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Hu T, Fang H, Pan Q, Xu H, Lv T, Fan X, Wang Y, Guo Y, Mou L, Xu J, Zhu J, Matsumoto H, Wang M. Seed microbiome-mediated herbicide resistance evolution in weeds. THE NEW PHYTOLOGIST 2024; 242:333-343. [PMID: 38062878 DOI: 10.1111/nph.19459] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 11/17/2023] [Indexed: 03/22/2024]
Abstract
See also the Commentary on this article by Zhang et al., 242: 327–330.
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Affiliation(s)
- Tingting Hu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Hongda Fang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Qianqian Pan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Haorong Xu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Tianxing Lv
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyan Fan
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Yue Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Yichun Guo
- Phytobiome Ecological Science & Technology, Shanghai, 200122, China
| | - Lei Mou
- Phytobiome Ecological Science & Technology, Shanghai, 200122, China
| | - Jiayu Xu
- Phytobiome Ecological Science & Technology, Shanghai, 200122, China
| | - Jinwen Zhu
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Haruna Matsumoto
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
| | - Mengcen Wang
- Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Ministry of Agriculture, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- State Key Laboratory of Rice Biology and Breeding, Zhejiang University, Hangzhou, 310058, China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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Yao Y, Liu C, Zhang Y, Lin Y, Chen T, Xie J, Chang H, Fu Y, Cheng J, Li B, Yu X, Lyu X, Feng Y, Bian X, Jiang D. The Dynamic Changes of Brassica napus Seed Microbiota across the Entire Seed Life in the Field. PLANTS (BASEL, SWITZERLAND) 2024; 13:912. [PMID: 38592934 PMCID: PMC10975644 DOI: 10.3390/plants13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/11/2024]
Abstract
The seed microbiota is an important component given by nature to plants, protecting seeds from damage by other organisms and abiotic stress. However, little is known about the dynamic changes and potential functions of the seed microbiota during seed development. In this study, we investigated the composition and potential functions of the seed microbiota of rapeseed (Brassica napus). A total of 2496 amplicon sequence variants (ASVs) belonging to 504 genera in 25 phyla were identified, and the seed microbiota of all sampling stages were divided into three groups. The microbiota of flower buds, young pods, and seeds at 20 days after flowering (daf) formed the first group; that of seeds at 30 daf, 40 daf and 50 daf formed the second group; that of mature seeds and parental seeds were clustered into the third group. The functions of seed microbiota were identified by using PICRUSt2, and it was found that the substance metabolism of seed microbiota was correlated with those of the seeds. Finally, sixty-one core ASVs, including several potential human pathogens, were identified, and a member of the seed core microbiota, Sphingomonas endophytica, was isolated from seeds and found to promote seedling growth and enhance resistance against Sclerotinia sclerotiorum, a major pathogen in rapeseed. Our findings provide a novel perspective for understanding the composition and functions of microbiota during seed development and may enhance the efficiency of mining beneficial seed microbes.
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Affiliation(s)
- Yao Yao
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Changxing Liu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yu Zhang
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Yang Lin
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Tao Chen
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Haibin Chang
- Huanggang Academy of Agricultural Science, Huanggang 438000, China;
| | - Yanping Fu
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
| | - Bo Li
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xiao Yu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Yanbo Feng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xuefeng Bian
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Y.); (C.L.); (T.C.); (J.X.); (B.L.); (X.Y.); (X.L.); (Y.F.); (X.B.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China; (Y.Z.); (Y.L.); (Y.F.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Peng D, Wang Z, Tian J, Wang W, Guo S, Dai X, Yin H, Li L. Phyllosphere bacterial community dynamics in response to bacterial wildfire disease: succession and interaction patterns. FRONTIERS IN PLANT SCIENCE 2024; 15:1331443. [PMID: 38533399 PMCID: PMC10963427 DOI: 10.3389/fpls.2024.1331443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 02/08/2024] [Indexed: 03/28/2024]
Abstract
Plants interact with complex microbial communities in which microorganisms play different roles in plant development and health. While certain microorganisms may cause disease, others promote nutrient uptake and resistance to stresses through a variety of mechanisms. Developing plant protection measures requires a deeper comprehension of the factors that influence multitrophic interactions and the organization of phyllospheric communities. High-throughput sequencing was used in this work to investigate the effects of climate variables and bacterial wildfire disease on the bacterial community's composition and assembly in the phyllosphere of tobacco (Nicotiana tabacum L.). The samples from June (M1), July (M2), August (M3), and September (M4) formed statistically separate clusters. The assembly of the whole bacterial population was mostly influenced by stochastic processes. PICRUSt2 predictions revealed genes enriched in the M3, a period when the plant wildfire disease index reached climax, were associated with the development of the wildfire disease (secretion of virulence factor), the enhanced metabolic capacity and environmental adaption. The M3 and M4 microbial communities have more intricate molecular ecological networks (MENs), bursting with interconnections within a densely networked bacterial population. The relative abundances of plant-beneficial and antagonistic microbes Clostridiales, Bacillales, Lactobacillales, and Sphingobacteriales, showed significant decrease in severally diseased sample (M3) compared to the pre-diseased samples (M1/M2). Following the results of MENs, we further test if the correlating bacterial pairs within the MEN have the possibility to share functional genes and we have unraveled 139 entries of such horizontal gene transfer (HGT) events, highlighting the significance of HGT in shaping the adaptive traits of plant-associated bacteria across the MENs, particularly in relation to host colonization and pathogenicity.
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Affiliation(s)
- Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Jinyan Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Wei Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Shijie Guo
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
| | - Liangzhi Li
- School of Minerals Processing and Bioengineering, Central South University, Changsha, China
- Key Laboratory of Biometallurgy of Ministry of Education, Central South University, Changsha, China
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Li X, Wang C, Zhu X, Ntoukakis V, Cernava T, Jin D. Exploration of phyllosphere microbiomes in wheat varieties with differing aphid resistance. ENVIRONMENTAL MICROBIOME 2023; 18:78. [PMID: 37876011 PMCID: PMC10594911 DOI: 10.1186/s40793-023-00534-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
BACKGROUND Leaf-associated microbes play an important role in plant development and response to exogenous stress. Insect herbivores are known to alter the phyllosphere microbiome. However, whether the host plant's defense against insects is related to the phyllosphere microbiome remains mostly elusive. Here, we investigated bacterial communities in the phyllosphere and endosphere of eight wheat cultivars with differing aphid resistance, grown in the same farmland. RESULTS The bacterial community in both the phyllosphere and endosphere showed significant differences among most wheat cultivars. The phyllosphere was connected to more complex and stable microbial networks than the endosphere in most wheat cultivars. Moreover, the genera Pantoea, Massilia, and Pseudomonas were found to play a major role in shaping the microbial community in the wheat phyllosphere. Additionally, wheat plants showed phenotype-specific associations with the genera Massilia and Pseudomonas. The abundance of the genus Exiguobacterium in the phyllosphere exhibited a significant negative correlation with the aphid hazard grade in the wheat plants. CONCLUSION Communities of leaf-associated microbes in wheat plants were mainly driven by the host genotype. Members of the genus Exiguobacterium may have adverse effects on wheat aphids. Our findings provide new clues supporting the development of aphid control strategies based on phyllosphere microbiome engineering.
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Affiliation(s)
- Xinan Li
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, School of Resource and Environmental Sciences, Henan Institute of Science and Technology, 453003, Xinxiang, China
| | - Chao Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, 100193, Beijing, China.
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, CV4 7AL, Coventry, UK
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ, Southampton, UK
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, 100085, Beijing, China.
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Chen H, Song Y, Wang S, Fan K, Wang H, Mao Y, Zhang J, Xu Y, Yin X, Wang Y, Ding Z. Improved phyllosphere microbiome composition of tea plant with the application of small peptides in combination with rhamnolipid. BMC Microbiol 2023; 23:302. [PMID: 37872475 PMCID: PMC10591406 DOI: 10.1186/s12866-023-03043-0] [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: 04/14/2023] [Accepted: 10/03/2023] [Indexed: 10/25/2023] Open
Abstract
BACKGROUND Small peptides play a crucial role in plant growth and adaptation to the environment. Exogenous small peptides are often applied together with surfactants as foliar fertilizers, but the impact of small peptides and surfactants on the tea phyllosphere microbiome remains unknown. RESULTS In this study, we investigated the effects of small peptides and different surfactants on the tea phyllosphere microbiome using 16S and ITS sequencing. Our results showed that the use of small peptides reduced the bacterial diversity of the tea phyllosphere microbiome and increased the fungal diversity, while the use of surfactants influenced the diversity of bacteria and fungi. Furthermore, the addition of rhamnolipid to small peptides significantly improved the tea phyllosphere microbiome community structure, making beneficial microorganisms such as Pseudomonas, Chryseobacterium, Meyerozyma, and Vishniacozyma dominant populations. CONCLUSION Our study suggests that the combined use of small peptides and surfactants can significantly modify the tea phyllosphere microbiome community structure, particularly for beneficial microorganisms closely related to tea plant health. Thus, this preliminary study offers initial insights that could guide the application of small peptides and surfactants in agricultural production, particularly with respect to their potential for modulating the phyllosphere microbiome community in tea plant management.
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Affiliation(s)
- Hao Chen
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yujie Song
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Shuangshuang Wang
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
| | - Kai Fan
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Hui Wang
- Rizhao Tea Research Institute, Rizhao, 276827, China
| | - Yilin Mao
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Jie Zhang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yang Xu
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Xinyue Yin
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China
| | - Yu Wang
- Tea Research Institute, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Zhaotang Ding
- Tea Research Institute, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
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Du XD, Wang J, Shen C, Wang J, Jing Z, Huang LN, Luo ZH, Ge Y. Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion? PLANTS (BASEL, SWITZERLAND) 2023; 12:1406. [PMID: 36987094 PMCID: PMC10052042 DOI: 10.3390/plants12061406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.
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Affiliation(s)
- Xiang-Deng Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Wang
- School of Life Science, Taizhou University, Taizhou 318000, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongwang Jing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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Yin J, Zhang Z, Zhu C, Wang T, Wang R, Ruan L. Heritability of tomato rhizobacteria resistant to Ralstonia solanacearum. MICROBIOME 2022; 10:227. [PMID: 36517876 PMCID: PMC9753271 DOI: 10.1186/s40168-022-01413-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 11/04/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome from soil to resist Rs. However, whether this recruitment is inheritable from resistant parent to progeny has not been determined. RESULTS In the present study, we investigated the rhizosphere microbiomes of tomatoes with clear kinship and different resistance against Rs. Resistant tomatoes grown with the additions of natural soil or its extract showed lower disease indexes than those grown in the sterile soil, demonstrating the importance of soil microbiome in resisting Rs. The results of 16S ribosomal RNA gene amplicon sequencing revealed that the resistant cultivars had more robust rhizosphere microbiomes than the susceptible ones. Besides, the resistant progeny HF12 resembled its resistant parent HG64 in the rhizosphere microbiome. The rhizosphere microbiome had functional consistency between HF12 and HG64 as revealed by metagenomics. Based on multi-omics analysis and experimental validation, two rhizobacteria (Sphingomonas sp. Cra20 and Pseudomonas putida KT2440) were enriched in HF12 and HG64 with the ability to offer susceptible tomatoes considerable protection against Rs. Multiple aspects were involved in the protection, including reducing the virulence-related genes of Rs and reshaping the transcriptomes of the susceptible tomatoes. CONCLUSIONS We found promising bacteria to suppress the tomato bacterial wilt in sustainable agriculture. And our research provides insights into the heritability of Rs-resistant tomato rhizobacteria, echoing the inheritance of tomato genetic material. Video Abstract.
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Affiliation(s)
- Jiakang Yin
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Ziliang Zhang
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Chengcheng Zhu
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Taotao Wang
- Key Laboratory of Horticulture Plant Biology, Ministry of Education, Huazhong Agriculture University, Wuhan, 430070, China
| | - Ruihong Wang
- Key Laboratory of Forest Ecology in Tibet Plateau (Tibet Agricultural & Animal Husbandry University), Ministry of Education, Nyingchi, 860000, Tibet, China
| | - Lifang Ruan
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
- College of Resources & Environment, Tibet Agriculture & Animal Husbandry University, Nyingchi, 860000, Tibet, China.
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8
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Tan X, Xie H, Yu J, Wang Y, Xu J, Xu P, Ma B. Host genetic determinants drive compartment-specific assembly of tea plant microbiomes. PLANT BIOTECHNOLOGY JOURNAL 2022; 20:2174-2186. [PMID: 35876474 PMCID: PMC9616527 DOI: 10.1111/pbi.13897] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/17/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Diverse host factors drive microbial variation in plant-associated environments, whereas their genetic mechanisms remain largely unexplored. To address this, we coupled the analyses of plant genetics and microbiomes in this study. Using 100 tea plant (Camellia sinensis) cultivars, the microbiomes of rhizosphere, root endosphere and phyllosphere showed clear compartment-specific assembly, whereas the subpopulation differentiation of tea cultivars exhibited small effects on microbial variation in each compartment. Through microbiome genome-wide association studies, we examined the interactions between tea genetic loci and microbial variation. Notably, genes related to the cell wall and carbon catabolism were heavily linked to root endosphere microbial composition, whereas genes related to the metabolism of metal ions and small organic molecules were overrepresented in association with rhizosphere microbial composition. Moreover, a set of tea genetic variants, including the cytoskeleton-related formin homology interacting protein 1 gene, were strongly associated with the β-diversity of phyllosphere microbiomes, implying their interactions with the overall structure of microbial communities. Our results create a catalogue of tea genetic determinants interacting with microbiomes and reveal the compartment-specific microbiome assembly driven by host genetics.
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Affiliation(s)
- Xiangfeng Tan
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Hengtong Xie
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jingwen Yu
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
| | - Yuefei Wang
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Jianming Xu
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
| | - Ping Xu
- Institution of Tea ScienceZhejiang UniversityHangzhouChina
| | - Bin Ma
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource SciencesZhejiang UniversityHangzhouChina
- Zhejiang Provincial Key Laboratory of Agricultural, Resources and EnvironmentZhejiang UniversityHangzhouChina
- ZJU‐Hangzhou Global Scientific and Technological Innovation CenterZhejiang UniversityHangzhouChina
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