1
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Pierroz G. Seeing red: a modified RUBY reporter assay for visualizing in planta protein-protein interactions. Plant J 2023; 114:1207-1208. [PMID: 37323060 DOI: 10.1111/tpj.16325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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2
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Pierroz G. Welcome to the machine: how machine learning identified metabolomic changes in Brachypodium distachyon under stress. Plant J 2023; 114:461-462. [PMID: 37119519 DOI: 10.1111/tpj.16243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
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3
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Pierroz G. 2D or not 2D: how mRNA methylation regulates the transition to 3-dimensional growth in Physcomitrium patens. Plant J 2023; 114:5-6. [PMID: 36974889 DOI: 10.1111/tpj.16173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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4
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Pierroz G. Picture perfect: non-destructive, image-based phenotyping of bacterial wilt severity in tomato. Plant J 2023; 113:885-886. [PMID: 36853846 DOI: 10.1111/tpj.16138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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5
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Pierroz G. Need for speed: a breakthrough speed breeding protocol for hemp. Plant J 2023; 113:435-436. [PMID: 36744477 DOI: 10.1111/tpj.16108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
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6
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Pierroz G. Making babies: how auxin regulates somatic embryogenesis in Arabidopsis tissue culture. Plant J 2023; 113:5-6. [PMID: 36585767 DOI: 10.1111/tpj.16062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
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7
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Pierroz G. Super modeling: integrating photosynthetic and metabolic models to enhance algal bioproduction. Plant J 2022; 112:601-602. [PMID: 36308721 DOI: 10.1111/tpj.16001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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8
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Pierroz G. Stress management: how NOD and LGN coordinate growth-defence tradeoffs in maize. Plant J 2022; 112:879-880. [PMID: 36415090 DOI: 10.1111/tpj.16016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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9
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Pierroz G. Feeling the heat: discovery of a feedback loop regulating thermotolerance in tomato and Arabidopsis. Plant J 2022; 112:5-6. [PMID: 36189500 DOI: 10.1111/tpj.15978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
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10
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Pierroz G. Shady deals: how Setaria viridis compensates for smaller bundle sheaths in low light. Plant J 2022; 111:1221-1222. [PMID: 36045544 DOI: 10.1111/tpj.15940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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11
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Pierroz G. Glycosylation in the Golgi guides cellulose synthesis at the cell wall. Plant J 2022; 111:921-922. [PMID: 35971865 DOI: 10.1111/tpj.15932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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12
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Pierroz G. Genomics reveal a complicated past and suggest a possible future for Nicotiana benthamiana. Plant J 2022; 111:5-6. [PMID: 35789508 DOI: 10.1111/tpj.15869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
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13
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Aregawi K, Shen J, Pierroz G, Sharma MK, Dahlberg J, Owiti J, Lemaux PG. Morphogene-assisted transformation of Sorghum bicolor allows more efficient genome editing. Plant Biotechnol J 2022; 20:748-760. [PMID: 34837319 PMCID: PMC8989502 DOI: 10.1111/pbi.13754] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [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: 06/15/2021] [Revised: 11/12/2021] [Accepted: 11/15/2021] [Indexed: 05/08/2023]
Abstract
Sorghum bicolor (L.) Moench, the fifth most important cereal worldwide, is a multi-use crop for feed, food, forage and fuel. To enhance the sorghum and other important crop plants, establishing gene function is essential for their improvement. For sorghum, identifying genes associated with its notable abiotic stress tolerances requires a detailed molecular understanding of the genes associated with those traits. The limits of this knowledge became evident from our earlier in-depth sorghum transcriptome study showing that over 40% of its transcriptome had not been annotated. Here, we describe a full spectrum of tools to engineer, edit, annotate and characterize sorghum's genes. Efforts to develop those tools began with a morphogene-assisted transformation (MAT) method that led to accelerated transformation times, nearly half the time required with classical callus-based, non-MAT approaches. These efforts also led to expanded numbers of amenable genotypes, including several not previously transformed or historically recalcitrant. Another transformation advance, termed altruistic, involved introducing a gene of interest in a separate Agrobacterium strain from the one with morphogenes, leading to plants with the gene of interest but without morphogenes. The MAT approach was also successfully used to edit a target exemplary gene, phytoene desaturase. To identify single-copy transformed plants, we adapted a high-throughput technique and also developed a novel method to determine transgene independent integration. These efforts led to an efficient method to determine gene function, expediting research in numerous genotypes of this widely grown, multi-use crop.
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Affiliation(s)
- Kiflom Aregawi
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Jianqiang Shen
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Grady Pierroz
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Manoj K. Sharma
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Jeffery Dahlberg
- University of California Ag & Natural ResourcesKearney Agricultural Research & Extension CenterParlierCAUSA
| | - Judith Owiti
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
| | - Peggy G. Lemaux
- Department of Plant and Microbial BiologyUniversity of CaliforniaBerkeleyCAUSA
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14
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Willing CE, Pierroz G, Guzman A, Anderegg LDL, Gao C, Coleman-Derr D, Taylor JW, Bruns TD, Dawson TE. Keep your friends close: Host compartmentalisation of microbial communities facilitates decoupling from effects of habitat fragmentation. Ecol Lett 2021; 24:2674-2686. [PMID: 34523223 DOI: 10.1111/ele.13886] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 08/25/2021] [Accepted: 08/30/2021] [Indexed: 11/28/2022]
Abstract
Root-associated fungal communities modify the climatic niches and even the competitive ability of their hosts, yet how the different components of the root microbiome are modified by habitat loss remains a key knowledge gap. Using principles of landscape ecology, we tested how free-living versus host-associated microbes differ in their response to landscape heterogeneity. Further, we explore how compartmentalisation of microbes into specialised root structures filters for key fungal symbionts. Our study demonstrates that free-living fungal community structure correlates with landscape heterogeneity, but that host-associated fungal communities depart from these patterns. Specifically, biotic filtering in roots, especially via compartmentalisation within specialised root structures, decouples the biogeographic patterns of host-associated fungal communities from the soil community. In this way, even as habitat loss and fragmentation threaten fungal diversity in the soils, plant hosts exert biotic controls to ensure associations with critical mutualists, helping to preserve the root mycobiome.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,Plant Gene Expression Center, USDA-ARS, Albany, California, USA
| | - Aidee Guzman
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA
| | - Leander D L Anderegg
- Department of Integrative Biology, UC Berkeley, Berkeley, California, USA.,Department of Ecology, Evolution & Marine Biology, UC Santa Barbara, Santa Barbara, California, USA
| | - Cheng Gao
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,State Key Laboratory of Mycology, Chinese Academy of Sciences, Beijing, China
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA.,Plant Gene Expression Center, USDA-ARS, Albany, California, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA
| | - Tom D Bruns
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA.,Department of Plant and Microbial Biology, UC Berkeley, Berkeley, California, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, California, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, California, USA
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15
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Xu L, Dong Z, Chiniquy D, Pierroz G, Deng S, Gao C, Diamond S, Simmons T, Wipf HML, Caddell D, Varoquaux N, Madera MA, Hutmacher R, Deutschbauer A, Dahlberg JA, Guerinot ML, Purdom E, Banfield JF, Taylor JW, Lemaux PG, Coleman-Derr D. Genome-resolved metagenomics reveals role of iron metabolism in drought-induced rhizosphere microbiome dynamics. Nat Commun 2021; 12:3209. [PMID: 34050180 PMCID: PMC8163885 DOI: 10.1038/s41467-021-23553-7] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [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: 08/28/2020] [Accepted: 04/27/2021] [Indexed: 02/04/2023] Open
Abstract
Recent studies have demonstrated that drought leads to dramatic, highly conserved shifts in the root microbiome. At present, the molecular mechanisms underlying these responses remain largely uncharacterized. Here we employ genome-resolved metagenomics and comparative genomics to demonstrate that carbohydrate and secondary metabolite transport functionalities are overrepresented within drought-enriched taxa. These data also reveal that bacterial iron transport and metabolism functionality is highly correlated with drought enrichment. Using time-series root RNA-Seq data, we demonstrate that iron homeostasis within the root is impacted by drought stress, and that loss of a plant phytosiderophore iron transporter impacts microbial community composition, leading to significant increases in the drought-enriched lineage, Actinobacteria. Finally, we show that exogenous application of iron disrupts the drought-induced enrichment of Actinobacteria, as well as their improvement in host phenotype during drought stress. Collectively, our findings implicate iron metabolism in the root microbiome's response to drought and may inform efforts to improve plant drought tolerance to increase food security.
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Affiliation(s)
- Ling Xu
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA ,grid.22935.3f0000 0004 0530 8290State Key Laboratory of Plant Physiology and Biochemistry, Department of Microbiology and Immunology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Zhaobin Dong
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Dawn Chiniquy
- grid.184769.50000 0001 2231 4551Department of Energy, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | - Grady Pierroz
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Siwen Deng
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Cheng Gao
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Spencer Diamond
- grid.47840.3f0000 0001 2181 7878Department of Earth and Planetary Science, University of California, Berkeley, CA USA
| | - Tuesday Simmons
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Heidi M.-L. Wipf
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Daniel Caddell
- grid.507310.0Plant Gene Expression Center, USDA-ARS, Albany, CA USA
| | - Nelle Varoquaux
- grid.463716.10000 0004 4687 1979CNRS, University Grenoble Alpes, TIMC-IMAG, Grenoble, France
| | - Mary A. Madera
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Robert Hutmacher
- grid.27860.3b0000 0004 1936 9684Westside Research & Extension Center, UC Department of Plant Sciences, University of California, Davis, CA USA
| | - Adam Deutschbauer
- grid.184769.50000 0001 2231 4551Department of Energy, Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA USA
| | | | - Mary Lou Guerinot
- grid.254880.30000 0001 2179 2404Department of Biological Scienes, Dartmouth College, Hanover, NH USA
| | - Elizabeth Purdom
- grid.47840.3f0000 0001 2181 7878Department of Statistics, University of California, Berkeley, CA USA
| | - Jillian F. Banfield
- grid.47840.3f0000 0001 2181 7878Department of Earth and Planetary Science, University of California, Berkeley, CA USA
| | - John W. Taylor
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Peggy G. Lemaux
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Devin Coleman-Derr
- grid.47840.3f0000 0001 2181 7878Department of Plant and Microbial Biology, University of California, Berkeley, CA USA ,grid.507310.0Plant Gene Expression Center, USDA-ARS, Albany, CA USA
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16
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Xu L, Pierroz G, Wipf HML, Gao C, Taylor JW, Lemaux PG, Coleman-Derr D. Holo-omics for deciphering plant-microbiome interactions. Microbiome 2021; 9:69. [PMID: 33762001 PMCID: PMC7988928 DOI: 10.1186/s40168-021-01014-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 02/02/2021] [Indexed: 05/02/2023]
Abstract
Host-microbiome interactions are recognized for their importance to host health. An improved understanding of the molecular underpinnings of host-microbiome relationships will advance our capacity to accurately predict host fitness and manipulate interaction outcomes. Within the plant microbiome research field, unlocking the functional relationships between plants and their microbial partners is the next step to effectively using the microbiome to improve plant fitness. We propose that strategies that pair host and microbial datasets-referred to here as holo-omics-provide a powerful approach for hypothesis development and advancement in this area. We discuss several experimental design considerations and present a case study to highlight the potential for holo-omics to generate a more holistic perspective of molecular networks within the plant microbiome system. In addition, we discuss the biggest challenges for conducting holo-omics studies; specifically, the lack of vetted analytical frameworks, publicly available tools, and required technical expertise to process and integrate heterogeneous data. Finally, we conclude with a perspective on appropriate use-cases for holo-omics studies, the need for downstream validation, and new experimental techniques that hold promise for the plant microbiome research field. We argue that utilizing a holo-omics approach to characterize host-microbiome interactions can provide important opportunities for broadening system-level understandings and significantly inform microbial approaches to improving host health and fitness. Video abstract.
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Affiliation(s)
- Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Heidi M.-L. Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Cheng Gao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - John W. Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Peggy G. Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA USA
- Plant Gene Expression Center, USDA-ARS, Albany, CA USA
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17
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Willing CE, Pierroz G, Coleman-Derr D, Dawson TE. The generalizability of water-deficit on bacterial community composition; Site-specific water-availability predicts the bacterial community associated with coast redwood roots. Mol Ecol 2020; 29:4721-4734. [PMID: 33000868 DOI: 10.1111/mec.15666] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 09/18/2020] [Accepted: 09/21/2020] [Indexed: 12/01/2022]
Abstract
Experimental drought has been shown to delay the development of the root microbiome and increase the relative abundance of Actinobacteria, however, the generalizability of these findings to natural systems or other diverse plant hosts remains unknown. Bacterial cell wall thickness and growth morphology (e.g., filamentous or unicellular) have been proposed as traits that may mediate bacterial responses to environmental drivers. Leveraging a natural gradient of water-availability across the coast redwood (Sequoia sempervirens) range, we tested three hypotheses: (a) that site-specific water-availability is an important predictor of bacterial community composition for redwood roots and rhizosphere soils; (b) that there is relative enrichment of Actinobacteria and other monoderm bacterial groups within the redwood microbiome in response to drier conditions; and (c) that bacterial growth morphology is an important predictor of bacteria response to water-availability, where filamentous taxa will become more dominant at drier sites compared to unicellular bacteria. We find that both α- and β-diversity of redwood bacterial communities is partially explained by water-availability and that Actinobacterial enrichment is a conserved response of land plants to water-deficit. Further, we highlight how the trend of Actinobacterial enrichment in the redwood system is largely driven by the Actinomycetales. We propose bacterial growth morphology (filamentous vs. unicellular) as an additional mechanism behind the increase in Actinomycetales with increasing aridity. A trait-based approach including cell-wall thickness and growth morphology may explain the distribution of bacterial taxa across environmental gradients and help to predict patterns of bacterial community composition for a wide range of host plants.
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Affiliation(s)
- Claire E Willing
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, UC Berkeley, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Todd E Dawson
- Department of Environmental Science, Policy and Management, UC Berkeley, Berkeley, CA, USA.,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA
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18
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Simmons T, Styer AB, Pierroz G, Gonçalves AP, Pasricha R, Hazra AB, Bubner P, Coleman-Derr D. Drought Drives Spatial Variation in the Millet Root Microbiome. Front Plant Sci 2020; 11:599. [PMID: 32547572 PMCID: PMC7270290 DOI: 10.3389/fpls.2020.00599] [Citation(s) in RCA: 12] [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] [Subscribe] [Scholar Register] [Received: 12/07/2019] [Accepted: 04/20/2020] [Indexed: 05/29/2023]
Abstract
Efforts to boost crop yield and meet global food demands while striving to reach sustainability goals are hindered by the increasingly severe impacts of abiotic stress, such as drought. One strategy for alleviating drought stress in crops is to utilize root-associated bacteria, yet knowledge concerning the relationship between plant hosts and their microbiomes during drought remain under-studied. One broad pattern that has recently been reported in a variety of monocot and dicot species from both native and agricultural environments, is the enrichment of Actinobacteria within the drought-stressed root microbiome. In order to better understand the causes of this phenomenon, we performed a series of experiments in millet plants to explore the roles of drought severity, drought localization, and root development in provoking Actinobacteria enrichment within the root endosphere. Through 16S rRNA amplicon-based sequencing, we demonstrate that the degree of drought is correlated with levels of Actinobacterial enrichment in four species of millet. Additionally, we demonstrate that the observed drought-induced enrichment of Actinobacteria occurs along the length of the root, but the response is localized to portions of the root experiencing drought. Finally, we demonstrate that Actinobacteria are depleted in the dead root tissue of Japanese millet, suggesting saprophytic activity is not the main cause of observed shifts in drought-treated root microbiome structure. Collectively, these results help narrow the list of potential causes of drought-induced Actinobacterial enrichment in plant roots by showing that enrichment is dependent upon localized drought responses but not root developmental stage or root death.
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Affiliation(s)
- Tuesday Simmons
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Alexander B. Styer
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Grady Pierroz
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Antonio Pedro Gonçalves
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Ramji Pasricha
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Amrita B. Hazra
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Patricia Bubner
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
| | - Devin Coleman-Derr
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, United States
- Plant Gene Expression Center, United States Department of Agriculture–Agriculture Research Service, Albany, CA, United States
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19
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Deng S, Wipf HML, Pierroz G, Raab TK, Khanna R, Coleman-Derr D. A Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome. Sci Rep 2019; 9:17677. [PMID: 31776356 PMCID: PMC6881409 DOI: 10.1038/s41598-019-53623-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 11/01/2019] [Indexed: 12/22/2022] Open
Abstract
Despite growing interest in utilizing microbial-based methods for improving crop growth, much work still remains in elucidating how beneficial plant-microbe associations are established, and what role soil amendments play in shaping these interactions. Here, we describe a set of experiments that test the effect of a commercially available soil amendment, VESTA, on the soil and strawberry (Fragaria x ananassa Monterey) root bacterial microbiome. The bacterial communities of the soil, rhizosphere, and root from amendment-treated and untreated fields were profiled at four time points across the strawberry growing season using 16S rRNA gene amplicon sequencing on the Illumina MiSeq platform. In all sample types, bacterial community composition and relative abundance were significantly altered with amendment application. Importantly, time point effects on composition are more pronounced in the root and rhizosphere, suggesting an interaction between plant development and treatment effect. Surprisingly, there was slight overlap between the taxa within the amendment and those enriched in plant and soil following treatment, suggesting that VESTA may act to rewire existing networks of organisms through an, as of yet, uncharacterized mechanism. These findings demonstrate that a commercial microbial soil amendment can impact the bacterial community structure of both roots and the surrounding environment.
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Affiliation(s)
- Siwen Deng
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Heidi M-L Wipf
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Grady Pierroz
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA
| | - Ted K Raab
- Carnegie Institution for Science, Department of Plant Biology, Stanford, CA, USA
| | - Rajnish Khanna
- i-Cultiver, Inc., 404 Clipper Cove Way, San Francisco, CA, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA. .,Plant Gene Expression Center, USDA-ARS, Albany, CA, USA.
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