productivity. Gas exchange and nutrient content data were collected from 144 observations of upper canopy leaves from at least 65 species at two forest sites in Panama, differing in species composition, rainfall and soil fertility. Photosynthetic parameters were derived from analysis of assimilation rate vs internal CO2 concentration curves (A/Ci ), and relationships with foliar nitrogen (N) and P content were developed. The relationships between area-based photosynthetic parameters and nutrients were of similar strength for N and P and robust across diverse species and site conditions. The strongest relationship expressed maximum electron transport rate (Jmax ) as a multivariate function of both N and P, and this relationship was improved with the inclusion of independent data on wood density. Models that estimate photosynthesis from foliar N would be improved only modestly by including additional data on foliar P, but doing so may increase the capability of models to predict future conditions in P-limited tropical forests, especially when combined with data on edaphic conditions and other environmental drivers.
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Affiliation(s)
- Richard J Norby
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Ivan C Haworth
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Anna M Jensen
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
- Department of Forestry and Wood Technology, Linnaeus University, Växjö, Sweden
| | - Benjamin L Turner
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
| | - Anthony P Walker
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Jeffrey M Warren
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - David J Weston
- Biosciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37830-6301, USA
| | - Chonggang Xu
- Earth and Environmental Science Division, Los Alamos National Laboratory, Los Alamos, NM, 87545, USA
| | - Klaus Winter
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
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Abraham PE, Yin H, Borland AM, Weighill D, Lim SD, De Paoli HC, Engle N, Jones PC, Agh R, Weston DJ, Wullschleger SD, Tschaplinski T, Jacobson D, Cushman JC, Hettich RL, Tuskan GA, Yang X. Transcript, protein and metabolite temporal dynamics in the CAM plant Agave. Nat Plants 2016; 2:16178. [PMID: 27869799 DOI: 10.1038/nplants.2016.178] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2016] [Accepted: 10/20/2016] [Indexed: 05/19/2023]
Abstract
Already a proven mechanism for drought resilience, crassulacean acid metabolism (CAM) is a specialized type of photosynthesis that maximizes water-use efficiency by means of an inverse (compared to C3 and C4 photosynthesis) day/night pattern of stomatal closure/opening to shift CO2 uptake to the night, when evapotranspiration rates are low. A systems-level understanding of temporal molecular and metabolic controls is needed to define the cellular behaviour underpinning CAM. Here, we report high-resolution temporal behaviours of transcript, protein and metabolite abundances across a CAM diel cycle and, where applicable, compare the observations to the well-established C3 model plant Arabidopsis. A mechanistic finding that emerged is that CAM operates with a diel redox poise that is shifted relative to that in Arabidopsis. Moreover, we identify widespread rescheduled expression of genes associated with signal transduction mechanisms that regulate stomatal opening/closing. Controlled production and degradation of transcripts and proteins represents a timing mechanism by which to regulate cellular function, yet knowledge of how this molecular timekeeping regulates CAM is unknown. Here, we provide new insights into complex post-transcriptional and -translational hierarchies that govern CAM in Agave. These data sets provide a resource to inform efforts to engineer more efficient CAM traits into economically valuable C3 crops.
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Affiliation(s)
- Paul E Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Hengfu Yin
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- School of Biology, University of Newcastle, Newcastle upon Tyne NE1 7RU, UK
| | - Deborah Weighill
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, Nevada 89557-0330, USA
| | | | - Nancy Engle
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Piet C Jones
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - Ryan Agh
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Timothy Tschaplinski
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Daniel Jacobson
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Tennessee 37996, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, Nevada 89557-0330, USA
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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Henning JA, Weston DJ, Pelletier DA, Timm CM, Jawdy SS, Classen AT. Root bacterial endophytes alter plant phenotype, but not physiology. PeerJ 2016; 4:e2606. [PMID: 27833797 PMCID: PMC5101591 DOI: 10.7717/peerj.2606] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 09/24/2016] [Indexed: 12/15/2022] Open
Abstract
Plant traits, such as root and leaf area, influence how plants interact with their environment and the diverse microbiota living within plants can influence plant morphology and physiology. Here, we explored how three bacterial strains isolated from the Populus root microbiome, influenced plant phenotype. We chose three bacterial strains that differed in predicted metabolic capabilities, plant hormone production and metabolism, and secondary metabolite synthesis. We inoculated each bacterial strain on a single genotype of Populus trichocarpa and measured the response of plant growth related traits (root:shoot, biomass production, root and leaf growth rates) and physiological traits (chlorophyll content, net photosynthesis, net photosynthesis at saturating light-Asat, and saturating CO2-Amax). Overall, we found that bacterial root endophyte infection increased root growth rate up to 184% and leaf growth rate up to 137% relative to non-inoculated control plants, evidence that plants respond to bacteria by modifying morphology. However, endophyte inoculation had no influence on total plant biomass and photosynthetic traits (net photosynthesis, chlorophyll content). In sum, bacterial inoculation did not significantly increase plant carbon fixation and biomass, but their presence altered where and how carbon was being allocated in the plant host.
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Affiliation(s)
- Jeremiah A. Henning
- Department of Ecology & Evolutionary Biology, University of Tennessee–Knoxville, Knoxville, Tennessee, United States
| | - David J. Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Collin M. Timm
- Joint Institute for Biological Sciences, University of Tennessee, Oak Ridge, TN, United States
| | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - Aimée T. Classen
- Department of Ecology & Evolutionary Biology, University of Tennessee–Knoxville, Knoxville, Tennessee, United States
- Center for Macroecology, Evolution, and Climate, The Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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Kostka JE, Weston DJ, Glass JB, Lilleskov EA, Shaw AJ, Turetsky MR. The Sphagnum microbiome: new insights from an ancient plant lineage. New Phytol 2016; 211:57-64. [PMID: 27173909 DOI: 10.1111/nph.13993] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 02/15/2016] [Indexed: 05/03/2023]
Abstract
57 I. 57 II. 58 III. 59 IV. 59 V. 61 VI. 62 63 References 63 SUMMARY: Peat mosses of the genus Sphagnum play a major role in global carbon storage and dominate many northern peatland ecosystems, which are currently being subjected to some of the most rapid climate changes on Earth. A rapidly expanding database indicates that a diverse community of microorganisms is intimately associated with Sphagnum, inhabiting the tissues and surface of the plant. Here we summarize the current state of knowledge regarding the Sphagnum microbiome and provide a perspective for future research directions. Although the majority of the microbiome remains uncultivated and its metabolic capabilities uncharacterized, prokaryotes and fungi have the potential to act as mutualists, symbionts, or antagonists of Sphagnum. For example, methanotrophic and nitrogen-fixing bacteria may benefit the plant host by providing up to 20-30% of Sphagnum carbon and nitrogen, respectively. Next-generation sequencing approaches have enabled the detailed characterization of microbiome community composition in peat mosses. However, as with other ecologically or economically important plants, our knowledge of Sphagnum-microbiome associations is in its infancy. In order to attain a predictive understanding of the role of the microbiome in Sphagnum productivity and ecosystem function, the mechanisms of plant-microbiome interactions and the metabolic potential of constituent microbial populations must be revealed.
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Affiliation(s)
- Joel E Kostka
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Lab, Oak Ridge, TN, 37831, USA
| | - Jennifer B Glass
- Schools of Biology and Earth & Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Erik A Lilleskov
- Northern Research Station, USDA Forest Service, Houghton, MI, 49931, USA
| | | | - Merritt R Turetsky
- Department of Integrative Biology, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Devos N, Szövényi P, Weston DJ, Rothfels CJ, Johnson MG, Shaw AJ. Analyses of transcriptome sequences reveal multiple ancient large-scale duplication events in the ancestor of Sphagnopsida (Bryophyta). New Phytol 2016; 211:300-18. [PMID: 26900928 DOI: 10.1111/nph.13887] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/04/2016] [Indexed: 05/07/2023]
Abstract
The goal of this research was to investigate whether there has been a whole-genome duplication (WGD) in the ancestry of Sphagnum (peatmoss) or the class Sphagnopsida, and to determine if the timing of any such duplication(s) and patterns of paralog retention could help explain the rapid radiation and current ecological dominance of peatmosses. RNA sequencing (RNA-seq) data were generated for nine taxa in Sphagnopsida (Bryophyta). Analyses of frequency plots for synonymous substitutions per synonymous site (Ks ) between paralogous gene pairs and reconciliation of 578 gene trees were conducted to assess evidence of large-scale or genome-wide duplication events in each transcriptome. Both Ks frequency plots and gene tree-based analyses indicate multiple duplication events in the history of the Sphagnopsida. The most recent WGD event predates divergence of Sphagnum from the two other genera of Sphagnopsida. Duplicate retention is highly variable across species, which might be best explained by local adaptation. Our analyses indicate that the last WGD could have been an important factor underlying the diversification of peatmosses and facilitated their rise to ecological dominance in peatlands. The timing of the duplication events and their significance in the evolutionary history of peat mosses are discussed.
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Affiliation(s)
- Nicolas Devos
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Péter Szövényi
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, 8008, Zurich, Switzerland
- Institute of Systematic Botany, University of Zurich, 8057, Zurich, Switzerland
- Swiss Institute of Bioinformatics, Quartier Sorge-Batiment Genopode, 1015, Lausanne, Switzerland
- MTA ELTE-MTM Ecology Research Group, ELTE, Biological Institute, H1117, Budapest, Hungary
| | - David J Weston
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, 37831, USA
| | - Carl J Rothfels
- University Herbarium & Department of Integrative Biology, University of California, Berkeley, CA, 24720, USA
| | - Matthew G Johnson
- Chicago Botanic Garden, 1000 Lake Cook Road, Glencoe, IL, 60022, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
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Bible AN, Fletcher SJ, Pelletier DA, Schadt CW, Jawdy SS, Weston DJ, Engle NL, Tschaplinski T, Masyuko R, Polisetti S, Bohn PW, Coutinho TA, Doktycz MJ, Morrell-Falvey JL. A Carotenoid-Deficient Mutant in Pantoea sp. YR343, a Bacteria Isolated from the Rhizosphere of Populus deltoides, Is Defective in Root Colonization. Front Microbiol 2016; 7:491. [PMID: 27148182 PMCID: PMC4834302 DOI: 10.3389/fmicb.2016.00491] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Accepted: 03/24/2016] [Indexed: 11/13/2022] Open
Abstract
The complex interactions between plants and their microbiome can have a profound effect on the health and productivity of the plant host. A better understanding of the microbial mechanisms that promote plant health and stress tolerance will enable strategies for improving the productivity of economically important plants. Pantoea sp. YR343 is a motile, rod-shaped bacterium isolated from the roots of Populus deltoides that possesses the ability to solubilize phosphate and produce the phytohormone indole-3-acetic acid (IAA). Pantoea sp. YR343 readily colonizes plant roots and does not appear to be pathogenic when applied to the leaves or roots of selected plant hosts. To better understand the molecular mechanisms involved in plant association and rhizosphere survival by Pantoea sp. YR343, we constructed a mutant in which the crtB gene encoding phytoene synthase was deleted. Phytoene synthase is responsible for converting geranylgeranyl pyrophosphate to phytoene, an important precursor to the production of carotenoids. As predicted, the ΔcrtB mutant is defective in carotenoid production, and shows increased sensitivity to oxidative stress. Moreover, we find that the ΔcrtB mutant is impaired in biofilm formation and production of IAA. Finally we demonstrate that the ΔcrtB mutant shows reduced colonization of plant roots. Taken together, these data suggest that carotenoids are important for plant association and/or rhizosphere survival in Pantoea sp. YR343.
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Affiliation(s)
- Amber N. Bible
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Sarah J. Fletcher
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Nancy L. Engle
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | - Rachel Masyuko
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Sneha Polisetti
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Paul W. Bohn
- Department of Chemical and Biomolecular Engineering, University of Notre DameNotre Dame, IN, USA
| | - Teresa A. Coutinho
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute, University of PretoriaPretoria, South Africa
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Timm CM, Pelletier DA, Jawdy SS, Gunter LE, Henning JA, Engle N, Aufrecht J, Gee E, Nookaew I, Yang Z, Lu TY, Tschaplinski TJ, Doktycz MJ, Tuskan GA, Weston DJ. Two Poplar-Associated Bacterial Isolates Induce Additive Favorable Responses in a Constructed Plant-Microbiome System. Front Plant Sci 2016; 7:497. [PMID: 27200001 PMCID: PMC4845692 DOI: 10.3389/fpls.2016.00497] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 03/29/2016] [Indexed: 05/18/2023]
Abstract
The biological function of the plant-microbiome system is the result of contributions from the host plant and microbiome members. The Populus root microbiome is a diverse community that has high abundance of β- and γ-Proteobacteria, both classes which include multiple plant-growth promoting representatives. To understand the contribution of individual microbiome members in a community, we studied the function of a simplified community consisting of Pseudomonas and Burkholderia bacterial strains isolated from Populus hosts and inoculated on axenic Populus cutting in controlled laboratory conditions. Both strains increased lateral root formation and root hair production in Arabidopsis plate assays and are predicted to encode for different functions related to growth and plant growth promotion in Populus hosts. Inoculation individually, with either bacterial isolate, increased root growth relative to uninoculated controls, and while root area was increased in mixed inoculation, the interaction term was insignificant indicating additive effects of root phenotype. Complementary data including photosynthetic efficiency, whole-transcriptome gene expression and GC-MS metabolite expression data in individual and mixed inoculated treatments indicate that the effects of these bacterial strains are unique and additive. These results suggest that the function of a microbiome community may be predicted from the additive functions of the individual members.
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Affiliation(s)
- Collin M. Timm
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- *Correspondence: Collin M. Timm
| | - Dale A. Pelletier
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Sara S. Jawdy
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Lee E. Gunter
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jeremiah A. Henning
- Department of Ecology and Evolutionary Biology, University of TennesseeKnoxville, TN, USA
| | - Nancy Engle
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Jayde Aufrecht
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of TennesseeKnoxville, TN, USA
| | - Emily Gee
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Intawat Nookaew
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Zamin Yang
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - Tse-Yuan Lu
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | | | | | - Gerald A. Tuskan
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
| | - David J. Weston
- Biosciences Division, Oak Ridge National LaboratoryOak Ridge, TN, USA
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Timm CM, Campbell AG, Utturkar SM, Jun SR, Parales RE, Tan WA, Robeson MS, Lu TYS, Jawdy S, Brown SD, Ussery DW, Schadt CW, Tuskan GA, Doktycz MJ, Weston DJ, Pelletier DA. Metabolic functions of Pseudomonas fluorescens strains from Populus deltoides depend on rhizosphere or endosphere isolation compartment. Front Microbiol 2015; 6:1118. [PMID: 26528266 PMCID: PMC4604316 DOI: 10.3389/fmicb.2015.01118] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 09/28/2015] [Indexed: 12/13/2022] Open
Abstract
The bacterial microbiota of plants is diverse, with 1000s of operational taxonomic units (OTUs) associated with any individual plant. In this work, we used phenotypic analysis, comparative genomics, and metabolic models to investigate the differences between 19 sequenced Pseudomonas fluorescens strains. These isolates represent a single OTU and were collected from the rhizosphere and endosphere of Populus deltoides. While no traits were exclusive to either endosphere or rhizosphere P. fluorescens isolates, multiple pathways relevant for plant-bacterial interactions are enriched in endosphere isolate genomes. Further, growth phenotypes such as phosphate solubilization, protease activity, denitrification and root growth promotion are biased toward endosphere isolates. Endosphere isolates have significantly more metabolic pathways for plant signaling compounds and an increased metabolic range that includes utilization of energy rich nucleotides and sugars, consistent with endosphere colonization. Rhizosphere P. fluorescens have fewer pathways representative of plant-bacterial interactions but show metabolic bias toward chemical substrates often found in root exudates. This work reveals the diverse functions that may contribute to colonization of the endosphere by bacteria and are enriched among closely related isolates.
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Affiliation(s)
- Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Alisha G Campbell
- Department of Natural Sciences, Northwest Missouri State University Maryville, MO, USA
| | - Sagar M Utturkar
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Se-Ran Jun
- Joint Institute for Computational Sciences, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Rebecca E Parales
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Watumesa A Tan
- Microbiology and Molecular Genetics, University of California, Davis Davis, CA, USA
| | - Michael S Robeson
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Fish, Wildlife and Conservation Biology, Colorado State University Fort Collins, CO, USA
| | - Tse-Yuan S Lu
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Sara Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Steven D Brown
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Graduate School of Genome Science and Technology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - David W Ussery
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Christopher W Schadt
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA ; Department of Microbiology, University of Tennessee, Knoxville Knoxville, TN, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Mitchel J Doktycz
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
| | - Dale A Pelletier
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, TN, USA
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Weston DJ, Timm CM, Walker AP, Gu L, Muchero W, Schmutz J, Shaw AJ, Tuskan GA, Warren JM, Wullschleger SD. Sphagnum physiology in the context of changing climate: emergent influences of genomics, modelling and host-microbiome interactions on understanding ecosystem function. Plant Cell Environ 2015; 38:1737-1751. [PMID: 25266403 DOI: 10.1111/pce.12458] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2014] [Revised: 09/16/2014] [Accepted: 09/18/2014] [Indexed: 06/03/2023]
Abstract
Peatlands harbour more than one-third of terrestrial carbon leading to the argument that the bryophytes, as major components of peatland ecosystems, store more organic carbon in soils than any other collective plant taxa. Plants of the genus Sphagnum are important components of peatland ecosystems and are potentially vulnerable to changing climatic conditions. However, the response of Sphagnum to rising temperatures, elevated CO2 and shifts in local hydrology have yet to be fully characterized. In this review, we examine Sphagnum biology and ecology and explore the role of this group of keystone species and its associated microbiome in carbon and nitrogen cycling using literature review and model simulations. Several issues are highlighted including the consequences of a variable environment on plant-microbiome interactions, uncertainty associated with CO2 diffusion resistances and the relationship between fixed N and that partitioned to the photosynthetic apparatus. We note that the Sphagnum fallax genome is currently being sequenced and outline potential applications of population-level genomics and corresponding plant photosynthesis and microbial metabolic modelling techniques. We highlight Sphagnum as a model organism to explore ecosystem response to a changing climate and to define the role that Sphagnum can play at the intersection of physiology, genetics and functional genomics.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Collin M Timm
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Anthony P Walker
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Lianhong Gu
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Wellington Muchero
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeremy Schmutz
- Department of Energy Joint Genome Institute, Walnut Creek, CA, 94598, USA
- HudsonAlpha Institute of Biotechnology, Huntsville, AL, 35806, USA
| | - A Jonathan Shaw
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Jeffrey M Warren
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Stan D Wullschleger
- Environmental Sciences Division and Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
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47
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Borland AM, Wullschleger SD, Weston DJ, Hartwell J, Tuskan GA, Yang X, Cushman JC. Climate-resilient agroforestry: physiological responses to climate change and engineering of crassulacean acid metabolism (CAM) as a mitigation strategy. Plant Cell Environ 2015; 38:1833-49. [PMID: 25366937 DOI: 10.1111/pce.12479] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 10/16/2014] [Accepted: 10/27/2014] [Indexed: 05/20/2023]
Abstract
Global climate change threatens the sustainability of agriculture and agroforestry worldwide through increased heat, drought, surface evaporation and associated soil drying. Exposure of crops and forests to warmer and drier environments will increase leaf:air water vapour-pressure deficits (VPD), and will result in increased drought susceptibility and reduced productivity, not only in arid regions but also in tropical regions with seasonal dry periods. Fast-growing, short-rotation forestry (SRF) bioenergy crops such as poplar (Populus spp.) and willow (Salix spp.) are particularly susceptible to hydraulic failure following drought stress due to their isohydric nature and relatively high stomatal conductance. One approach to sustaining plant productivity is to improve water-use efficiency (WUE) by engineering crassulacean acid metabolism (CAM) into C3 crops. CAM improves WUE by shifting stomatal opening and primary CO2 uptake and fixation to the night-time when leaf:air VPD is low. CAM members of the tree genus Clusia exemplify the compatibility of CAM performance within tree species and highlight CAM as a mechanism to conserve water and maintain carbon uptake during drought conditions. The introduction of bioengineered CAM into SRF bioenergy trees is a potentially viable path to sustaining agroforestry production systems in the face of a globally changing climate.
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Affiliation(s)
- Anne M Borland
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
- Biosciences Division, Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Stan D Wullschleger
- Climate Change Science Institute, Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - David J Weston
- Biosciences Division, Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Gerald A Tuskan
- Biosciences Division, Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Xiaohan Yang
- Biosciences Division, Bioenergy Science Center, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, MS330, University of Nevada, Reno, NV, 89557-0330, USA
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48
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Yang X, Cushman JC, Borland AM, Edwards EJ, Wullschleger SD, Tuskan GA, Owen NA, Griffiths H, Smith JAC, De Paoli HC, Weston DJ, Cottingham R, Hartwell J, Davis SC, Silvera K, Ming R, Schlauch K, Abraham P, Stewart JR, Guo HB, Albion R, Ha J, Lim SD, Wone BWM, Yim WC, Garcia T, Mayer JA, Petereit J, Nair SS, Casey E, Hettich RL, Ceusters J, Ranjan P, Palla KJ, Yin H, Reyes-García C, Andrade JL, Freschi L, Beltrán JD, Dever LV, Boxall SF, Waller J, Davies J, Bupphada P, Kadu N, Winter K, Sage RF, Aguilar CN, Schmutz J, Jenkins J, Holtum JAM. A roadmap for research on crassulacean acid metabolism (CAM) to enhance sustainable food and bioenergy production in a hotter, drier world. New Phytol 2015; 207:491-504. [PMID: 26153373 DOI: 10.1111/nph.13393] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Crassulacean acid metabolism (CAM) is a specialized mode of photosynthesis that features nocturnal CO2 uptake, facilitates increased water-use efficiency (WUE), and enables CAM plants to inhabit water-limited environments such as semi-arid deserts or seasonally dry forests. Human population growth and global climate change now present challenges for agricultural production systems to increase food, feed, forage, fiber, and fuel production. One approach to meet these challenges is to increase reliance on CAM crops, such as Agave and Opuntia, for biomass production on semi-arid, abandoned, marginal, or degraded agricultural lands. Major research efforts are now underway to assess the productivity of CAM crop species and to harness the WUE of CAM by engineering this pathway into existing food, feed, and bioenergy crops. An improved understanding of CAM has potential for high returns on research investment. To exploit the potential of CAM crops and CAM bioengineering, it will be necessary to elucidate the evolution, genomic features, and regulatory mechanisms of CAM. Field trials and predictive models will be required to assess the productivity of CAM crops, while new synthetic biology approaches need to be developed for CAM engineering. Infrastructure will be needed for CAM model systems, field trials, mutant collections, and data management.
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Affiliation(s)
- Xiaohan Yang
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - John C Cushman
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Anne M Borland
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Erika J Edwards
- Department of Ecology and Evolutionary Biology, Brown University, Box G-W, Providence, RI, 02912, USA
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Nick A Owen
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - Howard Griffiths
- Department of Plant Sciences, University of Cambridge, Downing Street, Cambridge, CB2 3EA, UK
| | - J Andrew C Smith
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Henrique C De Paoli
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - David J Weston
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Robert Cottingham
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - James Hartwell
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Sarah C Davis
- Voinovich School of Leadership and Public Affairs and Department of Environmental and Plant Biology, Ohio University, Athens, OH, 45701, USA
| | - Katia Silvera
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Karen Schlauch
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Paul Abraham
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - J Ryan Stewart
- Department of Plant and Wildlife Sciences, Brigham Young University, 4105 Life Sciences Building, Provo, UT, 84602, USA
| | - Hao-Bo Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Rebecca Albion
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jungmin Ha
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sung Don Lim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Bernard W M Wone
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Won Cheol Yim
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Travis Garcia
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Jesse A Mayer
- Department of Biochemistry and Molecular Biology, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Juli Petereit
- Nevada Center for Bioinformatics, University of Nevada, MS330, Reno, NV, 89557-0330, USA
| | - Sujithkumar S Nair
- Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
| | - Erin Casey
- School of Biology, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK
| | - Robert L Hettich
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Johan Ceusters
- Department of M²S, Faculty of Engineering Technology, TC Bioengineering Technology, KU Leuven, Campus Geel, Kleinhoefstraat 4, B-2440, Geel, Belgium
| | - Priya Ranjan
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Kaitlin J Palla
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6407, USA
| | - Hengfu Yin
- Key Laboratory of Forest Genetics and Breeding, Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Fuyang, 311400, China
| | - Casandra Reyes-García
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - José Luis Andrade
- Centro de Investigación Científica de Yucatán, Calle 43 No. 130, Colonia Chuburná de Hidalgo, CP 97200, Mérida, México
| | - Luciano Freschi
- Department of Botany, University of São Paulo, São Paulo, 05508-090, Brazil
| | - Juan D Beltrán
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - Louisa V Dever
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Susanna F Boxall
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jade Waller
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Jack Davies
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Phaitun Bupphada
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Nirja Kadu
- Department of Plant Sciences, Institute of Integrative Biology, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Klaus Winter
- Smithsonian Tropical Research Institute, PO Box 0843-03092, Balboa, Ancon, Republic of Panama
| | - Rowan F Sage
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S3B2, Canada
| | - Cristobal N Aguilar
- Department of Food Research, School of Chemistry, Universidad Autónoma de Coahuila, Saltillo, México
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
- US Department of Energy Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, CA, 94598, USA
| | - Jerry Jenkins
- HudsonAlpha Institute for Biotechnology, 601 Genome Way, Huntsville, AL, 35801, USA
| | - Joseph A M Holtum
- College of Marine and Environmental Sciences, James Cook University, Townsville, 4811, QLD, Australia
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Weston DJ, Rogers A, Tschaplinski TJ, Gunter LE, Jawdy SA, Engle NL, Heady LE, Tuskan GA, Wullschleger SD. Scaling nitrogen and carbon interactions: what are the consequences of biological buffering? Ecol Evol 2015; 5:2839-50. [PMID: 26306170 PMCID: PMC4541989 DOI: 10.1002/ece3.1565] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2015] [Accepted: 05/26/2015] [Indexed: 11/27/2022] Open
Abstract
Understanding the consequences of elevated CO2 (eCO2; 800 ppm) on terrestrial ecosystems is a central theme in global change biology, but relatively little is known about how altered plant C and N metabolism influences higher levels of biological organization. Here, we investigate the consequences of C and N interactions by genetically modifying the N-assimilation pathway in Arabidopsis and initiating growth chamber and mesocosm competition studies at current CO2 (cCO2; 400 ppm) and eCO2 over multiple generations. Using a suite of ecological, physiological, and molecular genomic tools, we show that a single-gene mutant of a key enzyme (nia2) elicited a highly orchestrated buffering response starting with a fivefold increase in the expression of a gene paralog (nia1) and a 63% increase in the expression of gene network module enriched for N-assimilation genes. The genetic perturbation reduced amino acids, protein, and TCA-cycle intermediate concentrations in the nia2 mutant compared to the wild-type, while eCO2 mainly increased carbohydrate concentrations. The mutant had reduced net photosynthetic rates due to a 27% decrease in carboxylation capacity and an 18% decrease in electron transport rates. The expression of these buffering mechanisms resulted in a penalty that negatively correlated with fitness and population dynamics yet showed only minor alterations in our estimates of population function, including total per unit area biomass, ground cover, and leaf area index. This study provides insight into the consequences of buffering mechanisms that occur post-genetic perturbations in the N pathway and the associated outcomes these buffering systems have on plant populations relative to eCO2.
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Affiliation(s)
- David J Weston
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Alistair Rogers
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory Upton, New York, 11973-5000
| | | | - Lee E Gunter
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Sara A Jawdy
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Nancy L Engle
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Lindsey E Heady
- Biological, Environmental & Climate Sciences Department, Brookhaven National Laboratory Upton, New York, 11973-5000
| | - Gerald A Tuskan
- Biosciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6407
| | - Stan D Wullschleger
- Environmental Sciences Division, Oak Ridge National Laboratory Oak Ridge, Tennessee, 37831-6301
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50
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Wullschleger SD, Breen AL, Iversen CM, Olson MS, Näsholm T, Ganeteg U, Wallenstein MD, Weston DJ. Genomics in a changing arctic: critical questions await the molecular ecologist. Mol Ecol 2015; 24:2301-9. [PMID: 25809088 DOI: 10.1111/mec.13166] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 03/13/2015] [Accepted: 03/18/2015] [Indexed: 12/24/2022]
Abstract
Molecular ecology is poised to tackle a host of interesting questions in the coming years. The Arctic provides a unique and rapidly changing environment with a suite of emerging research needs that can be addressed through genetics and genomics. Here we highlight recent research on boreal and tundra ecosystems and put forth a series of questions related to plant and microbial responses to climate change that can benefit from technologies and analytical approaches contained within the molecular ecologist's toolbox. These questions include understanding (i) the mechanisms of plant acquisition and uptake of N in cold soils, (ii) how these processes are mediated by root traits, (iii) the role played by the plant microbiome in cycling C and nutrients within high-latitude ecosystems and (iv) plant adaptation to extreme Arctic climates. We highlight how contributions can be made in these areas through studies that target model and nonmodel organisms and emphasize that the sequencing of the Populus and Salix genomes provides a valuable resource for scientific discoveries related to the plant microbiome and plant adaptation in the Arctic. Moreover, there exists an exciting role to play in model development, including incorporating genetic and evolutionary knowledge into ecosystem and Earth System Models. In this regard, the molecular ecologist provides a valuable perspective on plant genetics as a driver for community biodiversity, and how ecological and evolutionary forces govern community dynamics in a rapidly changing climate.
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Affiliation(s)
- Stan D Wullschleger
- Environmental Sciences Division, Climate Change Science Institute, Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6301, USA
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