1
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Ladau J, Brodie EL, Falco N, Bansal I, Hoffman EB, Joachimiak MP, Mora AM, Walker AM, Wainwright HM, Wu Y, Pavicic M, Jacobson D, Hess M, Brown JB, Abuabara K. Estimating geographic variation of infection fatality ratios during epidemics. Infect Dis Model 2024; 9:634-643. [PMID: 38572058 PMCID: PMC10990719 DOI: 10.1016/j.idm.2024.02.009] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 02/10/2024] [Accepted: 02/16/2024] [Indexed: 04/05/2024] Open
Abstract
Objectives We aim to estimate geographic variability in total numbers of infections and infection fatality ratios (IFR; the number of deaths caused by an infection per 1,000 infected people) when the availability and quality of data on disease burden are limited during an epidemic. Methods We develop a noncentral hypergeometric framework that accounts for differential probabilities of positive tests and reflects the fact that symptomatic people are more likely to seek testing. We demonstrate the robustness, accuracy, and precision of this framework, and apply it to the United States (U.S.) COVID-19 pandemic to estimate county-level SARS-CoV-2 IFRs. Results The estimators for the numbers of infections and IFRs showed high accuracy and precision; for instance, when applied to simulated validation data sets, across counties, Pearson correlation coefficients between estimator means and true values were 0.996 and 0.928, respectively, and they showed strong robustness to model misspecification. Applying the county-level estimators to the real, unsimulated COVID-19 data spanning April 1, 2020 to September 30, 2020 from across the U.S., we found that IFRs varied from 0 to 44.69, with a standard deviation of 3.55 and a median of 2.14. Conclusions The proposed estimation framework can be used to identify geographic variation in IFRs across settings.
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Affiliation(s)
- Joshua Ladau
- Departments of Computational Precision Health and Dermatology, University of California, San Francisco, CA, 94115, USA
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Nicola Falco
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ishan Bansal
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Elijah B. Hoffman
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Graduate Group in Biostatistics, University of California, Berkeley, CA, 94720, USA
| | - Marcin P. Joachimiak
- Biosystems Data Science, Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Ana M. Mora
- Center for Environmental Research and Community Health (CERCH), School of Public Health, University of California, Berkeley, CA, 94720, USA
| | - Angelica M. Walker
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, TN, 37996, USA
| | - Haruko M. Wainwright
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Boston, MA, 02139, USA
| | - Yulun Wu
- Graduate Group in Biostatistics, University of California, Berkeley, CA, 94720, USA
| | - Mirko Pavicic
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | - Daniel Jacobson
- Biosciences, Oak Ridge National Laboratory, Oak Ridge, TN, 37830, USA
| | | | - James B. Brown
- Arva Intelligence, Inc., Salt Lake City, UT, 84101, USA
- Computational Biosciences Group, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Statistics Department, University of California, Berkeley, CA, 94720, USA
| | - Katrina Abuabara
- Departments of Computational Precision Health and Dermatology, University of California, San Francisco, CA, 94115, USA
- Division of Epidemiology and Biostatistics, University of California Berkeley School of Public Health, 2121 Berkeley Way, Berkeley, CA, 94720, USA
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2
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Alvarez-Aponte ZI, Govindaraju AM, Hallberg ZF, Nicolas AM, Green MA, Mok KC, Fonseca-Garcia C, Coleman-Derr D, Brodie EL, Carlson HK, Taga ME. Phylogenetic distribution and experimental characterization of corrinoid production and dependence in soil bacterial isolates. ISME J 2024:wrae068. [PMID: 38648288 DOI: 10.1093/ismejo/wrae068] [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] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/15/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
Soil microbial communities impact carbon sequestration and release, biogeochemical cycling, and agricultural yields. These global effects rely on metabolic interactions that modulate community composition and function. However, the physicochemical and taxonomic complexity of soil and the scarcity of available isolates for phenotypic testing are significant barriers to studying soil microbial interactions. Corrinoids-the vitamin B12 family of cofactors-are critical for microbial metabolism, yet they are synthesized by only a subset of microbiome members. Here, we evaluated corrinoid production and dependence in soil bacteria as a model to investigate the ecological roles of microorganisms involved in metabolic interactions. We isolated and characterized a taxonomically diverse collection of 161 soil bacteria from a single study site. Most corrinoid-dependent bacteria in the collection prefer B12 over other corrinoids, while all tested producers synthesize B12, indicating metabolic compatibility between producers and dependents in the collection. Furthermore, a subset of producers release B12 at levels sufficient to support dependent isolates in laboratory culture at estimated ratios of up to 1000 dependents per producer. Within our isolate collection, we did not find strong phylogenetic patterns in corrinoid production or dependence. Upon investigating trends in the phylogenetic dispersion of corrinoid metabolism categories across sequenced bacteria from various environments, we found that these traits are conserved in 47 out of 85 genera. Together, these phenotypic and genomic results provide evidence for corrinoid-based metabolic interactions among bacteria and provide a framework for the study of nutrient-sharing ecological interactions in microbial communities.
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Affiliation(s)
- Zoila I Alvarez-Aponte
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Alekhya M Govindaraju
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Zachary F Hallberg
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Alexa M Nicolas
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Myka A Green
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Kenny C Mok
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Citlali Fonseca-Garcia
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, USDA-ARS, Albany, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans K Carlson
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Michiko E Taga
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
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3
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Marschmann GL, Tang J, Zhalnina K, Karaoz U, Cho H, Le B, Pett-Ridge J, Brodie EL. Predictions of rhizosphere microbiome dynamics with a genome-informed and trait-based energy budget model. Nat Microbiol 2024; 9:421-433. [PMID: 38316928 PMCID: PMC10847045 DOI: 10.1038/s41564-023-01582-w] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 12/08/2023] [Indexed: 02/07/2024]
Abstract
Soil microbiomes are highly diverse, and to improve their representation in biogeochemical models, microbial genome data can be leveraged to infer key functional traits. By integrating genome-inferred traits into a theory-based hierarchical framework, emergent behaviour arising from interactions of individual traits can be predicted. Here we combine theory-driven predictions of substrate uptake kinetics with a genome-informed trait-based dynamic energy budget model to predict emergent life-history traits and trade-offs in soil bacteria. When applied to a plant microbiome system, the model accurately predicted distinct substrate-acquisition strategies that aligned with observations, uncovering resource-dependent trade-offs between microbial growth rate and efficiency. For instance, inherently slower-growing microorganisms, favoured by organic acid exudation at later plant growth stages, exhibited enhanced carbon use efficiency (yield) without sacrificing growth rate (power). This insight has implications for retaining plant root-derived carbon in soils and highlights the power of data-driven, trait-based approaches for improving microbial representation in biogeochemical models.
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Affiliation(s)
- Gianna L Marschmann
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jinyun Tang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kateryna Zhalnina
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Beatrice Le
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
- Life and Environmental Sciences Department, University of California Merced, Merced, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
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4
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Coclet C, Sorensen PO, Karaoz U, Wang S, Brodie EL, Eloe-Fadrosh EA, Roux S. Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem. Microbiome 2023; 11:237. [PMID: 37891627 PMCID: PMC10604447 DOI: 10.1186/s40168-023-01666-z] [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: 03/15/2023] [Accepted: 09/07/2023] [Indexed: 10/29/2023]
Abstract
BACKGROUND Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. RESULTS We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth. CONCLUSION Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.
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Affiliation(s)
- Clement Coclet
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Patrick O Sorensen
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Shi Wang
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, USA
| | - Emiley A Eloe-Fadrosh
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Simon Roux
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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5
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Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL. Publisher Correction: Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nat Commun 2023; 14:6306. [PMID: 37813907 PMCID: PMC10562389 DOI: 10.1038/s41467-023-42217-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/11/2023] Open
Affiliation(s)
- Javier A Ceja-Navarro
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA.
| | - Fernando E Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Building 001, BARC-W, Beltsville, Maryland, 20705, USA.
| | - Ulas Karaoz
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Zhao Hao
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Stefan Jenkins
- Genome Dynamics Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Hsiao Chien Lim
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Petr Kosina
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El Batán, Texcoco, 56130, Mexico
| | - Francisco Infante
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, Tapachula, Chiapas, 30700, Mexico
| | - Trent R Northen
- Genome Dynamics Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA
| | - Eoin L Brodie
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, 94720, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, 94720, USA.
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6
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Dodge R, Jones EW, Zhu H, Obadia B, Martinez DJ, Wang C, Aranda-Díaz A, Aumiller K, Liu Z, Voltolini M, Brodie EL, Huang KC, Carlson JM, Sivak DA, Spradling AC, Ludington WB. A symbiotic physical niche in Drosophila melanogaster regulates stable association of a multi-species gut microbiota. Nat Commun 2023; 14:1557. [PMID: 36944617 PMCID: PMC10030875 DOI: 10.1038/s41467-023-36942-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 02/22/2023] [Indexed: 03/23/2023] Open
Abstract
The gut is continuously invaded by diverse bacteria from the diet and the environment, yet microbiome composition is relatively stable over time for host species ranging from mammals to insects, suggesting host-specific factors may selectively maintain key species of bacteria. To investigate host specificity, we used gnotobiotic Drosophila, microbial pulse-chase protocols, and microscopy to investigate the stability of different strains of bacteria in the fly gut. We show that a host-constructed physical niche in the foregut selectively binds bacteria with strain-level specificity, stabilizing their colonization. Primary colonizers saturate the niche and exclude secondary colonizers of the same strain, but initial colonization by Lactobacillus species physically remodels the niche through production of a glycan-rich secretion to favor secondary colonization by unrelated commensals in the Acetobacter genus. Our results provide a mechanistic framework for understanding the establishment and stability of a multi-species intestinal microbiome.
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Affiliation(s)
- Ren Dodge
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Eric W Jones
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
- Department of Physics, University of California, Santa Barbara, CA, 93106, USA
| | - Haolong Zhu
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Benjamin Obadia
- Molecular and Cell Biology Department, University of California, Berkeley, CA, 94720, USA
| | - Daniel J Martinez
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
| | - Chenhui Wang
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21218, USA
| | - Andrés Aranda-Díaz
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Kevin Aumiller
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Zhexian Liu
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Marco Voltolini
- Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
- Dipartimento di Scienze della Terra, Università degli Studi di Milano, Milano, Italy
| | - Eoin L Brodie
- Lawrence Berkeley National Lab, Berkeley, CA, 94720, USA
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Microbiology and Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Jean M Carlson
- Department of Physics, University of California, Santa Barbara, CA, 93106, USA
| | - David A Sivak
- Department of Physics, Simon Fraser University, Burnaby, BC, V5A 1S6, Canada
| | - Allan C Spradling
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA
- Howard Hughes Medical Institute, Baltimore, MD, 21218, USA
| | - William B Ludington
- Department of Embryology, Carnegie Institution for Science, Baltimore, MD, 21218, USA.
- Department of Biology, Johns Hopkins University, Baltimore, MD, 21218, USA.
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7
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Thullner M, Brodie EL, Meile C, Pagel H. Editorial: Modeling the link between microbial ecology and biogeochemical process dynamics. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.994090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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8
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Karaoz U, Brodie EL. microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes. Front Bioinform 2022; 2:918853. [PMID: 36304272 PMCID: PMC9580909 DOI: 10.3389/fbinf.2022.918853] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2023] Open
Abstract
Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.
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Affiliation(s)
- Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, United States
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9
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Hao Y, Karaoz U, Yang L, Yachimski PS, Tseng W, Nossa CW, Ye W, Tseng M, Poles M, Francois F, Traube M, Brown SM, Chen Y, Torralba M, Peek RM, Brodie EL, Pei Z. Progressive dysbiosis of human orodigestive microbiota along the sequence of gastroesophageal reflux, Barrett's esophagus, and esophageal adenocarcinoma. Int J Cancer 2022; 151:1703-1716. [PMID: 35751398 DOI: 10.1002/ijc.34191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [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: 11/03/2021] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/06/2022]
Abstract
The incidence of esophageal adenocarcinoma (EA) has drastically increased in the United States since 1970s for unclear reasons. We hypothesized that the widespread usage of antibiotics has increased the procarcinogenic potential of the orodigestive microbiota along the sequence of gastroesophageal reflux (GR), Barrett's esophagus (BE), and EA phenotypes. This case control study included normal controls (NC) and three disease phenotypes GR, BE, and EA. Microbiota in the mouth, esophagus, and stomach, and rectum were analyzed using 16S rRNA gene sequencing. Overall, we discovered 44 significant pairwise differences in abundance of microbial taxa between the four phenotypes, with 12 differences in the mouth, 21 in the esophagus, two in the stomach, and nine in the rectum. Along the GR→BE→EA sequence, oral and esophageal microbiota were more diversified, the dominant genus Streptococcus was progressively depleted while six other genera Atopobium, Actinomyces, Veillonella, Ralstonia, Burkholderia, and Lautropia progressively enriched. In NC, Streptococcus appeared to control populations of other genera in the foregut via numerous negative and positive connections, while in disease states, the rich network was markedly simplified. Inferred gene functional content showed a progressive enrichment through the stages of EA development in genes encoding antibiotic resistance, ligands of Toll-like and NOD-like receptors, nitrate-nitrite-nitric oxide pathway, and acetaldehyde metabolism. The orodigestive microbiota is in a progressive dysbiotic state along the GR-BE-EA sequence. The increasing dysbiosis and antibiotic and procarcinogenic genes in the disease states warrants further study to define their roles in EA pathogenesis. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Yuhan Hao
- Department of Pathology, NYU School of Medicine, New York, New York, USA.,Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Liying Yang
- Department of Medicine, NYU School of Medicine, New York, New York, USA
| | - Patrick S Yachimski
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Wenzhi Tseng
- Department of Pathology, NYU School of Medicine, New York, New York, USA.,Amherst College, Amherst, Massachusetts, USA
| | - Carlos W Nossa
- Department of Medicine, NYU School of Medicine, New York, New York, USA
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Mengkao Tseng
- Department of Medicine, NYU School of Medicine, New York, New York, USA
| | - Michael Poles
- Department of Medicine, NYU School of Medicine, New York, New York, USA.,Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, USA
| | - Fritz Francois
- Department of Medicine, NYU School of Medicine, New York, New York, USA
| | - Morris Traube
- Department of Medicine, NYU School of Medicine, New York, New York, USA
| | - Stuart M Brown
- Department of Cell Biology, NYU School of Medicine, New York, New York, USA
| | - Yu Chen
- Department of Population Health and Department of Environmental Medicine, NYU School of Medicine, New York, New York, USA
| | | | - Richard M Peek
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Zhiheng Pei
- Department of Pathology, NYU School of Medicine, New York, New York, USA.,Department of Medicine, NYU School of Medicine, New York, New York, USA.,Department of Veterans Affairs New York Harbor Healthcare System, New York, New York, USA
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10
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Alves RJE, Callejas IA, Marschmann GL, Mooshammer M, Singh HW, Whitney B, Torn MS, Brodie EL. Kinetic Properties of Microbial Exoenzymes Vary With Soil Depth but Have Similar Temperature Sensitivities Through the Soil Profile. Front Microbiol 2021; 12:735282. [PMID: 34917043 PMCID: PMC8669745 DOI: 10.3389/fmicb.2021.735282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 07/02/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
Current knowledge of the mechanisms driving soil organic matter (SOM) turnover and responses to warming is mainly limited to surface soils, although over 50% of global soil carbon is contained in subsoils. Deep soils have different physicochemical properties, nutrient inputs, and microbiomes, which may harbor distinct functional traits and lead to different SOM dynamics and temperature responses. We hypothesized that kinetic and thermal properties of soil exoenzymes, which mediate SOM depolymerization, vary with soil depth, reflecting microbial adaptation to distinct substrate and temperature regimes. We determined the Michaelis-Menten (MM) kinetics of three ubiquitous enzymes involved in carbon (C), nitrogen (N) and phosphorus (P) acquisition at six soil depths down to 90 cm at a temperate forest, and their temperature sensitivity based on Arrhenius/Q10 and Macromolecular Rate Theory (MMRT) models over six temperatures between 4–50°C. Maximal enzyme velocity (Vmax) decreased strongly with depth for all enzymes, both on a dry soil mass and a microbial biomass C basis, whereas their affinities increased, indicating adaptation to lower substrate availability. Surprisingly, microbial biomass-specific catalytic efficiencies also decreased with depth, except for the P-acquiring enzyme, indicating distinct nutrient demands at depth relative to microbial abundance. These results suggested that deep soil microbiomes encode enzymes with intrinsically lower turnover and/or produce less enzymes per cell, reflecting distinct life strategies. The relative kinetics between different enzymes also varied with depth, suggesting an increase in relative P demand with depth, or that phosphatases may be involved in C acquisition. Vmax and catalytic efficiency increased consistently with temperature for all enzymes, leading to overall higher SOM-decomposition potential, but enzyme temperature sensitivity was similar at all depths and between enzymes, based on both Arrhenius/Q10 and MMRT models. In a few cases, however, temperature affected differently the kinetic properties of distinct enzymes at discrete depths, suggesting that it may alter the relative depolymerization of different compounds. We show that soil exoenzyme kinetics may reflect intrinsic traits of microbiomes adapted to distinct soil depths, although their temperature sensitivity is remarkably uniform. These results improve our understanding of critical mechanisms underlying SOM dynamics and responses to changing temperatures through the soil profile.
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Affiliation(s)
- Ricardo J Eloy Alves
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ileana A Callejas
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Civil and Environmental Engineering, University of California, Los Angeles, Los Angeles, CA, United States
| | - Gianna L Marschmann
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Maria Mooshammer
- Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Hans W Singh
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Bizuayehu Whitney
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Margaret S Torn
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Energy and Resources Group, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy, and Management, University of California, Berkeley, Berkeley, CA, United States
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11
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Leonard LT, Brodie EL, Williams KH, Sharp JO. Effect of elevation, season and accelerated snowmelt on biogeochemical processes during isolated conifer needle litter decomposition. PeerJ 2021; 9:e11926. [PMID: 34434657 PMCID: PMC8362670 DOI: 10.7717/peerj.11926] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/13/2021] [Accepted: 07/17/2021] [Indexed: 01/04/2023] Open
Abstract
Increased drought and temperatures associated with climate change have implications for ecosystem stress with risk for enhanced carbon release in sensitive biomes. Litter decomposition is a key component of biogeochemical cycling in terrestrial ecosystems, but questions remain regarding the local response of decomposition processes to climate change. This is particularly complex in mountain ecosystems where the variable nature of the slope, aspect, soil type, and snowmelt dynamics play a role. Hence, the goal of this study was to determine the role of elevation, soil type, seasonal shifts in soil moisture, and snowmelt timing on litter decomposition processes. Experimental plots containing replicate deployments of harvested lodgepole and spruce needle litter alongside needle-free controls were established in open meadows at three elevations ranging from 2,800–3,500 m in Crested Butte, Colorado. Soil biogeochemistry variables including gas flux, porewater chemistry, and microbial ecology were monitored over three climatically variable years that shifted from high monsoon rains to drought. Results indicated that elevation and soil type influenced baseline soil biogeochemical indicators; however, needle mass loss and chemical composition were consistent across the 700 m elevation gradient. Rates of gas flux were analogously consistent across a 300 m elevation gradient. The additional variable of early snowmelt by 2–3 weeks had little impact on needle chemistry, microbial composition and gas flux; however, it did result in increased dissolved organic carbon in lodgepole porewater collections suggesting a potential for aqueous export. In contrast to elevation, needle presence and seasonal variability of soil moisture and temperature both played significant roles in soil carbon fluxes. During a pronounced period of lower moisture and higher temperatures, bacterial community diversity increased across elevation with new members supplanting more dominant taxa. Microbial ecological resilience was demonstrated with a return to pre-drought structure and abundance after snowmelt rewetting the following year. These results show similar decomposition processes across a 700 m elevation gradient and reveal the sensitivity but resilience of soil microbial ecology to low moisture conditions.
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Affiliation(s)
- Laura T Leonard
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, United States
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Berkeley, California, United States
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Berkeley, California, United States.,Rocky Mountain Biological Laboratory, Crested Butte, Colorado, United States
| | - Jonathan O Sharp
- Department of Civil and Environmental Engineering, Colorado School of Mines, Golden, Colorado, United States.,Hydrologic Science and Engineering Program, Colorado School of Mines, Golden, Colorado, United States
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12
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Wang S, Walker R, Schicklberger M, Nico PS, Fox PM, Karaoz U, Chakraborty R, Brodie EL. Microbial Phosphorus Mobilization Strategies Across a Natural Nutrient Limitation Gradient and Evidence for Linkage With Iron Solubilization Traits. Front Microbiol 2021; 12:572212. [PMID: 34248859 PMCID: PMC8261140 DOI: 10.3389/fmicb.2021.572212] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2020] [Accepted: 03/12/2021] [Indexed: 01/04/2023] Open
Abstract
Microorganisms have evolved several mechanisms to mobilize and mineralize occluded and insoluble phosphorus (P), thereby promoting plant growth in terrestrial ecosystems. However, the linkages between microbial P-solubilization traits and the preponderance of insoluble P in natural ecosystems are not well known. We tested the P solubilization traits of hundreds of culturable bacteria representative of the rhizosphere from a natural gradient where P concentration and bioavailability decline as soil becomes progressively more weathered. Aluminum, iron phosphate and organic P (phytate) were expected to dominate in more weathered soils. A defined cultivation medium with these chemical forms of P was used for isolation. A combination of soil chemical, spectroscopic analyses and 16S rRNA gene sequencing were used to understand the in situ ability for solubilization of these predominant forms of P. Locations with more occluded and organic P harbored the greatest abundance of P-mobilizing microorganisms, especially Burkholderiaceae (Caballeronia and Paraburkholderia spp.). Nearly all bacteria utilized aluminum phosphate, however fewer could subsist on iron phosphate (FePO4) or phytate. Microorganisms isolated from phytic acid were also most effective at solubilizing FePO4, suggesting that phytate solubilization may be linked to the ability to solubilize Fe. Significantly, we observed Fe to be co-located with P in organic patches in soil. Siderophore addition in lab experiments reinstated phytase mediated P-solubilization from Fe-phytate complexes. Taken together, these results indicate that metal-organic-P complex formation may limit enzymatic P solubilization from phytate in soil. Additionally, the linked traits of phytase and siderophore production were mostly restricted to specific clades within the Burkholderiaceae. We propose that Fe complexation of organic P (e.g., phytate) represents a major constraint on P turnover and availability in acidic soils, as only a limited subset of bacteria appear to possess the traits required to access this persistent pool of soil P.
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Affiliation(s)
- Shi Wang
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Robert Walker
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,School of BioSciences, University of Melbourne, Parkville, VIC, Australia
| | - Marcus Schicklberger
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Peter S Nico
- Energy Geosciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Patricia M Fox
- Energy Geosciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ulas Karaoz
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Romy Chakraborty
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L Brodie
- Ecology Department, Climate and Ecosystem Sciences Division, Earth and Environmental Sciences Area, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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13
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Kim J, Goldstein AH, Chakraborty R, Jardine K, Weber R, Sorensen PO, Wang S, Faybishenko B, Misztal PK, Brodie EL. Measurement of Volatile Compounds for Real-Time Analysis of Soil Microbial Metabolic Response to Simulated Snowmelt. Front Microbiol 2021; 12:679671. [PMID: 34248891 PMCID: PMC8261151 DOI: 10.3389/fmicb.2021.679671] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 05/31/2021] [Indexed: 11/24/2022] Open
Abstract
Snowmelt dynamics are a significant determinant of microbial metabolism in soil and regulate global biogeochemical cycles of carbon and nutrients by creating seasonal variations in soil redox and nutrient pools. With an increasing concern that climate change accelerates both snowmelt timing and rate, obtaining an accurate characterization of microbial response to snowmelt is important for understanding biogeochemical cycles intertwined with soil. However, observing microbial metabolism and its dynamics non-destructively remains a major challenge for systems such as soil. Microbial volatile compounds (mVCs) emitted from soil represent information-dense signatures and when assayed non-destructively using state-of-the-art instrumentation such as Proton Transfer Reaction-Time of Flight-Mass Spectrometry (PTR-TOF-MS) provide time resolved insights into the metabolism of active microbiomes. In this study, we used PTR-TOF-MS to investigate the metabolic trajectory of microbiomes from a subalpine forest soil, and their response to a simulated wet-up event akin to snowmelt. Using an information theory approach based on the partitioning of mutual information, we identified mVC metabolite pairs with robust interactions, including those that were non-linear and with time lags. The biological context for these mVC interactions was evaluated by projecting the connections onto the Kyoto Encyclopedia of Genes and Genomes (KEGG) network of known metabolic pathways. Simulated snowmelt resulted in a rapid increase in the production of trimethylamine (TMA) suggesting that anaerobic degradation of quaternary amine osmo/cryoprotectants, such as glycine betaine, may be important contributors to this resource pulse. Unique and synergistic connections between intermediates of methylotrophic pathways such as dimethylamine, formaldehyde and methanol were observed upon wet-up and indicate that the initial pulse of TMA was likely transformed into these intermediates by methylotrophs. Increases in ammonia oxidation signatures (transformation of hydroxylamine to nitrite) were observed in parallel, and while the relative role of nitrifiers or methylotrophs cannot be confirmed, the inferred connection to TMA oxidation suggests either a direct or indirect coupling between these processes. Overall, it appears that such mVC time-series from PTR-TOF-MS combined with causal inference represents an attractive approach to non-destructively observe soil microbial metabolism and its response to environmental perturbation.
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Affiliation(s)
- Junhyeong Kim
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Allen H Goldstein
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Romy Chakraborty
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Kolby Jardine
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Robert Weber
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Patrick O Sorensen
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Shi Wang
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Boris Faybishenko
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States
| | - Pawel K Misztal
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Climate and Ecosystems Sciences, Earth and Environmental Sciences, Berkeley, CA, United States.,Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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14
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Ceja-Navarro JA, Wang Y, Ning D, Arellano A, Ramanculova L, Yuan MM, Byer A, Craven KD, Saha MC, Brodie EL, Pett-Ridge J, Firestone MK. Protist diversity and community complexity in the rhizosphere of switchgrass are dynamic as plants develop. Microbiome 2021; 9:96. [PMID: 33910643 PMCID: PMC8082632 DOI: 10.1186/s40168-021-01042-9] [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] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/26/2021] [Indexed: 05/06/2023]
Abstract
BACKGROUND Despite their widespread distribution and ecological importance, protists remain one of the least understood components of the soil and rhizosphere microbiome. Knowledge of the roles that protists play in stimulating organic matter decomposition and shaping microbiome dynamics continues to grow, but there remains a need to understand the extent to which biological and environmental factors mediate protist community assembly and dynamics. We hypothesize that protists communities are filtered by the influence of plants on their rhizosphere biological and physicochemical environment, resulting in patterns of protist diversity and composition that mirror previously observed diversity and successional dynamics in rhizosphere bacterial communities. RESULTS We analyzed protist communities associated with the rhizosphere and bulk soil of switchgrass (SG) plants (Panicum virgatum) at different phenological stages, grown in two marginal soils as part of a large-scale field experiment. Our results reveal that the diversity of protists is lower in rhizosphere than bulk soils, and that temporal variations depend on soil properties but are less pronounced in rhizosphere soil. Patterns of significantly prevalent protists groups in the rhizosphere suggest that most protists play varied ecological roles across plant growth stages and that some plant pathogenic protists and protists with omnivorous diets reoccur over time in the rhizosphere. We found that protist co-occurrence network dynamics are more complex in the rhizosphere compared to bulk soil. A phylogenetic bin-based null model analysis showed that protists' community assembly in our study sites is mainly controlled by homogenous selection and dispersal limitation, with stronger selection in rhizosphere than bulk soil as SG grew and senesced. CONCLUSIONS We demonstrate that environmental filtering is a dominant determinant of overall protist community properties and that at the rhizosphere level, plant control on the physical and biological environment is a critical driver of protist community composition and dynamics. Since protists are key contributors to plant nutrient availability and bacterial community composition and abundance, mapping and understanding their patterns in rhizosphere soil is foundational to understanding the ecology of the root-microbe-soil system. Video Abstract.
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Affiliation(s)
- Javier A. Ceja-Navarro
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
- Institute for Biodiversity Science and Sustainability, California Academy of Sciences, San Francisco, CA USA
| | - Yuan Wang
- Noble Research Institute, LLC, Ardmore, OK USA
| | - Daliang Ning
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Abelardo Arellano
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Leila Ramanculova
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Mengting Maggie Yuan
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | - Alyssa Byer
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
| | | | | | - Eoin L. Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA USA
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA USA
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15
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Pessotti RDC, Hansen BL, Reaso JN, Ceja-Navarro JA, El-Hifnawi L, Brodie EL, Traxler MF. Multiple lineages of Streptomyces produce antimicrobials within passalid beetle galleries across eastern North America. eLife 2021; 10:65091. [PMID: 33942718 PMCID: PMC8096431 DOI: 10.7554/elife.65091] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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: 11/22/2020] [Accepted: 03/25/2021] [Indexed: 02/06/2023] Open
Abstract
Some insects form symbioses in which actinomycetes provide defense against pathogens by making antimicrobials. The range of chemical strategies employed across these associations, and how these strategies relate to insect lifestyle, remains underexplored. We assessed subsocial passalid beetles of the species Odontotaenius disjunctus, and their frass (fecal material), which is an important food resource within their galleries, as a model insect/actinomycete system. Through chemical and phylogenetic analyses, we found that O. disjunctus frass collected across eastern North America harbored multiple lineages of Streptomyces and diverse antimicrobials. Metabolites detected in frass displayed synergistic and antagonistic inhibition of a fungal entomopathogen, Metarhizium anisopliae, and multiple streptomycete isolates inhibited this pathogen when co-cultivated directly in frass. These findings support a model in which the lifestyle of O. disjunctus accommodates multiple Streptomyces lineages in their frass, resulting in a rich repertoire of antimicrobials that likely insulates their galleries against pathogenic invasion.
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Affiliation(s)
- Rita de Cassia Pessotti
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Bridget L Hansen
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Jewel N Reaso
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
| | - Javier A Ceja-Navarro
- Bioengineering and Biomedical Sciences Department, Biological Systems and Engineering Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States,Institute for Biodiversity Science and Sustainability, California Academy of SciencesBerkeleyUnited States
| | - Laila El-Hifnawi
- Department of Molecular and Cellular Biology, University of California, BerkeleyBerkeleyUnited States
| | - Eoin L Brodie
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeleyUnited States,Department of Environmental Science, Policy and Management, University of California, BerkeleyBerkeleyUnited States
| | - Matthew F Traxler
- Department of Plant and Microbial Biology, University of California, BerkeleyBerkeleyUnited States
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16
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Chadwick KD, Brodrick PG, Grant K, Goulden T, Henderson A, Falco N, Wainwright H, Williams KH, Bill M, Breckheimer I, Brodie EL, Steltzer H, Williams CFR, Blonder B, Chen J, Dafflon B, Damerow J, Hancher M, Khurram A, Lamb J, Lawrence CR, McCormick M, Musinsky J, Pierce S, Polussa A, Hastings Porro M, Scott A, Singh HW, Sorensen PO, Varadharajan C, Whitney B, Maher K. Integrating airborne remote sensing and field campaigns for ecology and Earth system science. Methods Ecol Evol 2020. [DOI: 10.1111/2041-210x.13463] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- K. Dana Chadwick
- Department of Earth System Science Stanford University Stanford CA USA
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Philip G. Brodrick
- Jet Propulsion Laboratory California Institute of Technology Pasadena CA USA
| | - Kathleen Grant
- Department of Earth System Science Stanford University Stanford CA USA
| | | | | | - Nicola Falco
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Haruko Wainwright
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
- Jet Propulsion Laboratory California Institute of Technology Pasadena CA USA
| | - Markus Bill
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Eoin L. Brodie
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
| | - Heidi Steltzer
- Environment and Sustainability Department Fort Lewis College Durango CO USA
| | | | - Benjamin Blonder
- Rocky Mountain Biological Laboratory Crested Butte CO USA
- Department of Environmental Science, Policy, and Management University of California Berkeley CA USA
- School of Life Sciences Arizona State University Tempe AZ USA
| | - Jiancong Chen
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Baptiste Dafflon
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Joan Damerow
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Aizah Khurram
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Jack Lamb
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Corey R. Lawrence
- U.S. Geological Survey, Geosciences and Environmental Change Science Center Denver CO USA
| | - Maeve McCormick
- Department of Earth System Science Stanford University Stanford CA USA
| | - John Musinsky
- National Ecological Observatory Network Boulder CO USA
| | - Samuel Pierce
- SLAC National Accelerator Laboratory Menlo Park CA USA
| | - Alexander Polussa
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | | | - Andea Scott
- Department of Earth System Science Stanford University Stanford CA USA
| | - Hans Wu Singh
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Patrick O. Sorensen
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Charuleka Varadharajan
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Bizuayehu Whitney
- Earth and Environmental Sciences Area Lawrence Berkeley National Laboratory Berkeley CA USA
| | - Katharine Maher
- Department of Earth System Science Stanford University Stanford CA USA
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17
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Leonard LT, Mikkelson K, Hao Z, Brodie EL, Williams KH, Sharp JO. A comparison of lodgepole and spruce needle chemistry impacts on terrestrial biogeochemical processes during isolated decomposition. PeerJ 2020; 8:e9538. [PMID: 32742804 PMCID: PMC7369028 DOI: 10.7717/peerj.9538] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 02/17/2020] [Accepted: 06/23/2020] [Indexed: 12/01/2022] Open
Abstract
This study investigates the isolated decomposition of spruce and lodgepole conifer needles to enhance our understanding of how needle litter impacts near-surface terrestrial biogeochemical processes. Harvested needles were exported to a subalpine meadow to enable a discrete analysis of the decomposition processes over 2 years. Initial chemistry revealed the lodgepole needles to be less recalcitrant with a lower carbon to nitrogen (C:N) ratio. Total C and N fundamentally shifted within needle species over time with decreased C:N ratios for spruce and increased ratios for lodgepole. Differences in chemistry correlated with CO2 production and soil microbial communities. The most pronounced trends were associated with lodgepole needles in comparison to the spruce and needle-free controls. Increased organic carbon and nitrogen concentrations associated with needle presence in soil extractions further corroborate the results with clear biogeochemical signatures in association with needle chemistry. Interestingly, no clear differentiation was observed as a function of bark beetle impacted spruce needles vs those derived from healthy spruce trees despite initial differences in needle chemistry. These results reveal that the inherent chemistry associated with tree species has a greater impact on soil biogeochemical signatures during isolated needle decomposition. By extension, biogeochemical shifts associated with bark beetle infestation are likely driven more by changes such as the cessation of rhizospheric processes than by needle litter decomposition.
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Affiliation(s)
| | | | - Zhao Hao
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
| | - Jonathan O Sharp
- Colorado School of Mines, Golden, CO, USA.,Rocky Mountain Biological Laboratory, Crested Butte, CO, USA
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18
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Blazewicz SJ, Hungate BA, Koch BJ, Nuccio EE, Morrissey E, Brodie EL, Schwartz E, Pett-Ridge J, Firestone MK. Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil. ISME J 2020; 14:1520-1532. [PMID: 32203117 PMCID: PMC7242442 DOI: 10.1038/s41396-020-0617-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [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: 03/25/2019] [Revised: 02/10/2020] [Accepted: 02/17/2020] [Indexed: 02/01/2023]
Abstract
Microbial activity increases after rewetting dry soil, resulting in a pulse of carbon mineralization and nutrient availability. The biogeochemical responses to wet-up are reasonably well understood and known to be microbially mediated. Yet, the population level dynamics, and the resulting changes in microbial community patterns, are not well understood as ecological phenomena. Here, we used sequencing of 16S rRNA genes coupled with heavy water (H218O) DNA quantitative stable isotope probing to estimate population-specific rates of growth and mortality in response to a simulated wet-up event in a California annual grassland soil. Bacterial growth and mortality responded rapidly to wet-up, within 3 h, and continued throughout the 168 h incubation, with patterns of sequential growth observed at the phylum level. Of the 37 phyla detected in the prewet community, growth was found in 18 phyla while mortality was measured in 26 phyla. Rapid growth and mortality rates were measurable within 3 h of wet-up but had contrasting characteristics; growth at 3 h was dominated by select taxa within the Proteobacteria and Firmicutes, whereas mortality was taxonomically widespread. Furthermore, across the community, mortality exhibited density-independence, consistent with the indiscriminate shock resulting from dry-down and wet-up, whereas growth was density-dependent, consistent with control by competition or predation. Total aggregated growth across the community was highly correlated with total soil CO2 production. Together, these results illustrate how previously "invisible" population responses can translate quantitatively to emergent observations of ecosystem-scale biogeochemistry.
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Affiliation(s)
- Steven J Blazewicz
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA.
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA.
- Lawrence Livermore National Laboratory, 7000 East Ave L-231, Livermore, CA, 94550, USA.
| | - Bruce A Hungate
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Benjamin J Koch
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Ember Morrissey
- Division of Plant and Soil Sciences, West Virginia University, Morgantown, WV, 26505, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, USA
| | - Egbert Schwartz
- Center for Ecosystem Science and Society, Northern Arizona University, Flagstaff, AZ, 86011, USA
- Department of Biological Sciences, Northern Arizona University, Flagstaff, AZ, 86011, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA, 94550, USA
| | - Mary K Firestone
- Department of Environmental Science, Policy, and Management, University of California, 137 Mulford Hall, Berkeley, CA, 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, 1 Cyclotron Rd. MS70A-3317, Berkeley, CA, 94720, USA
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19
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Sorensen PO, Beller HR, Bill M, Bouskill NJ, Hubbard SS, Karaoz U, Polussa A, Steltzer H, Wang S, Williams KH, Wu Y, Brodie EL. The Snowmelt Niche Differentiates Three Microbial Life Strategies That Influence Soil Nitrogen Availability During and After Winter. Front Microbiol 2020; 11:871. [PMID: 32477299 PMCID: PMC7242569 DOI: 10.3389/fmicb.2020.00871] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 11/08/2019] [Accepted: 04/14/2020] [Indexed: 12/13/2022] Open
Abstract
Soil microbial biomass can reach its annual maximum pool size beneath the winter snowpack and is known to decline abruptly following snowmelt in seasonally snow-covered ecosystems. Observed differences in winter versus summer microbial taxonomic composition also suggests that phylogenetically conserved traits may permit winter- versus summer-adapted microorganisms to occupy distinct niches. In this study, we sought to identify archaea, bacteria, and fungi that are associated with the soil microbial bloom overwinter and the subsequent biomass collapse following snowmelt at a high-altitude watershed in central Colorado, United States. Archaea, bacteria, and fungi were categorized into three life strategies (Winter-Adapted, Snowmelt-Specialist, Spring-Adapted) based upon changes in abundance during winter, the snowmelt period, and after snowmelt in spring. We calculated indices of phylogenetic relatedness (archaea and bacteria) or assigned functional attributes (fungi) to organisms within life strategies to infer whether phylogenetically conserved traits differentiate Winter-Adapted, Snowmelt-Specialist, and Spring-Adapted groups. We observed that the soil microbial bloom was correlated in time with a pulse of snowmelt infiltration, which commenced 65 days prior to soils becoming snow-free. A pulse of nitrogen (N, as nitrate) occurred after snowmelt, along with a collapse in the microbial biomass pool size, and an increased abundance of nitrifying archaea and bacteria (e.g., Thaumarchaeota, Nitrospirae). Winter- and Spring-Adapted archaea and bacteria were phylogenetically clustered, suggesting that phylogenetically conserved traits allow Winter- and Spring-Adapted archaea and bacteria to occupy distinct niches. In contrast, Snowmelt-Specialist archaea and bacteria were phylogenetically overdispersed, suggesting that the key mechanism(s) of the microbial biomass crash are likely to be density-dependent (e.g., trophic interactions, competitive exclusion) and affect organisms across a broad phylogenetic spectrum. Saprotrophic fungi were the dominant functional group across fungal life strategies, however, ectomycorrhizal fungi experienced a large increase in abundance in spring. If well-coupled plant-mycorrhizal phenology currently buffers ecosystem N losses in spring, then changes in snowmelt timing may alter ecosystem N retention potential. Overall, we observed that snowmelt separates three distinct soil niches that are occupied by ecologically distinct groups of microorganisms. This ecological differentiation is of biogeochemical importance, particularly with respect to the mobilization of nitrogen during winter, before and after snowmelt.
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Affiliation(s)
- Patrick O. Sorensen
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Harry R. Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Nicholas J. Bouskill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Alexander Polussa
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- School of Forestry and Environmental Studies, Yale University, New Haven, CT, United States
| | - Heidi Steltzer
- Fort Lewis College, Durango, CO, United States
- Rocky Mountain Biological Laboratory, Gothic, CO, United States
| | - Shi Wang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Rocky Mountain Biological Laboratory, Gothic, CO, United States
| | - Yuxin Wu
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA, United States
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20
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Isobe K, Bouskill NJ, Brodie EL, Sudderth EA, Martiny JBH. Phylogenetic conservation of soil bacterial responses to simulated global changes. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190242. [PMID: 32200749 PMCID: PMC7133522 DOI: 10.1098/rstb.2019.0242] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2020] [Indexed: 01/03/2023] Open
Abstract
Soil bacterial communities are altered by anthropogenic drivers such as climate change-related warming and fertilization. However, we lack a predictive understanding of how bacterial communities respond to such global changes. Here, we tested whether phylogenetic information might be more predictive of the response of bacterial taxa to some forms of global change than others. We analysed the composition of soil bacterial communities from perturbation experiments that simulated warming, drought, elevated CO2 concentration and phosphorus (P) addition. Bacterial responses were phylogenetically conserved to all perturbations. The phylogenetic depth of these responses varied minimally among the types of perturbations and was similar when merging data across locations, implying that the context of particular locations did not affect the phylogenetic pattern of response. We further identified taxonomic groups that responded consistently to each type of perturbation. These patterns revealed that, at the level of family and above, most groups responded consistently to only one or two types of perturbations, suggesting that traits with different patterns of phylogenetic conservation underlie the responses to different perturbations. We conclude that a phylogenetic approach may be useful in predicting how soil bacterial communities respond to a variety of global changes. This article is part of the theme issue 'Conceptual challenges in microbial community ecology'.
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Affiliation(s)
- Kazuo Isobe
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Nicholas J. Bouskill
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Eoin L. Brodie
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Erika A. Sudderth
- Center for Environmental Studies, Brown University, Providence, RI, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
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21
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Nuccio EE, Starr E, Karaoz U, Brodie EL, Zhou J, Tringe SG, Malmstrom RR, Woyke T, Banfield JF, Firestone MK, Pett-Ridge J. Niche differentiation is spatially and temporally regulated in the rhizosphere. ISME J 2020; 14:999-1014. [PMID: 31953507 PMCID: PMC7082339 DOI: 10.1038/s41396-019-0582-x] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 04/28/2019] [Revised: 10/28/2019] [Accepted: 12/18/2019] [Indexed: 01/14/2023]
Abstract
The rhizosphere is a hotspot for microbial carbon transformations, and is the entry point for root polysaccharides and polymeric carbohydrates that are important precursors to soil organic matter (SOM). However, the ecological mechanisms that underpin rhizosphere carbohydrate depolymerization are poorly understood. Using Avena fatua, a common annual grass, we analyzed time-resolved metatranscriptomes to compare microbial functions in rhizosphere, detritusphere, and combined rhizosphere-detritusphere habitats. Transcripts were binned using a unique reference database generated from soil isolate genomes, single-cell amplified genomes, metagenomes, and stable isotope probing metagenomes. While soil habitat significantly affected both community composition and overall gene expression, the succession of microbial functions occurred at a faster time scale than compositional changes. Using hierarchical clustering of upregulated decomposition genes, we identified four distinct microbial guilds populated by taxa whose functional succession patterns suggest specialization for substrates provided by fresh growing roots, decaying root detritus, the combination of live and decaying root biomass, or aging root material. Carbohydrate depolymerization genes were consistently upregulated in the rhizosphere, and both taxonomic and functional diversity were highest in the combined rhizosphere-detritusphere, suggesting coexistence of rhizosphere guilds is facilitated by niche differentiation. Metatranscriptome-defined guilds provide a framework to model rhizosphere succession and its consequences for soil carbon cycling.
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Affiliation(s)
- Erin E Nuccio
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
| | - Evan Starr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jizhong Zhou
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, and School of Civil Engineering and Environmental Sciences, University of Oklahoma, Norman, OK, 73019, USA
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, 100084, China
| | - Susannah G Tringe
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Rex R Malmstrom
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Tanja Woyke
- Department of Energy Joint Genome Institute, Berkeley, CA, 94720, USA
| | - Jillian F Banfield
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Mary K Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, 94720, USA
| | - Jennifer Pett-Ridge
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, 94551, USA.
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22
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Malik AA, Martiny JBH, Brodie EL, Martiny AC, Treseder KK, Allison SD. Defining trait-based microbial strategies with consequences for soil carbon cycling under climate change. ISME J 2020; 14:1-9. [PMID: 31554911 PMCID: PMC6908601 DOI: 10.1038/s41396-019-0510-0] [Citation(s) in RCA: 237] [Impact Index Per Article: 59.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Revised: 06/07/2019] [Accepted: 08/16/2019] [Indexed: 12/22/2022]
Affiliation(s)
- Ashish A Malik
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA.
| | - Jennifer B H Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Adam C Martiny
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology & Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
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23
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Wood LF, Brown BP, Lennard K, Karaoz U, Havyarimana E, Passmore JAS, Hesseling AC, Edlefsen PT, Kuhn L, Mulder N, Brodie EL, Sodora DL, Jaspan HB. Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants. Clin Infect Dis 2019; 67:1237-1246. [PMID: 29659737 DOI: 10.1093/cid/ciy265] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 04/03/2018] [Indexed: 12/31/2022] Open
Abstract
Background Exclusive breastfeeding reduces the rate of postnatal human immunodeficiency virus (HIV) transmission compared to nonexclusive breastfeeding; however, the mechanisms of this protection are unknown. Our study aimed to interrogate the mechanisms underlying the protective effect of exclusive breastfeeding. Methods We performed a prospective, longitudinal study of infants from a high-HIV-prevalence, low-income setting in South Africa. We evaluated the role of any non-breast milk feeds, excluding prescribed medicines on stool microbial communities via 16S rRNA gene sequencing, peripheral T-cell activation via flow cytometry, and buccal mucosal gene expression via quantitative polymerase chain reaction assay. Results A total of 155 infants were recruited at birth with mean gestational age of 38.9 weeks and mean birth weight of 3.2 kg. All infants were exclusively breastfed (EBF) at birth, but only 43.5% and 20% remained EBF at 6 or 14 weeks of age, respectively. We observed lower stool microbial diversity and distinct microbial composition in exclusively breastfed infants. These microbial communities, and the relative abundance of key taxa, were correlated with peripheral CD4+ T-cell activation, which was lower in EBF infants. In the oral mucosa, gene expression of chemokine and chemokine receptors involved in recruitment of HIV target cells to tissues, as well as epithelial cytoskeletal proteins, was lower in EBF infants. Conclusions These data suggest that nonexclusive breastfeeding alters the gut microbiota, increasing T-cell activation and, potentially, mucosal recruitment of HIV target cells. Study findings highlight a biologically plausible mechanistic explanation for the reduced postnatal HIV transmission observed in EBF infants.
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Affiliation(s)
- Lianna F Wood
- University of Washington Schools of Medicine and Public Health, Seattle
| | - Bryan P Brown
- Duke University, Durham, North Carolina.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Katie Lennard
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Ulas Karaoz
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley.,University of California, Berkeley
| | - Enock Havyarimana
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Jo-Ann S Passmore
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa.,National Health Laboratory Services, Cape Town, South Africa
| | - Anneke C Hesseling
- Desmond Tutu TB Centre, Stellenbosch University, Cape Town, South Africa
| | | | | | - Nicola Mulder
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa
| | - Eoin L Brodie
- Earth and Environmental Science, Lawrence Berkeley National Laboratories, Berkeley.,University of California, Berkeley
| | | | - Heather B Jaspan
- University of Washington Schools of Medicine and Public Health, Seattle.,Institute of Infectious Disease and Molecular Medicine, University of Cape Town Health Sciences Faculty, South Africa.,Seattle Children's Research Institute, Washington
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24
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Zhalnina K, Louie KB, Hao Z, Mansoori N, da Rocha UN, Shi S, Cho H, Karaoz U, Loqué D, Bowen BP, Firestone MK, Northen TR, Brodie EL. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 2018. [PMID: 29556109 DOI: 10.1016/b978-0-12-520920-5.50016-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 04/21/2023]
Abstract
Like all higher organisms, plants have evolved in the context of a microbial world, shaping both their evolution and their contemporary ecology. Interactions between plant roots and soil microorganisms are critical for plant fitness in natural environments. Given this co-evolution and the pivotal importance of plant-microbial interactions, it has been hypothesized, and a growing body of literature suggests, that plants may regulate the composition of their rhizosphere to promote the growth of microorganisms that improve plant fitness in a given ecosystem. Here, using a combination of comparative genomics and exometabolomics, we show that pre-programmed developmental processes in plants (Avena barbata) result in consistent patterns in the chemical composition of root exudates. This chemical succession in the rhizosphere interacts with microbial metabolite substrate preferences that are predictable from genome sequences. Specifically, we observed a preference by rhizosphere bacteria for consumption of aromatic organic acids exuded by plants (nicotinic, shikimic, salicylic, cinnamic and indole-3-acetic). The combination of these plant exudation traits and microbial substrate uptake traits interact to yield the patterns of microbial community assembly observed in the rhizosphere of an annual grass. This discovery provides a mechanistic underpinning for the process of rhizosphere microbial community assembly and provides an attractive direction for the manipulation of the rhizosphere microbiome for beneficial outcomes.
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Affiliation(s)
- Kateryna Zhalnina
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Katherine B Louie
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Zhao Hao
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nasim Mansoori
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Biosystems Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
| | - Ulisses Nunes da Rocha
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Microbiology, Helmholtz Centre for Environmental Research-UFZ, Leipzig, Germany
| | - Shengjing Shi
- Lincoln Science Centre, AgResearch Ltd, Christchurch, New Zealand
| | - Heejung Cho
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Dominique Loqué
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Joint BioEnergy Institute, Biosystems Engineering Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- INSA de Lyon, CNRS, UMR5240, Microbiologie, Adaptation et Pathogénie, Université Claude Bernard Lyon 1, Villeurbanne, France
| | - Benjamin P Bowen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mary K Firestone
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA.
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25
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D'haeseleer P, Lee JZ, Prufert-Bebout L, Burow LC, Detweiler AM, Weber PK, Karaoz U, Brodie EL, Glavina Del Rio T, Tringe SG, Bebout BM, Pett-Ridge J. Metagenomic analysis of intertidal hypersaline microbial mats from Elkhorn Slough, California, grown with and without molybdate. Stand Genomic Sci 2017; 12:67. [PMID: 29167704 PMCID: PMC5688640 DOI: 10.1186/s40793-017-0279-6] [Citation(s) in RCA: 3] [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: 07/14/2017] [Accepted: 10/25/2017] [Indexed: 11/10/2022] Open
Abstract
Cyanobacterial mats are laminated microbial ecosystems which occur in highly diverse environments and which may provide a possible model for early life on Earth. Their ability to produce hydrogen also makes them of interest from a biotechnological and bioenergy perspective. Samples of an intertidal microbial mat from the Elkhorn Slough estuary in Monterey Bay, California, were transplanted to a greenhouse at NASA Ames Research Center to study a 24-h diel cycle, in the presence or absence of molybdate (which inhibits biohydrogen consumption by sulfate reducers). Here, we present metagenomic analyses of four samples that will be used as references for future metatranscriptomic analyses of this diel time series.
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Affiliation(s)
| | | | | | - Luke C Burow
- NASA Ames Research Center, Moffett Field, CA USA.,Stanford University, Stanford, CA USA
| | - Angela M Detweiler
- NASA Ames Research Center, Moffett Field, CA USA.,Bay Area Environmental Research Institute, Petaluma, CA USA
| | - Peter K Weber
- Lawrence Livermore National Laboratory, Livermore, CA USA
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Tijana Glavina Del Rio
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA USA
| | - Susannah G Tringe
- Lawrence Berkeley National Laboratory, Berkeley, CA USA.,Department of Energy Joint Genome Institute, Walnut Creek, CA USA
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26
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Obadia B, Güvener ZT, Zhang V, Ceja-Navarro JA, Brodie EL, Ja WW, Ludington WB. Probabilistic Invasion Underlies Natural Gut Microbiome Stability. Curr Biol 2017; 27:1999-2006.e8. [PMID: 28625783 PMCID: PMC5555957 DOI: 10.1016/j.cub.2017.05.034] [Citation(s) in RCA: 92] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 04/28/2017] [Accepted: 05/05/2017] [Indexed: 01/04/2023]
Abstract
Species compositions of gut microbiomes impact host health [1-3], but the processes determining these compositions are largely unknown. An unexplained observation is that gut species composition varies widely between individuals but is largely stable over time within individuals [4, 5]. Stochastic factors during establishment may drive these alternative stable states (colonized versus non-colonized) [6, 7], which can influence susceptibility to pathogens, such as Clostridium difficile. Here we sought to quantify and model the dose response, dynamics, and stability of bacterial colonization in the fruit fly (Drosophila melanogaster) gut. Our precise, high-throughput technique revealed stable between-host variation in colonization when individual germ-free flies were fed their own natural commensals (including the probiotic Lactobacillus plantarum). Some flies were colonized while others remained germ-free even at extremely high bacterial doses. Thus, alternative stable states of colonization exist even in this low-complexity model of host-microbe interactions. These alternative states are driven by a fundamental asymmetry between the inoculum population and the stably colonized population that is mediated by spatial localization and a population bottleneck, which makes stochastic effects important by lowering the effective population size. Prior colonization with other bacteria reduced the chances of subsequent colonization, thus increasing the stability of higher-diversity guts. Therefore, stable gut diversity may be driven by inherently stochastic processes, which has important implications for combatting infectious diseases and for stably establishing probiotics in the gut.
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Affiliation(s)
- Benjamin Obadia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Z T Güvener
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Vivian Zhang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Javier A Ceja-Navarro
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, CA 94720, USA
| | - William W Ja
- Department of Metabolism and Aging, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - William B Ludington
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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27
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Varadharajan C, Beller HR, Bill M, Brodie EL, Conrad ME, Han R, Irwin C, Larsen JT, Lim HC, Molins S, Steefel CI, van Hise A, Yang L, Nico PS. Reoxidation of Chromium(III) Products Formed under Different Biogeochemical Regimes. Environ Sci Technol 2017; 51:4918-4927. [PMID: 28365989 DOI: 10.1021/acs.est.6b06044] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Hexavalent chromium, Cr(VI), is a widespread and toxic groundwater contaminant. Reductive immobilization to Cr(III) is a treatment option, but its success depends on the long-term potential for reduced chromium precipitates to remain immobilized under oxidizing conditions. In this unique long-term study, aquifer sediments subjected to reductive Cr(VI) immobilization under different biogeochemical regimes were tested for their susceptibility to reoxidation. After reductive treatment for 1 year, sediments were exposed to oxygenated conditions for another 2 years in flow-through, laboratory columns. Under oxidizing conditions, immobilized chromium reduced under predominantly denitrifying conditions was mobilized at low concentrations (≪1 μM Cr(VI); ∼ 3% of Cr(III) deposited) that declined over time. A conceptual model of a limited pool of more soluble Cr(III), and a larger pool of relatively insoluble Cr(III), is proposed. In contrast, almost no chromium was mobilized from columns reduced under predominantly fermentative conditions, and where reducing conditions persisted for several months after introduction of oxidizing conditions, presumably due to the presence of a reservoir of reduced species generated during reductive treatment. The results from this 3-year study demonstrate that biogeochemical conditions present during reductive treatment, and the potential for buildup of reducing species, will impact the long-term sustainability of the remediation effort.
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Affiliation(s)
- Charuleka Varadharajan
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Harry R Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Mark E Conrad
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Ruyang Han
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Courtney Irwin
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Joern T Larsen
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Hsiao-Chien Lim
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Sergi Molins
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Carl I Steefel
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - April van Hise
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Li Yang
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
| | - Peter S Nico
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory , One Cyclotron Road, Berkeley, California 94720, United States
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Yabusaki SB, Wilkins MJ, Fang Y, Williams KH, Arora B, Bargar J, Beller HR, Bouskill NJ, Brodie EL, Christensen JN, Conrad ME, Danczak RE, King E, Soltanian MR, Spycher NF, Steefel CI, Tokunaga TK, Versteeg R, Waichler SR, Wainwright HM. Water Table Dynamics and Biogeochemical Cycling in a Shallow, Variably-Saturated Floodplain. Environ Sci Technol 2017; 51:3307-3317. [PMID: 28218533 DOI: 10.1021/acs.est.6b04873] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Three-dimensional variably saturated flow and multicomponent biogeochemical reactive transport modeling, based on published and newly generated data, is used to better understand the interplay of hydrology, geochemistry, and biology controlling the cycling of carbon, nitrogen, oxygen, iron, sulfur, and uranium in a shallow floodplain. In this system, aerobic respiration generally maintains anoxic groundwater below an oxic vadose zone until seasonal snowmelt-driven water table peaking transports dissolved oxygen (DO) and nitrate from the vadose zone into the alluvial aquifer. The response to this perturbation is localized due to distinct physico-biogeochemical environments and relatively long time scales for transport through the floodplain aquifer and vadose zone. Naturally reduced zones (NRZs) containing sediments higher in organic matter, iron sulfides, and non-crystalline U(IV) rapidly consume DO and nitrate to maintain anoxic conditions, yielding Fe(II) from FeS oxidative dissolution, nitrite from denitrification, and U(VI) from nitrite-promoted U(IV) oxidation. Redox cycling is a key factor for sustaining the observed aquifer behaviors despite continuous oxygen influx and the annual hydrologically induced oxidation event. Depth-dependent activity of fermenters, aerobes, nitrate reducers, sulfate reducers, and chemolithoautotrophs (e.g., oxidizing Fe(II), S compounds, and ammonium) is linked to the presence of DO, which has higher concentrations near the water table.
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Affiliation(s)
- Steven B Yabusaki
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | | | - Yilin Fang
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Kenneth H Williams
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Bhavna Arora
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John Bargar
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Harry R Beller
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Nicholas J Bouskill
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - John N Christensen
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Mark E Conrad
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | - Eric King
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | | | - Nicolas F Spycher
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Carl I Steefel
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Tetsu K Tokunaga
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Roelof Versteeg
- Subsurface Insights , Hanover, New Hampshire 03755, United States
| | - Scott R Waichler
- Pacific Northwest National Laboratory , Richland, Washington 99354, United States
| | - Haruko M Wainwright
- Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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29
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Martiny JBH, Martiny AC, Weihe C, Lu Y, Berlemont R, Brodie EL, Goulden ML, Treseder KK, Allison SD. Microbial legacies alter decomposition in response to simulated global change. ISME J 2017; 11:490-499. [PMID: 27740610 PMCID: PMC5270563 DOI: 10.1038/ismej.2016.122] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/11/2016] [Accepted: 08/05/2016] [Indexed: 01/19/2023]
Abstract
Terrestrial ecosystem models assume that microbial communities respond instantaneously, or are immediately resilient, to environmental change. Here we tested this assumption by quantifying the resilience of a leaf litter community to changes in precipitation or nitrogen availability. By manipulating composition within a global change experiment, we decoupled the legacies of abiotic parameters versus that of the microbial community itself. After one rainy season, more variation in fungal composition could be explained by the original microbial inoculum than the litterbag environment (18% versus 5.5% of total variation). This compositional legacy persisted for 3 years, when 6% of the variability in fungal composition was still explained by the microbial origin. In contrast, bacterial composition was generally more resilient than fungal composition. Microbial functioning (measured as decomposition rate) was not immediately resilient to the global change manipulations; decomposition depended on both the contemporary environment and rainfall the year prior. Finally, using metagenomic sequencing, we showed that changes in precipitation, but not nitrogen availability, altered the potential for bacterial carbohydrate degradation, suggesting why the functional consequences of the two experiments may have differed. Predictions of how terrestrial ecosystem processes respond to environmental change may thus be improved by considering the legacies of microbial communities.
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Affiliation(s)
- Jennifer BH Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Adam C Martiny
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Renaud Berlemont
- Department of Earth System Science, University of California, Irvine, CA, USA
- Department of Biology, California State University, Long Beach, CA, USA
| | - Eoin L Brodie
- Ecology Department, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, CA, USA
| | - Michael L Goulden
- Department of Earth System Science, University of California, Irvine, CA, USA
| | - Kathleen K Treseder
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
| | - Steven D Allison
- Department of Ecology and Evolutionary Biology, University of California, Irvine, CA, USA
- Department of Earth System Science, University of California, Irvine, CA, USA
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30
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Jewell TNM, Karaoz U, Bill M, Chakraborty R, Brodie EL, Williams KH, Beller HR. Metatranscriptomic Analysis Reveals Unexpectedly Diverse Microbial Metabolism in a Biogeochemical Hot Spot in an Alluvial Aquifer. Front Microbiol 2017; 8:40. [PMID: 28179898 PMCID: PMC5264521 DOI: 10.3389/fmicb.2017.00040] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [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: 10/09/2016] [Accepted: 01/06/2017] [Indexed: 02/05/2023] Open
Abstract
Organic matter deposits in alluvial aquifers have been shown to result in the formation of naturally reduced zones (NRZs), which can modulate aquifer redox status and influence the speciation and mobility of metals, affecting groundwater geochemistry. In this study, we sought to better understand how natural organic matter fuels microbial communities within anoxic biogeochemical hot spots (NRZs) in a shallow alluvial aquifer at the Rifle (CO) site. We conducted a 20-day microcosm experiment in which NRZ sediments, which were enriched in buried woody plant material, served as the sole source of electron donors and microorganisms. The microcosms were constructed and incubated under anaerobic conditions in serum bottles with an initial N2 headspace and were sampled every 5 days for metagenome and metatranscriptome profiles in combination with biogeochemical measurements. Biogeochemical data indicated that the decomposition of native organic matter occurred in different phases, beginning with mineralization of dissolved organic matter (DOM) to CO2 during the first week of incubation, followed by a pulse of acetogenesis that dominated carbon flux after 2 weeks. A pulse of methanogenesis co-occurred with acetogenesis, but only accounted for a small fraction of carbon flux. The depletion of DOM over time was strongly correlated with increases in expression of many genes associated with heterotrophy (e.g., amino acid, fatty acid, and carbohydrate metabolism) belonging to a Hydrogenophaga strain that accounted for a relatively large percentage (~8%) of the metatranscriptome. This Hydrogenophaga strain also expressed genes indicative of chemolithoautotrophy, including CO2 fixation, H2 oxidation, S-compound oxidation, and denitrification. The pulse of acetogenesis appears to have been collectively catalyzed by a number of different organisms and metabolisms, most prominently pyruvate:ferredoxin oxidoreductase. Unexpected genes were identified among the most highly expressed (>98th percentile) transcripts, including acetone carboxylase and cell-wall-associated hydrolases with unknown substrates (numerous lesser expressed cell-wall-associated hydrolases targeted peptidoglycan). Many of the most highly expressed hydrolases belonged to a Ca. Bathyarchaeota strain and may have been associated with recycling of bacterial biomass. Overall, these results highlight the complex nature of organic matter transformation in NRZs and the microbial metabolic pathways that interact to mediate redox status and elemental cycling.
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Affiliation(s)
- Talia N M Jewell
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Markus Bill
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Romy Chakraborty
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Kenneth H Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Harry R Beller
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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31
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Ben Guerrero E, Soria M, Salvador R, Ceja-Navarro JA, Campos E, Brodie EL, Talia P. Effect of Different Lignocellulosic Diets on Bacterial Microbiota and Hydrolytic Enzyme Activities in the Gut of the Cotton Boll Weevil ( Anthonomus grandis). Front Microbiol 2016; 7:2093. [PMID: 28082962 PMCID: PMC5186755 DOI: 10.3389/fmicb.2016.02093] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [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: 08/01/2016] [Accepted: 12/09/2016] [Indexed: 11/13/2022] Open
Abstract
Cotton boll weevils, Anthonomus grandis, are omnivorous coleopteran that can feed on diets with different compositions, including recalcitrant lignocellulosic materials. We characterized the changes in the prokaryotic community structure and the hydrolytic activities of A. grandis larvae fed on different lignocellulosic diets. A. grandis larvae were fed on three different artificial diets: cottonseed meal (CM), Napier grass (NG) and corn stover (CS). Total DNA was extracted from the gut samples for amplification and sequencing of the V3-V4 hypervariable region of the 16S rRNA gene. Proteobacteria and Firmicutes dominated the gut microbiota followed by Actinobacteria, Spirochaetes and a small number of unclassified phyla in CM and NG microbiomes. In the CS feeding group, members of Spirochaetes were the most prevalent, followed by Proteobacteria and Firmicutes. Bray-Curtis distances showed that the samples from the CS community were clearly separated from those samples of the CM and NG diets. Gut extracts from all three diets exhibited endoglucanase, xylanase, β-glucosidase and pectinase activities. These activities were significantly affected by pH and temperature across different diets. We observed that the larvae reared on a CM showed significantly higher activities than larvae reared on NG and CS. We demonstrated that the intestinal bacterial community structure varies depending on diet composition. Diets with more variable and complex compositions, such as CS, showed higher bacterial diversity and richness than the two other diets. In spite of the detected changes in composition and diversity, we identified a core microbiome shared between the three different lignocellulosic diets. These results suggest that feeding with diets of different lignocellulosic composition could be a viable strategy to discover variants of hemicellulose and cellulose breakdown systems.
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Affiliation(s)
- Emiliano Ben Guerrero
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Marcelo Soria
- Instituto de Investigaciones en Biociencias Agrícolas y Ambientales-Consejo Nacional de Investigaciones Científicas y Técnicas, Cátedra de Microbiología Agrícola, Facultad de Agronomía, Universidad de Buenos Aires Buenos Aires, Argentina
| | - Ricardo Salvador
- Instituto de Microbiología y Zoología Agrícola, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria Castelar Hurlingham, Argentina
| | - Javier A Ceja-Navarro
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eleonora Campos
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Paola Talia
- Instituto de Biotecnología, Centro de Investigación en Ciencias Veterinarias y Agronómicas, Centro Nacional de Investigaciones Agropecuarias - Instituto Nacional de Tecnología Agropecuaria CastelarHurlingham, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)Buenos Aires, Argentina
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32
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Anantharaman K, Brown CT, Hug LA, Sharon I, Castelle CJ, Probst AJ, Thomas BC, Singh A, Wilkins MJ, Karaoz U, Brodie EL, Williams KH, Hubbard SS, Banfield JF. Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nat Commun 2016; 7:13219. [PMID: 27774985 PMCID: PMC5079060 DOI: 10.1038/ncomms13219] [Citation(s) in RCA: 572] [Impact Index Per Article: 71.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 09/13/2016] [Indexed: 01/05/2023] Open
Abstract
The subterranean world hosts up to one-fifth of all biomass, including microbial communities that drive transformations central to Earth's biogeochemical cycles. However, little is known about how complex microbial communities in such environments are structured, and how inter-organism interactions shape ecosystem function. Here we apply terabase-scale cultivation-independent metagenomics to aquifer sediments and groundwater, and reconstruct 2,540 draft-quality, near-complete and complete strain-resolved genomes that represent the majority of known bacterial phyla as well as 47 newly discovered phylum-level lineages. Metabolic analyses spanning this vast phylogenetic diversity and representing up to 36% of organisms detected in the system are used to document the distribution of pathways in coexisting organisms. Consistent with prior findings indicating metabolic handoffs in simple consortia, we find that few organisms within the community can conduct multiple sequential redox transformations. As environmental conditions change, different assemblages of organisms are selected for, altering linkages among the major biogeochemical cycles.
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Affiliation(s)
- Karthik Anantharaman
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Christopher T. Brown
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | - Laura A. Hug
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Itai Sharon
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Cindy J. Castelle
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Alexander J. Probst
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Brian C. Thomas
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Andrea Singh
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
| | - Michael J. Wilkins
- School of Earth Sciences and Department of Microbiology, The Ohio State University, Columbus, Ohio 43210, USA
| | - Ulas Karaoz
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Kenneth H. Williams
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Susan S. Hubbard
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Jillian F. Banfield
- Department of Earth and Planetary Science, University of California, Berkeley, California 94720, USA
- Earth and Environmental Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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33
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Blaser MJ, Cardon ZG, Cho MK, Dangl JL, Donohue TJ, Green JL, Knight R, Maxon ME, Northen TR, Pollard KS, Brodie EL. Toward a Predictive Understanding of Earth's Microbiomes to Address 21st Century Challenges. mBio 2016; 7:e00714-16. [PMID: 27178263 PMCID: PMC4895116 DOI: 10.1128/mbio.00714-16] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Microorganisms have shaped our planet and its inhabitants for over 3.5 billion years. Humankind has had a profound influence on the biosphere, manifested as global climate and land use changes, and extensive urbanization in response to a growing population. The challenges we face to supply food, energy, and clean water while maintaining and improving the health of our population and ecosystems are significant. Given the extensive influence of microorganisms across our biosphere, we propose that a coordinated, cross-disciplinary effort is required to understand, predict, and harness microbiome function. From the parallelization of gene function testing to precision manipulation of genes, communities, and model ecosystems and development of novel analytical and simulation approaches, we outline strategies to move microbiome research into an era of causality. These efforts will improve prediction of ecosystem response and enable the development of new, responsible, microbiome-based solutions to significant challenges of our time.
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Affiliation(s)
- Martin J Blaser
- Departments of Microbiology and Medicine, New York University School of Medicine, New York, New York, USA
| | - Zoe G Cardon
- The Ecosystems Center, Marine Biological Laboratory, Woods Hole, Massachusetts, USA
| | - Mildred K Cho
- Stanford Center for Biomedical Ethics, Stanford University, Palo Alto, California, USA
| | - Jeffrey L Dangl
- Department of Biology and Howard Hughes Medical Institute, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Timothy J Donohue
- Department of Bacteriology, Great Lakes Bioenergy Research Center and Wisconsin Energy Institute, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Jessica L Green
- Biology and the Built Environment Center, University of Oregon, Eugene, Oregon, USA Department of Biology, Institute of Ecology and Evolution, University of Oregon, Eugene, Oregon, USA
| | - Rob Knight
- Departments of Pediatrics and Computer Science & Engineering, and Center for Microbiome Innovation, University of California San Diego, La Jolla, California, USA
| | - Mary E Maxon
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Trent R Northen
- Biosciences, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Katherine S Pollard
- Division of Biostatistics, Gladstone Institutes and Institute for Human Genetics, Institute for Computational Health Science, University of California, San Francisco, California, USA
| | - Eoin L Brodie
- Earth and Environmental Sciences, Lawrence Berkeley National Lab, Berkeley, California, USA Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
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34
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Nuccio EE, Anderson‐Furgeson J, Estera KY, Pett‐Ridge J, Valpine P, Brodie EL, Firestone MK. Climate and edaphic controllers influence rhizosphere community assembly for a wild annual grass. Ecology 2016; 97:1307-18. [DOI: 10.1890/15-0882.1] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Erin E. Nuccio
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California USA
- Department of Plant and Microbial Biology University of California Berkeley, Berkeley California USA
| | - James Anderson‐Furgeson
- Department of Plant and Microbial Biology University of California Berkeley, Berkeley California USA
| | - Katerina Y. Estera
- Department of Environmental Science, Policy, and Management University of California Berkeley, Berkeley California USA
| | - Jennifer Pett‐Ridge
- Physical and Life Sciences Directorate Lawrence Livermore National Laboratory Livermore California USA
| | - Perry Valpine
- Department of Environmental Science, Policy, and Management University of California Berkeley, Berkeley California USA
| | - Eoin L. Brodie
- Department of Environmental Science, Policy, and Management University of California Berkeley, Berkeley California USA
- Earth and Environmental Sciences Lawrence Berkeley National Laboratory Berkeley California USA
| | - Mary K. Firestone
- Department of Environmental Science, Policy, and Management University of California Berkeley, Berkeley California USA
- Earth and Environmental Sciences Lawrence Berkeley National Laboratory Berkeley California USA
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35
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Bouskill NJ, Wood TE, Baran R, Ye Z, Bowen BP, Lim H, Zhou J, Nostrand JDV, Nico P, Northen TR, Silver WL, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. I. Changes in Microbial Functional Potential and Metabolism. Front Microbiol 2016; 7:525. [PMID: 27148214 PMCID: PMC4837414 DOI: 10.3389/fmicb.2016.00525] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [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: 12/29/2015] [Accepted: 03/30/2016] [Indexed: 11/15/2022] Open
Abstract
Global climate models predict a future of increased severity of drought in many tropical forests. Soil microbes are central to the balance of these systems as sources or sinks of atmospheric carbon (C), yet how they respond metabolically to drought is not well-understood. We simulated drought in the typically aseasonal Luquillo Experimental Forest, Puerto Rico, by intercepting precipitation falling through the forest canopy. This approach reduced soil moisture by 13% and water potential by 0.14 MPa (from -0.2 to -0.34). Previous results from this experiment have demonstrated that the diversity and composition of these soil microbial communities are sensitive to even small changes in soil water. Here, we show prolonged drought significantly alters the functional potential of the community and provokes a clear osmotic stress response, including the production of compatible solutes that increase intracellular C demand. Subsequently, a microbial population emerges with a greater capacity for extracellular enzyme production targeting macromolecular carbon. Significantly, some of these drought-induced functional shifts in the soil microbiota are attenuated by prior exposure to a short-term drought suggesting that acclimation may occur despite a lack of longer-term drought history.
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Affiliation(s)
- Nicholas J Bouskill
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, USDA Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin P Bowen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - HsiaoChien Lim
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Jizhong Zhou
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of OklahomaNorman, OK, USA; State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua UniversityBeijing, China
| | - Joy D Van Nostrand
- Institute for Environmental Genomics and Department of Microbiology and Plant Biology, University of Oklahoma Norman, OK, USA
| | - Peter Nico
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Trent R Northen
- Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy and Management, University of California-Berkeley Berkeley, CA, USA
| | - Eoin L Brodie
- Earth Sciences Division, Ecology Department, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy and Management, University of California-BerkeleyBerkeley, CA, USA
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36
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Bouskill NJ, Wood TE, Baran R, Hao Z, Ye Z, Bowen BP, Lim HC, Nico PS, Holman HY, Gilbert B, Silver WL, Northen TR, Brodie EL. Belowground Response to Drought in a Tropical Forest Soil. II. Change in Microbial Function Impacts Carbon Composition. Front Microbiol 2016; 7:323. [PMID: 27014243 PMCID: PMC4791749 DOI: 10.3389/fmicb.2016.00323] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 12/29/2015] [Accepted: 02/29/2016] [Indexed: 01/29/2023] Open
Abstract
Climate model projections for tropical regions show clear perturbation of precipitation patterns leading to increased frequency and severity of drought in some regions. Previous work has shown declining soil moisture to be a strong driver of changes in microbial trait distribution, however, the feedback of any shift in functional potential on ecosystem properties related to carbon cycling are poorly understood. Here we show that drought-induced changes in microbial functional diversity and activity shape, and are in turn shaped by, the composition of dissolved and soil-associated carbon. We also demonstrate that a shift in microbial functional traits that favor the production of hygroscopic compounds alter the efflux of carbon dioxide following soil rewetting. Under drought the composition of the dissolved organic carbon pool changed in a manner consistent with a microbial metabolic response. We hypothesize that this microbial ecophysiological response to changing soil moisture elevates the intracellular carbon demand stimulating extracellular enzyme production, that prompts the observed decline in more complex carbon compounds (e.g., cellulose and lignin). Furthermore, a metabolic response to drought appeared to condition (biologically and physically) the soil, notably through the production of polysaccharides, particularly in experimental plots that had been pre-exposed to a short-term drought. This hysteretic response, in addition to an observed drought-related decline in phosphorus concentration, may have been responsible for a comparatively modest CO2 efflux following wet-up in drought plots relative to control plots.
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Affiliation(s)
- Nicholas J Bouskill
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Tana E Wood
- International Institute of Tropical Forestry, United States Department of Agriculture Forest ServiceRio Piedras, PR, USA; Fundación Puertorriqueña de ConservaciónSan Juan, PR, USA
| | - Richard Baran
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zhao Hao
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Zaw Ye
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Ben P Bowen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hsiao Chien Lim
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Peter S Nico
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Hoi-Ying Holman
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Benjamin Gilbert
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Whendee L Silver
- Department of Environmental Science, Policy, and Management, University of California, Berkeley Berkeley, CA, USA
| | - Trent R Northen
- Environmental Genomics and Systems Biology, Life Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
| | - Eoin L Brodie
- Climate and Ecosystem Sciences, Earth and Environmental Sciences, Lawrence Berkeley National LaboratoryBerkeley, CA, USA; Department of Environmental Science, Policy, and Management, University of California, BerkeleyBerkeley, CA, USA
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Alivisatos AP, Blaser MJ, Brodie EL, Chun M, Dangl JL, Donohue TJ, Dorrestein PC, Gilbert JA, Green JL, Jansson JK, Knight R, Maxon ME, McFall-Ngai MJ, Miller JF, Pollard KS, Ruby EG, Taha SA. MICROBIOME. A unified initiative to harness Earth's microbiomes. Science 2015; 350:507-8. [PMID: 26511287 DOI: 10.1126/science.aac8480] [Citation(s) in RCA: 147] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- A P Alivisatos
- See the supplementary materials for authors' affiliations
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Shi S, Nuccio E, Herman DJ, Rijkers R, Estera K, Li J, da Rocha UN, He Z, Pett-Ridge J, Brodie EL, Zhou J, Firestone M. Successional Trajectories of Rhizosphere Bacterial Communities over Consecutive Seasons. mBio 2015; 6:e00746. [PMID: 26242625 PMCID: PMC4526712 DOI: 10.1128/mbio.00746-15] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/20/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED It is well known that rhizosphere microbiomes differ from those of surrounding soil, and yet we know little about how these root-associated microbial communities change through the growing season and between seasons. We analyzed the response of soil bacteria to roots of the common annual grass Avena fatua over two growing seasons using high-throughput sequencing of 16S rRNA genes. Over the two periods of growth, the rhizosphere bacterial communities followed consistent successional patterns as plants grew, although the starting communities were distinct. Succession in the rhizosphere was characterized by a significant decrease in both taxonomic and phylogenetic diversity relative to background soil communities, driven by reductions in both richness and evenness of the bacterial communities. Plant roots selectively stimulated the relative abundance of Alphaproteobacteria, Betaproteobacteria, and Bacteroidetes but reduced the abundance of Acidobacteria, Actinobacteria, and Firmicutes. Taxa that increased in relative abundance in the rhizosphere soil displayed phylogenetic clustering, suggesting some conservation and an evolutionary basis for the response of complex soil bacterial communities to the presence of plant roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence. IMPORTANCE We document the successional patterns of rhizosphere bacterial communities associated with a "wild" annual grass, Avena fatua, which is commonly a dominant plant in Mediterranean-type annual grasslands around the world; the plant was grown in its grassland soil. Most studies documenting rhizosphere microbiomes address "domesticated" plants growing in soils to which they are introduced. Rhizosphere bacterial communities exhibited a pattern of temporal succession that was consistent and repeatable over two growing seasons. There are few studies assessing the reproducibility over multiple seasons. Through the growing season, the rhizosphere community became progressively less diverse, likely reflecting root homogenization of soil microniches. Phylogenetic clustering of the rhizosphere dynamic taxa suggests evolutionary adaptation to Avena roots. The reproducibility of rhizosphere succession and the apparent phylogenetic conservation of rhizosphere competence traits suggest adaptation of the indigenous bacterial community to this common grass over the many decades of its presence.
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Affiliation(s)
- Shengjing Shi
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Erin Nuccio
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Donald J Herman
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruud Rijkers
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Katerina Estera
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA
| | - Jiabao Li
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Ulisses Nunes da Rocha
- Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Zhili He
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA
| | - Jennifer Pett-Ridge
- Nuclear and Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, California, USA
| | - Eoin L Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Jizhong Zhou
- Department of Microbiology and Plant Biology, Institute for Environmental Genomics, University of Oklahoma, Norman, Oklahoma, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing, China
| | - Mary Firestone
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California, USA Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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Ceja-Navarro JA, Vega FE, Karaoz U, Hao Z, Jenkins S, Lim HC, Kosina P, Infante F, Northen TR, Brodie EL. Gut microbiota mediate caffeine detoxification in the primary insect pest of coffee. Nat Commun 2015; 6:7618. [PMID: 26173063 PMCID: PMC4510693 DOI: 10.1038/ncomms8618] [Citation(s) in RCA: 241] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 05/26/2015] [Indexed: 01/23/2023] Open
Abstract
The coffee berry borer (Hypothenemus hampei) is the most devastating insect pest of coffee worldwide with its infestations decreasing crop yield by up to 80%. Caffeine is an alkaloid that can be toxic to insects and is hypothesized to act as a defence mechanism to inhibit herbivory. Here we show that caffeine is degraded in the gut of H. hampei, and that experimental inactivation of the gut microbiota eliminates this activity. We demonstrate that gut microbiota in H. hampei specimens from seven major coffee-producing countries and laboratory-reared colonies share a core of microorganisms. Globally ubiquitous members of the gut microbiota, including prominent Pseudomonas species, subsist on caffeine as a sole source of carbon and nitrogen. Pseudomonas caffeine demethylase genes are expressed in vivo in the gut of H. hampei, and re-inoculation of antibiotic-treated insects with an isolated Pseudomonas strain reinstates caffeine-degradation ability confirming their key role.
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Affiliation(s)
- Javier A. Ceja-Navarro
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Fernando E. Vega
- Sustainable Perennial Crops Laboratory, United States Department of Agriculture, Agricultural Research Service, Building 001, BARC-W, Beltsville, Maryland 20705, USA
| | - Ulas Karaoz
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Zhao Hao
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Stefan Jenkins
- Genome Dynamics Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Hsiao Chien Lim
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Petr Kosina
- International Maize and Wheat Improvement Center (CIMMYT), Carretera Mexico-Veracruz Km. 45, El Batán, Texcoco 56130, Mexico
| | - Francisco Infante
- El Colegio de la Frontera Sur (ECOSUR), Carretera Antiguo Aeropuerto Km. 2.5, Tapachula, Chiapas 30700, Mexico
| | - Trent R. Northen
- Genome Dynamics Department, Life Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Eoin L. Brodie
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
- Department of Environmental Science, Policy and Management, University of California, Berkeley, California 94720, USA
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40
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Nunes da Rocha U, Cadillo-Quiroz H, Karaoz U, Rajeev L, Klitgord N, Dunn S, Truong V, Buenrostro M, Bowen BP, Garcia-Pichel F, Mukhopadhyay A, Northen TR, Brodie EL. Isolation of a significant fraction of non-phototroph diversity from a desert Biological Soil Crust. Front Microbiol 2015; 6:277. [PMID: 25926821 PMCID: PMC4396413 DOI: 10.3389/fmicb.2015.00277] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 03/19/2015] [Indexed: 01/10/2023] Open
Abstract
Biological Soil Crusts (BSCs) are organosedimentary assemblages comprised of microbes and minerals in topsoil of terrestrial environments. BSCs strongly impact soil quality in dryland ecosystems (e.g., soil structure and nutrient yields) due to pioneer species such as Microcoleus vaginatus; phototrophs that produce filaments that bind the soil together, and support an array of heterotrophic microorganisms. These microorganisms in turn contribute to soil stability and biogeochemistry of BSCs. Non-cyanobacterial populations of BSCs are less well known than cyanobacterial populations. Therefore, we attempted to isolate a broad range of numerically significant and phylogenetically representative BSC aerobic heterotrophs. Combining simple pre-treatments (hydration of BSCs under dark and light) and isolation strategies (media with varying nutrient availability and protection from oxidative stress) we recovered 402 bacterial and one fungal isolate in axenic culture, which comprised 116 phylotypes (at 97% 16S rRNA gene sequence homology), 115 bacterial and one fungal. Each medium enriched a mostly distinct subset of phylotypes, and cultivated phylotypes varied due to the BSC pre-treatment. The fraction of the total phylotype diversity isolated, weighted by relative abundance in the community, was determined by the overlap between isolate sequences and OTUs reconstructed from metagenome or metatranscriptome reads. Together, more than 8% of relative abundance of OTUs in the metagenome was represented by our isolates, a cultivation efficiency much larger than typically expected from most soils. We conclude that simple cultivation procedures combined with specific pre-treatment of samples afford a significant reduction in the culturability gap, enabling physiological and metabolic assays that rely on ecologically relevant axenic cultures.
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Affiliation(s)
- Ulisses Nunes da Rocha
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Quantitative Microbial Ecology Group, Department of Molecular and Cell Physiology, Faculty of Earth and Life Sciences, VU Amsterdam Amsterdam, Netherlands
| | - Hinsby Cadillo-Quiroz
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA
| | - Lara Rajeev
- Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA
| | - Niels Klitgord
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Sean Dunn
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Viet Truong
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Mayra Buenrostro
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA
| | - Benjamin P Bowen
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Ferran Garcia-Pichel
- Faculty of Genomics, Evolution and Bioinformatics, School of Life Sciences, Arizona State University Tucson, AZ, USA ; Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Aindrila Mukhopadhyay
- Lawrence Berkeley National Laboratory, Physical Biosciences Division Berkeley, CA, USA
| | - Trent R Northen
- Lawrence Berkeley National Laboratory, Life Sciences Division Berkeley, CA, USA
| | - Eoin L Brodie
- Lawrence Berkeley National Laboratory, Earth Sciences Division Berkeley, CA, USA ; Department of Environmental Science, Policy and Management, University of California, Berkeley Berkeley, CA, USA
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Srinivasan R, Karaoz U, Volegova M, MacKichan J, Kato-Maeda M, Miller S, Nadarajan R, Brodie EL, Lynch SV. Use of 16S rRNA gene for identification of a broad range of clinically relevant bacterial pathogens. PLoS One 2015; 10:e0117617. [PMID: 25658760 PMCID: PMC4319838 DOI: 10.1371/journal.pone.0117617] [Citation(s) in RCA: 207] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 12/29/2014] [Indexed: 01/06/2023] Open
Abstract
According to World Health Organization statistics of 2011, infectious diseases remain in the top five causes of mortality worldwide. However, despite sophisticated research tools for microbial detection, rapid and accurate molecular diagnostics for identification of infection in humans have not been extensively adopted. Time-consuming culture-based methods remain to the forefront of clinical microbial detection. The 16S rRNA gene, a molecular marker for identification of bacterial species, is ubiquitous to members of this domain and, thanks to ever-expanding databases of sequence information, a useful tool for bacterial identification. In this study, we assembled an extensive repository of clinical isolates (n = 617), representing 30 medically important pathogenic species and originally identified using traditional culture-based or non-16S molecular methods. This strain repository was used to systematically evaluate the ability of 16S rRNA for species level identification. To enable the most accurate species level classification based on the paucity of sequence data accumulated in public databases, we built a Naïve Bayes classifier representing a diverse set of high-quality sequences from medically important bacterial organisms. We show that for species identification, a model-based approach is superior to an alignment based method. Overall, between 16S gene based and clinical identities, our study shows a genus-level concordance rate of 96% and a species-level concordance rate of 87.5%. We point to multiple cases of probable clinical misidentification with traditional culture based identification across a wide range of gram-negative rods and gram-positive cocci as well as common gram-negative cocci.
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Affiliation(s)
- Ramya Srinivasan
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
| | - Ulas Karaoz
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Marina Volegova
- University of California, Berkeley, CA 94720, United States of America
| | - Joanna MacKichan
- School of Biological Sciences, Victoria University of Wellington, 34 Kenepuru Drive, Porirua, Wellington, New Zealand
| | - Midori Kato-Maeda
- San Francisco General Hospital, Department of Medicine, Bldg 100, San Francisco, CA 94110, United States of America
| | - Steve Miller
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Rohan Nadarajan
- University of California San Francisco, Clinical Microbiology Laboratory, 185 Berry Street, Suite 290, San Francisco, CA 94107, United States of America
| | - Eoin L. Brodie
- Lawrence Berkeley National Laboratory, Earth Sciences Division, 1 Cyclotron Rd., MS70A-3317, Berkeley, CA 94720, United States of America
| | - Susan V. Lynch
- University of California San Francisco, Department of Medicine, Gastroenterology Division, 513 Parnassus Ave, San Francisco, CA 94143–0538, United States of America
- * E-mail:
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42
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Berlemont R, Allison SD, Weihe C, Lu Y, Brodie EL, Martiny JBH, Martiny AC. Cellulolytic potential under environmental changes in microbial communities from grassland litter. Front Microbiol 2014; 5:639. [PMID: 25505459 PMCID: PMC4243572 DOI: 10.3389/fmicb.2014.00639] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [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: 06/20/2014] [Accepted: 11/06/2014] [Indexed: 12/02/2022] Open
Abstract
In many ecosystems, global changes are likely to profoundly affect microorganisms. In Southern California, changes in precipitation and nitrogen deposition may influence the composition and functional potential of microbial communities and their resulting ability to degrade plant material. To test whether such environmental changes impact the distribution of functional groups involved in leaf litter degradation, we determined how the genomic diversity of microbial communities in a semi-arid grassland ecosystem changed under reduced precipitation or increased N deposition. We monitored communities seasonally over a period of 2 years to place environmental change responses into the context of natural variation. Fungal and bacterial communities displayed strong seasonal patterns, Fungi being mostly detected during the dry season whereas Bacteria were common during wet periods. Most putative cellulose degraders were associated with 33 bacterial genera and predicted to constitute 18% of the microbial community. Precipitation reduction reduced bacterial abundance and cellulolytic potential whereas nitrogen addition did not affect the cellulolytic potential of the microbial community. Finally, we detected a strong correlation between the frequencies of genera of putative cellulose degraders and cellulase genes. Thus, microbial taxonomic composition was predictive of cellulolytic potential. This work provides a framework for how environmental changes affect microorganisms responsible for plant litter deconstruction.
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Affiliation(s)
- Renaud Berlemont
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Biological Science, California State UniversityLong Beach, CA, USA
| | - Steven D. Allison
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Claudia Weihe
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Ying Lu
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Eoin L. Brodie
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National LaboratoryBerkeley, CA, USA
- Department of Environmental Science, Policy and Management, University of CaliforniaBerkeley, CA, USA
| | - Jennifer B. H. Martiny
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
| | - Adam C. Martiny
- Department of Earth System Science, University of California, IrvineIrvine, CA, USA
- Department of Ecology and Evolutionary Biology, University of California, IrvineIrvine, CA, USA
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Beller HR, Yang L, Varadharajan C, Han R, Lim HC, Karaoz U, Molins S, Marcus MA, Brodie EL, Steefel CI, Nico PS. Divergent aquifer biogeochemical systems converge on similar and unexpected Cr(VI) reduction products. Environ Sci Technol 2014; 48:10699-10706. [PMID: 25084058 DOI: 10.1021/es5016982] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
In this study of reductive chromium immobilization, we found that flow-through columns constructed with homogenized aquifer sediment and continuously infused with lactate, chromate, and various native electron acceptors diverged to have very different Cr(VI)-reducing biogeochemical regimes characterized by either denitrifying or fermentative conditions (as indicated by effluent chemical data, 16S rRNA pyrotag data, and metatranscriptome data). Despite the two dramatically different biogeochemical environments that evolved in the columns, these regimes created similar Cr(III)-Fe(III) hydroxide precipitates as the predominant Cr(VI) reduction product, as characterized by micro-X-ray fluorescence and micro-X-ray absorption near-edge structure analysis. We discuss two conflicting scenarios of microbially mediated formation of Cr(III)-Fe(III) precipitates, each of which is both supported and contradicted by different lines of evidence: (1) enzymatic reduction of Cr(VI) to Cr(III) followed by coprecipitation of Cr(III) and Fe(III) and (2) both regimes generated at least small amounts of Fe(II), which abiotically reduced Cr(VI) to form a Cr-Fe precipitate. Evidence of zones with different levels of Cr(VI) reduction suggest that local heterogeneity may have confounded interpretation of processes based on bulk measurements. This study indicates that the bulk redox status and biogeochemical regime, as categorized by the dominant electron-accepting process, do not necessarily control the final product of Cr(VI) reduction.
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Affiliation(s)
- Harry R Beller
- Earth Sciences Division and ‡Advanced Light Source, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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44
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Closek CJ, Sunagawa S, DeSalvo MK, Piceno YM, DeSantis TZ, Brodie EL, Weber MX, Voolstra CR, Andersen GL, Medina M. Coral transcriptome and bacterial community profiles reveal distinct Yellow Band Disease states in Orbicella faveolata. ISME J 2014; 8:2411-22. [PMID: 24950107 DOI: 10.1038/ismej.2014.85] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/30/2014] [Accepted: 04/08/2014] [Indexed: 11/09/2022]
Abstract
Coral diseases impact reefs globally. Although we continue to describe diseases, little is known about the etiology or progression of even the most common cases. To examine a spectrum of coral health and determine factors of disease progression we examined Orbicella faveolata exhibiting signs of Yellow Band Disease (YBD), a widespread condition in the Caribbean. We used a novel combined approach to assess three members of the coral holobiont: the coral-host, associated Symbiodinium algae, and bacteria. We profiled three conditions: (1) healthy-appearing colonies (HH), (2) healthy-appearing tissue on diseased colonies (HD), and (3) diseased lesion (DD). Restriction fragment length polymorphism analysis revealed health state-specific diversity in Symbiodinium clade associations. 16S ribosomal RNA gene microarrays (PhyloChips) and O. faveolata complimentary DNA microarrays revealed the bacterial community structure and host transcriptional response, respectively. A distinct bacterial community structure marked each health state. Diseased samples were associated with two to three times more bacterial diversity. HD samples had the highest bacterial richness, which included components associated with HH and DD, as well as additional unique families. The host transcriptome under YBD revealed a reduced cellular expression of defense- and metabolism-related processes, while the neighboring HD condition exhibited an intermediate expression profile. Although HD tissue appeared visibly healthy, the microbial communities and gene expression profiles were distinct. HD should be regarded as an additional (intermediate) state of disease, which is important for understanding the progression of YBD.
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Affiliation(s)
- Collin J Closek
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
| | - Shinichi Sunagawa
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | | | - Yvette M Piceno
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | - Eoin L Brodie
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Michele X Weber
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
| | - Christian R Voolstra
- Red Sea Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Gary L Andersen
- Center for Environmental Biotechnology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Mónica Medina
- 1] Department of Biology, The Pennsylvania State University, University Park, PA, USA [2] School of Natural Sciences, University of California, Merced, CA, USA
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Ganz HH, Turner WC, Brodie EL, Kusters M, Shi Y, Sibanda H, Torok T, Getz WM. Interactions between Bacillus anthracis and plants may promote anthrax transmission. PLoS Negl Trop Dis 2014; 8:e2903. [PMID: 24901846 PMCID: PMC4046938 DOI: 10.1371/journal.pntd.0002903] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/14/2014] [Indexed: 01/06/2023] Open
Abstract
Environmental reservoirs are essential in the maintenance and transmission of anthrax but are poorly characterized. The anthrax agent, Bacillus anthracis was long considered an obligate pathogen that is dormant and passively transmitted in the environment. However, a growing number of laboratory studies indicate that, like some of its close relatives, B. anthracis has some activity outside of its vertebrate hosts. Here we show in the field that B. anthracis has significant interactions with a grass that could promote anthrax spore transmission to grazing hosts. Using a local, virulent strain of B. anthracis, we performed a field experiment in an enclosure within a grassland savanna. We found that B. anthracis increased the rate of establishment of a native grass (Enneapogon desvauxii) by 50% and that grass seeds exposed to blood reached heights that were 45% taller than controls. Further we detected significant effects of E. desvauxii, B. anthracis, and their interaction on soil bacterial taxa richness and community composition. We did not find any evidence for multiplication or increased longevity of B. anthracis in bulk soil associated with grass compared to controls. Instead interactions between B. anthracis and plants may result in increased host grazing and subsequently increased transmission to hosts. Anthrax is a neglected zoonotic disease affecting livestock, wildlife, and humans in developing countries, particularly in Africa and Asia, and it occurs regularly in rural parts of North America. The causative agent of anthrax, Bacillus anthracis is transmitted by spores that persist for long periods of time in the environment. The transmission mechanisms of socioeconomically important and environmentally maintained pathogens are poorly understood, yet essential for understanding disease dynamics and devising appropriate control measures. Recent laboratory studies show that B. anthracis interacts with plants and other soil-dwelling organisms that may affect its survival and transmission. In this paper, we describe the results of a field experiment designed to test whether the interaction of B. anthracis with plants might affect its persistence and potential transmission to grazing hosts. We found that like some of its close relatives, B. anthracis promotes plant growth. Rather than simply lying in wait as a dormant spore in soil, instead B. anthracis may promote plant growth as a way of attracting hosts to graze on infectious material at carcass sites.
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Affiliation(s)
- Holly H. Ganz
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Wendy C. Turner
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, United States of America
| | - Eoin L. Brodie
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, United States of America
- Ecology Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | | | - Ying Shi
- Department of Statistics, University of California, Berkeley, California, United States of America
| | - Heniritha Sibanda
- Ministry of Fisheries and Marine Resources, Inland Aquaculture, Katima Mulilo Regional Office, Katima Mulilo, Namibia
| | - Tamas Torok
- Ecology Department, Earth Science Division, Lawrence Berkeley National Laboratory, Berkeley, California, United States of America
| | - Wayne M. Getz
- Department of Environmental Science, Policy and Management, University of California, Berkeley, Berkeley, California, United States of America
- School of Mathematical Sciences, University of KwaZulu-Natal, Durban, South Africa
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46
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Wells GF, Wu CH, Piceno YM, Eggleston B, Brodie EL, DeSantis TZ, Andersen GL, Hazen TC, Francis CA, Criddle CS. Microbial biogeography across a full-scale wastewater treatment plant transect: evidence for immigration between coupled processes. Appl Microbiol Biotechnol 2014; 98:4723-36. [DOI: 10.1007/s00253-014-5564-3] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 01/20/2014] [Accepted: 01/21/2014] [Indexed: 11/28/2022]
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47
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Briggs BR, Brodie EL, Tom LM, Dong H, Jiang H, Huang Q, Wang S, Hou W, Wu G, Huang L, Hedlund BP, Zhang C, Dijkstra P, Hungate BA. Seasonal patterns in microbial communities inhabiting the hot springs of Tengchong, Yunnan Province, China. Environ Microbiol 2013; 16:1579-91. [PMID: 24148100 DOI: 10.1111/1462-2920.12311] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 10/08/2013] [Indexed: 11/30/2022]
Abstract
Studies focusing on seasonal dynamics of microbial communities in terrestrial and marine environments are common; however, little is known about seasonal dynamics in high-temperature environments. Thus, our objective was to document the seasonal dynamics of both the physicochemical conditions and the microbial communities inhabiting hot springs in Tengchong County, Yunnan Province, China. The PhyloChip microarray detected 4882 operational taxonomic units (OTUs) within 79 bacterial phylum-level groups and 113 OTUs within 20 archaeal phylum-level groups, which are additional 54 bacterial phyla and 11 archaeal phyla to those that were previously described using pyrosequencing. Monsoon samples (June 2011) showed increased concentrations of potassium, total organic carbon, ammonium, calcium, sodium and total nitrogen, and decreased ferrous iron relative to the dry season (January 2011). At the same time, the highly ordered microbial communities present in January gave way to poorly ordered communities in June, characterized by higher richness of Bacteria, including microbes related to mesophiles. These seasonal changes in geochemistry and community structure are likely due to high rainfall influx during the monsoon season and indicate that seasonal dynamics occurs in high-temperature environments experiencing significant changes in seasonal recharge. Thus, geothermal environments are not isolated from the surrounding environment and seasonality affects microbial ecology.
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Affiliation(s)
- Brandon R Briggs
- Department of Geology and Environmental Earth Science, Miami University, Oxford, OH, 45056, USA
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48
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Nyyssönen M, Tran HM, Karaoz U, Weihe C, Hadi MZ, Martiny JBH, Martiny AC, Brodie EL. Coupled high-throughput functional screening and next generation sequencing for identification of plant polymer decomposing enzymes in metagenomic libraries. Front Microbiol 2013; 4:282. [PMID: 24069019 PMCID: PMC3779933 DOI: 10.3389/fmicb.2013.00282] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [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: 06/13/2013] [Accepted: 09/02/2013] [Indexed: 12/13/2022] Open
Abstract
Recent advances in sequencing technologies generate new predictions and hypotheses about the functional roles of environmental microorganisms. Yet, until we can test these predictions at a scale that matches our ability to generate them, most of them will remain as hypotheses. Function-based mining of metagenomic libraries can provide direct linkages between genes, metabolic traits and microbial taxa and thus bridge this gap between sequence data generation and functional predictions. Here we developed high-throughput screening assays for function-based characterization of activities involved in plant polymer decomposition from environmental metagenomic libraries. The multiplexed assays use fluorogenic and chromogenic substrates, combine automated liquid handling and use a genetically modified expression host to enable simultaneous screening of 12,160 clones for 14 activities in a total of 170,240 reactions. Using this platform we identified 374 (0.26%) cellulose, hemicellulose, chitin, starch, phosphate and protein hydrolyzing clones from fosmid libraries prepared from decomposing leaf litter. Sequencing on the Illumina MiSeq platform, followed by assembly and gene prediction of a subset of 95 fosmid clones, identified a broad range of bacterial phyla, including Actinobacteria, Bacteroidetes, multiple Proteobacteria sub-phyla in addition to some Fungi. Carbohydrate-active enzyme genes from 20 different glycoside hydrolase (GH) families were detected. Using tetranucleotide frequency (TNF) binning of fosmid sequences, multiple enzyme activities from distinct fosmids were linked, demonstrating how biochemically-confirmed functional traits in environmental metagenomes may be attributed to groups of specific organisms. Overall, our results demonstrate how functional screening of metagenomic libraries can be used to connect microbial functionality to community composition and, as a result, complement large-scale metagenomic sequencing efforts.
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Affiliation(s)
- Mari Nyyssönen
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory Berkeley, CA, USA
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49
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Ceja-Navarro JA, Nguyen NH, Karaoz U, Gross SR, Herman DJ, Andersen GL, Bruns TD, Pett-Ridge J, Blackwell M, Brodie EL. Compartmentalized microbial composition, oxygen gradients and nitrogen fixation in the gut of Odontotaenius disjunctus. ISME J 2013; 8:6-18. [PMID: 23985746 DOI: 10.1038/ismej.2013.134] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 07/03/2013] [Accepted: 07/13/2013] [Indexed: 11/09/2022]
Abstract
Coarse woody debris is an important biomass pool in forest ecosystems that numerous groups of insects have evolved to take advantage of. These insects are ecologically important and represent useful natural analogs for biomass to biofuel conversion. Using a range of molecular approaches combined with microelectrode measurements of oxygen, we have characterized the gut microbiome and physiology of Odontotaenius disjunctus, a wood-feeding beetle native to the eastern United States. We hypothesized that morphological and physiological differences among gut regions would correspond to distinct microbial populations and activities. In fact, significantly different communities were found in the foregut (FG), midgut (MG)/posterior hindgut (PHG) and anterior hindgut (AHG), with Actinobacteria and Rhizobiales being more abundant toward the FG and PHG. Conversely, fermentative bacteria such as Bacteroidetes and Clostridia were more abundant in the AHG, and also the sole region where methanogenic Archaea were detected. Although each gut region possessed an anaerobic core, micron-scale profiling identified radial gradients in oxygen concentration in all regions. Nitrogen fixation was confirmed by (15)N2 incorporation, and nitrogenase gene (nifH) expression was greatest in the AHG. Phylogenetic analysis of nifH identified the most abundant transcript as related to Ni-Fe nitrogenase of a Bacteroidetes species, Paludibacter propionicigenes. Overall, we demonstrate not only a compartmentalized microbiome in this beetle digestive tract but also sharp oxygen gradients that may permit aerobic and anaerobic metabolism to occur within the same regions in close proximity. We provide evidence for the microbial fixation of N2 that is important for this beetle to subsist on woody biomass.
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Affiliation(s)
- Javier A Ceja-Navarro
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Nhu H Nguyen
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
| | - Ulas Karaoz
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Stephanie R Gross
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Donald J Herman
- Department of Environmental Science Policy and Management, University of California, Berkeley, CA, USA
| | - Gary L Andersen
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Thomas D Bruns
- Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jennifer Pett-Ridge
- Chemical Sciences Division, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Meredith Blackwell
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA
| | - Eoin L Brodie
- 1] Ecology Department, Earth Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA [2] Department of Environmental Science Policy and Management, University of California, Berkeley, CA, USA
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50
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Rajeev L, da Rocha UN, Klitgord N, Luning EG, Fortney J, Axen SD, Shih PM, Bouskill NJ, Bowen BP, Kerfeld CA, Garcia-Pichel F, Brodie EL, Northen TR, Mukhopadhyay A. Dynamic cyanobacterial response to hydration and dehydration in a desert biological soil crust. ISME J 2013; 7:2178-91. [PMID: 23739051 PMCID: PMC3806265 DOI: 10.1038/ismej.2013.83] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2013] [Accepted: 04/21/2013] [Indexed: 12/22/2022]
Abstract
Biological soil crusts (BSCs) cover extensive portions of the earth's deserts. In order to survive desiccation cycles and utilize short periods of activity during infrequent precipitation, crust microorganisms must rely on the unique capabilities of vegetative cells to enter a dormant state and be poised for rapid resuscitation upon wetting. To elucidate the key events involved in the exit from dormancy, we performed a wetting experiment of a BSC and followed the response of the dominant cyanobacterium, Microcoleus vaginatus, in situ using a whole-genome transcriptional time course that included two diel cycles. Immediate, but transient, induction of DNA repair and regulatory genes signaled the hydration event. Recovery of photosynthesis occurred within 1 h, accompanied by upregulation of anabolic pathways. Onset of desiccation was characterized by the induction of genes for oxidative and photo-oxidative stress responses, osmotic stress response and the synthesis of C and N storage polymers. Early expression of genes for the production of exopolysaccharides, additional storage molecules and genes for membrane unsaturation occurred before drying and hints at preparedness for desiccation. We also observed signatures of preparation for future precipitation, notably the expression of genes for anaplerotic reactions in drying crusts, and the stable maintenance of mRNA through dormancy. These data shed light on possible synchronization between this cyanobacterium and its environment, and provides key mechanistic insights into its metabolism in situ that may be used to predict its response to climate, and or, land-use driven perturbations.
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Affiliation(s)
- Lara Rajeev
- Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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