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de Celis M, Fernández-Alonso MJ, Belda I, García C, Ochoa-Hueso R, Palomino J, Singh BK, Yin Y, Wang JT, Abdala-Roberts L, Alfaro FD, Angulo-Pérez D, Arthikala MK, Corwin J, Gui-Lan D, Hernandez-Lopez A, Nanjareddy K, Pasari B, Quijano-Medina T, Rivera DS, Shaaf S, Trivedi P, Yang Q, Zaady E, Zhu YG, Delgado-Baquerizo M, Milla R, García-Palacios P. The abundant fraction of soil microbiomes regulates the rhizosphere function in crop wild progenitors. Ecol Lett 2024; 27:e14462. [PMID: 39031813 DOI: 10.1111/ele.14462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Revised: 04/30/2024] [Accepted: 05/27/2024] [Indexed: 07/22/2024]
Abstract
The rhizosphere influence on the soil microbiome and function of crop wild progenitors (CWPs) remains virtually unknown, despite its relevance to develop microbiome-oriented tools in sustainable agriculture. Here, we quantified the rhizosphere influence-a comparison between rhizosphere and bulk soil samples-on bacterial, fungal, protists and invertebrate communities and on soil multifunctionality across nine CWPs at their sites of origin. Overall, rhizosphere influence was higher for abundant taxa across the four microbial groups and had a positive influence on rhizosphere soil organic C and nutrient contents compared to bulk soils. The rhizosphere influence on abundant soil microbiomes was more important for soil multifunctionality than rare taxa and environmental conditions. Our results are a starting point towards the use of CWPs for rhizosphere engineering in modern crops.
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Affiliation(s)
- Miguel de Celis
- Departamento de Suelo, Planta y Calidad Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - María José Fernández-Alonso
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
- Departamento de Geología y Geoquímica, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Ignacio Belda
- Department of Genetics, Physiology and Microbiology, Microbiology Unit, Faculty of Biology, Complutense University of Madrid, Madrid, Spain
| | - Carlos García
- Department of Soil and Water Conservation and Organic Waste Management, CEBAS-CSIC, Murcia, Spain
| | - Raúl Ochoa-Hueso
- Department of Biology, IVAGRO, University of Cádiz, Cádiz, Spain
| | - Javier Palomino
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Brajesh K Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Luis Abdala-Roberts
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Fernando D Alfaro
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Diego Angulo-Pérez
- Unidad de Recursos Naturales, Centro de Investigación Científica de Yucatán, A.C., Mérida, Yucatán, Mexico
| | - Manoj-Kumar Arthikala
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato, Mexico
| | - Jason Corwin
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Duan Gui-Lan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Antonio Hernandez-Lopez
- Escuela Nacional de Estudios Superiores Unidad León, Universidad Nacional Autónoma de México, Guanajuato, Mexico
| | - Kalpana Nanjareddy
- Ciencias Agrogenómicas, Escuela Nacional de Estudios Superiores Unidad León-Universidad Nacional Autónoma de México (UNAM), León, Guanajuato, Mexico
| | - Babak Pasari
- Department of Agronomy and Plant Breeding, Sanandaj Branch, Islamic Azad University, Sanandaj, Iran
| | - Teresa Quijano-Medina
- Departamento de Ecología Tropical, Universidad Autónoma de Yucatán, Mérida, Yucatán, Mexico
| | - Daniela S Rivera
- GEMA Center for Genomics, Ecology and Environment, Universidad Mayor, Santiago, Chile
| | - Salar Shaaf
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, Germany
| | - Pankaj Trivedi
- Microbiome Network and Department of Agricultural Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Qingwen Yang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Eli Zaady
- Department of Natural Resources, Agricultural Research Organization, Gilat Research Center, Institute of Plant Sciences, Mobile Post Negev, Israel
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
| | - Rubén Milla
- Area of Biodiversity and Conservation, Department of Biology and Geology, Physics and Inorganic Chemistry, Universidad Rey Juan Carlos, Móstoles, Spain
- Global Change Research Institute, Universidad Rey Juan Carlos, Móstoles, Spain
| | - Pablo García-Palacios
- Departamento de Suelo, Planta y Calidad Ambiental, Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
- Department of Plant and Microbial Biology, University of Zurich, Zurich, Switzerland
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Soldan R, Fusi M, Cardinale M, Homma F, Santos LG, Wenzl P, Bach-Pages M, Bitocchi E, Chacon Sanchez MI, Daffonchio D, Preston GM. Consistent effects of independent domestication events on the plant microbiota. Curr Biol 2024; 34:557-567.e4. [PMID: 38232731 DOI: 10.1016/j.cub.2023.12.056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 12/01/2023] [Accepted: 12/18/2023] [Indexed: 01/19/2024]
Abstract
The effect of plant domestication on plant-microbe interactions remains difficult to prove. In this study, we provide evidence of a domestication effect on the composition and abundance of the plant microbiota. We focused on the genus Phaseolus, which underwent four independent domestication events within two species (P. vulgaris and P. lunatus), providing multiple replicates of a process spanning thousands of years. We targeted Phaseolus seeds to identify a link between domesticated traits and bacterial community composition as Phaseolus seeds have been subject to large and consistent phenotypic changes during these independent domestication events. The seed bacterial communities of representative plant accessions from subpopulations descended from each domestication event were analyzed under controlled and field conditions. The results showed that independent domestication events led to similar seed bacterial community signatures in independently domesticated plant populations, which could be partially explained by selection for common domesticated plant phenotypes. Our results therefore provide evidence of a consistent effect of plant domestication on seed microbial community composition and abundance and offer avenues for applying knowledge of the impact of plant domestication on the plant microbiota to improve microbial applications in agriculture.
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Affiliation(s)
| | - Marco Fusi
- Center for Conservation and Restoration Science, Edinburgh Napier University, Edinburgh, UK
| | - Massimiliano Cardinale
- University of Salento, Department of Biological and Environmental Sciences and Technologies, Lecce, Italy
| | - Felix Homma
- University of Oxford, Department of Biology, Oxford, UK
| | - Luis Guillermo Santos
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | - Peter Wenzl
- The Alliance Biodiversity International and the International Center for Tropical Agriculture (CIAT), Palmira, Colombia
| | | | - Elena Bitocchi
- Dipartimento di Scienze Agrarie, Alimentari ed Ambientali, Università Politecnica delle Marche, Ancona, Italy
| | - Maria Isabel Chacon Sanchez
- Departamento de Agronomía, Facultad de Ciencias Agrarias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Daniele Daffonchio
- Red Sea Research Center (RSRC), 4700 King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Gail M Preston
- University of Oxford, Department of Biology, Oxford, UK.
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Andargie YE, Lee G, Jeong M, Tagele SB, Shin JH. Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere. FRONTIERS IN PLANT SCIENCE 2023; 14:1301698. [PMID: 38116158 PMCID: PMC10728675 DOI: 10.3389/fpls.2023.1301698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 11/20/2023] [Indexed: 12/21/2023]
Abstract
In a plant-microbe symbiosis, the host plant plays a key role in promoting the association of beneficial microbes and maintaining microbiome homeostasis through microbe-associated molecular patterns (MAMPs). The associated microbes provide an additional layer of protection for plant immunity and help in nutrient acquisition. Despite identical MAMPs in pathogens and commensals, the plant distinguishes between them and promotes the enrichment of beneficial ones while defending against the pathogens. The rhizosphere is a narrow zone of soil surrounding living plant roots. Hence, various biotic and abiotic factors are involved in shaping the rhizosphere microbiome responsible for pathogen suppression. Efforts have been devoted to modifying the composition and structure of the rhizosphere microbiome. Nevertheless, systemic manipulation of the rhizosphere microbiome has been challenging, and predicting the resultant microbiome structure after an introduced change is difficult. This is due to the involvement of various factors that determine microbiome assembly and result in an increased complexity of microbial networks. Thus, a comprehensive analysis of critical factors that influence microbiome assembly in the rhizosphere will enable scientists to design intervention techniques to reshape the rhizosphere microbiome structure and functions systematically. In this review, we give highlights on fundamental concepts in soil suppressiveness and concisely explore studies on how plants monitor microbiome assembly and homeostasis. We then emphasize key factors that govern pathogen-suppressive microbiome assembly. We discuss how pathogen infection enhances plant immunity by employing a cry-for-help strategy and examine how domestication wipes out defensive genes in plants experiencing domestication syndrome. Additionally, we provide insights into how nutrient availability and pH determine pathogen suppression in the rhizosphere. We finally highlight up-to-date endeavors in rhizosphere microbiome manipulation to gain valuable insights into potential strategies by which microbiome structure could be reshaped to promote pathogen-suppressive soil development.
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Affiliation(s)
- Yohannes Ebabuye Andargie
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Plant Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - GyuDae Lee
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Minsoo Jeong
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
| | - Setu Bazie Tagele
- Department of Microbiology and Plant Pathology, University of California, Riverside, Riverside, CA, United States
| | - Jae-Ho Shin
- Department of Applied Biosciences, Kyungpook National University, Daegu, Republic of Korea
- Department of Integrative Biology, Kyungpook National University, Daegu, Republic of Korea
- Next Generation Sequencing (NGS) Core Facility, Kyungpook National University, Daegu, Republic of Korea
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