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Jones P, Garcia BJ, Furches A, Tuskan GA, Jacobson D. Plant Host-Associated Mechanisms for Microbial Selection. FRONTIERS IN PLANT SCIENCE 2019; 10:862. [PMID: 31333701 PMCID: PMC6618679 DOI: 10.3389/fpls.2019.00862] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 06/14/2019] [Indexed: 05/18/2023]
Abstract
Plants serve as host to numerous microorganisms. The members of these microbial communities interact among each other and with the plant, and there is increasing evidence to suggest that the microbial community may promote plant growth, improve drought tolerance, facilitate pathogen defense and even assist in environmental remediation. Therefore, it is important to better understand the mechanisms that influence the composition and structure of microbial communities, and what role the host may play in the recruitment and control of its microbiome. In particular, there is a growing body of research to suggest that plant defense systems not only provide a layer of protection against pathogens but may also actively manage the composition of the overall microbiome. In this review, we provide an overview of the current research into mechanisms employed by the plant host to select for and control its microbiome. We specifically review recent research that expands upon the role of keystone microbial species, phytohormones, and abiotic stress, and in how they relate to plant driven dynamic microbial structuring.
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Affiliation(s)
- Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Benjamin J. Garcia
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Anna Furches
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
| | - Gerald A. Tuskan
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, The Center for Bioenergy Innovation, Oak Ridge, TN, United States
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee, Knoxville, Knoxville, TN, United States
- *Correspondence: Daniel Jacobson
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252
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Cernava T, Aschenbrenner IA, Soh J, Sensen CW, Grube M, Berg G. Plasticity of a holobiont: desiccation induces fasting-like metabolism within the lichen microbiota. ISME JOURNAL 2018; 13:547-556. [PMID: 30310167 PMCID: PMC6331575 DOI: 10.1038/s41396-018-0286-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/31/2018] [Accepted: 09/08/2018] [Indexed: 01/08/2023]
Abstract
The role of host-associated microbiota in enduring dehydration and drought is largely unknown. We have used lichens to study this increasingly important problem because they are the organisms that are optimally adapted to reoccurring hydration/dehydration cycles, and they host a defined and persistent bacterial community. The analysis of metatranscriptomic datasets from bacterial communities of the lung lichen (Lobaria pulmonaria (L.) Hoffm.), sampled under representative hydration stages, revealed significant structural shifts and functional specialization to host conditions. The hydrated samples showed upregulated transcription of transport systems, tRNA modification and various porins (Omp2b by Rhizobiales), whereas the desiccated samples showed different functions related to stress adaption prominently. Carbohydrate metabolism was activated under both conditions. Under dry conditions, upregulation of a specialized ketone metabolism indicated a switch to lipid-based nutrition. Several bacterial lineages were involved in a functional transition that was reminiscent of a 'fasting metaorganism'. Similar functional adaptions were assigned to taxonomically unrelated groups, indicating hydration-related specialization of the microbiota. We were able to show that host-associated bacterial communities are well adapted to dehydration by stress protection and changes of the metabolism. Moreover, our results indicate an intense interplay in holobiont functioning under drought stress.
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Affiliation(s)
- Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Ines Aline Aschenbrenner
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Jung Soh
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
| | - Christoph W Sensen
- Institute of Computational Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria.,BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Austria
| | - Martin Grube
- Institute of Plant Sciences, University of Graz, Holteigasse 6, 8010, Graz, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria. .,BioTechMed Graz, Mozartgasse 12/II, 8010, Graz, Austria.
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Gao C, Montoya L, Xu L, Madera M, Hollingsworth J, Purdom E, Hutmacher RB, Dahlberg JA, Coleman-Derr D, Lemaux PG, Taylor JW. Strong succession in arbuscular mycorrhizal fungal communities. ISME JOURNAL 2018; 13:214-226. [PMID: 30171254 PMCID: PMC6298956 DOI: 10.1038/s41396-018-0264-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Revised: 06/08/2018] [Accepted: 07/24/2018] [Indexed: 12/26/2022]
Abstract
The ecology of fungi lags behind that of plants and animals because most fungi are microscopic and hidden in their substrates. Here, we address the basic ecological process of fungal succession in nature using the microscopic, arbuscular mycorrhizal fungi (AMF) that form essential mutualisms with 70-90% of plants. We find a signal for temporal change in AMF community similarity that is 40-fold stronger than seen in the most recent studies, likely due to weekly samplings of roots, rhizosphere and soil throughout the 17 weeks from seedling to fruit maturity and the use of the fungal DNA barcode to recognize species in a simple, agricultural environment. We demonstrate the patterns of nestedness and turnover and the microbial equivalents of the processes of immigration and extinction, that is, appearance and disappearance. We also provide the first evidence that AMF species co-exist rather than simply co-occur by demonstrating negative, density-dependent population growth for multiple species. Our study shows the advantages of using fungi to test basic ecological hypotheses (e.g., nestedness v. turnover, immigration v. extinction, and coexistence theory) over periods as short as one season.
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Affiliation(s)
- Cheng Gao
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Liliam Montoya
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Ling Xu
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.,Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, 94710, USA
| | - Mary Madera
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - Joy Hollingsworth
- University of California Kearney Agricultural Research & Extension Center, Parlier, CA, 93648, USA
| | - Elizabeth Purdom
- Department of Statistics, University of California, Berkeley, CA, 94720, USA
| | - Robert B Hutmacher
- University of California West Side Research & Extension Center, UC Davis Department of Plant Sciences, Five Points, CA, 93624, USA
| | - Jeffery A Dahlberg
- University of California Kearney Agricultural Research & Extension Center, Parlier, CA, 93648, USA
| | - Devin Coleman-Derr
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.,Plant Gene Expression Center, US Department of Agriculture-Agricultural Research Service, Albany, CA, 94710, USA
| | - Peggy G Lemaux
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA
| | - John W Taylor
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, 94720-3102, USA.
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