Consistent Microbial Assembly in the Rhizosphere of Crop Wild Progenitors

ABSTRACT Aim Microbiome rewilding seeks to harness plant‐microbe interactions for sustainable agriculture, assuming that ancestral microbial partners have been lost during domestication and geographical spread. Designing microbiome rewilding strategies requires a quantitative and predictive understanding of the fundamental ecological processes—selection, dispersal, and drift—driving microbial assembly and persistence in the rhizosphere of crop wild progenitors (CWPs). Location Global. Time Period Present. Major Taxa Studied Rhizosphere bacteria and fungi. Methods Here, we leveraged a global survey of the CWPs of 10 major crops across their native habitats to assess the roles of selection, dispersal, and drift in shaping rhizosphere microbial communities. We combined compositional and phylogenetic turnover metrics with local network analyses to evaluate community assembly and structure in response to environmental gradients. Results We found host‐driven selection, reflected by low phylogenetic turnover at the whole‐tree level, but also selection driven by differences among individual plants, as indicated by high turnover among closely related taxa. The high level of compositional turnover found suggests dispersal limitations, which in the context of CWPs, may indicate host‐mediated filtering of external microbial taxa. The network structure was constant across CWPs; however, bacterial and fungal structures diverged, pointing to distinct community organisations. Bacterial communities presented higher modularity and lower clustering than fungal communities. Climate, especially seasonal temperature and precipitation, was the main driver of both bacterial and fungal structures. However, host identity best predicted bacterial structure, while NDVI, a proxy for vegetation status, better explained fungal patterns. Main Conclusions Bacterial and fungal communities are shaped by consistent assembly processes across CWPs, but their structures diverge. With the identification of the assembly processes driving microbiome composition in the rhizosphere of CWPs, this work paves the road to incorporate microbiome rewilding in the toolbox of sustainable agriculture.

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Publication Details

Journal
Global Ecology and Biogeography
Published
2026-03-27
DOI
https://doi.org/10.1111/geb.70228
Primary Topic
Plant-Microbe Interactions and Immunity
Type
article
Field-Weighted Citation Impact
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article

Consistent Microbial Assembly in the Rhizosphere of Crop Wild Progenitors

Pablo García‐Palacios, Daniela S. Rivera, Prerana Sarma, Ignacio Belda et al.
Global Ecology and Biogeography
Plant-Microbe Interactions and Immunity
article

Consistent Microbial Assembly in the Rhizosphere of Crop Wild Progenitors

Pablo García‐Palacios, Daniela S. Rivera, Prerana Sarma, Ignacio Belda, Teresa Quijano‐Medina, Miguel de Celis, Antonio Hernández‐López, Rubén Milla, Salar Shaaf, María Leo, Qin Yang, Jason Corwin, Luis Abdala‐Roberts, Kalpana Nanjareddy, Fernando D. Alfaro, Juan Gaitán, Danteswari Chalasani, Appa Rao Podile, Ji Wang, Yong‐Guan Zhu, Yue Yin, S. Chandra Nayaka, Diego Francisco Angulo, Pankaj Trivedi, Gui‐Lan Duan, Brajesh K. Singh, Eli Zaady, María José Fernández‐Alonso, Thanuku S. S. K. Patro, Manoj‐Kumar Arthikala, Babak Pasari, Carlos García
article en

Abstract

ABSTRACT Aim Microbiome rewilding seeks to harness plant‐microbe interactions for sustainable agriculture, assuming that ancestral microbial partners have been lost during domestication and geographical spread. Designing microbiome rewilding strategies requires a quantitative and predictive understanding of the fundamental ecological processes—selection, dispersal, and drift—driving microbial assembly and persistence in the rhizosphere of crop wild progenitors (CWPs). Location Global. Time Period Present. Major Taxa Studied Rhizosphere bacteria and fungi. Methods Here, we leveraged a global survey of the CWPs of 10 major crops across their native habitats to assess the roles of selection, dispersal, and drift in shaping rhizosphere microbial communities. We combined compositional and phylogenetic turnover metrics with local network analyses to evaluate community assembly and structure in response to environmental gradients. Results We found host‐driven selection, reflected by low phylogenetic turnover at the whole‐tree level, but also selection driven by differences among individual plants, as indicated by high turnover among closely related taxa. The high level of compositional turnover found suggests dispersal limitations, which in the context of CWPs, may indicate host‐mediated filtering of external microbial taxa. The network structure was constant across CWPs; however, bacterial and fungal structures diverged, pointing to distinct community organisations. Bacterial communities presented higher modularity and lower clustering than fungal communities. Climate, especially seasonal temperature and precipitation, was the main driver of both bacterial and fungal structures. However, host identity best predicted bacterial structure, while NDVI, a proxy for vegetation status, better explained fungal patterns. Main Conclusions Bacterial and fungal communities are shaped by consistent assembly processes across CWPs, but their structures diverge. With the identification of the assembly processes driving microbiome composition in the rhizosphere of CWPs, this work paves the road to incorporate microbiome rewilding in the toolbox of sustainable agriculture.

Global Ecology and BiogeographyVol. 35(4)
Universidad Mayor (CL), Universidad Complutense de Madrid (ES), Acharya N. G. Ranga Agricultural University (IN), University of Quintana Roo (MX), Sapir College (IL), National University of Luján (AR), Universidad Autónoma del Estado de México (MX), Universidad Rey Juan Carlos (ES), Chinese Academy of Sciences (CN), University of Zurich (CH), University of Mysore (IN), Autonomous University of Yucatán (MX), Islamic Azad University Sanandaj Branch (IR), University of Hyderabad (IN), Centro de Edafología y Biología Aplicada del Segura (ES), Institute of Urban Environment (CN), Leibniz-Institut für Pflanzengenetik und Kulturpflanzenforschung (IPK) (DE), Chinese Academy of Agricultural Sciences (CN), Instituto de Agricultura Sostenible (ES), Research Center for Eco-Environmental Sciences (CN), Institute of Crop Sciences (CN), Ministry of Agriculture and Rural Development (IL), Western Sydney University (AU), Universidad Autónoma de Madrid (ES), Universidad Nacional Autónoma de México (MX), Colorado State University (US)
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