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Pan Q, Lv T, Xu H, Fang H, Li M, Zhu J, Wang Y, Fan X, Xu P, Wang X, Wang Q, Matsumoto H, Wang M. Gut pathobiome mediates behavioral and developmental disorders in biotoxin-exposed amphibians. ENVIRONMENTAL SCIENCE AND ECOTECHNOLOGY 2024; 21:100415. [PMID: 38577706 PMCID: PMC10992726 DOI: 10.1016/j.ese.2024.100415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 03/15/2024] [Accepted: 03/16/2024] [Indexed: 04/06/2024]
Abstract
Emerging evidence suggests a link between alterations in the gut microbiome and adverse health outcomes in the hosts exposed to environmental pollutants. Yet, the causal relationships and underlying mechanisms remain largely undefined. Here we show that exposure to biotoxins can affect gut pathobiome assembly in amphibians, which in turn triggers the toxicity of exogenous pollutants. We used Xenopus laevis as a model in this study. Tadpoles exposed to tropolone demonstrated notable developmental impairments and increased locomotor activity, with a reduction in total length by 4.37%-22.48% and an increase in swimming speed by 49.96%-84.83%. Fusobacterium and Cetobacterium are predominant taxa in the gut pathobiome of tropolone-exposed tadpoles. The tropolone-induced developmental and behavioral disorders in the host were mediated by assembly of the gut pathobiome, leading to transcriptome reprogramming. This study not only advances our understanding of the intricate interactions between environmental pollutants, the gut pathobiome, and host health but also emphasizes the potential of the gut pathobiome in mediating the toxicological effects of environmental contaminants.
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Affiliation(s)
- Qianqian Pan
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Tianxing Lv
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haorong Xu
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Hongda Fang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Meng Li
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiaping Zhu
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Yue Wang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Xiaoyan Fan
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Ping Xu
- Institution of Tea Science, Zhejiang University, Hangzhou, 310058, China
| | - Xiuguo Wang
- The Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao, 266101, China
| | - Qiangwei Wang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haruna Matsumoto
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Mengcen Wang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058, China
- Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan
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2
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Luo X, Hounmanou YMG, Ndayisenga F, Yu Z. Spontaneous fermentation mitigates the frequency of genes encoding antimicrobial resistance spreading from the phyllosphere reservoir to the diet. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 931:172712. [PMID: 38677439 DOI: 10.1016/j.scitotenv.2024.172712] [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: 01/22/2024] [Revised: 04/18/2024] [Accepted: 04/21/2024] [Indexed: 04/29/2024]
Abstract
The phyllosphere microbiome of vegetable products constitutes an important reservoir for multidrug resistant bacteria and Antibiotic Resistance Genes (ARG). Vegetable products including fermented products such as Paocai therefore may serve as a shuttle for extrinsic microorganisms with ARGs into the gut of consumers. Here we study the effect of fermentation on Paocai ARG dissemination by metagenomic analysis. Microbial abundance and diversity of the Paocai microbiome were diminished during fermentation, which correlated with the reduction of abundance in ARGs. Specifically, as fermentation progressed, Enterobacterales overtook Pseudomonadales as the predominant ARG carriers, and Lactobacillales and Enterobacteriales became the determinants of Paocai resistome variation. Moreover, the dual effect of microbes and metal resistance genes (MRGs) was the major contributor driving Paocai resistome dynamics. We recovered several metagenome-assembled genomes (MAGs) carrying acquired ARGs in the phyllosphere microbiome. ARGs of potential clinical and epidemiological relevance such as tet M and emrB-qacA, were mainly hosted by non-dominant bacterial genera. Overall, our study provides evidence that changes in microbial community composition by fermentation aid in constraining ARG dispersal from raw ingredients to the human microbiome but does not eliminate them.
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Affiliation(s)
- Xiao Luo
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China
| | - Yaovi Mahuton Gildas Hounmanou
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Stigbojlen 4, 1870 Frederiksberg, Denmark
| | - Fabrice Ndayisenga
- College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China
| | - Zhisheng Yu
- Sino-Danish College, University of Chinese Academy of Sciences, Beijing 101408, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing 100049, China; RCEES-IMCAS-UCAS Joint-Lab of Microbial Technology for Environmental Science, Beijing 100085, China.
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3
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An H, Li X, Huang Y, Wang W, Wu Y, Liu L, Ling W, Li W, Zhao H, Lu D, Liu Q, Jiang G. A new ChatGPT-empowered, easy-to-use machine learning paradigm for environmental science. ECO-ENVIRONMENT & HEALTH 2024; 3:131-136. [PMID: 38638173 PMCID: PMC11021822 DOI: 10.1016/j.eehl.2024.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 04/20/2024]
Abstract
The quantity and complexity of environmental data show exponential growth in recent years. High-quality big data analysis is critical for performing a sophisticated characterization of the complex network of environmental pollution. Machine learning (ML) has been employed as a powerful tool for decoupling the complexities of environmental big data based on its remarkable fitting ability. Yet, due to the knowledge gap across different subjects, ML concepts and algorithms have not been well-popularized among researchers in environmental sustainability. In this context, we introduce a new research paradigm-"ChatGPT + ML + Environment", providing an unprecedented chance for environmental researchers to reduce the difficulty of using ML models. For instance, each step involved in applying ML models to environmental sustainability, including data preparation, model selection and construction, model training and evaluation, and hyper-parameter optimization, can be easily performed with guidance from ChatGPT. We also discuss the challenges and limitations of using this research paradigm in the field of environmental sustainability. Furthermore, we highlight the importance of "secondary training" for future application of "ChatGPT + ML + Environment".
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Affiliation(s)
- Haoyuan An
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- Biomedical Engineering Institute, School of Control Science and Engineering, Shandong University, Jinan 250061, China
| | - Xiangyu Li
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuming Huang
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weichao Wang
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Yuehan Wu
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Lin Liu
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Weibo Ling
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Wei Li
- Biomedical Engineering Institute, School of Control Science and Engineering, Shandong University, Jinan 250061, China
| | - Hanzhu Zhao
- Biomedical Engineering Institute, School of Control Science and Engineering, Shandong University, Jinan 250061, China
| | - Dawei Lu
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qian Liu
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Guibin Jiang
- State Key Laboratory of Environmental Chemistry and Toxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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4
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Shen J, Wang M, Wang E. Exploitation of the microbiome for crop breeding. NATURE PLANTS 2024; 10:533-534. [PMID: 38514786 DOI: 10.1038/s41477-024-01657-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Affiliation(s)
- Jiayong Shen
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Mingxing Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Ertao Wang
- New Cornerstone Science Laboratory, National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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5
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Li Y, Jin L, Wu M, Wang B, Qu N, Zhou H, Chen T, Liu G, Yue M, Zhang G. Forest management positively reshapes the phyllosphere bacterial community and improves community stability. ENVIRONMENT INTERNATIONAL 2024; 186:108611. [PMID: 38603812 DOI: 10.1016/j.envint.2024.108611] [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: 01/10/2024] [Revised: 02/29/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Research has shown that forest management can improve the post-drought growth and resilience of Qinghai spruce in the eastern Qilian Mountains, located on the northeastern Tibetan Plateau. However, the impact of such management on the tree-associated phyllosphere microbiome is not yet fully understood. This study provides new evidence of positive forest management effects on the phyllosphere microbiome after extreme drought, from the perspectives of community diversity, structure, network inference, keystone species, and assembly processes. In managed Qinghai spruce forest, the α-diversity of the phyllosphere bacterial communities increased, whereas the β-diversity decreased. In addition, the phyllosphere bacterial community became more stable and resistant, yet less complex, following forest management. Keystone species inferred from a bacterial network also changed under forest management. Furthermore, forest management mediated changes in community assembly processes, intensifying the influence of determinacy, while diminishing that of stochasticity. These findings support the hypothesis that management can re-assemble the phyllosphere bacterial community, enhance community stability, and ultimately improve tree growth. Overall, the study highlights the importance of forest management on the phyllosphere microbiome and furnishes new insights into forest conservation from the perspective of managing microbial processes and effects.
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Affiliation(s)
- Yunshi Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China
| | - Ling Jin
- College of Pharmacy, Gansu University of Chinese Medicine, Lanzhou 730000, China
| | - Minghui Wu
- Key Laboratory of Soil Ecology and Health in Universities of Yunnan Province, School of Ecology and Environmental Sciences, Yunnan University, Kunming 650091, China
| | - Bo Wang
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Na Qu
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China
| | - Huaizhe Zhou
- Test Center, National University of Defense Technology, Xi'an 710106, China
| | - Tuo Chen
- State Key Laboratory of Cryospheric Science, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China; Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China
| | - Guangxiu Liu
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western China, Xi'an 710069, China; Department of Life Science, Northwest University, Xi'an 710069, China.
| | - Gaosen Zhang
- Key Laboratory of Extreme Environmental Microbial Resources and Engineering, Lanzhou 730000, China; Key Laboratory of Desert and Desertification, Northwest Institute of Eco-Environment and Resources, Chinese Academy of Sciences, Lanzhou 730000, China.
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6
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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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Zobel M, Koorem K, Moora M, Semchenko M, Davison J. Symbiont plasticity as a driver of plant success. THE NEW PHYTOLOGIST 2024; 241:2340-2352. [PMID: 38308116 DOI: 10.1111/nph.19566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 01/12/2024] [Indexed: 02/04/2024]
Abstract
We discuss which plant species are likely to become winners, that is achieve the highest global abundance, in changing landscapes, and whether plant-associated microbes play a determining role. Reduction and fragmentation of natural habitats in historic landscapes have led to the emergence of patchy, hybrid landscapes, and novel landscapes where anthropogenic ecosystems prevail. In patchy landscapes, species with broad niches are favoured. Plasticity in the degree of association with symbiotic microbes may contribute to broader plant niches and optimization of symbiosis costs and benefits, by downregulating symbiosis when it is unnecessary and upregulating it when it is beneficial. Plasticity can also be expressed as the switch from one type of mutualism to another, for example from nutritive to defensive mutualism with increasing soil fertility and the associated increase in parasite load. Upon dispersal, wide mutualistic partner receptivity is another facet of symbiont plasticity that becomes beneficial, because plants are not limited by the availability of specialist partners when arriving at new locations. Thus, under conditions of global change, symbiont plasticity allows plants to optimize the activity of mutualistic relationships, potentially allowing them to become winners by maximizing geographic occupancy and local abundance.
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Affiliation(s)
- Martin Zobel
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Kadri Koorem
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Mari Moora
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - Marina Semchenko
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
| | - John Davison
- Institute of Ecology and Earth Sciences, University of Tartu, J. Liivi 2, Tartu, 50409, Estonia
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8
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Zhan C, Wang M. Disease resistance through M genes. NATURE PLANTS 2024; 10:352-353. [PMID: 38409293 DOI: 10.1038/s41477-024-01644-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Affiliation(s)
- Chengfang Zhan
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China
- State Key Laboratory of Rice Biology & Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
- State Key Laboratory of Rice Biology & Breeding, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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9
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Ren P, Sun A, Jiao X, Chen QL, Li F, He JZ, Hu HW. National-scale investigation reveals the dominant role of phyllosphere fungal pathogens in sorghum yield loss. ENVIRONMENT INTERNATIONAL 2024; 185:108511. [PMID: 38382404 DOI: 10.1016/j.envint.2024.108511] [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: 01/23/2024] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 02/23/2024]
Abstract
Fungal plant pathogens threaten crop production and sustainable agricultural development. However, the environmental factors driving their diversity and nationwide biogeographic model remain elusive, impacting our capacity to predict their changes under future climate scenarios. Here, we analyzed potential fungal plant pathogens from 563 samples collected from 57 agricultural fields across China. Over 28.0% of fungal taxa in the phyllosphere were identified as potential plant pathogens, compared to 22.3% in the rhizosphere. Dominant fungal plant pathogen groups were Cladosporium (in the phyllosphere) and Fusarium (in the rhizosphere), with higher diversity observed in the phyllosphere than in rhizosphere soil. Deterministic processes played an important role in shaping the potential fungal plant pathogen community assembly in both habitats. Mean annual precipitation and temperature were the most important factor influencing phyllosphere fungal plant pathogen richness. Significantly negative relationships were found between fungal pathogen diversity and sorghum yield. Notably, compared to the rhizosphere, the phyllosphere fungal plant pathogen diversity played a more crucial role in sorghum yield. Together, our work provides novel insights into the factors governing the spatial patterns of fungal plant pathogens in the crop microbiome, and highlights the potential significance of aboveground phyllosphere fungal plant pathogens in crop productivity.
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Affiliation(s)
- Peixin Ren
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Xiaoyan Jiao
- College of Resource and Environment, Shanxi Agricultural University, Taiyuan 030031, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Fangfang Li
- Key Laboratory for Humid Subtropical Eco-geographical Processes of the Ministry of Education, School of Geographical Sciences, Fujian Normal University, Fuzhou 350007, China
| | - Ji-Zheng He
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Hang-Wei Hu
- School of Agriculture, Food and Ecosystem Sciences, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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10
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Muneer MA, Chen X, Wang H, Munir MZ, Afridi MS, Yan X, Ji B, Li W, Wu L, Zheng C. Unraveling two decades of phyllosphere endophytes: tracing research trends and insights through visualized knowledge maps, with emphasis on microbial interactions as emerging frontiers. STRESS BIOLOGY 2024; 4:12. [PMID: 38319560 PMCID: PMC10847081 DOI: 10.1007/s44154-024-00148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/07/2024] [Indexed: 02/07/2024]
Abstract
Phyllosphere endophytes play a critical role in a myriad of biological functions, such as maintaining plant health and overall fitness. They play a determinative role in crop yield and quality by regulating vital processes, such as leaf functionality and longevity, seed mass, apical growth, flowering, and fruit development. This study conducted a comprehensive bibliometric analysis aiming to review the prevailing research trajectories in phyllosphere endophytes and harness both primary areas of interest and emerging challenges. A total of 156 research articles on phyllosphere endophytes, published between 2002 and 2022, were retrieved from the Web of Science Core Collection (WoSCC). A systematic analysis was conducted using CiteSpace to visualize the evolution of publication frequency, the collaboration network, the co-citation network, and keywords co-occurrence. The findings indicated that initially, there were few publications on the topic of phyllosphere endophytes. However, from 2011 onwards, there was a notable increase in the number of publications on phyllosphere endophytes, gaining worldwide attention. Among authors, Arnold, A Elizabeth is widely recognized as a leading author in this research area. In terms of countries, the USA and China hold the highest rankings. As for institutional ranking, the University of Arizona is the most prevalent and leading institute in this particular subject. Collaborative efforts among the authors and institutions tend to be confined to small groups, and a large-scale collaborative network needs to be established. This study identified the influential journals, literature, and hot research topics. These findings also highlight the interconnected nature of key themes, e.g., phyllosphere endophyte research revolves around the four pillars: diversity, fungal endophytes, growth, and endophytic fungi. This study provides an in-depth perspective on phyllosphere endophytes studies, revealing the identification of biodiversity and microbial interaction of phyllosphere endophytes as the principal research frontiers. These analytical findings not only elucidate the recent trajectory of phyllosphere endophyte research but also provide invaluable insights for similar studies and their potential applications on a global scale.
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Affiliation(s)
- Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention; Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Hexin Wang
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention; Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Zeeshan Munir
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199, Lishui Rd, Shenzhen, 518055, China
| | - Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras (UFLA), Lavras, MG, CEP 37200-900, Brazil
| | - Xiaojun Yan
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baoming Ji
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Wenqing Li
- Fujian Institute of Tobacco Sciences, Fuzhou, 350013, China
| | - Liangquan Wu
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaoyuan Zheng
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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11
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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [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: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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12
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [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: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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13
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Liu D, Iqbal S, Gui H, Xu J, An S, Xing B. Nano-Iron Oxide (Fe 3O 4) Mitigates the Effects of Microplastics on a Ryegrass Soil-Microbe-Plant System. ACS NANO 2023; 17:24867-24882. [PMID: 38084717 DOI: 10.1021/acsnano.3c05809] [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: 12/27/2023]
Abstract
To understand microplastic-nanomaterial interactions in agricultural systems, a randomized block 90-day pot experiment was set up to cultivate ryegrass seedings in a typical red sandy soil amended with compost (1:9 ratio). Polyvinyl chloride (PVC) and polyethylene (PE) microplastic (MP) contaminants were added into pot soils at 0.1 and 10%, whereas nano-Fe3O4 (as nanoenabled agrochemicals) was added at 0.1% and 0.5% in comparison with chemical-free controls. The combination of nano-Fe3O4 and MPs significantly increased the soil pH (+3% to + 17%) but decreased the total nitrogen content (-9% to - 30%; P < 0.05). The treatment group with both nano-Fe3O4 and PE had the highest total soil C (29 g kg-1 vs 20 g kg-1 in control) and C/N ratio (13 vs 8 in control). Increased rhizosphere nano-Fe3O4 concentrations promoted ryegrass growth (+42% dry weight) by enhancing the chlorophyll (+20%) and carotenoid (+15%) activities. Plant leaf and root peroxidase enzyme activity was more significantly affected by nano-Fe3O4 with PVC (+15%) than with PE (+6%). Nano-Fe3O4 significantly changed the ryegrass bacterial community structure from belowground (the rhizoplane and root endosphere) to aboveground (the phylloplane). Under MP contamination, the addition of nano-Fe3O4 increased bacterial diversity (+0.35%) and abundance (+30%) in the phylloplane and further intensified the connectivity of ryegrass aboveground bacterial networks (positive association increased 17%). The structural equation model showed that the change in the plant microbiome was associated with the rhizosphere microbiome. Overall, these findings imply the positive influences of nano-Fe3O4 on the soil-microbe-plant system and establish a method to alleviate the harmful effects of MP accumulation in soils.
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Affiliation(s)
- Dong Liu
- The Germplasm Bank of Wild Species, Yunnan Key Laboratory for Fungal Diversity and Green Development, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, Yunnan, People's Republic of China
| | - Shahid Iqbal
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Heng Gui
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Jianchu Xu
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
- Centre for Mountain Futures (CMF), Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, People's Republic of China
| | - Shaoshan An
- State Key Laboratory of Soil Erosion and Dryland Farming on the Loess Plateau, Institute of Soil and Water Conservation, Northwest A&F University, Yangling 712100, People's Republic of China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts, Amherst, Massachusetts 01003, United States
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14
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Meyer KM, Muscettola IE, Vasconcelos ALS, Sherman JK, Metcalf CJE, Lindow SE, Koskella B. Conspecific versus heterospecific transmission shapes host specialization of the phyllosphere microbiome. Cell Host Microbe 2023; 31:2067-2079.e5. [PMID: 38029741 DOI: 10.1016/j.chom.2023.11.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 09/09/2023] [Accepted: 11/01/2023] [Indexed: 12/01/2023]
Abstract
In disease ecology, pathogen transmission among conspecific versus heterospecific hosts is known to shape pathogen specialization and virulence, but we do not yet know if similar effects occur at the microbiome level. We tested this idea by experimentally passaging leaf-associated microbiomes either within conspecific or across heterospecific plant hosts. Although conspecific transmission results in persistent host-filtering effects and more within-microbiome network connections, heterospecific transmission results in weaker host-filtering effects but higher levels of interconnectivity. When transplanted onto novel plants, heterospecific lines are less differentiated by host species than conspecific lines, suggesting a shift toward microbiome generalism. Finally, conspecific lines from tomato exhibit a competitive advantage on tomato hosts against those passaged on bean or pepper, suggesting microbiome-level host specialization. Overall, we find that transmission mode and previous host history shape microbiome diversity, with repeated conspecific transmission driving microbiome specialization and repeated heterospecific transmission promoting microbiome generalism.
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Affiliation(s)
- Kyle M Meyer
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Isabella E Muscettola
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ana Luisa S Vasconcelos
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Soil Science, College of Agriculture "Luiz de Queiroz", Universidade de São Paulo, Piracicaba 13418-900, Brazil
| | - Julia K Sherman
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - C Jessica E Metcalf
- Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
| | - Steven E Lindow
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, San Francisco, CA 94158, USA
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15
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Emmenegger B, Massoni J, Pestalozzi CM, Bortfeld-Miller M, Maier BA, Vorholt JA. Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning. Nat Commun 2023; 14:7983. [PMID: 38042924 PMCID: PMC10693592 DOI: 10.1038/s41467-023-43793-z] [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: 06/20/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.
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Affiliation(s)
| | - Julien Massoni
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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16
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Li R, Chen S, Matsumoto H, Gouda M, Gafforov Y, Wang M, Liu Y. Predicting rice diseases using advanced technologies at different scales: present status and future perspectives. ABIOTECH 2023; 4:359-371. [PMID: 38106429 PMCID: PMC10721578 DOI: 10.1007/s42994-023-00126-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 10/30/2023] [Indexed: 12/19/2023]
Abstract
The past few years have witnessed significant progress in emerging disease detection techniques for accurately and rapidly tracking rice diseases and predicting potential solutions. In this review we focus on image processing techniques using machine learning (ML) and deep learning (DL) models related to multi-scale rice diseases. Furthermore, we summarize applications of different detection techniques, including genomic, physiological, and biochemical approaches. In addition, we also present the state-of-the-art in contemporary optical sensing applications of pathogen-plant interaction phenotypes. This review serves as a valuable resource for researchers seeking effective solutions to address the challenges of high-throughput data and model recognition for early detection of issues affecting rice crops through ML and DL models.
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Affiliation(s)
- Ruyue Li
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
- College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, 310058 China
| | - Sishi Chen
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058 China
| | - Mostafa Gouda
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
- Department of Nutrition and Food Science, National Research Centre, Giza, 12622 Egypt
| | - Yusufjon Gafforov
- Central Asian Center for Development Studies, New Uzbekistan University, Tashkent, 100000 Uzbekistan
| | - Mengcen Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, 310058 China
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, 060-8589 Japan
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, 310058 China
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17
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Hu JP, Zhang MX, Lü ZL, He YY, Yang XX, Khan A, Xiong YC, Fang XL, Dong QM, Zhang JL. Grazing practices affect phyllosphere and rhizosphere bacterial communities of Kobresia humilis by altering their network stability. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 900:165814. [PMID: 37517723 DOI: 10.1016/j.scitotenv.2023.165814] [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: 06/09/2023] [Revised: 07/22/2023] [Accepted: 07/24/2023] [Indexed: 08/01/2023]
Abstract
The primary utilization strategy for meadow grasslands on the Qinghai-Tibet Plateau (QTP) is livestock grazing. This practice is considered as one of the major drivers of plant-associated bacterial community construction and changes in soil properties. The species of Kobresia humilis is considered as the most dominant one in grasslands. However, how different grazing practices affect the phyllosphere and rhizosphere bacterial communities of K. humilis is unknown. To address this issue, the effects of the grazing enclosure (GE), single-species grazing (YG and SG, representing yak only and sheep only, respectively), and different ratios of grazing (ratio of yak to sheep is 1:2, 1:4, and 1:6, represented by MG1:2, MG1:4, and MG1:6, respectively) on the dominant plant of K. humilis, it's phyllosphere and rhizosphere bacteria, and soil properties were investigated using artificially controlled grazing and grazing enclosure. Our data showed that grazing enclosure enhanced vegetation coverage, and rhizosphere bacterial richness and diversity, while reduced plant number and bacterial network stability of K. humilis. The NO3--N, K+, and Cl- concentrations were lower under grazing compared to GE. SG reduced the concentration of NH4+-N, TN, K+, and Na+ compared to YG. Moderate grazing intensity had a lower relative abundance of the r-strategists (Bacteroidota and Gammaproteobacteria) with higher bacterial network stability. Yak and sheep grazing showed reversed impacts on the bacterial network stability between the phyllosphere and rhizosphere of K. humilis. Proteobacteria and Actinobacteriota were identified in the molecular ecological network analysis as keystone taxa in the phyllosphere and rhizosphere networks, respectively, under all treatments. This study explained why sheep grazing has more adverse effects on grazing-tolerant grass species, K. humilis, than yak grazing, and will contribute to a better understanding of the impacts of different grazing practices and grazing enclosure on alpine grassland ecosystems on the QTP.
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Affiliation(s)
- Jin-Peng Hu
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Ming-Xu Zhang
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Zhao-Long Lü
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Yuan-Yuan He
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xiao-Xia Yang
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, People's Republic of China
| | - Aziz Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - You-Cai Xiong
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; College of Ecology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Xiang-Ling Fang
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China
| | - Quan-Min Dong
- Qinghai Provincial Key Laboratory of Adaptive Management on Alpine Grassland, Qinghai Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining 810016, People's Republic of China.
| | - Jin-Lin Zhang
- Center for Grassland Microbiome; State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Engineering Research Center of Grassland Industry, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730000, People's Republic of China.
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18
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Wang M, Cernava T. Soterobionts: disease-preventing microorganisms and proposed strategies to facilitate their discovery. Curr Opin Microbiol 2023; 75:102349. [PMID: 37369150 DOI: 10.1016/j.mib.2023.102349] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 05/25/2023] [Accepted: 05/26/2023] [Indexed: 06/29/2023]
Abstract
Crop production and the food security that it provides are currently threatened worldwide by plant pathogens. Conventional control measures, such as breeding for resistant plants, are progressively losing their efficacy due to rapidly evolving pathogens. The plant microbiota contributes to essential functions of host plants, among which is protection against pathogens. Only recently, microorganisms that provide holistic protection against certain plant diseases were identified. They were termed as 'soterobionts' and extend their host's immune system, which results in disease-resistant phenotypes. Further exploration of such microorganisms could not only provide answers to better understand the implications of the plant microbiota in health and disease, but also contribute to new developments in agriculture and beyond. The aim of this work is to point out how the identification of plant-associated soterobionts can be facilitated, and to discuss technologies that will be required to enable this.
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Affiliation(s)
- Mengcen Wang
- College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China; State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou 310058, China; Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom.
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19
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Sha H, Liu X, Xiao X, Zhang H, Gu X, Chen W, Mao B. Nigrospora oryzae Causing Leaf Spot Disease on Chrysanthemum × morifolium Ramat and Screening of Its Potential Antagonistic Bacteria. Microorganisms 2023; 11:2224. [PMID: 37764068 PMCID: PMC10537370 DOI: 10.3390/microorganisms11092224] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/29/2023] Open
Abstract
Chrysanthemum × morifolium Ramat. is a famous perennial herb with medicinal, edible, and ornamental purposes, but the occurrence of plant diseases can reduce its value. A serious disease that caused leaf spots in C. morifolium appeared in 2022 in Tongxiang City, Zhejiang Province, China. The C. morifolium leaves with brown spots were collected and used for pathogen isolation. By completing Koch's postulates, it was proven that the isolate had pathogenicity to infect C. morifolium. It was determined that the pathogen isolated from chrysanthemum leaves was Nigrospora oryzae, through morphology and a multilocus sequence analysis method using a combination of the internal transcribed spacer gene (ITS), beta-tubulin gene (TUB2), and translation elongation factor 1-alpha gene (TEF1-α). This is the first report of C. morifolium disease caused by N. oryzae in the world. Through dual culture assay on PDA plates, 12 strains of bacteria with antagonistic effects were selected from 231 strains from the C. morifolium phyllosphere, among which Bacillus siamensis D65 had the best inhibitory effect on N. oryzae growth. In addition, the components of a strain D65 fermentation broth were profiled by SPME-GC-Q-TOF analysis, providing a foundation for further application and research of biological control.
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Affiliation(s)
- Haodong Sha
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Xinyi Liu
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Xiaoe Xiao
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
| | - Han Zhang
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Xueting Gu
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Weiliang Chen
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
| | - Bizeng Mao
- Institute of Biotechnology, College of Agriculture & Biotechnology, Zhejiang University, Hangzhou 310058, China
- Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects, Hangzhou 310058, China
- Zhejiang Tongxiang Hangbaiju Technology Academy, Tongxiang 314500, China
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20
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Thomazella DPDT, Teixeira PJPL. Microbiome-mediated metabolic defence. NATURE PLANTS 2023; 9:1174-1175. [PMID: 37433973 DOI: 10.1038/s41477-023-01470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
| | - Paulo José Pereira Lima Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil.
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21
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Liu X, Matsumoto H, Lv T, Zhan C, Fang H, Pan Q, Xu H, Fan X, Chu T, Chen S, Qiao K, Ma Y, Sun L, Wang Q, Wang M. Phyllosphere microbiome induces host metabolic defence against rice false-smut disease. Nat Microbiol 2023; 8:1419-1433. [PMID: 37142774 DOI: 10.1038/s41564-023-01379-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 04/04/2023] [Indexed: 05/06/2023]
Abstract
Mutualistic interactions between host plants and their microbiota have the potential to provide disease resistance. Most research has focused on the rhizosphere, but it is unclear how the microbiome associated with the aerial surface of plants protects against infection. Here we identify a metabolic defence underlying the mutualistic interaction between the panicle and the resident microbiota in rice to defend against a globally prevalent phytopathogen, Ustilaginoidea virens, which causes false-smut disease. Analysis of the 16S ribosomal RNA gene and internal transcribed spacer sequencing data identified keystone microbial taxa enriched in the disease-suppressive panicle, in particular Lactobacillus spp. and Aspergillus spp. Integration of these data with primary metabolism profiling, host genome editing and microbial isolate transplantation experiments revealed that plants with these taxa could resist U. virens infection in a host branched-chain amino acid (BCAA)-dependent manner. Leucine, a predominant BCAA, suppressed U. virens pathogenicity by inducing apoptosis-like cell death through H2O2 overproduction. Additionally, preliminary field experiments showed that leucine could be used in combination with chemical fungicides with a 50% reduction in dose but similar efficacy to higher fungicide concentrations. These findings may facilitate protection of crops from panicle diseases prevalent at a global scale.
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Affiliation(s)
- Xiaoyu Liu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- Australian Research Council Centre of Excellence in Plant Energy Biology, The University of Western Australia, Perth, Western Australia, Australia
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Tianxing Lv
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Hongda Fang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Qianqian Pan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haorong Xu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Xiaoyan Fan
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
- CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Tianyi Chu
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Sunlu Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, China
| | - Kun Qiao
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Youning Ma
- China National Rice Research Institute, Hangzhou, China
| | - Li Sun
- Department of Neurobiology, School of Medicine, Zhejiang University, Hangzhou, China
| | - Qiangwei Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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22
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Lv T, Zhan C, Pan Q, Xu H, Fang H, Wang M, Matsumoto H. Plant pathogenesis: Toward multidimensional understanding of the microbiome. IMETA 2023; 2:e129. [PMID: 38867927 PMCID: PMC10989765 DOI: 10.1002/imt2.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 06/14/2024]
Abstract
Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.
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Affiliation(s)
- Tianxing Lv
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qianqian Pan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Haorong Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hongda Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Global Education Program for AgriScience Frontiers, Graduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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23
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Zhang G, Shi L, Liu C, Mao R, Xia B, Huang Z, Wei X, Wu L, Zheng Y, Wei G, Xu J, Gao S, Chen S, Dong L. Modules in robust but low-efficiency phyllosphere fungal networks drive saponin accumulation in leaves of different Panax species. ENVIRONMENTAL MICROBIOME 2023; 18:57. [PMID: 37438802 DOI: 10.1186/s40793-023-00516-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 07/07/2023] [Indexed: 07/14/2023]
Abstract
BACKGROUND The phyllosphere mycobiome plays a crucial role in plant fitness and ecosystem functions. The complex microbial ecological networks (MEN) formed by these fungi remain poorly understood, particularly with regard to their organization strategy and their contributions to plant secondary metabolites such as saponin. RESULTS In this study, we constructed six MENs from leaf epiphytic and endophytic mycobiomes of three Panax species distributed in the northeast and southwest ends of mainland China. Hub nodes were absent in these MENs, which were significantly more complex, robust, and less efficient compared to random graphs (P < 0.05), indicating a hub-independent high-robustness strategy to maintain structural homeostasis. The important roles of specific MEN modules in shaping leaf saponin profiles of each Panax species were proved by multiple machine learning algorithms. Positive regulation modules (PRMs) of total saponin content were further identified, which exhibited more deterministic ecological assembly and comprised of highly connected nodes as well as higher proportion of plant-associated fungal guilds compared to other network members, indicating their tight links with host plant. The significant and direct effects (P < 0.05) of PRMs on total saponin accumulation were validated by well-fitted structural equation models (χ2 < 0.3, P > 0.5). Taxonomic analysis revealed that Pleosporales and Chaetothyriales were significantly overrepresented by positive regulation taxa (PRT) of total saponin content (FDR < 0.05). Across PRT identified in three Panax species, Epicoccum and Coniothyrium were conservatively present, while species-specific taxa such as Agaricales were also found, indicating the conservatism and specificity of plant-fungi interactions associated with leaf saponin accumulation in Panax genus. CONCLUSIONS These findings provide a foundation for understanding mechanisms maintaining the steady state of phyllosphere mycobiome in healthy plant, and offer clues for engineering phyllosphere mycobiome to improve the accumulation of bioactive secondary metabolites on the basis of network modules.
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Affiliation(s)
- Guozhuang Zhang
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liping Shi
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Congsheng Liu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Fujian, 363000, China
| | - Renjun Mao
- School of Life Sciences, Yan' an University, Yan' an, 716000, China
| | - Bing Xia
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Zhixin Huang
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Fujian, 363000, China
| | - Xiuye Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Lixuan Wu
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Fujian, 363000, China
| | - Yuqing Zheng
- Zhangzhou Pien Tze Huang Pharmaceutical Co., Ltd., Fujian, 363000, China
| | - Guangfei Wei
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Jia Xu
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shuangrong Gao
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Shilin Chen
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, China
| | - Linlin Dong
- Key Laboratory of Beijing for Identification and Safety Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
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24
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Wang M, Cernava T. Editorial: The phyllosphere microbiome. FRONTIERS IN PLANT SCIENCE 2023; 14:1234843. [PMID: 37426976 PMCID: PMC10325780 DOI: 10.3389/fpls.2023.1234843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Accepted: 06/12/2023] [Indexed: 07/11/2023]
Affiliation(s)
- Mengcen Wang
- State Key Laboratory of Rice Biology, and Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, United Kingdom
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
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