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Yuan L, Zhao T, Yang J, Wu N, Zhang P, Zhang H, Xu T. Characteristics of the Perianthic Endophytic Fungal Communities of the Rare Horticultural Plant Lirianthe delavayi and Their Changes under Artificial Cultivation. Microorganisms 2024; 12:1491. [PMID: 39065259 PMCID: PMC11278761 DOI: 10.3390/microorganisms12071491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2024] [Revised: 07/18/2024] [Accepted: 07/19/2024] [Indexed: 07/28/2024] Open
Abstract
Flower endophytic fungi play a major role in plant reproduction, stress resistance, and growth and development. However, little is known about how artificial cultivation affects the endophytic fungal community found in the tepals of rare horticultural plants. In this research, we used high-throughput sequencing technology combined with bioinformatics analysis to reveal the endophytic fungal community of tepals in Lirianthe delavayi and the effects of artificial cultivation on the community composition and function of these plants, using tepals of L. delavayi from wild habitat, cultivated campus habitat, and cultivated field habitat as research objects. The results showed that the variety of endophytic fungi in the tepals of L. delavayi was abundant, with a total of 907 Amplicon sequencing variants (ASVs) obtained from all the samples, which were further classified into 4 phyla, 23 classes, 51 orders, 97 families, 156 genera, and 214 species. We also found that artificial cultivation had a significant impact on the community composition of endophytic fungi. Although there was no significant difference at the phylum level, with Ascomycota and Basidiomycota being the main phyla, there were significant differences in dominant and unique genera. Artificial cultivation has led to the addition of new pathogenic fungal genera, such as Phaeosphaeria, Botryosphaeria, and Paraconiothyrium, increasing the risk of disease in L. delavayi. In addition, the abundance of the endophytic fungus Rhodotorula, which is typical in plant reproductive organs, decreased. Artificial cultivation also altered the metabolic pathways of endophytic fungi, decreasing their ability to resist pests and diseases and reducing their ability to reproduce. A comparison of endophytic fungi in tepals and leaves revealed significant differences in community composition and changes in the endophytic diversity caused by artificial cultivation. To summarize, our results indicate that endophytic fungi in the tepals of L. delavayi mainly consist of pathogenic and saprophytic fungi. Simultaneously, artificial cultivation introduces a great number of pathogenic fungi that alter the metabolic pathways associated with plant resistance to disease and pests, as well as reproduction, which can increase the risk of plant disease and reduce plant reproductive capacity. Our study provides an important reference for the conservation and breeding of rare horticultural plants.
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Affiliation(s)
- Lang Yuan
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
| | - Tongxing Zhao
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
| | - Jing Yang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
| | - Nannan Wu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
| | - Pinzheng Zhang
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
| | - Hanbo Zhang
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming 650106, China
| | - Tao Xu
- School of Ecology and Environmental Science, Yunnan University, Kunming 650106, China (J.Y.)
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Li F, Lyu H, Li H, Xi K, Yi Y, Zhang Y. Domestication and Genetic Improvement Alter the Symbiotic Microbiome Structure and Function of Tomato Leaf and Fruit Pericarp. Microorganisms 2024; 12:1351. [PMID: 39065120 PMCID: PMC11279011 DOI: 10.3390/microorganisms12071351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 06/22/2024] [Accepted: 06/22/2024] [Indexed: 07/28/2024] Open
Abstract
Many studies have attempted to explore the changes in the structure and function of symbiotic microbiomes, as well as the underlying genetic mechanism during crop domestication. However, most of these studies have focused on crop root microbiomes, while those on leaf and fruit are rare. In this study, we generated a comprehensive dataset including the metagenomic (leaf) and metatranscriptomic (fruit pericarp in the orange stage) data of hundreds of germplasms from three tomato clades: Solanum pimpinellifolium (PIM), cherry tomato (S. lycopersicum var. cerasiforme) (CER), and S. lycopersicum group (BIG). We investigated the effect of domestication and improvement processes on the structure of the symbiotic microbiome of tomato leaf and fruit pericarp, as well as its genetic basis. We were able to obtain the composition of the symbiotic microbiome of tomato leaf and fruit pericarp, based on which the tomato clade (PIM, CER, or BIG) was predicted with high accuracy through machine learning methods. In the processes of tomato domestication and improvement, changes were observed in the relative abundance of specific bacterial taxa, Bacillus for example, in the tomato leaf and fruit pericarp symbiotic microbiomes, as well as in the function of these symbiotic microbiomes. In addition, SNP loci that were significantly associated with microbial species that are characteristic of tomato leaf were identified. Our results show that domestication and genetic improvement processes alter the symbiotic microbiome structure and function of tomato leaf and fruit pericarp. We propose that leaf and fruit microbiomes are more suitable for revealing changes in symbiotic microbiomes during the domestication process and the underlying genetic basis for these changes due to the exclusion of the influence of environmental factors such as soil types on the microbiome structure.
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Affiliation(s)
- Fei Li
- Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang 550001, China; (H.L.); (K.X.); (Y.Y.); (Y.Z.)
| | - Hongjun Lyu
- Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang 550001, China; (H.L.); (K.X.); (Y.Y.); (Y.Z.)
- Shandong Province Key Laboratory for Biology of Greenhouse Vegetables, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Shandong Branch of National Improvement Center for Vegetables, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Ministry of Agriculture and Rural Affairs, Jinan 250100, China
| | - Henan Li
- Shandong Province Key Laboratory for Biology of Greenhouse Vegetables, Institute of Vegetables, Shandong Academy of Agricultural Sciences, Shandong Branch of National Improvement Center for Vegetables, Huang-Huai-Hai Region Scientific Observation and Experimental Station of Vegetables, Ministry of Agriculture and Rural Affairs, Jinan 250100, China
| | - Kuanling Xi
- Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang 550001, China; (H.L.); (K.X.); (Y.Y.); (Y.Z.)
| | - Yin Yi
- Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang 550001, China; (H.L.); (K.X.); (Y.Y.); (Y.Z.)
| | - Yubin Zhang
- Key Laboratory of Biodiversity Conservation in Karst Mountain Area of Southwest of China, Forestry Ministry, School of Life Sciences, Guizhou Normal University, Guiyang 550001, China; (H.L.); (K.X.); (Y.Y.); (Y.Z.)
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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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Abdullaeva Y, Ratering S, Rosado-Porto D, Ambika Manirajan B, Glatt A, Schnell S, Cardinale M. Domestication caused taxonomical and functional shifts in the wheat rhizosphere microbiota, and weakened the natural bacterial biocontrol against fungal pathogens. Microbiol Res 2024; 281:127601. [PMID: 38218094 DOI: 10.1016/j.micres.2024.127601] [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: 11/12/2023] [Revised: 12/14/2023] [Accepted: 01/02/2024] [Indexed: 01/15/2024]
Abstract
Modern crops might have lost some of their functional traits, required for interacting with beneficial microbes, as a result of the genotypic/phenotypic modifications that occurred during domestication. Here, we studied the bacterial and fungal microbiota in the rhizosphere of two cultivated wheat species (Triticum aestivum and T. durum) and their respective ancestors (Aegilops tauschii and T. dicoccoides), in three experimental fields, by using metabarcoding of 16S rRNA genes and ITS2, coupled with co-occurrence network analysis. Moreover, the abundance of bacterial genes involved in N- and P-cycles was estimated by quantitative PCR, and urease, alkaline phosphatase and phosphomonoesterase activities were assessed by enzymatic tests. The relationships between microbiota and environmental metadata were tested by correlation analysis. The assemblage of core microbiota was affected by both site and plant species. No significant differences in the abundance of potential fungal pathogens between wild and cultivated wheat species were found; however, co-occurrence analysis showed more bacterial-fungal negative correlations in the wild species. Concerning functions, the nitrogen denitrification nirS gene was consistently more abundant in the rhizosphere of A. tauschii than T. aestivum. Urease activity was higher in the rhizosphere of each wild wheat species in at least two of the research locations. Several microbiota members, including potentially beneficial taxa such as Lysobacter and new taxa such as Blastocatellaceae, were found to be strongly correlated to rhizospheric soil metadata. Our results showed that a functional microbiome shift occurred as a result of wheat domestication. Notably, these changes also included the reduction of the natural biocontrol potential of rhizosphere-associated bacteria against pathogenic fungi, suggesting that domestication disrupted the equilibrium of plant-microbe relationships that had been established during million years of co-evolution.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - Andrea Glatt
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany.
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany; Department of Biological and Environmental Sciences and Technologies - DiSTeBA, University of Salento, Lecce, Italy.
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5
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Li J, Hou L, Zhang G, Cheng L, Liu Y. Comparative Analysis of Rhizosphere and Endosphere Fungal Communities in Healthy and Diseased Faba Bean Plants. J Fungi (Basel) 2024; 10:84. [PMID: 38276030 PMCID: PMC10817651 DOI: 10.3390/jof10010084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 01/17/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
This study used the ITS approach based on Illumina MiSeq sequencing to assess the endosphere and rhizosphere fungal communities in healthy and diseased faba bean plants. The findings indicate that the most predominant phyla in all samples were Ascomycota (49.89-99.56%) and Basidiomycota (0.33-25.78%). In healthy endosphere samples, Glomeromycota (0.08-1.17%) was the only predominant phylum. In diseased endosphere samples, Olpidiomycota (0.04-1.75%) was the only predominant phylum. At the genus level, Penicillium (0.47-35.21%) was more abundant in rhizosphere soil, while Paraphoma (3.48-91.16%) was predominant in the endosphere roots of faba bean plants. Significant differences were observed in the alpha diversity of rhizosphere samples from different germplasm resources (p < 0.05). The fungal community structures were clearly distinguished between rhizosphere and endosphere samples and between healthy and diseased endosphere samples (p < 0.05). Saccharomyces was significantly enriched in diseased endosphere samples, whereas Apiotrichum was enriched in healthy endosphere samples. Vishniacozyma and Phialophora were enriched in diseased rhizosphere samples, while Pseudogymnoascus was enriched in healthy rhizosphere samples. Diseased samples displayed more strongly correlated genera than healthy samples. Saprotrophs accounted for a larger proportion of the fungal microbes in rhizosphere soil than in endosphere roots. This study provides a better understanding of the composition and diversity of fungal communities in the rhizosphere and endosphere of faba bean plants as well as a theoretical guidance for future research on the prevention or control of faba bean root rot disease.
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Affiliation(s)
- Juan Li
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Lu Hou
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Gui Zhang
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Liang Cheng
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Yujiao Liu
- Qinghai Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (J.L.); (G.Z.); (L.C.)
- Key Laboratory of Agricultural Integrated Pest Management, Xining 810016, China
- Key Laboratory of Qinghai Tibetan Plateau Biotechnology, Ministry of Education, Qinghai University, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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Yan K, Lu DS, Ding CJ, Wang Y, Tian YR, Su XH, Dong YF, Wang YP. Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 908:168216. [PMID: 37923276 DOI: 10.1016/j.scitotenv.2023.168216] [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: 05/24/2023] [Revised: 10/27/2023] [Accepted: 10/28/2023] [Indexed: 11/07/2023]
Abstract
Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.
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Affiliation(s)
- Kun Yan
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - De Shan Lu
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Chang Jun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Yan Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Yong Ren Tian
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China
| | - Xiao Hua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | | | - Yan Ping Wang
- Key Laboratory of the State Forestry and Grassland Administration for the Cultivation of Forests in the Lower Reaches of the Yellow River, College of Forestry, Shandong Agricultural University, Tai'an 271018, China.
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Zeng Q, Zhao Y, Shen W, Han D, Yang M. Seed-to-Seed: Plant Core Vertically Transmitted Microbiota. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19255-19264. [PMID: 38044571 DOI: 10.1021/acs.jafc.3c07092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The plant core microbiota transmitted by seeds have been demonstrated to exist in seeds and adult plants of several crops for multiple generations. They are closely related to plants and are relatively conserved throughout evolution, domestication, and breeding. These microbiota play a vital role in the early stages of plant growth. However, information about their colonization routes, transmission pathways, and final fate remains fragmentary. This review delves into the concept of these microbiota, their colonization sources, transmission pathways, and how they change throughout plant evolution, domestication, and breeding, as well as their effects on plants, based on relevant literature. Finally, the significant potential of incorporating the practical application of seed-transmitted microbiota into plant microbial breeding is emphasized.
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Affiliation(s)
- Quan Zeng
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yang Zhao
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wei Shen
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mingming Yang
- College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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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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9
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Zhang L, Huang X, Tong B, Chen M, Huang L, Liu J. Composition, functional, and niche differentiation of fungal communities in the rhizosphere and root endosphere of Cinnamomum migao in southwestern China. J Appl Microbiol 2023; 134:lxad239. [PMID: 37935485 DOI: 10.1093/jambio/lxad239] [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: 04/04/2023] [Revised: 09/25/2023] [Accepted: 11/02/2023] [Indexed: 11/09/2023]
Abstract
AIMS Roots are key parts of plant material circulation and energy flow, creating two distinct niches for the plant microbiome, such as the rhizosphere and root endosphere, which interact to maintain plant growth and health. In this study, two niches of plant rhizosphere and root endosphere were selected to study the composition and differences of fungi communities in order to better understand how differences in the structure and function of plant fungi communities affect plant health. METHODS AND RESULTS The community structure, diversity, and ecological function of fungi in the rhizosphere and root endosphere of Cinnamomum migao were studied using high-throughput sequencing techniques, traditional culture methods, and the FUNGuild database. The results of the analysis of alpha diversity showed that the diversity of rhizosphere fungal communities in C. migao was much higher than that of root endosphere communities. Some similarities and differences were noted between the two niche fungal communities, and some fungi had niche preferences. Functional prediction results demonstrated that fungi in the rhizosphere and root endosphere adopt multiple trophic modes, mostly saprophytic fungi. CONCLUSIONS This study provided a basis for an in-depth understanding of the structural variation, niche differentiation, and function of plant root-related fungal microbiota. We believe that it could provide guidance on the subsequent development of beneficial fungi.
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Affiliation(s)
- Lan Zhang
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Xiaolong Huang
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Bingli Tong
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou 550025, China
| | - Meng Chen
- Guizhou Academy of Forestry, Guiyang, Guizhou 550005, China
| | - Luting Huang
- Xiangzhong Normal College for Preschool Education, Shaoyang, Hunan 422099, China
| | - Jiming Liu
- College of Forestry, Guizhou University, Guiyang, Guizhou 550025, China
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10
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [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] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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11
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Valente J, Gerin F, Mini A, Richard R, Le Gouis J, Prigent-Combaret C, Moënne-Loccoz Y. Symbiotic Variations among Wheat Genotypes and Detection of Quantitative Trait Loci for Molecular Interaction with Auxin-Producing Azospirillum PGPR. Microorganisms 2023; 11:1615. [PMID: 37375117 DOI: 10.3390/microorganisms11061615] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/13/2023] [Accepted: 06/17/2023] [Indexed: 06/29/2023] Open
Abstract
Crop varieties differ in their ability to interact with Plant Growth-Promoting Rhizobacteria (PGPR), but the genetic basis for these differences is unknown. This issue was addressed with the PGPR Azospirillum baldaniorum Sp245, using 187 wheat accessions. We screened the accessions based on the seedling colonization by the PGPR and the expression of the phenylpyruvate decarboxylase gene ppdC (for synthesis of the auxin indole-3-acetic acid), using gusA fusions. Then, the effects of the PGPR on the selected accessions stimulating Sp245 (or not) were compared in soil under stress. Finally, a genome-wide association approach was implemented to identify the quantitative trait loci (QTL) associated with PGPR interaction. Overall, the ancient genotypes were more effective than the modern genotypes for Azospirillum root colonization and ppdC expression. In non-sterile soil, A. baldaniorum Sp245 improved wheat performance for three of the four PGPR-stimulating genotypes and none of the four non-PGPR-stimulating genotypes. The genome-wide association did not identify any region for root colonization but revealed 22 regions spread on 11 wheat chromosomes for ppdC expression and/or ppdC induction rate. This is the first QTL study focusing on molecular interaction with PGPR bacteria. The molecular markers identified provide the possibility to improve the capacity of modern wheat genotypes to interact with Sp245, as well as, potentially, other Azospirillum strains.
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Affiliation(s)
- Jordan Valente
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Florence Gerin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Agathe Mini
- GDEC, INRAE, UCA, F-63000 Clermont-Ferrand, France
| | | | | | - Claire Prigent-Combaret
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
| | - Yvan Moënne-Loccoz
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, UMR5557 Ecologie Microbienne, 43 Bd du 11 Novembre 1918, F-69622 Villeurbanne, France
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12
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Che J, Wu Y, Yang H, Wang S, Wu W, Lyu L, Wang X, Li W. Root Niches of Blueberry Imprint Increasing Bacterial-Fungal Interkingdom Interactions along the Soil-Rhizosphere-Root Continuum. Microbiol Spectr 2023; 11:e0533322. [PMID: 37222589 PMCID: PMC10269492 DOI: 10.1128/spectrum.05333-22] [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: 12/28/2022] [Accepted: 05/10/2023] [Indexed: 05/25/2023] Open
Abstract
Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
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Affiliation(s)
- Jilu Che
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Hao Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Shaoyi Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Xiaomin Wang
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Nanjing, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
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13
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Balogun FO, Abdulsalam RA, Ojo AO, Cason E, Sabiu S. Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower ( Helianthus annus) Seeds. Microorganisms 2023; 11:microorganisms11040988. [PMID: 37110411 PMCID: PMC10146784 DOI: 10.3390/microorganisms11040988] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/01/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3-V4) regions of the rRNA operon. The oil contents ranged between 41-52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower.
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Affiliation(s)
- Fatai Oladunni Balogun
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | - Rukayat Abiola Abdulsalam
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
| | - Abidemi Oluranti Ojo
- Centre for Applied Food Sustainability and Biotechnology, Central University of Technology, Bloemfontein 9300, South Africa
| | - Errol Cason
- Department of Animal Science, University of the Free State, Bloemfontein 9300, South Africa
| | - Saheed Sabiu
- Department of Biotechnology and Food Science, Durban University of Technology, Durban 4000, South Africa
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14
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Yue H, Yue W, Jiao S, Kim H, Lee YH, Wei G, Song W, Shu D. Plant domestication shapes rhizosphere microbiome assembly and metabolic functions. MICROBIOME 2023; 11:70. [PMID: 37004105 PMCID: PMC10064753 DOI: 10.1186/s40168-023-01513-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 03/07/2023] [Indexed: 05/23/2023]
Abstract
BACKGROUND The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments. RESULTS Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status. CONCLUSIONS Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.
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Affiliation(s)
- Hong Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Wenjie Yue
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Shuo Jiao
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Xianyang, 712100, Shaanxi, China
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China
| | - Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826, Korea
| | - Gehong Wei
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Xianyang, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
| | - Weining Song
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Agronomy, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
| | - Duntao Shu
- Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, Yangling, Xianyang, 712100, Shaanxi, China.
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Yangling, Xianyang, 712100, Shaanxi, China.
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15
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Yin Y, Wang YF, Cui HL, Zhou R, Li L, Duan GL, Zhu YG. Distinctive Structure and Assembly of Phyllosphere Microbial Communities between Wild and Cultivated Rice. Microbiol Spectr 2023; 11:e0437122. [PMID: 36625666 PMCID: PMC9927517 DOI: 10.1128/spectrum.04371-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 12/16/2022] [Indexed: 01/11/2023] Open
Abstract
Wild rice has been demonstrated to possess enriched genetic diversity and multiple valuable traits involved in disease/pest resistance and abiotic stress tolerance, which provides a potential resource for sustainable agriculture. However, unlike the plant compartments such as rhizosphere, the structure and assembly of phyllosphere microbial communities of wild rice remain largely unexplored. Through amplicon sequencing, this study compared the phyllosphere bacterial and fungal communities of wild rice and its neighboring cultivated rice. The core phyllosphere microbial taxa of both wild and cultivated rice are dominated with Pantoea, Methylobacterium, Nigrospora, and Papiliotrema, which are potentially beneficial to rice growth and health. Compared to the cultivated rice, Methylobacterium, Sphingomonas, Phaeosphaeria, and Khuskia were significantly enriched in the wild rice phyllosphere. The potentially nitrogen-fixing Methylobacterium is the dominated wild-enriched microbe; Sphingomonas is the hub taxon of wild rice networks. In addition, the microbiota of wild rice was more governed by deterministic assembly with a more complicated and stable community network than the cultivated rice. Our study provides a list of the beneficial microbes in the wild rice phyllosphere and reveals the microbial divergence between wild rice and cultivated rice in the original habitats, which highlights the potential selective role of wild rice in recruiting specific microbiomes for enhancing crop performance and promoting sustainable food production. IMPORTANCE Plant microbiota are being considered a lever to increase the sustainability of food production under a changing climate. In particular, the microbiomes associated with ancestors of modern cultivars have the potential to support their domesticated cultivars. However, few efforts have been devoted to studying the biodiversity and functions of microbial communities in the native habitats of ancestors of modern crop species. This study provides a list of the beneficial microbes in the wild rice phyllosphere and explores the microbial interaction patterns and the functional profiles of wild rice. This information could be useful for the future utilization of the plant microbiome to enhance crop performance and sustainability, especially in the framework of sustainable agroecosystems.
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Affiliation(s)
- Yue Yin
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi-Fei Wang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Rui Zhou
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong-Guan Zhu
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
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16
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Liu Z, Michalet R, Wang C, Wang Y, Chen J, Cui H, Song H, Wang J, Yang Z, An L, Xiao S, Chen S. Contrasting effects of two phenotypes of an alpine cushion plant on understory species drive community assembly. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 859:160154. [PMID: 36375548 DOI: 10.1016/j.scitotenv.2022.160154] [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: 07/02/2022] [Revised: 10/24/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
In alpine systems, cushion plants act as foundation species by ameliorating local environmental conditions. Empirical studies indicate that contrasting phenotypes of alpine cushion species have different effects on understory plant species, either facilitative or competitive. Furthermore, dependent species within each community type might also exhibit different responses to each cushion phenotype, which can be clustered into several "response groups". Additionally, these species-groups specific responses to alpine cushion species phenotypes could alter community assembly. However, very few studies have assessed responses of dependent communities at species-group levels, in particular for both above- and below-ground communities. Here, we selected a loose and a tight phenotype of the alpine cushion species Thylacospermum caespitosum in two sites of northwest China, and use the relative intensity of interactions index to quantify cushion plant effects on subordinate communities of plants and soil fungi and bacteria. We assessed variations in responses of both above- and below-ground organisms to cushion plant effects at species-group level. Species-group level analyses showed that the effects of the phenotype varied among groups of each of the three community types, and different species-groups were composed by unique taxa. Additionally, we found that loose cushions enhanced stochastic processes in community assembly, for plants and soil fungi but not for soil bacteria. These variations of phenotypic effects on different species-group induced contrasting taxonomic composition between groups, and alter community assembly thereby. Our study highlights the occurrence of contrasting effects of two phenotypes of a foundation cushion plant on understory plants, soil fungi and bacteria community composition, but not necessarily on their richness. We also showed that assessing responses of understory species at the species-group level allows a more realistic and mechanistic understanding of biotic interactions both for above- and below-ground communities.
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Affiliation(s)
- Ziyang Liu
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Richard Michalet
- Environnements et Paléoenvironnements Océaniques et Continentaux, University of Bordeaux, Bordeaux, France
| | - Chenyue Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Yajun Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jingwei Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hanwen Cui
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Hongxian Song
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Jiajia Wang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Zi Yang
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Lizhe An
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Sa Xiao
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China
| | - Shuyan Chen
- Key Laboratory of Cell Activities and Stress Adaptations Ministry of Education, School of Life Sciences, Lanzhou University, Tianshui Road 222, Lanzhou, Gansu, People's Republic of China.
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17
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Zhang YL, Guo XJ, Huang X, Guo RJ, Lu XH, Li SD, Zhang H. The Co-Association of Enterobacteriaceae and Pseudomonas with Specific Resistant Cucumber against Fusarium Wilt Disease. BIOLOGY 2023; 12:biology12020143. [PMID: 36829422 PMCID: PMC9952826 DOI: 10.3390/biology12020143] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023]
Abstract
The root microbiota contributes to the plant's defense against stresses and pathogens. However, the co-association pattern of functional bacteria that improves plant resistance has not been interpreted clearly. Using Illumina high-throughput sequencing technology, the root bacterial community profiles of six cucumber cultivars with different resistance in response to the causative agent of cucumber Fusarium wilt (CFW), Fusarium oxysporum f. sp. cucumerinum (Foc), were analyzed. The principal coordinate analysis indicated that the interactions of the cultivars and pathogens drove the cucumber root bacterial communities (p = 0.001). The resistance-specific differential genera across the cultivars were identified, including Massilia in the resistant cultivars, unclassified Enterobacteriaceae in resistant CL11 and JY409, Pseudomonas in JY409, Cronobacter in moderately resistant ZN106, and unclassified Rhizobiaceae and Streptomyces in susceptible ZN6. The predominant root bacterium Massilia accounted for the relative abundance of up to 28.08-61.55%, but dramatically declined to 9.36% in Foc-inoculated susceptible ZN6. Pseudomonas ASV103 and ASV48 of Pseudomonadaceae and Cronobacter ASV162 of Enterobacteriaceae were consistently differential across the cultivars at the phylum, genus, and ASV levels. Using the culture-based method, antagonistic strains of Enterobacteriaceae with a high proportion of 51% were isolated. Furthermore, the bacterial complexes of Pantoea dispersa E318 + Pseudomonas koreensis Ps213 and Cronobacter spp. C1 + C7 reduced the disease index of CFW by 77.2% and 60.0% in the pot experiment, respectively. This study reveals the co-association of specific root bacteria with host plants and reveals insight into the suppressing mechanism of resistant cultivars against CFW disease by regulating the root microbiota.
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Affiliation(s)
- Yu-Lu Zhang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xiao-Jing Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Xin Huang
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
| | - Rong-Jun Guo
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence:
| | - Xiao-Hong Lu
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Shi-Dong Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Hao Zhang
- College of Plant Protection, Jilin Agricultural University, Changchun 130118, China
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18
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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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19
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Gutierrez A, Grillo MA. Effects of Domestication on Plant-Microbiome Interactions. PLANT & CELL PHYSIOLOGY 2022; 63:1654-1666. [PMID: 35876043 DOI: 10.1093/pcp/pcac108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2022] [Revised: 07/15/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
Through the process of domestication, selection is targeted on a limited number of plant traits that are typically associated with yield. As an unintended consequence, domesticated plants often perform poorly compared to their wild progenitors for a multitude of traits that were not under selection during domestication, including abiotic and biotic stress tolerance. Over the past decade, advances in sequencing technology have allowed for the rigorous characterization of host-associated microbial communities, termed the microbiome. It is now clear that nearly every conceivable plant interaction with the environment is mediated by interactions with the microbiome. For this reason, plant-microbiome interactions are an area of great promise for plant breeding and crop improvement. Here, we review the literature to assess the potential impact that domestication has had on plant-microbiome interactions and the current understanding of the genetic basis of microbiome variation to inform plant breeding efforts. Overall, we find limited evidence that domestication impacts the diversity of microbiomes, but domestication is often associated with shifts in the abundance and composition of microbial communities, including taxa of known functional significance. Moreover, genome-wide association studies and mutant analysis have not revealed a consistent set of core candidate genes or genetic pathways that confer variation in microbiomes across systems. However, such studies do implicate a consistent role for plant immunity, root traits, root and leaf exudates and cell wall integrity as key traits that control microbiome colonization and assembly. Therefore, selection on these key traits may pose the most immediate promise for enhancing plant-microbiome interactions through breeding.
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Affiliation(s)
- Andres Gutierrez
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
| | - Michael A Grillo
- Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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20
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Chang J, Tian L, Leite MFA, Sun Y, Shi S, Xu S, Wang J, Chen H, Chen D, Zhang J, Tian C, Kuramae EE. Nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the wild rice Oryza rufipogon core rhizomicrobiome. MICROBIOME 2022; 10:196. [PMID: 36419170 PMCID: PMC9682824 DOI: 10.1186/s40168-022-01360-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 08/31/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The assembly of the rhizomicrobiome, i.e., the microbiome in the soil adhering to the root, is influenced by soil conditions. Here, we investigated the core rhizomicrobiome of a wild plant species transplanted to an identical soil type with small differences in chemical factors and the impact of these soil chemistry differences on the core microbiome after long-term cultivation. We sampled three natural reserve populations of wild rice (i.e., in situ) and three populations of transplanted in situ wild rice grown ex situ for more than 40 years to determine the core wild rice rhizomicrobiome. RESULTS Generalized joint attribute modeling (GJAM) identified a total of 44 amplicon sequence variants (ASVs) composing the core wild rice rhizomicrobiome, including 35 bacterial ASVs belonging to the phyla Actinobacteria, Chloroflexi, Firmicutes, and Nitrospirae and 9 fungal ASVs belonging to the phyla Ascomycota, Basidiomycota, and Rozellomycota. Nine core bacterial ASVs belonging to the genera Haliangium, Anaeromyxobacter, Bradyrhizobium, and Bacillus were more abundant in the rhizosphere of ex situ wild rice than in the rhizosphere of in situ wild rice. The main ecological functions of the core microbiome were nitrogen fixation, manganese oxidation, aerobic chemoheterotrophy, chemoheterotrophy, and iron respiration, suggesting roles of the core rhizomicrobiome in improving nutrient resource acquisition for rice growth. The function of the core rhizosphere bacterial community was significantly (p < 0.05) shaped by electrical conductivity, total nitrogen, and available phosphorus present in the soil adhering to the roots. CONCLUSION We discovered that nitrogen, manganese, iron, and carbon resource acquisition are potential functions of the core rhizomicrobiome of the wild rice Oryza rufipogon. Our findings suggest that further potential utilization of the core rhizomicrobiome should consider the effects of soil properties on the abundances of different genera. Video Abstract.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Marcio F A Leite
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Hongping Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, 130102, Jilin, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB, Wageningen, the Netherlands.
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH, Utrecht, the Netherlands.
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21
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Jia W, Wang S, He X, Zhao X. Different factors drive the assembly of pine and Panax notoginseng-associated microbiomes in Panax notoginseng-pine agroforestry systems. Front Microbiol 2022; 13:1018989. [DOI: 10.3389/fmicb.2022.1018989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/24/2022] [Indexed: 11/15/2022] Open
Abstract
Land-use conversion affects the composition and assembly of plant-associated microbiomes, which in turn affects plant growth, development, and ecosystem functioning. However, agroforestry systems, as sustainable land types, have received little attention regarding the dynamics of different plant-associated microbes. In this study, we used high-throughput sequencing technology to analyze the assembly mechanisms and the driving factors of pine- and Panax notoginseng (P.n.)-associated microbiomes during the conversion of different pine forests (Pinus kesiya var. langbianensis and Pinus armandii) into P.n.-pine agroforestry systems. The results showed that the conversion of pure pine forest into P.n.-pine agroforestry systems significantly altered the diversity of pine-associated fungi rather than the community structure, and the community structure of P.n.-associated fungi rather than the diversity. Additionally, plant-associated fungi were more responsive to land-use change than bacteria. Main effect analysis revealed that compartment rather than genotype was the driving factor of pine- and P.n.-associated microbiomes, but P.n. cultivation also significantly affected the assembly of pine-associated microbiomes. In addition, there was a transfer of P.n. endophytes to pine trees in agroforestry systems and the beneficial microbiomes (Massilia, Marmoricola, Herbaspirillum, etc.) were enlarged in pine roots. Therefore, the diversity of the assembly mechanisms of P.n.- and pine-associated microbiomes played an important role in the P.n.--pine agroforestry systems and were the basis for the sustainable development of the P.n.--pine agroforestry systems.
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22
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Nerva L, Sandrini M, Moffa L, Velasco R, Balestrini R, Chitarra W. Breeding toward improved ecological plant-microbiome interactions. TRENDS IN PLANT SCIENCE 2022; 27:1134-1143. [PMID: 35803843 DOI: 10.1016/j.tplants.2022.06.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Revised: 06/04/2022] [Accepted: 06/09/2022] [Indexed: 06/15/2023]
Abstract
Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.
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Affiliation(s)
- Luca Nerva
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
| | - Marco Sandrini
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Loredana Moffa
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; University of Udine, Department of Agricultural, Food, Environmental and Animal Sciences, Via delle Scienze 206, 33100, Udine, (UD), Italy
| | - Riccardo Velasco
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy
| | - Raffaella Balestrini
- National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy.
| | - Walter Chitarra
- Research Centre for Viticulture and Enology, Council for Agricultural Research and Economics (CREA-VE), Via XXVIII Aprile 26, 31015 Conegliano, (TV), Italy; National Research Council of Italy - Institute for Sustainable Plant Protection (CNR-IPSP), Strada delle Cacce, 73, 10135 Torino (TO), Italy
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23
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Chang J, van Veen JA, Tian C, Kuramae EE. A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 842:156706. [PMID: 35724776 DOI: 10.1016/j.scitotenv.2022.156706] [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: 01/22/2022] [Revised: 06/10/2022] [Accepted: 06/11/2022] [Indexed: 06/15/2023]
Abstract
The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China.
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, 6708 PB Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, 3584 CH Utrecht, the Netherlands.
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24
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Jacquiod S, Raynaud T, Pimet E, Ducourtieux C, Casieri L, Wipf D, Blouin M. Wheat Rhizosphere Microbiota Respond to Changes in Plant Genotype, Chemical Inputs, and Plant Phenotypic Plasticity. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.903008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Modern wheat varieties that were selected since the Green Revolution are generally grown with synthetic chemical inputs, and ancient varieties released before1960 without. Thus, when changes occur in rhizosphere microbiota structure, it is not possible to distinguish if they are due to (i) changes in wheat genotypes by breeding, (ii) modifications of the environment via synthetic chemical inputs, or (iii) phenotypic plasticity, the interaction between wheat genotype and the environment. Using a crossed factorial design in the field, we evaluated the effects of either modern or ancient wheat varieties grown with or without chemical inputs (a N fertilizer, a fungicide, and an herbicide) on “microbiome as a phenotype.” We analyzed the rhizosphere microbiota by bacterial and fungal amplicon sequencing, coupled with microscope observations of mycorrhizal associations. We found that plant genotype and phenotypic plasticity had the most influence on rhizosphere microbiota, whereas inputs had only marginal effects. Phenotypic plasticity was particularly important in explaining diversity variations in bacteria and fungi but had no impact on the mycorrhizal association. Our results show an interest in considering the interaction between wheat genotype and the environment in breeding programs, by focusing on genes involved in the phenotypic plasticity of plant-microbe interactions.
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25
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Medina-Paz F, Herrera-Estrella L, Heil M. All Set before Flowering: A 16S Gene Amplicon-Based Analysis of the Root Microbiome Recruited by Common Bean ( Phaseolus vulgaris) in Its Centre of Domestication. PLANTS (BASEL, SWITZERLAND) 2022; 11:1631. [PMID: 35807585 PMCID: PMC9269403 DOI: 10.3390/plants11131631] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 04/18/2022] [Accepted: 04/27/2022] [Indexed: 06/15/2023]
Abstract
Plant roots recruit most prokaryotic members of their root microbiota from the locally available inoculum, but knowledge on the contribution of native microorganisms to the root microbiota of crops in native versus non-native areas remains scarce. We grew common bean (Phaseolus vulgaris) at a field site in its centre of domestication to characterise rhizosphere and endosphere bacterial communities at the vegetative, flowering, and pod filling stage. 16S r RNA gene amplicon sequencing of ten samples yielded 9,401,757 reads, of which 8,344,070 were assigned to 17,352 operational taxonomic units (OTUs). Rhizosphere communities were four times more diverse than in the endosphere and dominated by Actinobacteria, Bacteroidetes, Crenarchaeota, and Proteobacteria (endosphere: 99% Proteobacteria). We also detected high abundances of Gemmatimonadetes (6%), Chloroflexi (4%), and the archaeal phylum Thaumarchaeota (Candidatus Nitrososphaera: 11.5%): taxa less frequently reported from common bean rhizosphere. Among 154 OTUs with different abundances between vegetative and flowering stage, we detected increased read numbers of Chryseobacterium in the endosphere and a 40-fold increase in the abundances of OTUs classified as Rhizobium and Aeromonas (equivalent to 1.5% and over 6% of all reads in the rhizosphere). Our results indicate that bean recruits specific taxa into its microbiome when growing 'at home'.
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Affiliation(s)
- Francisco Medina-Paz
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
| | - Luis Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad de Genómica Avanzada, Irapuato 36824, GTO, Mexico; or
- Institute of Genomics for Crop Abiotic Stress Tolerance, Texas Tech University, Lubbock, TX 79424, USA
| | - Martin Heil
- Laboratorio de Ecología de Plantas, Departamento de Ingeniería Genética, Centro de Investigación y de Estudios Avanzados (CINVESTAV)—Unidad Irapuato, Irapuato 36824, GTO, Mexico;
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26
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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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27
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Abdelfattah A, Tack AJM, Wasserman B, Liu J, Berg G, Norelli J, Droby S, Wisniewski M. Evidence for host-microbiome co-evolution in apple. THE NEW PHYTOLOGIST 2022; 234:2088-2100. [PMID: 34823272 PMCID: PMC9299473 DOI: 10.1111/nph.17820] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 10/18/2021] [Indexed: 05/07/2023]
Abstract
Plants evolved in association with a diverse community of microorganisms. The effect of plant phylogeny and domestication on host-microbiome co-evolutionary dynamics are poorly understood. Here we examined the effect of domestication and plant lineage on the composition of the endophytic microbiome of 11 Malus species, representing three major groups: domesticated apple (M. domestica), wild apple progenitors, and wild Malus species. The endophytic community of M. domestica and its wild progenitors showed higher microbial diversity and abundance than wild Malus species. Heirloom and modern cultivars harbored a distinct community composition, though the difference was not significant. A community-wide Bayesian model revealed that the endophytic microbiome of domesticated apple is an admixture of its wild progenitors, with clear evidence for microbiome introgression, especially for the bacterial community. We observed a significant correlation between the evolutionary distance of Malus species and their microbiome. This study supports co-evolution between Malus species and their microbiome during domestication. This finding has major implications for future breeding programs and our understanding of the evolution of plants and their microbiomes.
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Affiliation(s)
- Ahmed Abdelfattah
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
| | - Ayco J. M. Tack
- Department of Ecology, Environment and Plant SciencesStockholm UniversitySvante Arrhenius väg 20AStockholmSE‐106 91Sweden
| | - Birgit Wasserman
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
| | - Jia Liu
- Chongqing Key Laboratory of Economic Plant BiotechnologyCollege of Landscape Architecture and Life SciencesChongqing University of Arts and SciencesYongchuanChongquing402160China
| | - Gabriele Berg
- Institute of Environmental BiotechnologyGraz University of TechnologyPetersgasse 12Graz8010Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB)Max‐Eyth Allee 10014469PotsdamGermany
- Institute for Biochemistry and BiologyUniversity of Postdam14476Potsdam OT GolmGermany
| | - John Norelli
- Appalachian Fruit Research StationUnited States Department of Agriculture – Agricultural Research ServiceKearneysvilleWV25430USA
| | - Samir Droby
- Department of Postharvest ScienceAgricultural Research OrganizationThe Volcani InstitutePO Box 15159Rishon LeZion7505101Israel
| | - Michael Wisniewski
- Department of Biological SciencesVirginia Polytechnic Institute and State University220 Ag Quad LnBlacksburgVA24061USA
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Fréville H, Montazeaud G, Forst E, David J, papa R, Tenaillon MI. Shift in beneficial interactions during crop evolution. Evol Appl 2022; 15:905-918. [PMID: 35782010 PMCID: PMC9234679 DOI: 10.1111/eva.13390] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 03/30/2022] [Accepted: 04/22/2022] [Indexed: 11/30/2022] Open
Abstract
Plant domestication can be viewed as a form of co‐evolved interspecific mutualism between humans and crops for the benefit of the two partners. Here, we ask how this plant–human mutualism has, in turn, impacted beneficial interactions within crop species, between crop species, and between crops and their associated microbial partners. We focus on beneficial interactions resulting from three main mechanisms that can be promoted by manipulating genetic diversity in agrosystems: niche partitioning, facilitation, and kin selection. We show that a combination of factors has impacted either directly or indirectly plant–plant interactions during domestication and breeding, with a trend toward reduced benefits arising from niche partitioning and facilitation. Such factors include marked decrease of molecular and functional diversity of crops and other organisms present in the agroecosystem, mass selection, and increased use of chemical inputs. For example, the latter has likely contributed to the relaxation of selection pressures on nutrient‐mobilizing traits such as those associated to root exudation and plant nutrient exchanges via microbial partners. In contrast, we show that beneficial interactions arising from kin selection have likely been promoted since the advent of modern breeding. We highlight several issues that need further investigation such as whether crop phenotypic plasticity has evolved and could trigger beneficial interactions in crops, and whether human‐mediated selection has impacted cooperation via kin recognition. Finally, we discuss how plant breeding and agricultural practices can help promoting beneficial interactions within and between species in the context of agroecology where the mobilization of diversity and complexity of crop interactions is viewed as a keystone of agroecosystem sustainability.
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Affiliation(s)
- Hélène Fréville
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier France
| | - Germain Montazeaud
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier France
- Department of Ecology and Evolution University of Lausanne 1015 Lausanne Switzerland
| | - Emma Forst
- Department of Agricultural, Food and Environmental Sciences Università Politecnica delle Marche Ancona Italy
| | - Jacques David
- AGAP, Univ Montpellier, CIRAD, INRAE, Institut Agro Montpellier France
| | - Roberto papa
- Department of Agricultural, Food and Environmental Sciences Università Politecnica delle Marche Ancona Italy
| | - Maud I. Tenaillon
- Génétique Quantitative et Evolution – Le Moulon Université Paris‐Saclay INRAE CNRS AgroParisTech 91190 Gif‐sur‐Yvette France
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Tamošiūnė I, Andriūnaitė E, Vinskienė J, Stanys V, Rugienius R, Baniulis D. Enduring Effect of Antibiotic Timentin Treatment on Tobacco In Vitro Shoot Growth and Microbiome Diversity. PLANTS (BASEL, SWITZERLAND) 2022; 11:832. [PMID: 35336713 PMCID: PMC8954828 DOI: 10.3390/plants11060832] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 06/14/2023]
Abstract
Plant in vitro cultures initiated from surface-sterilized explants often harbor complex microbial communities. Antibiotics are commonly used to decontaminate plant tissue culture or during genetic transformation; however, the effect of antibiotic treatment on the diversity of indigenous microbial populations and the consequences on the performance of tissue culture is not completely understood. Therefore, the aim of this study was to assess the effect of antibiotic treatment on the growth and stress level of tobacco (Nicotiana tabacum L.) shoots in vitro as well as the composition of the plant-associated microbiome. The study revealed that shoot cultivation on a medium supplemented with 250 mg L-1 timentin resulted in 29 ± 4% reduced biomass accumulation and a 1.2-1.6-fold higher level of oxidative stress injury compared to the control samples. Moreover, the growth properties of shoots were only partially restored after transfer to a medium without the antibiotic. Microbiome analysis of the shoot samples using multivariable region-based 16S rRNA gene sequencing revealed a diverse microbial community in the control tobacco shoots, including 59 bacterial families; however, it was largely dominated by Mycobacteriaceae. Antibiotic treatment resulted in a decline in microbial diversity (the number of families was reduced 4.5-fold) and increased domination by the Mycobacteriaceae family. These results imply that the diversity of the plant-associated microbiome might represent a significant factor contributing to the efficient propagation of in vitro tissue culture.
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Wassermann B, Abdelfattah A, Müller H, Korsten L, Berg G. The microbiome and resistome of apple fruits alter in the post-harvest period. ENVIRONMENTAL MICROBIOME 2022; 17:10. [PMID: 35256002 PMCID: PMC8900306 DOI: 10.1186/s40793-022-00402-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 02/06/2022] [Indexed: 05/13/2023]
Abstract
BACKGROUND A detailed understanding of antimicrobial resistance trends among all human-related environments is key to combat global health threats. In food science, however, the resistome is still little considered. Here, we studied the apple microbiome and resistome from different cultivars (Royal Gala and Braeburn) and sources (freshly harvested in South Africa and exported apples in Austrian supermarkets) by metagenomic approaches, genome reconstruction and isolate sequencing. RESULTS All fruits harbor an indigenous, versatile resistome composed of 132 antimicrobial resistance genes (ARGs) encoding for 19 different antibiotic classes. ARGs are partially of clinical relevance and plasmid-encoded; however, their abundance within the metagenomes is very low (≤ 0.03%). Post-harvest, after intercontinental transport, the apple microbiome and resistome was significantly changed independently of the cultivar. In comparison to fresh apples, the post-harvest microbiome is characterized by higher abundance of Enterobacteriales, and a more diversified pool of ARGs, especially associated with multidrug resistance, as well as quinolone, rifampicin, fosfomycin and aminoglycoside resistance. The association of ARGs with metagenome-assembled genomes (MAGs) suggests resistance interconnectivity within the microbiome. Bacterial isolates of the phyla Gammaproteobacteria, Alphaproteobacteria and Actinobacteria served as representatives actively possessing multidrug resistance and ARGs were confirmed by genome sequencing. CONCLUSION Our results revealed intrinsic and potentially acquired antimicrobial resistance in apples and strengthen the argument that all plant microbiomes harbor diverse resistance features. Although the apple resistome appears comparatively inconspicuous, we identified storage and transport as potential risk parameters to distribute AMR globally and highlight the need for surveillance of resistance emergence along complex food chains.
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Affiliation(s)
- Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
| | - Lise Korsten
- Department of Plant and Soil Sciences, University of Pretoria, Pretoria, Republic of South Africa
- DSI-NRF Centre of Excellence in Food Security, Pretoria, Republic of South Africa
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010 Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
- Institute for Biochemistry and Biology, University of Postdam, 14476 Potsdam OT Golm, Germany
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31
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Muratova AY, Zelenova NA, Sungurtseva IY, Gorelova SV, Kolbas AP, Pleshakova YV. Comparative Study of the Rhizospheric Microflora of Sunflower Cultivars of Helianthus annuus (Asteraceae, Magnoliópsida) Grown on Soils with Anthropogenic Polyelemental Anomalies. BIOL BULL+ 2022. [DOI: 10.1134/s1062359021100198] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Abdullaeva Y, Ratering S, Ambika Manirajan B, Rosado-Porto D, Schnell S, Cardinale M. Domestication Impacts the Wheat-Associated Microbiota and the Rhizosphere Colonization by Seed- and Soil-Originated Microbiomes, Across Different Fields. FRONTIERS IN PLANT SCIENCE 2022; 12:806915. [PMID: 35095978 PMCID: PMC8789879 DOI: 10.3389/fpls.2021.806915] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 12/13/2021] [Indexed: 05/17/2023]
Abstract
The seed-transmitted microorganisms and the microbiome of the soil in which the plant grows are major drivers of the rhizosphere microbiome, a crucial component of the plant holobiont. The seed-borne microbiome can be even coevolved with the host plant as a result of adaptation and vertical transmission over generations. The reduced genome diversity and crossing events during domestication might have influenced plant traits that are important for root colonization by seed-borne microbes and also rhizosphere recruitment of microbes from the bulk soil. However, the impact of the breeding on seed-transmitted microbiome composition and the plant ability of microbiome selection from the soil remain unknown. Here, we analyzed both endorhiza and rhizosphere microbiome of two couples of genetically related wild and cultivated wheat species (Aegilops tauschii/Triticum aestivum and T. dicoccoides/T. durum) grown in three locations, using 16S rRNA gene and ITS2 metabarcoding, to assess the relative contribution of seed-borne and soil-derived microbes to the assemblage of the rhizosphere microbiome. We found that more bacterial and fungal ASVs are transmitted from seed to the endosphere of all species compared with the rhizosphere, and these transmitted ASVs were species-specific regardless of location. Only in one location, more microbial seed transmission occurred also in the rhizosphere of A. tauschii compared with other species. Concerning soil-derived microbiome, the most distinct microbial genera occurred in the rhizosphere of A. tauschii compared with other species in all locations. The rhizosphere of genetically connected wheat species was enriched with similar taxa, differently between locations. Our results demonstrate that host plant criteria for soil bank's and seed-originated microbiome recruitment depend on both plants' genotype and availability of microorganisms in a particular environment. This study also provides indications of coevolution between the host plant and its associated microbiome resulting from the vertical transmission of seed-originated taxa.
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Affiliation(s)
| | - Stefan Ratering
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | | | - David Rosado-Porto
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Sylvia Schnell
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
| | - Massimiliano Cardinale
- Institute of Applied Microbiology, Justus-Liebig-University, Giessen, Germany
- Department of Biological and Environmental Sciences and Technologies – DiSTeBA, University of Salento, Lecce, Italy
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Tian L, Chang J, Shi S, Ji L, Zhang J, Sun Y, Li X, Li X, Xie H, Cai Y, Chen D, Wang J, van Veen JA, Kuramae EE, Tran LSP, Tian C. Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 803:150131. [PMID: 34788940 DOI: 10.1016/j.scitotenv.2021.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 06/28/2021] [Accepted: 08/31/2021] [Indexed: 06/13/2023]
Abstract
Microbial communities from rhizosphere (rhizomicrobiomes) have been significantly impacted by domestication as evidenced by a comparison of the rhizomicrobiomes of wild and related cultivated rice accessions. While there have been many published studies focusing on the structure of the rhizomicrobiome, studies comparing the functional traits of the microbial communities in the rhizospheres of wild rice and cultivated rice accessions are not yet available. In this study, we used metagenomic data from experimental rice plots to analyze the potential functional traits of the microbial communities in the rhizospheres of wild rice accessions originated from Africa and Asia in comparison with their related cultivated rice accessions. The functional potential of rhizosphere microbial communities involved in alanine, aspartate and glutamate metabolism, methane metabolism, carbon fixation pathways, citrate cycle (TCA cycle), pyruvate metabolism and lipopolysaccharide biosynthesis pathways were found to be enriched in the rhizomicrobiomes of wild rice accessions. Notably, methane metabolism in the rhizomicrobiomes of wild and cultivated rice accessions clearly differed. Key enzymes involved in methane production and utilization were overrepresented in the rhizomicrobiome samples obtained from wild rice accessions, suggesting that the rhizomicrobiomes of wild rice maintain a different ecological balance for methane production and utilization compared with those of the related cultivated rice accessions. A novel assessment of the impact of rice domestication on the primary metabolic pathways associated with microbial taxa in the rhizomicrobiomes was performed. Results indicated a strong impact of rice domestication on methane metabolism; a process that represents a critical function of the rhizosphere microbial community of rice. The findings of this study provide important information for future breeding of rice varieties with reduced methane emission during cultivation for sustainable agriculture.
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Affiliation(s)
- Lei Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Jingjing Chang
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China; Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands
| | - Shaohua Shi
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Li Ji
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jianfeng Zhang
- College of Life Science, Jilin Agricultural University, Changchun, Jilin, China
| | - Yu Sun
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiaojie Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Xiujun Li
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China
| | - Hongwei Xie
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Yaohui Cai
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Dazhou Chen
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Jilin Wang
- Jiangxi Super-rice Research and Development Center, National Engineering Laboratory for Rice, Nanchang, China
| | - Johannes A van Veen
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands
| | - Eiko E Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, the Netherlands; Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, the Netherlands.
| | - Lam-Son Phan Tran
- Institute of Research and Development, Duy Tan University, Da Nang 550000, Viet Nam; Institute of Genomics for Crop Abiotic Stress Tolerance, Department of Plant and Soil Science, Texas Tech University, TX 79409, USA.
| | - Chunjie Tian
- Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin 130102, China.
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Mofini MT, Diedhiou AG, Simonin M, Dondjou DT, Pignoly S, Ndiaye C, Min D, Vigouroux Y, Laplaze L, Kane A. Cultivated and wild pearl millet display contrasting patterns of abundance and co-occurrence in their root mycobiome. Sci Rep 2022; 12:207. [PMID: 34997057 PMCID: PMC8741948 DOI: 10.1038/s41598-021-04097-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Accepted: 12/15/2021] [Indexed: 11/08/2022] Open
Abstract
Fungal communities associated with roots play a key role in nutrient uptake and in mitigating the abiotic and biotic stress of their host. In this study, we characterized the roots mycobiome of wild and cultivated pearl millet [Pennisetum glaucum (L.) R. Br., synonym: Cenchrus americanus (L.) Morrone] in three agro-ecological areas of Senegal following a rainfall gradient. We hypothesized that wild pearl millet could serve as a reservoir of endophytes for cultivated pearl millet. We therefore analyzed the soil factors influencing fungal community structure and whether cultivated and wild millet shared the same fungal communities. The fungal communities associated with pearl millet were significantly structured according to sites and plant type (wild vs cultivated). Besides, soil pH and phosphorus were the main factors influencing the fungal community structure. We observed a higher fungal diversity in cultivated compared to wild pearl millet. Interestingly, we detected higher relative abundance of putative pathotrophs, especially plant pathogen, in cultivated than in wild millet in semi-arid and semi-humid zones, and higher relative abundance of saprotrophs in wild millet in arid and semi-humid zones. A network analysis based on taxa co-occurrence patterns in the core mycobiome revealed that cultivated millet and wild relatives had dissimilar groups of hub taxa. The identification of the core mycobiome and hub taxa of cultivated and wild pearl millet could be an important step in developing microbiome engineering approaches for more sustainable management practices in pearl millet agroecosystems.
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Affiliation(s)
- Marie-Thérèse Mofini
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), BP 5005, Dakar Fann, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Abdala G Diedhiou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), BP 5005, Dakar Fann, Senegal.
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal.
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal.
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal.
| | - Marie Simonin
- IPME, IRD, Cirad, Université de Montpellier, Montpellier, France
- Université d'Angers, Institut Agro, INRAE, IRHS, SFR 4207 QuaSaV, 49000, Angers, France
| | - Donald Tchouomo Dondjou
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), BP 5005, Dakar Fann, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal
- Centre d'Etude Régional pour l'Amélioration de l'Adaptation à la Sécheresse (CERAAS), Institut Sénégalais de Recherches Agricoles (ISRA), Route de Khombole, Thiès, Sénégal
| | - Sarah Pignoly
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- DIADE, Université de Montpellier, IRD, Cirad, 911 Avenue Agropolis, 34394, Montpellier cedex 5, France
| | - Cheikh Ndiaye
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), BP 5005, Dakar Fann, Senegal
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal
| | - Doohong Min
- Department of Agronomy, Kansas State University, Manhattan, KS, USA
| | - Yves Vigouroux
- DIADE, Université de Montpellier, IRD, Cirad, 911 Avenue Agropolis, 34394, Montpellier cedex 5, France
| | - Laurent Laplaze
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal.
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal.
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal.
- DIADE, Université de Montpellier, IRD, Cirad, 911 Avenue Agropolis, 34394, Montpellier cedex 5, France.
| | - Aboubacry Kane
- Département de Biologie Végétale, Faculté des Sciences et Techniques, Université Cheikh Anta Diop (UCAD), BP 5005, Dakar Fann, Senegal.
- Laboratoire Mixte International Adaptation des Plantes et Microorganismes associés aux Stress Environnementaux (LAPSE), Centre de recherche de Bel-Air, Dakar, Sénégal.
- Laboratoire Commun de Microbiologie (LCM), Centre de Recherche de Bel-Air, Dakar, Sénégal.
- Centre d'Excellence Africain en Agriculture pour la Sécurité Alimentaire et Nutritionnelle (CEA-AGRISAN), UCAD, Dakar, Sénégal.
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Liu J, Abdelfattah A, Wasserman B, Wisniewski M, Droby S, Fazio G, Mazzola M, Wu X. Contrasting effects of genotype and root size on the fungal and bacterial communities associated with apple rootstocks. HORTICULTURE RESEARCH 2022; 9:6511261. [PMID: 35043188 PMCID: PMC8769040 DOI: 10.1093/hr/uhab013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/17/2021] [Accepted: 09/25/2021] [Indexed: 05/04/2023]
Abstract
The endophytic microbiome of plants is believed to have a significant impact on its physiology and disease resistance, however, the role of host genotype in determining the composition of the endophytic microbiome of apple root systems remains an open question that has important implications for defining breeding objectives. In the current study, the bacterial and fungal microbiota associated with four different apple rootstocks planted in April, 2018 in the same soil environment and harvested in May, 2019 were evaluated to determine the role of genotype on the composition of both the bacterial and fungal communities. Results demonstrated a clear impact of genotype and root size on microbial composition and diversity. The fungal community was more affected by plant genotype whereas the bacterial community was shaped by root size. Fungal and bacterial abundance was equal between different-sized roots however, significantly higher microbial counts were detected in rhizosphere samples compared to root endosphere samples. This study provides information that can be used to develop a comprehensive and readily applicable understanding of the impact of genotype and environmental factors on the establishment of plant microbiome, as well as its potential function and impact on host physiology.
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Affiliation(s)
- Jia Liu
- Chongqing Key Laboratory of Economic Plant Biotechnology, College of Landscape Architecture and Life Science/Institute of Special Plants, Chongqing University of Arts and Sciences, 317 Honghe Road, Yongchuan District, Chongqing 402160, China
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469 Potsdam, Germany
| | - Birgit Wasserman
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz 8010, Austria
| | - Michael Wisniewski
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, 220 Ag Quad Ln, Blacksburg, VA 24061, USA
- Corresponding authors: E-mails: ;
| | - Samir Droby
- Department of Postharvest Science, Agricultural Research Organization, The Volcani Center, PO Box 15159 Rishon LeZion 7505101, Israel
| | - Gennaro Fazio
- United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Plant Genetic Resources Unit, 21 Crabapple Drive, Geneva, NY 14456, USA
| | - Mark Mazzola
- USDA-ARS, Tree Fruit Research Laboratory,
1104 North Western Ave., Wenatchee, WA 98801, USA
| | - Xuehong Wu
- Department of Plant Pathology, College of Plant Protection, China Agricultural University, 2 Youanmingyuan West Road, Haidan District, Beijing 100193, China
- Corresponding authors: E-mails: ;
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Smulders L, Ferrero V, de la Peña E, Pozo MJ, Díaz Pendón JA, Benítez E, López-García Á. Resistance and Not Plant Fruit Traits Determine Root-Associated Bacterial Community Composition along a Domestication Gradient in Tomato. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010043. [PMID: 35009046 PMCID: PMC8747438 DOI: 10.3390/plants11010043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/20/2021] [Accepted: 12/20/2021] [Indexed: 05/12/2023]
Abstract
Soil bacterial communities are involved in multiple ecosystem services, key in determining plant productivity. Crop domestication and intensive agricultural practices often disrupt species interactions with unknown consequences for rhizosphere microbiomes. This study evaluates whether variation in plant traits along a domestication gradient determines the composition of root-associated bacterial communities; and whether these changes are related to targeted plant traits (e.g., fruit traits) or are side effects of less-often-targeted traits (e.g., resistance) during crop breeding. For this purpose, 18 tomato varieties (wild and modern species) differing in fruit and resistance traits were grown in a field experiment, and their root-associated bacterial communities were characterised. Root-associated bacterial community composition was influenced by plant resistance traits and genotype relatedness. When only considering domesticated tomatoes, the effect of resistance on bacterial OTU composition increases, while the effect due to phylogenetic relatedness decreases. Furthermore, bacterial diversity positively correlated with plant resistance traits. These results suggest that resistance traits not selected during domestication are related to the capacity of tomato varieties to associate with different bacterial groups. Taken together, these results evidence the relationship between plant traits and bacterial communities, pointing out the potential of breeding to affect plant microbiomes.
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Affiliation(s)
- Lisanne Smulders
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
- Correspondence:
| | - Victoria Ferrero
- Department of Biodiversity and Environmental Management, Campus de Vegazana s/n, University of León, 24071 León, Spain;
| | - Eduardo de la Peña
- Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000 Ghent, Belgium;
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - María J. Pozo
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
| | - Juan Antonio Díaz Pendón
- Finca Experimental “La Mayora” CSIC, Instituto de Hortofruticultura Subtropical y Mediterránea (IHSM-UMA-CSIC), 29750 Málaga, Spain;
| | - Emilio Benítez
- Department Enviromental Protection, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain;
| | - Álvaro López-García
- Department Soil Microbiology and Symbiotic Systems, Estación Experimental del Zaidín (EEZ), CSIC, 18008 Granada, Spain; (M.J.P.); (Á.L.-G.)
- Department Animal Biology, Plant Biology and Ecology, Universidad de Jaén, 23071 Jaén, Spain
- Instituto Interuniversitario de Investigación del Sistema Tierra en Andalucía (IISTA), 18006 Granada, Spain
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37
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Adeleke BS, Ayangbenro AS, Babalola OO. Bacterial community structure of the sunflower ( Helianthus annuus) endosphere. PLANT SIGNALING & BEHAVIOR 2021; 16:1974217. [PMID: 34590546 PMCID: PMC9208795 DOI: 10.1080/15592324.2021.1974217] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Agrochemical applications on farmland aim to enhance crop yield; however, the consequence of biodiversity loss has caused a reduction in ecological functions. The positive endosphere interactions and crop rotation systems may function in restoring a stable ecosystem. Employing culture-independent techniques will help access the total bacteria community in the sunflower endosphere. Limited information is available on the bacteria diversity in sunflower plants cultivated under different agricultural practices. Hence, this study was designed to investigate the endophytic bacterial community structure of sunflower at the growing stage. Plant root and stem samples were sourced from two locations (Itsoseng and Lichtenburg), for DNA extraction and sequenced on the Illumina Miseq platform. The sequence dataset was analyzed using online bioinformatics tools. Saccharibacteria and Acidobacteria were dominant in plant roots, while the stem is dominated by Proteobacteria, Bacteriodetes, and Gemmatimonadetes across the sites. Bacterial genera, Acidovorax, Flavobacterium, Hydrogenophaga, and Burkholderia-Paraburkhoderia were found dominant in the root, while the stem is dominated by Streptomyces. The diverse bacterial community structure at phyla and class levels were significantly different in plant organs across the sites. The influence of soil physical and chemical parameters analyzed was observed to induce bacterial distribution across the sites. This study provides information on the dominant bacteria community structure in sunflowers at the growing stage and their predictive functions, which suggest their future exploration as bioinoculants for improved agricultural yields.
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Affiliation(s)
- Bartholomew Saanu Adeleke
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Ayansina Segun Ayangbenro
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Olubukola Oluranti Babalola
- Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
- CONTACT Olubukola Oluranti Babalola Food Security and Safety Niche Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho2735, South Africa
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38
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Johnston-Monje D, Gutiérrez JP, Lopez-Lavalle LAB. Seed-Transmitted Bacteria and Fungi Dominate Juvenile Plant Microbiomes. Front Microbiol 2021; 12:737616. [PMID: 34745040 PMCID: PMC8569520 DOI: 10.3389/fmicb.2021.737616] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/13/2021] [Indexed: 11/13/2022] Open
Abstract
Plant microbiomes play an important role in agricultural productivity, but there is still much to learn about their provenance, diversity, and organization. In order to study the role of vertical transmission in establishing the bacterial and fungal populations of juvenile plants, we used high-throughput sequencing to survey the microbiomes of seeds, spermospheres, rhizospheres, roots, and shoots of the monocot crops maize (B73), rice (Nipponbare), switchgrass (Alamo), Brachiaria decumbens, wheat, sugarcane, barley, and sorghum; the dicot crops tomato (Heinz 1706), coffee (Geisha), common bean (G19833), cassava, soybean, pea, and sunflower; and the model plants Arabidopsis thaliana (Columbia-0) and Brachypodium distachyon (Bd21). Unsterilized seeds were planted in either sterile sand or farm soil inside hermetically sealed jars, and after as much as 60 days of growth, DNA was extracted to allow for amplicon sequence-based profiling of the bacterial and fungal populations that developed. Seeds of most plants were dominated by Proteobacteria and Ascomycetes, with all containing operational taxonomic units (OTUs) belonging to Pantoea and Enterobacter. All spermospheres also contained DNA belonging to Pseudomonas, Bacillus, and Fusarium. Despite having only seeds as a source of inoculum, all plants grown on sterile sand in sealed jars nevertheless developed rhizospheres, endospheres, and phyllospheres dominated by shared Proteobacteria and diverse fungi. Compared to sterile sand-grown seedlings, growth on soil added new microbial diversity to the plant, especially to rhizospheres; however, all 63 seed-transmitted bacterial OTUs were still present, and the most abundant bacteria (Pantoea, Enterobacter, Pseudomonas, Klebsiella, and Massilia) were the same dominant seed-transmitted microbes observed in sterile sand-grown plants. While most plant mycobiome diversity was observed to come from soil, judging by read abundance, the dominant fungi (Fusarium and Alternaria) were also vertically transmitted. Seed-transmitted fungi and bacteria appear to make up the majority of juvenile crop plant microbial populations by abundance, and based on occupancy, there seems to be a pan-angiosperm seed-transmitted core bacterial microbiome. Further study of these seed-transmitted microbes will be important to understand their role in plant growth and health, as well as their fate during the plant life cycle and may lead to innovations for agricultural inoculant development.
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Affiliation(s)
- David Johnston-Monje
- MaxPlanck Tandem Group in Plant Microbial Ecology, Universidad del Valle, Cali, Colombia.,International Center for Tropical Agriculture, Palmira, Colombia.,Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Cologne, Germany
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39
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Wille L, Kurmann M, Messmer MM, Studer B, Hohmann P. Untangling the Pea Root Rot Complex Reveals Microbial Markers for Plant Health. FRONTIERS IN PLANT SCIENCE 2021; 12:737820. [PMID: 34712258 PMCID: PMC8545811 DOI: 10.3389/fpls.2021.737820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 09/15/2021] [Indexed: 06/13/2023]
Abstract
Plant health is recognised as a key element to ensure global food security. While plant breeding has substantially improved crop resistance against individual pathogens, it showed limited success for diseases caused by the interaction of multiple pathogens such as root rot in pea (Pisum sativum L.). To untangle the causal agents of the pea root rot complex and determine the role of the plant genotype in shaping its own detrimental or beneficial microbiome, fungal and oomycete root rot pathogens, as well as previously identified beneficials, i.e., arbuscular mycorrhizal fungi (AMF) and Clonostachys rosea, were qPCR quantified in diseased roots of eight differently resistant pea genotypes grown in four agricultural soils under controlled conditions. We found that soil and pea genotype significantly determined the microbial compositions in diseased pea roots. Despite significant genotype x soil interactions and distinct soil-dependent pathogen complexes, our data revealed key microbial taxa that were associated with plant fitness. Our study indicates the potential of fungal and oomycete markers for plant health and serves as a precedent for other complex plant pathosystems. Such microbial markers can be used to complement plant phenotype- and genotype-based selection strategies to improve disease resistance in one of the world's most important pulse crops of the world.
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Affiliation(s)
- Lukas Wille
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Mario Kurmann
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Monika M. Messmer
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zürich, Zurich, Switzerland
| | - Pierre Hohmann
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Frick, Switzerland
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40
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Dong H, Fan S, Sun H, Chen C, Wang A, Jiang L, Ma D. Rhizosphere-Associated Microbiomes of Rice ( Oryza sativa L.) Under the Effect of Increased Nitrogen Fertilization. Front Microbiol 2021; 12:730506. [PMID: 34621256 PMCID: PMC8490883 DOI: 10.3389/fmicb.2021.730506] [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: 06/25/2021] [Accepted: 09/01/2021] [Indexed: 11/13/2022] Open
Abstract
Crops assemble and rely on rhizosphere-associated microbiomes for plant nutrition, which is crucial to their productivity. Historically, excessive nitrogen fertilization did not result in continuously increasing yields but rather caused environmental issues. A comprehensive understanding should be developed regarding the ways in which crops shape rhizosphere-associated microbiomes under conditions of increased nitrogen fertilization. In this study, we applied 16S and 18S ribosomal RNA gene profiling to characterize bacterial and fungal communities in bulk and rhizosphere soil of rice subjected to three levels of nitrogen fertilization for 5 years. Soil biochemical properties were characterized, and carbon-, nitrogen-, and phosphorus-related soil enzyme activities were investigated, by assays. Increasing nitrogen fertilization led to a decreasing trend in the variation of microbial community structures and demonstrated a more definite influence on fungal rather than bacterial community compositions and functions. Changes in the level of nitrogen fertilization significantly affected chemical properties such as soil pH, nutrient content, and microbial biomass levels in both rhizosphere and bulk soil. Soil enzyme activity levels varied substantially across nitrogen fertilization intensities and correlated more with the fungal than with the bacterial community. Our results indicated that increased nitrogen input drives alterations in the structures and functions of microbial communities, properties of soil carbon, nitrogen, and phosphorus, as well as enzyme activities. These results provide novel insights into the associations among increased nitrogen input, changes in biochemical properties, and shifts in microbial communities in the rhizosphere of agriculturally intensive ecosystems.
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Affiliation(s)
- Hangyu Dong
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Shuxiu Fan
- College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Haoyuan Sun
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Conglin Chen
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Aixin Wang
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Linlin Jiang
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
| | - Dianrong Ma
- Key Laboratory of Northeast Rice Biology and Breeding, National Rice Regional Technology Innovation Center, Rice Research Institute, Shenyang Agricultural University, Shenyang, China.,College of Agronomy, Shenyang Agricultural University, Shenyang, China
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41
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Brigham LM, Bueno de Mesquita CP, Smith JG, Sartwell SA, Schmidt SK, Suding KN. Do plant-soil interactions influence how the microbial community responds to environmental change? Ecology 2021; 103:e03554. [PMID: 34622953 DOI: 10.1002/ecy.3554] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 05/03/2021] [Accepted: 07/15/2021] [Indexed: 01/04/2023]
Abstract
Global change alters ecosystems and their functioning, and biotic interactions can either buffer or amplify such changes. We utilized a long-term nitrogen (N) addition and species removal experiment in the Front Range of Colorado, USA to determine whether a codominant forb and a codominant grass, with different effects on nutrient cycling and plant community structure, would buffer or amplify the effects of simulated N deposition on soil bacterial and fungal communities. While the plant community was strongly shaped by both the presence of dominant species and N addition, we did not find a mediating effect of the plant community on soil microbial response to N. In contrast to our hypothesis, we found a decoupling of the plant and microbial communities such that the soil microbial community shifted under N independently of directional shifts in the plant community. These findings suggest there are not strong cascading effects of N deposition across the plant-soil interface in our system.
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Affiliation(s)
- Laurel M Brigham
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Clifton P Bueno de Mesquita
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Jane G Smith
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Samuel A Sartwell
- Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
| | - Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA
| | - Katharine N Suding
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, 80309, USA.,Institute of Arctic and Alpine Research, University of Colorado, Boulder, Colorado, 80301, USA
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42
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Plant growth-promoting abilities and community structure of culturable endophytic bacteria from the fruit of an invasive plant Xanthium italicum. 3 Biotech 2021; 11:449. [PMID: 34631350 DOI: 10.1007/s13205-021-02997-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/16/2021] [Indexed: 10/20/2022] Open
Abstract
Diversity of endophytic bacterial communities of capsular fruit, upper and lower seeds of an invasive plant Xanthium italicum growing in Xinjiang, China, was investigated. All isolates from the seed capsules, the upper seeds, and the lower seeds were identified by 16S rRNA gene sequencing, and sequences were compared to bacterial databases to define operational taxonomic units (OTUs). Finally, we obtained 316 endophytic isolates corresponding to 58 OTUs based on 16S rRNA gene sequences. The most common OTU corresponded most closely to Bacillus zhangzhouensis and comprised 9.49% of all bacterial isolates. The richness and diversity of endophytes in lower seeds were higher than that of the upper seeds; moreover, the Chao estimator and Shannon index of endophytes in the lower seeds were approximate to that in the seed capsules. Bacillus and Staphylococcus were found as the common taxa in three different tissues that were investigated (OTUs belong to these genera constituted > 70% of the total community). The bacterial endophytic communities differed significantly among these three fruit tissues, especially Bacillus strains, which have been reported to contribute to plant growth promotion and stress resilience to their hosts in harsh environment; abundance of Bacillus species was in the following order: capsules (78 OTUs) > lower seeds (55 OTUs) > upper seeds (40 OTUs). The lower seeds harboring more Bacillus species might be responsible for their earlier seed germination compared with the upper seeds.
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43
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Wagner MR. Prioritizing host phenotype to understand microbiome heritability in plants. THE NEW PHYTOLOGIST 2021; 232:502-509. [PMID: 34287929 DOI: 10.1111/nph.17622] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 07/02/2021] [Indexed: 05/06/2023]
Abstract
Breeders and evolutionary geneticists have grappled with the complexity of the 'genotype-to-phenotype map' for decades. Now, recent studies highlight the relevance of this concept for understanding heritability of plant microbiomes. Because host phenotype is a more proximate cause of microbiome variation than host genotype, microbiome heritability varies across plant anatomy and development. Fine-scale variation of plant traits within organs suggests that the well-established concept of 'microbiome compartment' should be refined. Additionally, recent work shows that the balance of deterministic processes (including host genetic effects) vs stochastic processes also varies over time and space. Together, these findings suggest that re-centering plant phenotype - both as a predictor and a readout of microbiome function - will accelerate new insights into microbiome heritability.
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Affiliation(s)
- Maggie R Wagner
- Department of Ecology and Evolutionary Biology, Kansas Biological Survey, University of Kansas, Lawrence, KS, 66045, USA
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44
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Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype. THE ISME JOURNAL 2021; 15:2708-2722. [PMID: 33772106 PMCID: PMC8397763 DOI: 10.1038/s41396-021-00955-5] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2020] [Revised: 02/12/2021] [Accepted: 03/01/2021] [Indexed: 02/01/2023]
Abstract
The full potential of managing microbial communities to support plant health is yet-unrealized, in part because it remains difficult to ascertain which members are most important for the plant. However, microbes that consistently associate with a plant species across varied field conditions and over plant development likely engage with the host or host environment. Here, we applied abundance-occupancy concepts from macroecology to quantify the core membership of bacterial/archaeal and fungal communities in the rhizosphere of the common bean (Phaseolus vulgaris). Our study investigated the microbiome membership that persisted over multiple dimensions important for plant agriculture, including major U.S. growing regions (Michigan, Nebraska, Colorado, and Washington), plant development, annual plantings, and divergent genotypes, and also included re-analysis of public data from beans grown in Colombia. We found 48 core bacterial taxa that were consistently detected in all samples, inclusive of all datasets and dimensions. This suggests reliable enrichment of these taxa to the plant environment and time-independence of their association with the plant. More generally, the breadth of ecologically important dimensions included in this work (space, time, host genotype, and management) provides an example of how to systematically identify the most stably-associated microbiome members, and can be applied to other hosts or systems.
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45
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Lu H, Wei T, Lou H, Shu X, Chen Q. A Critical Review on Communication Mechanism within Plant-Endophytic Fungi Interactions to Cope with Biotic and Abiotic Stresses. J Fungi (Basel) 2021; 7:719. [PMID: 34575757 PMCID: PMC8466524 DOI: 10.3390/jof7090719] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/07/2021] [Accepted: 08/10/2021] [Indexed: 12/28/2022] Open
Abstract
Endophytic fungi infect plant tissues by evading the immune response, potentially stimulating stress-tolerant plant growth. The plant selectively allows microbial colonization to carve endophyte structures through phenotypic genes and metabolic signals. Correspondingly, fungi develop various adaptations through symbiotic signal transduction to thrive in mycorrhiza. Over the past decade, the regulatory mechanism of plant-endophyte interaction has been uncovered. Currently, great progress has been made on plant endosphere, especially in endophytic fungi. Here, we systematically summarize the current understanding of endophytic fungi colonization, molecular recognition signal pathways, and immune evasion mechanisms to clarify the transboundary communication that allows endophytic fungi colonization and homeostatic phytobiome. In this work, we focus on immune signaling and recognition mechanisms, summarizing current research progress in plant-endophyte communication that converge to improve our understanding of endophytic fungi.
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Affiliation(s)
- Hongyun Lu
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Tianyu Wei
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Hanghang Lou
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
| | - Xiaoli Shu
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China;
| | - Qihe Chen
- Department of Food Science and Nutrition, Zhejiang University, Hangzhou 310058, China; (H.L.); (T.W.); (H.L.)
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Adeleke BS, Ayangbenro AS, Babalola OO. Genomic Analysis of Endophytic Bacillus cereus T4S and Its Plant Growth-Promoting Traits. PLANTS 2021; 10:plants10091776. [PMID: 34579311 PMCID: PMC8467928 DOI: 10.3390/plants10091776] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 07/24/2021] [Accepted: 07/25/2021] [Indexed: 11/19/2022]
Abstract
Insights into plant endophytic microbes and their exploration in agriculture have provided opportunities for sustainable plant health and food safety. Notable endophytic Bacillus species with plant growth-promoting traits have been documented; nevertheless, information on genome analysis of B. cereus associated with the sunflower in South Africa has not been studied. Therefore, we present whole-genome sequence of agriculturally important B. cereus strain T4S isolated from sunflower plants. The NextSeq Illumina sequencing yielded 7,255,762 bp sequence reads, 151 bp average read length, 5,945,881 bp genome size, 56 tRNA, 63 rRNA, and G + C content of 34.8%. The phylogeny analysis of strain T4S was similar to B. cereus NJ-W. Secondary metabolites, such as petrobactin, bacillibactin, bacitracin, molybdenum factor, zwittermicin, and fengycin underlining bacterial biocontrol efficacy against phytopathogens were found in the T4S genome. The predicted novel genes in the bacterial genome mediating the complex metabolic pathways can provide a genetic basis in understanding endosphere biology and their multiple functions thereof in crop improvement. Interestingly, seed and root inoculation with strain T4S contributed to sunflower yield under greenhouse experiments. Hence, the detection of notable genes specific for plant growth promotion as validated under in vitro screening, promisingly, suggests the relevance of strain T4S in agricultural biotechnology.
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47
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Kim H, Lee YH. Spatiotemporal Assembly of Bacterial and Fungal Communities of Seed-Seedling-Adult in Rice. Front Microbiol 2021; 12:708475. [PMID: 34421867 PMCID: PMC8375405 DOI: 10.3389/fmicb.2021.708475] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 07/19/2021] [Indexed: 01/04/2023] Open
Abstract
Seeds harbor not only genetic information about plants but also microbial communities affecting plants’ vigor. Knowledge on the movement and formation of seed microbial communities during plant development remains insufficient. Here, we address this knowledge gap by investigating endophytic bacterial and fungal communities of seeds, seedlings, and adult rice plants. We found that seed coats act as microbial niches for seed bacterial and fungal communities. The presence or absence of the seed coat affected taxonomic composition and diversity of bacterial and fungal communities associated with seeds and seedlings. Ordination analysis showed that niche differentiation between above- and belowground compartments leads to compositional differences in endophytic bacterial and fungal communities originating from seeds. Longitudinal tracking of the composition of microbial communities from field-grown rice revealed that bacterial and fungal communities originating from seeds persist in the leaf, stem, and root endospheres throughout the life cycle. Our study provides ecological insights into the assembly of the initial endophytic microbial communities of plants from seeds.
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Affiliation(s)
- Hyun Kim
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea
| | - Yong-Hwan Lee
- Department of Agricultural Biotechnology, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Interdisciplinary Program in Agricultural Genomics, Seoul National University, Seoul, South Korea.,Center for Fungal Genetic Resources, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Plant Immunity Research Center, Seoul National University, Seoul, South Korea
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48
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Quiza L, Tremblay J, Greer CW, Hemmingsen SM, St-Arnaud M, Pozniak CJ, Yergeau E. Rhizosphere shotgun metagenomic analyses fail to show differences between ancestral and modern wheat genotypes grown under low fertilizer inputs. FEMS Microbiol Ecol 2021; 97:6279035. [PMID: 34014265 DOI: 10.1093/femsec/fiab071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 05/17/2021] [Indexed: 12/13/2022] Open
Abstract
It is thought that modern wheat genotypes have lost their capacity to associate with soil microbes that would help them acquire nutrients from the soil. To test this hypothesis, ten ancestral and modern wheat genotypes were seeded in a field experiment under low fertilization conditions. The rhizosphere soil was collected, its DNA extracted and submitted to shotgun metagenomic sequencing. In contrast to our hypothesis, there was no significant difference in the global rhizosphere metagenomes of the different genotypes, and this held true when focusing the analyses on specific taxonomic or functional categories of genes. Some genes were significantly more abundant in the rhizosphere of one genotype or another, but they comprised only a small portion of the total genes identified and did not affect the global rhizosphere metagenomes. Our study shows for the first time that the rhizosphere metagenome of wheat is stable across a wide variety of genotypes when growing under nutrient poor conditions.
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Affiliation(s)
- Liliana Quiza
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
| | - Julien Tremblay
- Energy, Mining, and Environment, National Research Council Canada, 6100 Royalmount Ave., Montréal, QC, H4P 2R2, Canada
| | - Charles W Greer
- Energy, Mining, and Environment, National Research Council Canada, 6100 Royalmount Ave., Montréal, QC, H4P 2R2, Canada
| | - Sean M Hemmingsen
- Aquatic and Crop Resource Development, National Research Council Canada, 110 Gymnasium Place Saskatoon, SK, S7N 0W9, Canada
| | - Marc St-Arnaud
- Institut de recherche en biologie végétale, Université de Montréal and Jardin botanique de Montréal, 4101 Sherbrooke East, Montréal, QC, H1X 2B2, Canada
| | - Curtis J Pozniak
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK, S7N 5A8, Canada
| | - Etienne Yergeau
- Centre Armand-Frappier Santé Biotechnologie, Institut national de la recherche scientifique, 531 boul. des Prairies, Laval, QC, H7V 1B7, Canada
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Abstract
The seed microbial community constitutes an initial inoculum for plant microbiota assembly. Still, the persistence of seed microbiota when seeds encounter soil during plant emergence and early growth is barely documented. We characterized the encounter event of seed and soil microbiota and how it structured seedling bacterial and fungal communities by using amplicon sequencing. We performed eight contrasting encounter events to identify drivers influencing seedling microbiota assembly. To do so, four contrasting seed lots of two Brassica napus genotypes were sown in two soils whose microbial diversity levels were manipulated by serial dilution and recolonization. Seedling root and stem microbiota were influenced by soil but not by initial seed microbiota composition or by plant genotype. A strong selection on the seed and soil communities occurred during microbiota assembly, with only 8% to 32% of soil taxa and 0.8% to 1.4% of seed-borne taxa colonizing seedlings. The recruitment of seedling microbiota came mainly from soil (35% to 72% of diversity) and not from seeds (0.3% to 15%). Soil microbiota transmission success was higher for the bacterial community than for the fungal community. Interestingly, seedling microbiota was primarily composed of initially rare taxa (from seed, soil, or unknown origin) and intermediate-abundance soil taxa. IMPORTANCE Seed microbiota can have a crucial role for crop installation by modulating dormancy, germination, seedling development, and recruitment of plant symbionts. Little knowledge is available on the fraction of the plant microbiota that is acquired through seeds. We characterize the encounter between seed and soil communities and how they colonize the seedling together. Transmission success and seedling community assemblage can be influenced by the variation of initial microbial pools, i.e., plant genotype and cropping year for seeds and diversity level for soils. Despite a supposed resident advantage of the seed microbiota, we show that transmission success is in favor of the soil microbiota. Our results also suggest that successful plant-microbiome engineering based on native seed or soil microbiota must include rare taxa.
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50
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Guo J, Ling N, Li Y, Li K, Ning H, Shen Q, Guo S, Vandenkoornhuyse P. Seed-borne, endospheric and rhizospheric core microbiota as predictors of plant functional traits across rice cultivars are dominated by deterministic processes. THE NEW PHYTOLOGIST 2021; 230:2047-2060. [PMID: 33626176 DOI: 10.1111/nph.17297] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 02/17/2021] [Indexed: 06/12/2023]
Abstract
A host-plant and its associated microbiota depend on one another. However, the assembly process and the functioning of host-associated microbiota are poorly understood. Herein, rice was used as model plant to investigate the assemblage of bacterial microbiota, including those in the seed, root endosphere and rhizosphere. We also assessed the degree to which endosphere and rhizosphere communities were influenced by vertical transmission through seed and identified the core microbes that potentially associated with plant phenotypic properties. Plant microhabitat, rather than subspecies type, was the major driver shaping plant-associated bacterial microbiota. Deterministic processes were primarily responsible for community assembly in all microhabitats. The influence of vertical transmission from seed to root-associated bacterial communities appeared to be quite weak (endosphere) or even absent (rhizosphere). A core microbial community composed of 15 generalist species persisted across different microhabitats and represented key connectors in networks. Host-plant functional traits were linked to the relative abundance of these generalist core microbes and could be predicted from them using machine learning algorithms. Overall, bacterial microbiota is assembled by host-plant interactions in a deterministic-based manner. This study enhances our understanding of the driving mechanisms and associations of microbiota in various plant microhabitats and provides new perspectives to improve plant performance.
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Affiliation(s)
- Junjie Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ning Ling
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- CNRS, UMR 6553 EcoBio, Université de Rennes 1, campus Beaulieu Avenue du Général Leclerc, Rennes Cedex, 35042, France
| | - Yong Li
- College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
| | - Kaisong Li
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Huiling Ning
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Qirong Shen
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shiwei Guo
- Jiangsu Provincial Key Lab for Solid Organic Waste Utilization, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Philippe Vandenkoornhuyse
- CNRS, UMR 6553 EcoBio, Université de Rennes 1, campus Beaulieu Avenue du Général Leclerc, Rennes Cedex, 35042, France
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