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López JL, Fourie A, Poppeliers SWM, Pappas N, Sánchez-Gil JJ, de Jonge R, Dutilh BE. Growth rate is a dominant factor predicting the rhizosphere effect. THE ISME JOURNAL 2023; 17:1396-1405. [PMID: 37322285 PMCID: PMC10432406 DOI: 10.1038/s41396-023-01453-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/17/2023]
Abstract
The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.
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Affiliation(s)
- José L López
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
- Instituto Andino Patagónico de Tecnologías Biológicas y Geoambientales, Bariloche, Rio Negro, Argentina
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany
| | - Arista Fourie
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Nikolaos Pappas
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Department of Biology, Science for Life, Utrecht University, Utrecht, The Netherlands.
- Institute of Biodiversity, Faculty of Biological Sciences, Cluster of Excellence Balance of the Microverse, Friedrich Schiller University Jena, Jena, Germany.
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Migration Rates on Swim Plates Vary between Escherichia coli Soil Isolates: Differences Are Associated with Variants in Metabolic Genes. Appl Environ Microbiol 2023; 89:e0172722. [PMID: 36695629 PMCID: PMC9972950 DOI: 10.1128/aem.01727-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
This study investigates migration phenotypes of 265 Escherichia coli soil isolates from the Buffalo River basin in Minnesota, USA. Migration rates on semisolid tryptone swim plates ranged from nonmotile to 190% of the migration rate of a highly motile E. coli K-12 strain. The nonmotile isolate, LGE0550, had mutations in flagellar and chemotaxis genes, including two IS3 elements in the flagellin-encoding gene fliC. A genome-wide association study (GWAS), associating the migration rates with genetic variants in specific genes, yielded two metabolic variants (rygD-serA and metR-metE) with previous implications in chemotaxis. As a novel way of confirming GWAS results, we used minimal medium swim plates to confirm the associations. Other variants in metabolic genes and genes that are associated with biofilm were positively or negatively associated with migration rates. A determination of growth phenotypes on Biolog EcoPlates yielded differential growth for the 10 tested isolates on d-malic acid, putrescine, and d-xylose, all of which are important in the soil environment. IMPORTANCE E. coli is a Gram-negative, facultative anaerobic bacterium whose life cycle includes extra host environments in addition to human, animal, and plant hosts. The bacterium has the genomic capability of being motile. In this context, the significance of this study is severalfold: (i) the great diversity of migration phenotypes that we observed within our isolate collection supports previous (G. NandaKafle, A. A. Christie, S. Vilain, and V. S. Brözel, Front Microbiol 9:762, 2018, https://doi.org/10.3389/fmicb.2018.00762; Y. Somorin, F. Abram, F. Brennan, and C. O'Byrne, Appl Environ Microbiol 82:4628-4640, 2016, https://doi.org/10.1128/AEM.01175-16) ideas of soil promoting phenotypic heterogeneity, (ii) such heterogeneity may facilitate bacterial growth in the many different soil niches, and (iii) such heterogeneity may enable the bacteria to interact with human, animal, and plant hosts.
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Singh P, Singh RK, Li HB, Guo DJ, Sharma A, Verma KK, Solanki MK, Upadhyay SK, Lakshmanan P, Yang LT, Li YR. Nitrogen fixation and phytohormone stimulation of sugarcane plant through plant growth promoting diazotrophic Pseudomonas. Biotechnol Genet Eng Rev 2023:1-21. [PMID: 36814143 DOI: 10.1080/02648725.2023.2177814] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 01/30/2023] [Indexed: 02/24/2023]
Abstract
Diazotrophic microorganisms are free-living groups of organisms that can convert atmospheric nitrogen (N) into bioavailable nitrogen for plants, which increases crop development and production. The purpose of the current study was to ascertain how diazotrophic plant growth promoting (PGP) Pseudomonas strains (P. koreensis CY4 and P. entomophila CN11) enhanced nitrogen fixation, defense activity, and PGP attributes of sugarcane varieties; GT11 and G×B9. A 15N isotope-dilution study was conducted to confirm the sugarcane strains' capacity to fix nitrogen, and the results indicated that between 21 to 35% of plant, nitrogen is fixed biologically by selected rhizobacteria. In comparison to the control, after 30, 60, and 90 days, both CY4 and CN11 strains significantly increased defense-related enzymes (catalase, peroxidase, phenylalanine ammonia-lyase, superoxide dismutase, glucanase, and chitinase) and phytohormones (abscisic acid, ABA, cytokinin, etc.) in GT11 and GXB. Additionally, the expression of SuCHI, SuGLU, SuCAT, SuSOD, and SuPAL genes was found to be elevated in Pseudomonas strains inoculated plants using real-time quantitative polymerase chain reaction (RT-qPCR). Both bacterial strains increased all physiological parameters and chlorophyll content in sugarcane plants more than their control. The effects of P. koreensis CY4 and P. entomophila CN11 strains on sugarcane growth promotion and nitrogen fixation under greenhouse conditions are described here for the first time systematically. The results of confirmation studies demonstrated that P. koreensis CY4 and P. entomophila are PGP bacterial strains with the potential to be employed as a biofertilizer for sugarcane growth, nitrogen nutrient absorption, and reduced application of chemical nitrogenous fertilizers in agricultural fields. .
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Affiliation(s)
- Pratiksha Singh
- School of Marine Sciences and Biotechnology, Guangxi Minzu University, Nanning, China
| | - Rajesh Kumar Singh
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Hai-Bi Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Dao-Jun Guo
- College of Life Sciences and Engineering, Hexi University, Zhangye, China
| | - Anjney Sharma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Krishan K Verma
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Manoj Kumar Solanki
- Plant Cytogenetics and Molecular Biology Group, Institute of Biology, Biotechnology and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Sudhir K Upadhyay
- Department of Environmental Science, V.B.S. Purvanchal University, Jaunpur, India
| | - Prakash Lakshmanan
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
| | - Li-Tao Yang
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Yang-Rui Li
- Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Guangxi Key Laboratory of Crop Genetic Improvement and Biotechnology, Nanning, China
- Key Laboratory of Sugarcane Biotechnology and Genetic Improvement (Guangxi), Ministry of Agriculture, Sugarcane Research Center, Chinese Academy of Agricultural Sciences, Guangxi Key Laboratory of Sugarcane Genetic Improvement, Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, China
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Investigation of bacterial diversity using 16S rRNA sequencing and prediction of its functionalities in Moroccan phosphate mine ecosystem. Sci Rep 2022; 12:3741. [PMID: 35260670 PMCID: PMC8904503 DOI: 10.1038/s41598-022-07765-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/21/2022] [Indexed: 11/28/2022] Open
Abstract
Native plants in extreme environments may harbor some unique microbial communities with particular functions to sustain their growth and tolerance to harsh conditions. The aim of this study was to investigate the bacterial communities profiles in some native plants and samples of the Moroccan phosphate mine ecosystem by assessing the percentages of taxonomic identification using six hypervariable regions of the 16S rRNA. The rhizosphere of the three wild plants in the Moroccan phosphate mine is characterized by interesting bacterial diversity including Proteobacteria (62.24%, 71.15% and 65.61%), Actinobacteria (22.53%, 15.24%, 22.30%), Bacteroidetes (7.57%; 4.23%; 7.63%), and Firmicutes (5.82%; 1.17%; 2.83%). The bulk phosphate mine samples were dominated by Actinobacteria with average relative abundance of 97.73% that are different from those inferred in the rhizosphere samples of the native plants. The regions V3, V4 and V67 performed better in the taxonomic profiling at different taxonomic levels. Results indicated that both plant genotype and mainly soil conditions may be involved in the shaping of bacterial diversity. Such indication was also confirmed by the prediction of functional profiles that showed enrichment of many functions related to biological nitrogen fixation in the rhizosphere of native plants and the stress related functions in the bulk phosphate mine in comparison with the wheat rhizosphere samples.
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Oni FE, Esmaeel Q, Onyeka JT, Adeleke R, Jacquard C, Clement C, Gross H, Ait Barka E, Höfte M. Pseudomonas Lipopeptide-Mediated Biocontrol: Chemotaxonomy and Biological Activity. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27020372. [PMID: 35056688 PMCID: PMC8777863 DOI: 10.3390/molecules27020372] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 12/29/2021] [Accepted: 01/05/2022] [Indexed: 12/14/2022]
Abstract
Pseudomonas lipopeptides (Ps-LPs) play crucial roles in bacterial physiology, host–microbe interactions and plant disease control. Beneficial LP producers have mainly been isolated from the rhizosphere, phyllosphere and from bulk soils. Despite their wide geographic distribution and host range, emerging evidence suggests that LP-producing pseudomonads and their corresponding molecules display tight specificity and follow a phylogenetic distribution. About a decade ago, biocontrol LPs were mainly reported from the P. fluorescens group, but this has drastically advanced due to increased LP diversity research. On the one hand, the presence of a close-knit relationship between Pseudomonas taxonomy and the molecule produced may provide a startup toolbox for the delineation of unknown LPs into existing (or novel) LP groups. Furthermore, a taxonomy–molecule match may facilitate decisions regarding antimicrobial activity profiling and subsequent agricultural relevance of such LPs. In this review, we highlight and discuss the production of beneficial Ps-LPs by strains situated within unique taxonomic groups and the lineage-specificity and coevolution of this relationship. We also chronicle the antimicrobial activity demonstrated by these biomolecules in limited plant systems compared with multiple in vitro assays. Our review further stresses the need to systematically elucidate the roles of diverse Ps-LP groups in direct plant–pathogen interactions and in the enhancement of plant innate immunity.
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Affiliation(s)
- Feyisara Eyiwumi Oni
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
- Department of Biological Sciences, Faculty of Science, Anchor University, Ayobo P.M.B 00001, Lagos State, Nigeria
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
- Correspondence:
| | - Qassim Esmaeel
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Joseph Tobias Onyeka
- Plant Pathology Unit, National Root Crops Research Institute (NRCRI), Umudike 440001, Abia State, Nigeria;
| | - Rasheed Adeleke
- Unit for Environmental Sciences and Management, Faculty of Natural and Agricultural Sciences, North-West University, Potchefstroom 2520, South Africa;
| | - Cedric Jacquard
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Christophe Clement
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Harald Gross
- Department of Pharmaceutical Biology, Institute of Pharmaceutical Sciences, University of Tubingen, Auf der Morgenstelle 8, 72076 Tübingen, Germany;
| | - Essaid Ait Barka
- Université de Reims Champagne Ardenne, Unité de Recherche RIBP EA4707 USC INRAE 1488, SFR Condorcet FR CNRS 3417, 51100 Reims, France; (Q.E.); (C.J.); (C.C.); (E.A.B.)
| | - Monica Höfte
- Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium;
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Liu TY, Ye N, Wang X, Das D, Tan Y, You X, Long M, Hu T, Dai L, Zhang J, Chen MX. Drought stress and plant ecotype drive microbiome recruitment in switchgrass rhizosheath. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:1753-1774. [PMID: 34288433 DOI: 10.1111/jipb.13154] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/18/2021] [Indexed: 05/27/2023]
Abstract
The rhizosheath, a layer of soil grains that adheres firmly to roots, is beneficial for plant growth and adaptation to drought environments. Switchgrass is a perennial C4 grass which can form contact rhizosheath under drought conditions. In this study, we characterized the microbiomes of four different rhizocompartments of two switchgrass ecotypes (Alamo and Kanlow) grown under drought or well-watered conditions via 16S ribosomal RNA amplicon sequencing. These four rhizocompartments, the bulk soil, rhizosheath soil, rhizoplane, and root endosphere, harbored both distinct and overlapping microbial communities. The root compartments (rhizoplane and root endosphere) displayed low-complexity communities dominated by Proteobacteria and Firmicutes. Compared to bulk soil, Cyanobacteria and Bacteroidetes were selectively enriched, while Proteobacteria and Firmicutes were selectively depleted, in rhizosheath soil. Taxa from Proteobacteria or Firmicutes were specifically selected in Alamo or Kanlow rhizosheath soil. Following drought stress, Citrobacter and Acinetobacter were further enriched in rhizosheath soil, suggesting that rhizosheath microbiome assembly is driven by drought stress. Additionally, the ecotype-specific recruitment of rhizosheath microbiome reveals their differences in drought stress responses. Collectively, these results shed light on rhizosheath microbiome recruitment in switchgrass and lay the foundation for the improvement of drought tolerance in switchgrass by regulating the rhizosheath microbiome.
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Affiliation(s)
- Tie-Yuan Liu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Nenghui Ye
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, College of Agriculture, Hunan Agricultural University, Changsha, 410128, China
| | - Xinyu Wang
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Debatosh Das
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Yuxiang Tan
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Xiangkai You
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Mingxiu Long
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Tianming Hu
- College of Grassland Agriculture, Northwest A&F University, Yangling, 712100, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Jianhua Zhang
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, 999077, China
- Department of Biology, Hong Kong Baptist University, Kowloon, Hong Kong, 999077, China
| | - Mo-Xian Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing, 210037, China
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
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Sweet Sorghum Genotypes Tolerant and Sensitive to Nitrogen Stress Select Distinct Root Endosphere and Rhizosphere Bacterial Communities. Microorganisms 2021; 9:microorganisms9061329. [PMID: 34207412 PMCID: PMC8234256 DOI: 10.3390/microorganisms9061329] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/14/2021] [Accepted: 06/15/2021] [Indexed: 12/17/2022] Open
Abstract
The belowground microbiomes have many beneficial functions that assist plant growth, including nutrient cycling, acquisition and transport, as well as alleviation of stresses caused by nutrient limitations such as nitrogen (N). Here we analyzed the root endosphere, rhizosphere and soil bacterial communities of seven sweet sorghum genotypes differing in sensitivity to N-stress. Sorghum genotypes were grown in fields with no (low-N) or sufficient (high-N) N. The dry shoot weight ratio (low-N/high-N) was used to determine N-stress sensitivity. Our hypothesis was that genotypes tolerant and sensitive to N-stress select distinct bacterial communities. The endosphere and rhizosphere bacterial community structure were significantly different between the N-stress sensitive and tolerant genotypes in the high-N field, but not in the low-N field. However, significant changes in the relative abundance of specific bacterial taxa were observed in both fields. Streptomyces, a bacterial genus known to alleviate plant abiotic stresses, was enriched in the endosphere and rhizosphere of the tolerant genotypes in the low-N field. Our study indicates that sweet sorghum genotypes tolerant to N-stress select taxa that can potentially mitigate the N-stress, suggesting that the interactions between N-stress tolerant lines and the root-associated microbiome might be vital for coping with N-stress.
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de la Fuente Cantó C, Simonin M, King E, Moulin L, Bennett MJ, Castrillo G, Laplaze L. An extended root phenotype: the rhizosphere, its formation and impacts on plant fitness. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 103:951-964. [PMID: 32324287 DOI: 10.1111/tpj.14781] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 04/03/2020] [Accepted: 04/09/2020] [Indexed: 05/13/2023]
Abstract
Plants forage soil for water and nutrients, whose distribution is patchy and often dynamic. To improve their foraging activities, plants have evolved mechanisms to modify the physicochemical properties and microbial communities of the rhizosphere, i.e. the soil compartment under the influence of the roots. This dynamic interplay in root-soil-microbiome interactions creates emerging properties that impact plant nutrition and health. As a consequence, the rhizosphere can be considered an extended root phenotype, a manifestation of the effects of plant genes on their environment inside and/or outside of the organism. Here, we review current understanding of how plants shape the rhizosphere and the benefits it confers to plant fitness. We discuss future research challenges and how applying their solutions in crops will enable us to harvest the benefits of the extended root phenotype.
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Affiliation(s)
- Carla de la Fuente Cantó
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
| | - Marie Simonin
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
- IRHS-UMR1345, Université d'Angers, INRAE, Institut Agro, SFR 4207 QuaSaV, 49071, Beaucouzé, France
| | - Eoghan King
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
| | - Lionel Moulin
- UMR IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
| | - Malcolm J Bennett
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Gabriel Castrillo
- Future Food Beacon of Excellence, School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Laurent Laplaze
- UMR DIADE, Université de Montpellier, Institut de Recherche pour le Développement (IRD), Montpellier, France
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes Associés aux Stress Environnementaux (LAPSE), Dakar, Senegal
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