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Gholizadeh S, Nemati I, Vestergård M, Barnes CJ, Kudjordjie EN, Nicolaisen M. Harnessing root-soil-microbiota interactions for drought-resilient cereals. Microbiol Res 2024; 283:127698. [PMID: 38537330 DOI: 10.1016/j.micres.2024.127698] [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: 01/16/2024] [Revised: 03/14/2024] [Accepted: 03/17/2024] [Indexed: 04/17/2024]
Abstract
Cereal plants form complex networks with their associated microbiome in the soil environment. A complex system including variations of numerous parameters of soil properties and host traits shapes the dynamics of cereal microbiota under drought. These multifaceted interactions can greatly affect carbon and nutrient cycling in soil and offer the potential to increase plant growth and fitness under drought conditions. Despite growing recognition of the importance of plant microbiota to agroecosystem functioning, harnessing the cereal root microbiota remains a significant challenge due to interacting and synergistic effects between root traits, soil properties, agricultural practices, and drought-related features. A better mechanistic understanding of root-soil-microbiota associations could lead to the development of novel strategies to improve cereal production under drought. In this review, we discuss the root-soil-microbiota interactions for improving the soil environment and host fitness under drought and suggest a roadmap for harnessing the benefits of these interactions for drought-resilient cereals. These methods include conservative trait-based approaches for the selection and breeding of plant genetic resources and manipulation of the soil environments.
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Affiliation(s)
- Somayeh Gholizadeh
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Iman Nemati
- Department of Plant Production and Genetics Engineering, Faculty of Agriculture and Natural Resources, University of Mohaghegh Ardabili, Ardabil, Iran
| | - Mette Vestergård
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Christopher James Barnes
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Enoch Narh Kudjordjie
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark
| | - Mogens Nicolaisen
- Faculty of Technical Sciences, Department of Agroecology, Aarhus University, Forsøgsvej 1, Slagelse 4200, Denmark.
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Li X, Zheng X, Yadav N, Saha S, Salama ES, Li X, Wang L, Jeon BH. Rational management of the plant microbiome for the Second Green Revolution. PLANT COMMUNICATIONS 2024; 5:100812. [PMID: 38213028 PMCID: PMC11009158 DOI: 10.1016/j.xplc.2024.100812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 11/06/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
The Green Revolution of the mid-20th century transformed agriculture worldwide and has resulted in environmental challenges. A new approach, the Second Green Revolution, seeks to enhance agricultural productivity while minimizing negative environmental impacts. Plant microbiomes play critical roles in plant growth and stress responses, and understanding plant-microbiome interactions is essential for developing sustainable agricultural practices that meet food security and safety challenges, which are among the United Nations Sustainable Development Goals. This review provides a comprehensive exploration of key deterministic processes crucial for developing microbiome management strategies, including the host effect, the facilitator effect, and microbe-microbe interactions. A hierarchical framework for plant microbiome modulation is proposed to bridge the gap between basic research and agricultural applications. This framework emphasizes three levels of modulation: single-strain, synthetic community, and in situ microbiome modulation. Overall, rational management of plant microbiomes has wide-ranging applications in agriculture and can potentially be a core technology for the Second Green Revolution.
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Affiliation(s)
- Xiaofang Li
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Xin Zheng
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Nikita Yadav
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea
| | - Shouvik Saha
- Natural Resources Research Institute, University of Minnesota Duluth, Hermantown, MN 55811, USA; Department of Biotechnology, Brainware University, Barasat, Kolkata 700125, West Bengal, India
| | - El-Sayed Salama
- Department of Occupational and Environmental Health, School of Public Health, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Xiangkai Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Science, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Likun Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China.
| | - Byong-Hun Jeon
- Department of Earth Resources and Environmental Engineering, Hanyang University, Seoul 04763, South Korea.
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Gruet C, Alaoui M, Gerin F, Prigent-Combaret C, Börner A, Muller D, Moënne-Loccoz Y. Genomic content of wheat has a higher influence than plant domestication status on the ability to interact with Pseudomonas plant growth-promoting rhizobacteria. PLANT, CELL & ENVIRONMENT 2023; 46:3933-3948. [PMID: 37614118 DOI: 10.1111/pce.14698] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/10/2023] [Accepted: 08/11/2023] [Indexed: 08/25/2023]
Abstract
Plant evolutionary history has had profound effects on belowground traits, which is likely to have impacted the ability to interact with microorganisms, but consequences on root colonization and gene expression by plant growth-promoting rhizobacteria (PGPR) remain poorly understood. Here, we tested the hypothesis that wheat genomic content and domestication are key factors determining the capacity for PGPR interaction. Thus, 331 wheat representatives from eight Triticum or Aegilops species were inoculated under standardized conditions with the generalist PGPR Pseudomonas ogarae F113, using an autofluorescent reporter system for monitoring F113 colonization and expression of phl genes coding for the auxinic inducing signal 2,4-diacetylphloroglucinol. The interaction with P. ogarae F113 was influenced by ploidy level, presence of genomes AA, BB, DD, and domestication. While root colonization was higher for hexaploid and tetraploid species, and phl expression level higher for hexaploid wheat, the diploid Ae. tauschii displayed higher phl induction rate (i.e., expression:colonisation ratio) on roots. However, a better potential of interaction with F113 (i.e., under non-stress gnotobiotic conditions) did not translate, after seed inoculation, into better performance of wheat landraces in non-sterile soil under drought. Overall, results showed that domestication and especially plant genomic content modulate the PGPR interaction potential of wheats.
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Affiliation(s)
- Cécile Gruet
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Maroua Alaoui
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Andreas Börner
- Genebank Department, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Seeland, OT Gatersleben, Germany
| | - Daniel Muller
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, Villeurbanne, France
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Schultz CR, Johnson M, Wallace JG. Effects of Inbreeding on Microbial Community Diversity of Zea mays. Microorganisms 2023; 11:microorganisms11040879. [PMID: 37110300 PMCID: PMC10145435 DOI: 10.3390/microorganisms11040879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 03/14/2023] [Accepted: 03/28/2023] [Indexed: 03/31/2023] Open
Abstract
Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.
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Rapeseed Domestication Affects the Diversity of Rhizosphere Microbiota. Microorganisms 2023; 11:microorganisms11030724. [PMID: 36985297 PMCID: PMC10056747 DOI: 10.3390/microorganisms11030724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/04/2023] [Accepted: 03/09/2023] [Indexed: 03/14/2023] Open
Abstract
Rhizosphere microbiota is important for plant growth and health. Domestication is a process to select suitable plants to satisfy the needs of humans, which may have great impacts on the interaction between the host and its rhizosphere microbiota. Rapeseed (Brassica napus) is an important oilseed crop derived from the hybridization between Brassica rapa and Brassica oleracea ~7500 years ago. However, variations in rhizosphere microbiota along with rapeseed domestication remain poorly understood. Here, we characterized the composition and structure of the rhizosphere microbiota among diverse rapeseed accessions, including ten B. napus, two B. rapa, and three B. oleracea accessions through bacterial 16S rRNA gene sequencing. B. napus exhibited a higher Shannon index and different bacterial relative abundance compared with its wild relatives in rhizosphere microbiota. Moreover, artificial synthetic B. napus lines G3D001 and No.2127 showed significantly different rhizosphere microbiota diversity and composition from other B. napus accessions and their ancestors. The core rhizosphere microbiota of B. napus and its wild relatives was also described. FAPROTAX annotation predicted that the synthetic B. napus lines had more abundant pathways related to nitrogen metabolism, and the co-occurrence network results demonstrated that Rhodoplanes acted as hub nodes to promote nitrogen metabolism in the synthetic B. napus lines. This study provides new insights into the impacts of rapeseed domestication on the diversity and community structure of rhizosphere microbiota, which may highlight the contribution of rhizosphere microbiota to plant health.
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Malacrinò A, Abdelfattah A, Belgacem I, Schena L. Plant genotype influence the structure of cereal seed fungal microbiome. Front Microbiol 2023; 13:1075399. [PMID: 36687609 PMCID: PMC9846234 DOI: 10.3389/fmicb.2022.1075399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 12/13/2022] [Indexed: 01/06/2023] Open
Abstract
Plant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, and whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon metagenomics, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute to fill the knowledge gap on the wheat seed microbiome assembly and, together with other studies, might contribute to understand how we can manipulate this process to improve agriculture sustainability.
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Affiliation(s)
- Antonino Malacrinò
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria,Leibniz-Institute for Agricultural Engineering Potsdam (ATB) and University of Potsdam, Potsdam, Germany,*Correspondence: Ahmed Abdelfattah, ✉
| | - Imen Belgacem
- Agrocampus Ouest, INRAE, Université de Rennes, IGEPP, Le Rheu, France
| | - Leonardo Schena
- Dipartimento di Agraria, Università Mediterranea di Reggio Calabria, Reggio Calabria, Italy
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Aswini K, Suman A, Sharma P, Singh PK, Gond S, Pathak D. Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity. FRONTIERS IN PLANT SCIENCE 2023; 14:1101818. [PMID: 37089648 PMCID: PMC10117849 DOI: 10.3389/fpls.2023.1101818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 03/10/2023] [Indexed: 05/03/2023]
Abstract
Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heatS (heat susceptible, GW322) and heatT (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heatS variety than in the heatT variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heatS variety, a greater number of isolates from the heatT variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heatT samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.
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Affiliation(s)
- Krishnan Aswini
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Archna Suman
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Archna Suman,
| | - Pushpendra Sharma
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Shrikant Gond
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Devashish Pathak
- Division of Microbiology, ICAR-Indian Agricultural Research Institute, New Delhi, India
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