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Qi M, Berry JC, Veley KW, O'Connor L, Finkel OM, Salas-González I, Kuhs M, Jupe J, Holcomb E, Glavina Del Rio T, Creech C, Liu P, Tringe SG, Dangl JL, Schachtman DP, Bart RS. Identification of beneficial and detrimental bacteria impacting sorghum responses to drought using multi-scale and multi-system microbiome comparisons. THE ISME JOURNAL 2022; 16:1957-1969. [PMID: 35523959 PMCID: PMC9296637 DOI: 10.1038/s41396-022-01245-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 12/12/2022]
Abstract
Drought is a major abiotic stress limiting agricultural productivity. Previous field-level experiments have demonstrated that drought decreases microbiome diversity in the root and rhizosphere. How these changes ultimately affect plant health remains elusive. Toward this end, we combined reductionist, transitional and ecological approaches, applied to the staple cereal crop sorghum to identify key root-associated microbes that robustly affect drought-stressed plant phenotypes. Fifty-three Arabidopsis-associated bacteria were applied to sorghum seeds and their effect on root growth was monitored. Two Arthrobacter strains caused root growth inhibition (RGI) in Arabidopsis and sorghum. In the context of synthetic communities, Variovorax strains were able to protect plants from Arthrobacter-caused RGI. As a transitional system, high-throughput phenotyping was used to test the synthetic communities. During drought stress, plants colonized by Arthrobacter had reduced growth and leaf water content. Plants colonized by both Arthrobacter and Variovorax performed as well or better than control plants. In parallel, we performed a field trial wherein sorghum was evaluated across drought conditions. By incorporating data on soil properties into the microbiome analysis, we accounted for experimental noise with a novel method and were able to observe the negative correlation between the abundance of Arthrobacter and plant growth. Having validated this approach, we cross-referenced datasets from the high-throughput phenotyping and field experiments and report a list of bacteria with high confidence that positively associated with plant growth under drought stress. In conclusion, a three-tiered experimental system successfully spanned the lab-to-field gap and identified beneficial and deleterious bacterial strains for sorghum under drought.
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Affiliation(s)
- Mingsheng Qi
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Kira W Veley
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Lily O'Connor
- Donald Danforth Plant Science Center, St. Louis, MO, USA.,Washington University, St. Louis, MO, USA
| | - Omri M Finkel
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Plant and Environmental Sciences, Institute of Life Science, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Isai Salas-González
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Molly Kuhs
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Julietta Jupe
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | - Emily Holcomb
- Donald Danforth Plant Science Center, St. Louis, MO, USA
| | | | - Cody Creech
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA
| | - Peng Liu
- Department of Statistics, Iowa State University, Ames, IA, USA
| | - Susannah G Tringe
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.,Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Curriculum in Genetics and Molecular Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.,Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Daniel P Schachtman
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE, USA.,Center for Plant Science Innovation, University of Nebraska - Lincoln, Lincoln, NE, USA
| | - Rebecca S Bart
- Donald Danforth Plant Science Center, St. Louis, MO, USA.
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