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Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies. mSystems 2022; 7:e0093422. [PMID: 36342125 PMCID: PMC9765016 DOI: 10.1128/msystems.00934-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.
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Escudero-Martinez C, Coulter M, Alegria Terrazas R, Foito A, Kapadia R, Pietrangelo L, Maver M, Sharma R, Aprile A, Morris J, Hedley PE, Maurer A, Pillen K, Naclerio G, Mimmo T, Barton GJ, Waugh R, Abbott J, Bulgarelli D. Identifying plant genes shaping microbiota composition in the barley rhizosphere. Nat Commun 2022; 13:3443. [PMID: 35710760 PMCID: PMC9203816 DOI: 10.1038/s41467-022-31022-y] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Accepted: 05/30/2022] [Indexed: 12/13/2022] Open
Abstract
A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant’s capacity of shaping rhizosphere microbes. A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere. Here, the authors report QTLs and the associated candidate genes underlying rhizosphere microbiome composition in barley.
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Affiliation(s)
| | - Max Coulter
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Rodrigo Alegria Terrazas
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Mohammed VI Polytechnic University, Agrobiosciences Program, Plant & Soil Microbiome Subprogram, Bengurir, Morocco
| | | | - Rumana Kapadia
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK
| | - Laura Pietrangelo
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Mauro Maver
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | | | - Alessio Aprile
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,Department of Biological and Environmental Sciences and Technologies, University of Salento, Lecce, Italy
| | | | | | - Andreas Maurer
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Klaus Pillen
- Institute of Agricultural and Nutritional Sciences, Martin-Luther-University, Halle-Wittenberg, Germany
| | - Gino Naclerio
- Department of Biosciences and Territory, University of Molise, Campobasso, Italy
| | - Tanja Mimmo
- Faculty of Science and Technology, Free University of Bozen-Bolzano, Bolzano, Italy.,Competence Centre for Plant Health, Free University of Bozen-Bolzano, Bolzano, Italy
| | - Geoffrey J Barton
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Robbie Waugh
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.,The James Hutton Institute, Invergowrie, UK
| | - James Abbott
- University of Dundee, Computational Biology, School of Life Sciences, Dundee, UK
| | - Davide Bulgarelli
- University of Dundee, Plant Sciences, School of Life Sciences, Dundee, UK.
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