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Zai X, Cordovez V, Zhu F, Zhao M, Diao X, Zhang F, Raaijmakers JM, Song C. C4 cereal and biofuel crop microbiomes. Trends Microbiol 2024:S0966-842X(24)00093-3. [PMID: 38772810 DOI: 10.1016/j.tim.2024.04.008] [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: 12/07/2023] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 05/23/2024]
Abstract
Microbiomes provide multiple life-support functions for plants, including nutrient acquisition and tolerance to abiotic and biotic stresses. Considering the importance of C4 cereal and biofuel crops for food security under climate change conditions, more attention has been given recently to C4 plant microbiome assembly and functions. Here, we review the current status of C4 cereal and biofuel crop microbiome research with a focus on beneficial microbial traits for crop growth and health. We highlight the importance of environmental factors and plant genetics in C4 crop microbiome assembly and pinpoint current knowledge gaps. Finally, we discuss the potential of foxtail millet as a C4 model species and outline future perspectives of C4 plant microbiome research.
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Affiliation(s)
- Xiaoyu Zai
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Viviane Cordovez
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands.
| | - Feng Zhu
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China
| | - Meicheng Zhao
- Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water-Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, 050021 Shijiazhuang, China; Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Xianmin Diao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, 100081 Beijing, China
| | - Fusuo Zhang
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen, The Netherlands; Institute of Biology, Leiden University, Leiden, The Netherlands
| | - Chunxu Song
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, China Agricultural University, Beijing, China; National Academy of Agriculture Green Development, China Agricultural University, Beijing, China; Key Laboratory of Plant-Soil Interactions, Ministry of Education, China Agricultural University, 100193 Beijing, China; National Observation and Research Station of Agriculture Green Development, 057250 Quzhou, Hebei, China.
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2
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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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3
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Zhang J, Liu W, Bu J, Lin Y, Bai Y. Host genetics regulate the plant microbiome. Curr Opin Microbiol 2023; 72:102268. [PMID: 36708613 DOI: 10.1016/j.mib.2023.102268] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weidong Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jingshu Bu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
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4
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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: 22] [Impact Index Per Article: 22.0] [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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5
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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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6
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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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Zhang L, Zhang J, Wei Y, Hu W, Liu G, Zeng H, Shi H. Microbiome-wide association studies reveal correlations between the structure and metabolism of the rhizosphere microbiome and disease resistance in cassava. PLANT BIOTECHNOLOGY JOURNAL 2021; 19:689-701. [PMID: 33095967 PMCID: PMC8051613 DOI: 10.1111/pbi.13495] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/18/2020] [Indexed: 05/07/2023]
Abstract
Cassava is one of the most important staple food crops in tropical regions. To date, an understanding of the relationship between microbial communities and disease resistance in cassava has remained elusive. In order to explore the relationship among microbiome and phenotypes for further targeted design of microbial community, 16S rRNA and ITS of microbiome of ten cassava varieties were analysed, and a distinctive microbial community in the rhizosphere showed significant interdependence with disease resistance. Shotgun metagenome sequencing was performed to elucidate the structure of microbiomes of cassava rhizosphere. Comprehensive microbiome studies were performed to assess the correlation between the rhizosphere microbiome and disease resistance. Subsequently, the metagenome of rhizosphere microbiome was annotated to obtain taxonomic information at species level and identify metabolic pathways that were significantly associated with cassava disease resistance. Notably, cassava disease resistance was significantly associated with Lactococcus sp., which specifically produces nisin. To definitively explain the role of nisin and underlying mechanism, analysis of nisin biosynthesis-associated genes together with in vitro and in vivo experiments highlighted the effect of nisin on inhibiting the growth of Xanthomonas axonopodis pv. manihotis (Xam) and activating immune response in cassava. The new insights between cassava rhizosphere microbiome especially Lactococcus sp. and disease resistance provide valuable information into further control of cassava disease.
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Affiliation(s)
- Lin Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Jiachao Zhang
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Yunxie Wei
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Wei Hu
- Key Laboratory of Biology and Genetic Resources of Tropical CropsInstitute of Tropical Bioscience and BiotechnologyChinese Academy of Tropical Agricultural SciencesHaikouChina
| | - Guoyin Liu
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Hongqiu Zeng
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
| | - Haitao Shi
- Hainan Key Laboratory for Sustainable Utilization of Tropical BioresourcesCollege of Tropical CropsCollege of Food Science and TechnologyCollege of Life and Pharmaceutical SciencesHainan UniversityHaikouChina
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8
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Peng X, Xie J, Li W, Xie H, Cai Y, Ding X. Comparison of wild rice (Oryza longistaminata) tissues identifies rhizome-specific bacterial and archaeal endophytic microbiomes communities and network structures. PLoS One 2021; 16:e0246687. [PMID: 33556120 PMCID: PMC7870070 DOI: 10.1371/journal.pone.0246687] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Accepted: 01/23/2021] [Indexed: 11/18/2022] Open
Abstract
Compared with root-associated habitats, little is known about the role of microbiota inside other rice organs, especially the rhizome of perennial wild rice, and this information may be of importance for agriculture. Oryza longistaminata is perennial wild rice with various agronomically valuable traits, including large biomass on poor soils, high nitrogen use efficiency, and resistance to insect pests and disease. Here, we compared the endophytic bacterial and archaeal communities and network structures of the rhizome to other compartments of O. longistaminata using 16S rRNA gene sequencing. Diverse microbiota and significant variation in community structure were identified among different compartments of O. longistaminata. The rhizome microbial community showed low taxonomic and phylogenetic diversity as well as the lowest network complexity among four compartments. Rhizomes exhibited less phylogenetic clustering than roots and leaves, but similar phylogenetic clustering with stems. Streptococcus, Bacillus, and Methylobacteriaceae were the major genera in the rhizome. ASVs belonging to the Enhydrobacter, YS2, and Roseburia are specifically present in the rhizome. The relative abundance of Methylobacteriaceae in the rhizome and stem was significantly higher than that in leaf and root. Noteworthy type II methanotrophs were observed across all compartments, including the dominant Methylobacteriaceae, which potentially benefits the host by facilitating CH4-dependent N2 fixation under nitrogen nutrient-poor conditions. Our data offers a robust knowledge of host and microbiome interactions across various compartments and lends guidelines to the investigation of adaptation mechanisms of O. longistaminata in nutrient-poor environments for biofertilizer development in agriculture.
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Affiliation(s)
- Xiaojue Peng
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
| | - Jian Xie
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Wenzhuo Li
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
| | - Hongwei Xie
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Yaohui Cai
- Jiangxi Super-Rice Research and Development Center, Jiangxi Academy of Agricultural Sciences, Nanchang, Jiangxi, China
| | - Xia Ding
- School of Life Sciences, Nanchang University, Nanchang, Jiangxi, China
- Jiangxi Provincial People’s Hospital, Nanchang University, Nanchang, Jiangxi, China
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9
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Chang J, Sun Y, Tian L, Ji L, Luo S, Nasir F, Kuramae EE, Tian C. The Structure of Rhizosphere Fungal Communities of Wild and Domesticated Rice: Changes in Diversity and Co-occurrence Patterns. Front Microbiol 2021; 12:610823. [PMID: 33613482 PMCID: PMC7890246 DOI: 10.3389/fmicb.2021.610823] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/06/2021] [Indexed: 01/16/2023] Open
Abstract
The rhizosphere fungal community affects the ability of crops to acquire nutrients and their susceptibility to pathogen invasion. However, the effects of rice domestication on the diversity and interactions of rhizosphere fungal community still remain largely unknown. Here, internal transcribed spacer amplicon sequencing was used to systematically analyze the structure of rhizosphere fungal communities of wild and domesticated rice. The results showed that domestication increased the alpha diversity indices of the rice rhizosphere fungal community. The changes of alpha diversity index may be associated with the enrichment of Acremonium, Lecythophora, and other specific rare taxa in the rhizosphere of domesticated rice. The co-occurrence network showed that the complexity of wild rice rhizosphere fungal community was higher than that of the domesticated rice rhizosphere fungal community. Arbuscular mycorrhizal fungi (AMF) and soilborne fungi were positively and negatively correlated with more fungi in the wild rice rhizosphere, respectively. For restructuring the rhizomicrobial community of domesticated crops, we hypothesize that microbes that hold positive connections with AMF and negative connections with soilborne fungi can be used as potential sources for bio-inoculation. Our findings provide a scientific basis for reshaping the structure of rhizomicrobial community and furthermore create potential for novel intelligent and sustainable agricultural solutions.
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Affiliation(s)
- Jingjing Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Yu Sun
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Li Ji
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, China
| | - Shasha Luo
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
| | - Eiko E. Kuramae
- Department of Microbial Ecology, Netherlands Institute of Ecology NIOO-KNAW, Wageningen, Netherlands
- Ecology and Biodiversity, Institute of Environmental Biology, Utrecht University, Utrecht, Netherlands
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, China
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Self-Crossing Leads to Weak Co-Variation of the Bacterial and Fungal Communities in the Rice Rhizosphere. Microorganisms 2021; 9:microorganisms9010175. [PMID: 33467504 PMCID: PMC7830547 DOI: 10.3390/microorganisms9010175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 01/05/2021] [Accepted: 01/10/2021] [Indexed: 12/23/2022] Open
Abstract
The rhizomicrobial community is influenced by plant genotype. However, the potential differences in the co-assembly of bacterial and fungal communities between parental lines and different generations of rice progenies have not been examined. Here we compared the bacterial and fungal communities in the rhizomicrobiomes of female parent Oryza rufipogon wild rice; male parent Oryza sativa cultivated rice; their F1 progeny; and the F2, F3 and F4 self-crossing generations. Our results showed that the bacterial and fungal α-diversities of the hybrid F1 and self-crossing generations (F2, F3, F4) were closer to one of the two parental lines, which may indicate a role of the parental line in the diversity of the rhizosphere microbial community assembly. Self-crossing from F1 to F4 led to weak co-variation of the bacterial and fungal communities and distinct rhizosphere microbiomes. In the parental and self-crossing progenies, the reduction of community dissimilarity was higher for the fungal community than for the bacterial community.
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11
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Research Advances of Beneficial Microbiota Associated with Crop Plants. Int J Mol Sci 2020; 21:ijms21051792. [PMID: 32150945 PMCID: PMC7084388 DOI: 10.3390/ijms21051792] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2020] [Revised: 03/02/2020] [Accepted: 03/03/2020] [Indexed: 12/14/2022] Open
Abstract
Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.
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12
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Nasir F, Shi S, Tian L, Chang C, Ma L, Li X, Gao Y, Tian C. Strigolactones shape the rhizomicrobiome in rice (Oryza sativa). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 286:118-133. [PMID: 31300137 DOI: 10.1016/j.plantsci.2019.05.016] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 05/13/2019] [Accepted: 05/18/2019] [Indexed: 05/03/2023]
Abstract
The rhizomicrobiome helps the host plant to better adapt to environmental stresses. In contrast, plant-derived metabolic substances, including phytohormones, play an active role in structuring rhizomicrobiome. Although strigolactones (SLs), a group of phytohormones, serve as potential rhizosphere signaling molecules, their contributions in shaping the rice (Oryza sativa) rhizomicrobiome remain elusive. To address this issue, we compared the rhizomicrobiome of rice mutants defective in either SL biosynthesis or signaling and wild-type (WT) plants. To understand whether SL-regulated metabolic pathways shape the rhizomicrobiome, a correlation network analysis was conducted among the metabolic pathway-related genes and the rhizomicrobiome of rice. Compared to WT, higher bacterial richness (evidenced by the operational taxonomic unit richness) and lower fungal diversity (evidenced by the Shannon index) were observed in both SL deficient dwarf17 (d17) and signaling (d14) mutants. Additionally, remarkable differences were observed in the composition of a large number of bacterial communities than the fungal communities in the d17 and d14 mutants with respect to the WT. The abundance of certain beneficial bacterial taxa, including Nitrosomonadaceae and Rhodanobacter, were significantly decreased in both mutants relative to the WT. Correlation network analysis between SL-regulated metabolic pathway-associated genes and rhizomicrobiome proposed a role for SL-dependent metabolic pathways in shaping rhizomicrobiome composition. Taken together, our study suggests that SL biosynthesis and signaling play a key role in determining the rice rhizomicrobiome, directly or indirectly, through the mediation of distinct metabolic pathways. Based on our findings, the genetic modulation of rice SL biosynthesis and/or signaling pathways may help to recruit/increase the abundance of the desired rhizomicrobiome, which may assist in the stress resilience of rice.
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Affiliation(s)
- Fahad Nasir
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China; Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China
| | - Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Lina Ma
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China
| | - Yingzhi Gao
- Key Laboratory of Vegetation Ecology, Ministry of Education, Institute of Grassland Science, Northeast Normal University, Changchun 130024, Jilin Province, China.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, Jilin Province, China.
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13
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Xu S, Tian L, Chang C, Li X, Tian C. Plants exhibit significant effects on the rhizospheric microbiome across contrasting soils in tropical and subtropical China. FEMS Microbiol Ecol 2019; 95:5526218. [DOI: 10.1093/femsec/fiz100] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 06/25/2019] [Indexed: 11/14/2022] Open
Abstract
ABSTRACT
The rhizospheric microbiome appears to be one of the key determinants of plant health and productivity. In this study, to understand the assembly process of the rhizospheric microbiome, the effects of different sites, soils and plants on the rhizospheric microbiome were compared and examined using high-throughput sequencing. A series of comparisons of rhizospheric microbiomes were conducted using two plants (wild rice (Oryza rufipogon Griff.) and L. hexandra (Leersia hexandra Swartz)), two soils (high nutrient and low nutrient) and two sites (Guangdong and Hainan provinces in China). The results of the redundancy analysis, between-class analysis and coinertia analysis indicated that the factors shaping the rhizospheric microbiome (in decreasing order of strength), were the site, soil and plant. The effects of plants on the rhizospheric microbiome were slight and unobvious, with relatively low-explained variations and few core groups and indicator groups; however, the effects were significant across different sites and soils, especially for specific microbial groups that are closely associated with plants, such as pathogens, symbionts, and saprotrophs. Furthermore, rhizospheric fungi were more strongly influenced by plants than rhizospheric bacteria. Our results provide insights into the relationships among multiple factors that shape the rhizospheric microbiome in natural ecosystems and highlight the effects of plants across regional environmental shifts.
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Affiliation(s)
- Shangqi Xu
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, P.R. China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, P.R. China
| | - Chunling Chang
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, P.R. China
- University of Chinese Academy of Sciences, Beijing 100049, P.R. China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, P.R. China
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, P.R. China
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14
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Shi S, Tian L, Nasir F, Li X, Li W, Tran LSP, Tian C. Impact of domestication on the evolution of rhizomicrobiome of rice in response to the presence of Magnaporthe oryzae. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2018; 132:156-165. [PMID: 30195107 DOI: 10.1016/j.plaphy.2018.08.023] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 07/23/2018] [Accepted: 08/19/2018] [Indexed: 05/16/2023]
Abstract
The rhizomicrobiome plays a key role in suppressing soil-borne plant diseases. It remains unclear if crop domestication has altered the rhizomicrobiome and reduced the resistance of domesticated crops to pathogens. To investigate this question, the pathogenic fungus Magnaporthe oryzae was administered to the rhizosphere of plants of cultivated and wild rice to compare the impact of the fungal pathogen on their rhizomicrobiome. The analysis of the results indicated that the presence of M. oryzae affected the community structure and diversity of the rhizomicrobiome of both cultivated and wild rice species. Bacterial and fungal α- and β-diversity of the rhizosphere of cultivated rice were altered more significantly than in wild rice. Furthermore, the abundance of the introduced pathogen was significantly lower in the rhizosphere of wild rice, while the relative abundance of putatively beneficial bacterial and fungal taxa was higher, relative to cultivated rice. These results suggest that the rhizomicrobiome of cultivated rice was more sensitive to the introduction of the fungal pathogen and more easily disturbed than the rhizosphere community of its wild relative. Additionally, a correlation analysis of microbiome and root transcriptome data, obtained under pathogenic and non-pathogenic conditions, indicated that fungal members of the Glomeromycota are important for promoting phenylpropanoid and lignin syntheses in wild rice, which plays a role in resisting M. oryzae infection. The identified differences between the responses of the rhizomicrobiomes of cultivated and wild rice to M. oryzae may provide information that can be used in developing novel strategies to control soil-borne pathogens, which include reconstructing the rhizomicrobiome of domesticated crops to be similar to their wild relatives.
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Affiliation(s)
- Shaohua Shi
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Lei Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Fahad Nasir
- School of Life Sciences, Northeast Normal University, Changchun City, Jilin, China
| | - Xiujun Li
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China
| | - Weiqiang Li
- Stress Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, 1-7-22, Suehiro-cho, Tsurumi, Yokohama, 230-0045, Japan
| | - Lam-Son Phan Tran
- Plant Stress Research Group & Faculty of Applied Sciences, Ton Duc Thang University, Ho Chi Minh City, Vietnam.
| | - Chunjie Tian
- Key Laboratory of Mollisols Agroecology, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun, Jilin, 130102, China.
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