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      The rhizosphere microbiome: Plant–microbial interactions for resource acquisition

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          Abstract

          While horticulture tools and methods have been extensively developed to improve the management of crops, systems to harness the rhizosphere microbiome to benefit plant crops are still in development. Plants and microbes have been coevolving for several millennia, conferring fitness advantages that expand the plant’s own genetic potential. These beneficial associations allow the plants to cope with abiotic stresses such as nutrient deficiency across a wide range of soils and growing conditions. Plants achieve these benefits by selectively recruiting microbes using root exudates, positively impacting their nutrition, health and overall productivity. Advanced knowledge of the interplay between root exudates and microbiome alteration in response to plant nutrient status, and the underlying mechanisms there of, will allow the development of technologies to increase crop yield. This review summarizes current knowledge and perspectives on plant–microbial interactions for resource acquisition and discusses promising advances for manipulating rhizosphere microbiomes and root exudation.

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          Most cited references162

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          Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.

          The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry (MS) techniques are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of 'living data' through continuous reanalysis of deposited data.
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            Induced systemic resistance by beneficial microbes.

            Beneficial microbes in the microbiome of plant roots improve plant health. Induced systemic resistance (ISR) emerged as an important mechanism by which selected plant growth-promoting bacteria and fungi in the rhizosphere prime the whole plant body for enhanced defense against a broad range of pathogens and insect herbivores. A wide variety of root-associated mutualists, including Pseudomonas, Bacillus, Trichoderma, and mycorrhiza species sensitize the plant immune system for enhanced defense without directly activating costly defenses. This review focuses on molecular processes at the interface between plant roots and ISR-eliciting mutualists, and on the progress in our understanding of ISR signaling and systemic defense priming. The central role of the root-specific transcription factor MYB72 in the onset of ISR and the role of phytohormones and defense regulatory proteins in the expression of ISR in aboveground plant parts are highlighted. Finally, the ecological function of ISR-inducing microbes in the root microbiome is discussed.
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              Embracing the unknown: disentangling the complexities of the soil microbiome

              Soil contains a vast diversity of microorganisms that can directly or indirectly modulate soil processes and terrestrial ecosystems. In this Review, Fierer summarizes the challenges in characterizing the composition and functions of the soil microbiome, and discusses key future research directions.
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                Author and article information

                Contributors
                hugopg@colostate.edu
                j.vivanco@colostate.edu
                Journal
                J Appl Microbiol
                J Appl Microbiol
                10.1111/(ISSN)1365-2672
                JAM
                Journal of Applied Microbiology
                John Wiley and Sons Inc. (Hoboken )
                1364-5072
                1365-2672
                16 July 2022
                November 2022
                : 133
                : 5 ( doiID: 10.1111/jam.v133.5 )
                : 2864-2876
                Affiliations
                [ 1 ] Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape Architecture Colorado State University Fort Collins Colorado 80523‐1173 United States
                Author notes
                [*] [* ] Correspondence

                Hugo Pantigoso and Jorge Vivanco, Center for Root and Rhizosphere Biology, Department of Horticulture and Landscape Architecture, Colorado State University, Fort Collins, CO 80523‐1173, USA.

                Email: hugopg@ 123456colostate.edu ; j.vivanco@ 123456colostate.edu

                Author information
                https://orcid.org/0000-0002-7121-7253
                Article
                JAM15686 JAMICRO-2022-0016.R3
                10.1111/jam.15686
                9796772
                36648151
                c41bc2fe-9bb0-4cbc-a2ba-e19c2cdc8de7
                © 2022 The Authors. Journal of Applied Microbiology published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

                This is an open access article under the terms of the http://creativecommons.org/licenses/by-nc-nd/4.0/ License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non‐commercial and no modifications or adaptations are made.

                History
                : 16 June 2022
                : 03 January 2022
                : 22 June 2022
                Page count
                Figures: 1, Tables: 1, Pages: 13, Words: 9239
                Categories
                Review Article
                Regular Issue
                Review Articles
                Custom metadata
                2.0
                November 2022
                Converter:WILEY_ML3GV2_TO_JATSPMC version:6.2.3 mode:remove_FC converted:28.12.2022

                Microbiology & Virology
                microbiome,nutrient,plant growth promoting rhizobacteria,rhizosphere,root exudates,signalling,soil

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