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Yan X, White JC, He E, Peijnenburg WJGM, Zhang P, Qiu H. Temporal Dynamics of Copper-Based Nanopesticide Transfer and Subsequent Modulation of the Interplay Between Host and Microbiota Across Trophic Levels. ACS NANO 2024. [PMID: 39171664 DOI: 10.1021/acsnano.4c06047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
During agricultural production, significant quantities of copper-based nanopesticides (CBNPs) may be released into terrestrial ecosystems through foliar spraying, thereby posing a potential risk of biological transmission via food chains. Consequently, we investigated the trophic transfer of two commonly available commercial CBNPs, Reap2000 (RP) and HolyCu (HC), in a plant-caterpillar terrestrial food chain and evaluated impacts on host microbiota. Upon foliar exposure (with 4 rounds of spraying, totaling 6.0 mg CBNPs per plant), leaf Cu accumulation levels were 726 ± 180 and 571 ± 121 mg kg-1 for RP and HC, respectively. HC exhibited less penetration through the cuticle compared to RP (RP: 55.5%; HC: 32.8%), possibly due to size exclusion limitations. While caterpillars accumulated higher amounts of RP, HC exhibited a slightly higher trophic transfer factor (TTF; RP: 0.69 ± 0.20; HC: 0.74 ± 0.17, p > 0.05) and was more likely to be transferred through the food chain. The application of RP promoted the dispersal of phyllosphere microbes and perturbed the original host intestinal microbiota, whereas the HC group was largely host-modulated (control: 65%; RP: 94%; HC: 34%). Integrating multiomics analyses and modeling approaches, we elucidated two pathways by which plants exert bottom-up control over caterpillar health. Beyond the direct transmission of phyllosphere microbes, the leaf microbiome recruited upon exposure to CBNPs further influenced the ingestion behavior and intestinal microbiota of caterpillars via altered leaf metabolites. Elevated Proteobacteria abundance benefited caterpillar growth with RP, while the reduction of Proteobacteria with HC increased the risk of lipid metabolism issues and gut disease. The recruited Bacteroidota in the RP phyllosphere proliferated more extensively into the caterpillar gut to enhance stress resistance. Overall, the gut microbes reshaped in RP caterpillars exerted a strong regulatory effect on host health. These findings expand our understanding of the dynamic transmission of host-microbiota interactions with foliar CBNPs exposure, and provide critical insight necessary to ensure the safety and sustainability of nanoenabled agricultural strategies.
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Affiliation(s)
- Xuchen Yan
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Jason C White
- The Connecticut Agricultural Experiment Station, New Haven06511, Connecticut, United States
| | - Erkai He
- School of Geographic Sciences, East China Normal University, Shanghai 200241, China
| | - Willie J G M Peijnenburg
- Center for the Safety of Substances and Products, National Institute of Public Health and the Environment, Bilthoven 3720BA, The Netherlands
- Institute of Environmental Sciences, Leiden University, Leiden 2300RA, The Netherlands
| | - Peng Zhang
- School of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston B15 2TT, Birmingham, U.K
| | - Hao Qiu
- School of Environmental Science and Engineering, Shanghai Jiao Tong University, Shanghai 200240, China
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Wu WF, Li XY, Chen SC, Jin BJ, Wu CY, Li G, Sun CL, Zhu YG, Lin XY. Nitrogen fertilization modulates rice phyllosphere functional genes and pathogens through fungal communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 929:172622. [PMID: 38642761 DOI: 10.1016/j.scitotenv.2024.172622] [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: 01/25/2024] [Revised: 04/16/2024] [Accepted: 04/17/2024] [Indexed: 04/22/2024]
Abstract
The phyllosphere is a vital yet often neglected habitat hosting diverse microorganisms with various functions. However, studies regarding how the composition and functions of the phyllosphere microbiome respond to agricultural practices, like nitrogen fertilization, are limited. This study investigated the effects of long-term nitrogen fertilization with different levels (CK, N90, N210, N330) on the functional genes and pathogens of the rice phyllosphere microbiome. Results showed that the relative abundance of many microbial functional genes in the rice phyllosphere was significantly affected by nitrogen fertilization, especially those involved in C fixation and denitrification genes. Different nitrogen fertilization levels have greater effects on fungal communities than bacteria communities in the rice phyllosphere, and network analysis and structural equation models further elucidate that fungal communities not only changed bacterial-fungal inter-kingdom interactions in the phyllosphere but also contributed to the variation of biogeochemical cycle potential. Besides, the moderate nitrogen fertilization level (N210) was associated with an enrichment of beneficial microbes in the phyllosphere, while also resulting in the lowest abundance of pathogenic fungi (1.14 %). In contrast, the highest abundance of pathogenic fungi (1.64 %) was observed in the highest nitrogen fertilization level (N330). This enrichment of pathogen due to high nitrogen level was also regulated by the fungal communities, as revealed through SEM analysis. Together, we demonstrated that the phyllosphere fungal communities were more sensitive to the nitrogen fertilization levels and played a crucial role in influencing phyllosphere functional profiles including element cycling potential and pathogen abundance. This study expands our knowledge regarding the role of phyllosphere fungal communities in modulating the element cycling and plant health in sustainable agriculture.
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Affiliation(s)
- Wei-Feng Wu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Xin-Yuan Li
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Song-Can Chen
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna 1030, Austria
| | - Bing-Jie Jin
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Chun-Yan Wu
- Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, PR China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, PR China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, PR China
| | - Cheng-Liang Sun
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China
| | - Yong-Guan Zhu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, PR China
| | - Xian-Yong Lin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, PR China.
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Ouyang Y, Cheng Q, Cheng C, Tang Z, Huang Y, Tan E, Ma S, Lin X, Xie Y, Zhou H. Effects of plants-associated microbiota on cultivation and quality of Chinese herbal medicines. CHINESE HERBAL MEDICINES 2024; 16:190-203. [PMID: 38706825 PMCID: PMC11064599 DOI: 10.1016/j.chmed.2022.12.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 10/24/2022] [Accepted: 12/29/2022] [Indexed: 02/05/2023] Open
Abstract
Microbial resource influences the life activities of medicinal plants from several perspectives. Endophytes, rhizosphere microorganisms, and other environmental microorganisms play essential roles in medicinal plant growth and development, plant yield, and clinical efficacy. The microbiota can influence the biosynthesis of active compounds in medicinal plants by stimulating specific metabolic pathways. They induce host plants to improve their resistance to environmental stresses by accumulating secondary metabolites. Microorganisms can interact with their host plants to produce long-term, targeted selection results and improve their ability to adapt to the environment. Due to the interdependence and interaction between microorganisms and medicinal plants, Chinese herbal medicines (CHMs) quality is closely related to the associated microorganisms. This review summarizes the relationship between medicinal plants and their associated microorganisms, including their species, distribution, life activities, and metabolites. Microorganisms can aid in quality control, improve the efficacy of medicinal plants, and provide markers for identifying the origin and storage time of CHMs. Therefore, a comprehensive understanding of the relationship between microorganisms and medicinal plants will help to control the quality of CHMs from different perspectives.
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Affiliation(s)
- Yue Ouyang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Qiqing Cheng
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- School of Pharmacy, Hubei University of Science and Technology, Xianning 437100, China
| | - Chunsong Cheng
- Key Laboratory of Plant Ex-situ Conservation and Research Center of Resource Plant, Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang 332900, China
| | - Ziyu Tang
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Yufeng Huang
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
| | - Eyu Tan
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
| | - Shaofeng Ma
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Xinheng Lin
- Jiangmen Wuyi Hospital of Traditional Chinese Medicine, Jiangmen 529020, China
| | - Ying Xie
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
| | - Hua Zhou
- Guangdong Provincial Hospital of Chinese Medicine, Guangdong Provincial Academy of Chinese Medical Sciences, State Key Laboratory of Dampness Syndrome of Chinese Medicine, Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong-Hong Kong-Macau Joint Lab on Chinese Medicine and Immune Disease Research, Guangzhou 510006, China
- Faculty of Chinese Medicine, Macau University of Science and Technology, Macao 999078, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, Ministry of Education, Guangzhou University of Chinese Medicine, Guangzhou 510006, China
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4
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Dang N, Xing W, Gai X, Chen G. Modulating phyllosphere microbiome structure and function in Loropetalum chinense and Osmanthus fragrans: The impact of foliar dust and heavy metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170250. [PMID: 38253107 DOI: 10.1016/j.scitotenv.2024.170250] [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: 10/04/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Trees can effectively capture airborne particles and improve air quality. However, the specific response of phyllosphere microbiome (PMo) in different plant species to particulate matter (PM) and the heavy metals it contains are not yet fully understood. In this study, we investigated the impact of PM on the diversity and function of PMo in Loropetalum chinense and Osmanthus fragrans trees grown in industrial and clean zones with varying levels of PM pollution. Our findings revealed that leaf dust had a significant negative effect on microbial richness, with O. fragrans exhibiting higher microbial diversity than L. chinense. The dominant phylum of phyllosphere bacteria in all samples was Proteobacteria, and the dominant genera were Stenotrophomonas and Delftia. The relative abundance of these genera varied significantly among plant species and regions. Our results showed that PM had a significant impact on the community composition of PMo, with the presence of heavy metals exerting a greater effect than particle size. Moreover, the foliar microbial community of plants grown in industrial zones exhibited significantly higher metabolic functions related to stress resistance and disease resistance compared to plants in control zones. These findings highlight the structural and functional responses of PMo to PM and indicate their potential for enhancing plant adaptation to environmental stress.
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Affiliation(s)
- Ning Dang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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5
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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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6
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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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7
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Shao Q, Ran Q, Li X, Dong C, Huang J, Han Y. Deciphering the effect of phytohormones on the phyllosphere microbiota of Eucommia ulmoides. Microbiol Res 2024; 278:127513. [PMID: 37837828 DOI: 10.1016/j.micres.2023.127513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/30/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
Phytohormones are key signals mediating plant-microbe molecular communication. However, their roles in driving phyllosphere microbiota assembly remain unclear. Here, high throughput target assays for 12 phytohormones and microbial amplicon sequencing techniques were used to reveal the effects of hormone components on phyllosphere microbiota of Eucommia ulmoides. Most of the phytohormone components in old leaves were lower than in tender leaves, such as indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acid (JA), but the phyllosphere microbial community diversity in the older leaves was significantly higher than in the tender leaves, with more complex and aggregated microbial cooccurrence network. The E. ulmoides phyllosphere microbiota at tender and older leaf stage were dominated by the same dominant taxa at the phylum level, with Ascomycota and Basidiomycota as the main fungal taxa and Actinobacteriota, Bacteroidota, Firmicutes and Proteobacteria as the main bacterial taxa. FUNGuild and FAPROTAX functional predictions revealed that the high abundance functional groups of the E. ulmoides phyllosphere microbes were similar at tender and old leaf stages, with fungal functions mainly involving in plant pathogen, undefined saprotroph and endophyte, and bacterial functions mainly involving in chemoheterotrophy, fermentation and aerobic_chemoheterotrophy. Additionally, mantel test and variance partitioning analysis showed that IAA and N6-(delta 2-isopentenyl)-adenine (IP) were key phytohormones impacting the E. ulmoides phyllosphere microbiota, and their effects were largely interdependent. Our results improve the understanding of composition, diversity, function and influencing factors of phyllosphere microbiota, which might provide cue for sustainable agriculture and forestry management via precise regulation of the phyllosphere microbiota.
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Affiliation(s)
- Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Qingsong Ran
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Xu Li
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350108, Fujian, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China.
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8
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Gao M, Zhang Q, Lei C, Lu T, Qian H. Atmospheric antibiotic resistome driven by air pollutants. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 902:165942. [PMID: 37543315 DOI: 10.1016/j.scitotenv.2023.165942] [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: 07/07/2023] [Revised: 07/29/2023] [Accepted: 07/29/2023] [Indexed: 08/07/2023]
Abstract
The atmosphere is an important reservoir and habitat for antibiotic resistance genes (ARGs) and is a main pathway to cause potential health risks through inhalation and ingestion. However, the distribution characteristics of ARGs in the atmosphere and whether they were driven by atmospheric pollutants remain unclear. We annotated 392 public air metagenomic data worldwide and identified 1863 ARGs, mainly conferring to tetracycline, MLS, and multidrug resistance. We quantified these ARG's risk to human health and identified their principal pathogenic hosts, Burkholderia and Staphylococcus. Additionally, we found that bacteria in particulate contaminated air carry more ARGs than in chemically polluted air. This study revealed the influence of typical pollutants in the global atmosphere on the dissemination and risk of ARGs, providing a theoretical basis for the prevention and mitigation of the global risks associated with ARGs.
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Affiliation(s)
- Mingyu Gao
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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9
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Liu Y, Zhang B, Yao Y, Wang B, Cao Y, Shen Y, Jia X, Xu F, Song Z, Zhao C, Gao H, Guo P. Insight into the plant-associated bacterial interactions: Role for plant arsenic extraction and carbon fixation. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 894:164960. [PMID: 37348724 DOI: 10.1016/j.scitotenv.2023.164960] [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: 04/05/2023] [Revised: 06/12/2023] [Accepted: 06/15/2023] [Indexed: 06/24/2023]
Abstract
This study investigated the interactions between rhizosphere and endosphere bacteria during phytoextraction and how the interactions affect arsenic (As) extraction and carbon (C) fixation of plants. Pot experiments, high-throughput sequencing, metabonomics, and network analysis were integrated. Results showed that positive correlations dominated the interconnections within modules (>95 %), among modules (100 %), and among keystone taxa (>72 %) in the bacterial networks of plant rhizosphere, root endosphere, and shoot endosphere. This confirmed that cooperative interactions occurred between bacteria in the rhizosphere and endosphere during phytoextraction. Modules and keystone taxa positively correlating with plant As extraction and C fixation were identified, indicating that modules and keystone taxa promoted plant As extraction and C fixation simultaneously. This is mainly because modules and keystone taxa in plant rhizosphere, root endosphere, and shoot endosphere carried arsenate reduction and C fixation genes. Meanwhile, they up-regulated the significant metabolites related to plant As tolerance. Additionally, shoot C fixation increased peroxidase activity and biomass thereby facilitating plant As extraction was confirmed. This study revealed the mechanisms of plant-associated bacterial interactions contributing to plant As extraction and C fixation. More importantly, this study provided a new angle of view that phytoextraction can be applied to achieve multiple environmental goals, such as simultaneous soil remediation and C neutrality.
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Affiliation(s)
- Yibo Liu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Baiyu Zhang
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada A1B 3X5
| | - Ye Yao
- College of Physics, Jilin University, Changchun 130012, PR China
| | - Bo Wang
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Yiqi Cao
- Department of Civil Engineering, Faculty of Engineering and Applied Science, Memorial University, St. John's, NL, Canada A1B 3X5
| | - Yanping Shen
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Xiaohui Jia
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Fukai Xu
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Ziwei Song
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - Chengpeng Zhao
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China
| | - HongJie Gao
- Chinese Research Academy of Environmental Science, Beijing 100012, PR China.
| | - Ping Guo
- Key Laboratory of Groundwater Resources and Environment Ministry of Education, College of New Energy and Environment, Jilin University, Changchun 130012, PR China; Jilin Provincial Key Laboratory of Water Resources and Environment, Jilin University, Changchun 130012, PR China.
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10
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De Mandal S, Jeon J. Phyllosphere Microbiome in Plant Health and Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:3481. [PMID: 37836221 PMCID: PMC10575124 DOI: 10.3390/plants12193481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.
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Affiliation(s)
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
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11
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Huang XR, Neilson R, Yang LY, Deng JJ, Zhou SYD, Li H, Zhu YG, Yang XR. Urban greenspace types influence the microbial community assembly and antibiotic resistome more in the phyllosphere than in the soil. CHEMOSPHERE 2023; 338:139533. [PMID: 37459932 DOI: 10.1016/j.chemosphere.2023.139533] [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: 06/08/2023] [Revised: 07/14/2023] [Accepted: 07/15/2023] [Indexed: 07/23/2023]
Abstract
Urban greenspace (UGS) is recognized to confer significant societal benefits, but few studies explored the microbial communities and antibiotic resistance genes (ARGs) from different urban greenspace types. Here, we collected leaf and soil samples from forest, greenbelt, and parkland to analyze microbial community assembly and ARG profile. For phyllosphere fungal community, the α-diversity was higher in forest, compared to those in greenbelt and parkland. Moreover, urban greenspace types altered the community assembly. Stochastic processes had a greater effect on phyllosphere fungal community in greenbelt and parkland, while in forest they were dominated by deterministic processes. In contrast, no significant differences in bacterial community diversity, community assembly were observed between the samples collected from different urban greenspace types. A total of 153 ARGs and mobile genetic elements (MGEs) were detected in phyllosphere and soil with resistance to the majority classes of antibiotics commonly applied to humans and animals. Structural equation model further revealed that a direct association between greenspace type and ARGs in the phyllosphere even after considering the effects of all other factors simultaneously. Our findings provide new insights into the microbial communities and antibiotic resistome of urban greenspaces and the potential risk linked with human health.
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Affiliation(s)
- Xin-Rong Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee, DD2 5DA, Scotland, UK
| | - Le-Yang Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Jing-Jun Deng
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Shu-Yi-Dan Zhou
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, 723Xingke Road, Tianhe District, Guangzhou, 510650, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China; University of the Chinese Academy of Sciences, 19A Yuquan Road, Beijing, 100049, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, Chinese Academy of Sciences Haixi Industrial Technology Innovation Centerin, Beilun, Ningbo, 315830, China.
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12
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Meena KK, Sorty AM, Bitla U, Shinde AL, Kumar S, Wakchaure GC, Kumar S, Kanwat M, Singh DP. Stress-responsive gene regulation conferring salinity tolerance in wheat inoculated with ACC deaminase producing facultative methylotrophic actinobacterium. FRONTIERS IN PLANT SCIENCE 2023; 14:1249600. [PMID: 37780501 PMCID: PMC10534068 DOI: 10.3389/fpls.2023.1249600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 08/21/2023] [Indexed: 10/03/2023]
Abstract
Microbes enhance crop resilience to abiotic stresses, aiding agricultural sustainability amid rising global land salinity. While microbes have proven effective via seed priming, soil amendments, and foliar sprays in diverse crops, their mechanisms remain less explored. This study explores the utilization of ACC deaminase-producing Nocardioides sp. to enhance wheat growth in saline environments and the molecular mechanisms underlying Nocardioides sp.-mediated salinity tolerance in wheat. The Nocardioides sp. inoculated seeds were grown under four salinity regimes viz., 0 dS m-1, 5 dS m-1, 10 dS m-1, and 15 dS m-1, and vegetative growth parameters including shoot-root length, germination percentage, seedling vigor index, total biomass, and shoot-root ratio were recorded. The Nocardioides inoculated wheat plants performed well under saline conditions compared to uninoculated plants and exhibited lower shoot:root (S:R) ratio (1.52 ± 0.14 for treated plants against 1.84 ± 0.08 for untreated plants) at salinity level of 15 dS m-1 and also showed improved biomass at 5 dS m-1 and 10 dS m-1. Furthermore, the inoculated plants also exhibited higher protein content viz., 22.13 mg g-1, 22.10 mg g-1, 22.63 mg g-1, and 23.62 mg g-1 fresh weight, respectively, at 0 dS m-1, 5 dS m-1, 10 dS m-1, and 15 dS m-1. The mechanisms were studied in terms of catalase, peroxidase, superoxide dismutase, and ascorbate peroxidase activity, free radical scavenging potential, in-situ localization of H2O2 and superoxide ions, and DNA damage. The inoculated seedlings maintained higher enzymatic and non-enzymatic antioxidant potential, which corroborated with reduced H2O2 and superoxide localization within the tissue. The gene expression profiles of 18 stress-related genes involving abscisic acid signaling, salt overly sensitive (SOS response), ion transporters, stress-related transcription factors, and antioxidant enzymes were also analyzed. Higher levels of stress-responsive gene transcripts, for instance, TaABARE (~+7- and +10-fold at 10 dS m-1 and 15 dS m-1); TaHAk1 and hkt1 (~+4- and +8-fold at 15 dS m-1); antioxidant enzymes CAT, MnSOD, POD, APX, GPX, and GR (~+4, +3, +5, +4, +9, and +8 folds and), indicated actively elevated combat mechanisms in inoculated seedlings. Our findings emphasize Nocardioides sp.-mediated wheat salinity tolerance via ABA-dependent cascade and salt-responsive ion transport system. This urges additional study of methylotrophic microbes to enhance crop abiotic stress resilience.
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Affiliation(s)
- Kamlesh K. Meena
- Division of Integrated Farming System, Indian Council of Agricultural Research (ICAR)-Central Arid Zone Research Institute, Jodhpur, India
| | - Ajay M. Sorty
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Baramati, India
- Department of Environmental Science–Environmental Microbiology, Aarhus University, Roskilde, Denmark
| | - Utkarsh Bitla
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Baramati, India
| | - Akash L. Shinde
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Baramati, India
| | - Satish Kumar
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Baramati, India
- Department of Biochemistry, Indian Council of Agricultural Research (ICAR)-Directorate of Onion and Garlic Research, Pune, India
| | - Goraksha C. Wakchaure
- School of Soil Stress Management, Indian Council of Agricultural Research (ICAR)-National Institute of Abiotic Stress Management, Baramati, India
| | - Shrvan Kumar
- Division of Integrated Farming System, Indian Council of Agricultural Research (ICAR)-Central Arid Zone Research Institute, Jodhpur, India
| | - Manish Kanwat
- Division of Integrated Farming System, Indian Council of Agricultural Research (ICAR)-Central Arid Zone Research Institute, Jodhpur, India
| | - Dhananjaya P. Singh
- Indian Council of Agricultural Research (ICAR)-Crop Improvement Division, Indian Institute of Vegetable Research, Varanasi, India
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13
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Eliasson T, Sun L, Lundh Å, Höjer A, Saedén KH, Hetta M, Gonda H. Epiphytic microbiota in Swedish grass-clover herbage and the effect of silage additives on fermentation profiles and bacterial community compositions of the resulting silages. J Appl Microbiol 2023; 134:lxad196. [PMID: 37667493 DOI: 10.1093/jambio/lxad196] [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: 07/03/2023] [Revised: 08/18/2023] [Accepted: 08/26/2023] [Indexed: 09/06/2023]
Abstract
AIMS To investigate the epiphytic microbiota in grass-clover herbage harvested at different sites and occasions and to explore the effect of different silage additives on the resulting silage microbiota. METHODS AND RESULTS Herbage was harvested from grass-clover leys at geographically distributed sites in a long-term field experiment in Sweden, in early and late season of two consecutive years. Different silages were made from the herbage using: (1) no additive, (2) acid-treatment, and (3) inoculation by starter culture. Herbages were analysed for botanical and chemical composition, and the resulting silages for products of fermentation. Bacterial DNA was extracted from herbage and silage samples, followed by sequencing using Illumina 16S rRNA amplicon sequencing. Herbage microbiota showed no clear correlation to site or harvesting time. Silage additives had a major effect on the ensiling process; inoculation resulted in well fermented silages comprising a homogenous microbiota dominated by the genera Lactobacillus and Pediococcus. A minor effect of harvest time was also observed, with generally a more diverse microbiota in second-harvest silages. Untreated silages showed a higher relative abundance (RA) from non-lactic acid bacteria compared to acid-treated silages. In most silages, only a few bacterial amplicon sequence variants contributed to most of the RA. CONCLUSIONS The epiphytic microbiota in grass-clover herbage were found to be random and not dependent on site. From a microbial point of view, the most predictable and preferable silage outcome was obtained by inoculation with a starter culture. Acid-treatment with formic- and propionic acid surprisingly resulted in a less preferable silage. Silage making without additives cannot be recommended based on our results.
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Affiliation(s)
- Thomas Eliasson
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
- Norrmejerier, Umeå, SE-906 22, Sweden
| | - Li Sun
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | - Åse Lundh
- Department of Molecular Sciences, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
| | | | | | - Mårten Hetta
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Umeå, SE-901 83, Sweden
| | - Horacio Gonda
- Department of Animal Nutrition and Management, Swedish University of Agricultural Sciences, Uppsala, SE-750 07, Sweden
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14
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Lim YZ, Poh YH, Lee KC, Pointing SB, Wainwright BJ, Tan EJ. Influence of native and exotic plant diet on the gut microbiome of the Gray's Malayan stick insect, Lonchodes brevipes. Front Microbiol 2023; 14:1199187. [PMID: 37577436 PMCID: PMC10412900 DOI: 10.3389/fmicb.2023.1199187] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Accepted: 07/05/2023] [Indexed: 08/15/2023] Open
Abstract
Herbivorous insects require an active lignocellulolytic microbiome to process their diet. Stick insects (phasmids) are common in the tropics and display a cosmopolitan host plant feeding preference. The microbiomes of social insects are vertically transmitted to offspring, while for solitary species, such as phasmids, it has been assumed that microbiomes are acquired from their diet. This study reports the characterization of the gut microbiome for the Gray's Malayan stick insect, Lonchodes brevipes, reared on native and introduced species of host plants and compared to the microbiome of the host plant and surrounding soil to gain insight into possible sources of recruitment. Clear differences in the gut microbiome occurred between insects fed on native and exotic plant diets, and the native diet displayed a more species-rich fungal microbiome. While the findings suggest that phasmids may be capable of adapting their gut microbiome to changing diets, it is uncertain whether this may lead to any change in dietary efficiency or organismal fitness. Further insight in this regard may assist conservation and management decision-making.
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Affiliation(s)
- Yan Zhen Lim
- Division of Science, Yale-NUS College, Singapore, Singapore
| | - Yan Hong Poh
- Division of Science, Yale-NUS College, Singapore, Singapore
| | - Kevin C. Lee
- School of Science, Auckland University of Technology, Auckland, New Zealand
| | - Stephen Brian Pointing
- Division of Science, Yale-NUS College, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Benjamin J. Wainwright
- Division of Science, Yale-NUS College, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | - Eunice Jingmei Tan
- Division of Science, Yale-NUS College, Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
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15
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Hu S, He R, He X, Zeng J, Zhao D. Niche-Specific Restructuring of Bacterial Communities Associated with Submerged Macrophyte under Ammonium Stress. Appl Environ Microbiol 2023; 89:e0071723. [PMID: 37404156 PMCID: PMC10370296 DOI: 10.1128/aem.00717-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023] Open
Abstract
Submerged macrophytes and their epiphytic microbes form a "holobiont" that plays crucial roles in regulating the biogeochemical cycles of aquatic ecosystems but is sensitive to environmental disturbances such as ammonium loadings. Increasingly more studies suggest that plants may actively seek help from surrounding microbial communities whereby conferring benefits in responding to particular abiotic stresses. However, empirical evidence is scarce regarding how aquatic plants reconstruct their microbiomes as a "cry-for-help" against acute ammonium stress. Here, we investigated the temporal dynamics of the phyllosphere and rhizosphere bacterial communities of Vallisneria natans following ammonium stress and recovery periods. The bacterial community diversity of different plant niches exhibited opposite patterns with ammonium stress, that is, decreasing in the phyllosphere while increasing in the rhizosphere. Furthermore, both phyllosphere and rhizosphere bacterial communities underwent large compositional changes at the end of ammonium stress, significantly enriching of several nitrifiers and denitrifiers. Meanwhile, bacterial legacies wrought by ammonium stress were detected for weeks; some plant growth-promoting and stress-relieving bacteria remained enriched even after stress disappeared. Structural equation model analysis showed that the reshaped bacterial communities in plant niches collectively had a positive effect on maintaining plant biomass. Additionally, we applied an age-prediction model to predict the bacterial community's successional trajectory, and the results revealed a persistent change in bacterial community development under ammonium treatment. Our findings highlight the importance of plant-microbe interactions in mitigating plant stress and fostering a better understanding of the assembly of plant-beneficial microbes under ammonium stress in aquatic ecosystems. IMPORTANCE Increasing anthropogenic input of ammonium is accelerating the decline of submerged macrophytes in aquatic ecosystems. Finding efficient ways to release submerged macrophytes from ammonium stress is crucial to maintain their ecological benefits. Microbial symbioses can alleviate abiotic stress in plants, but harnessing these beneficial interactions requires a detailed understanding of plant microbiome responses to ammonium stress, especially over a continuous time course. Here, we tracked the temporal changes in bacterial communities associated with the phyllosphere and rhizosphere of Vallisneria natans during ammonium stress and recovery periods. Our results showed that severe ammonium stress triggers a plant-driven timely reshaping of the associated bacterial community in a niche-specific strategy. The reassembled bacterial communities could potentially benefit the plant by positively contributing to nitrogen transformation and plant growth promotion. These findings provide empirical evidence regarding the adaptive strategy of aquatic plants whereby they recruit beneficial microbes against ammonium stress.
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Affiliation(s)
- Siwen Hu
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Rujia He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
| | - Xiaowei He
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
| | - Jin Zeng
- State Key Laboratory of Lake Science and Environment, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, China
- Sino-Danish Centre for Education and Research, University of Chinese Academy of Sciences, Beijing, China
| | - Dayong Zhao
- Joint International Research Laboratory of Global Change and Water Cycle, State Key Laboratory of Hydrology-Water Resources and Hydraulic Engineering, College of Hydrology and Water Resources, Hohai University, Nanjing, China
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16
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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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17
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Xu N, Zhou Z, Chen B, Zhang Z, Zhang J, Li Y, Lu T, Sun L, Peijnenburg WJGM, Qian H. Effect of chlorpyrifos on freshwater microbial community and metabolic capacity of zebrafish. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 262:115230. [PMID: 37413963 DOI: 10.1016/j.ecoenv.2023.115230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/30/2023] [Accepted: 07/02/2023] [Indexed: 07/08/2023]
Abstract
Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhigao Zhou
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China; Zhejiang Province Institute of Architectural Design and Research, Hangzhou 310000, PR China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Jinfeng Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, RA Leiden 2300, the Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, the Netherlands
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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18
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Qin G, Zhang Q, Zhang Z, Chen Y, Zhu J, Yang Y, Peijnenburg WJGM, Qian H. Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2023; 326:121518. [PMID: 36990340 DOI: 10.1016/j.envpol.2023.121518] [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: 01/12/2023] [Revised: 03/06/2023] [Accepted: 03/25/2023] [Indexed: 06/19/2023]
Abstract
Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.
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Affiliation(s)
- Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Ziyao Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Jichao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, Leiden, RA 2300, Netherlands; National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, P.O. Box 1, Bilthoven, Netherlands
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310032, PR China.
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Wang Y, Ni K, Zhang Z, Xu N, Lei C, Chen B, Zhang Q, Sun L, Chen Y, Lu T, Qian H. Metatranscriptome deciphers the effects of non-antibiotic antimicrobial agents on antibiotic resistance and virulence factors in freshwater microcosms. AQUATIC TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2023; 258:106513. [PMID: 37001199 DOI: 10.1016/j.aquatox.2023.106513] [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: 02/28/2023] [Revised: 03/26/2023] [Accepted: 03/27/2023] [Indexed: 06/19/2023]
Abstract
The emergence and transmission of antibiotic resistance genes (ARGs) and virulence factors (VFs) pose health risks to the ecosystem and humans. Understanding how non-antibiotic antimicrobial agents drive the expression of ARGs and VFs in freshwater ecosystems, however, remains large challenges. Here, we employed freshwater microcosms and performed metatranscriptomic analysis to investigate the expression profiles of ARGs and VFs in response to pollutants of non-antibiotic antimicrobial agents, including silver nanoparticles (AgNPs) and azoxystrobin. Results showed that AgNPs significantly inhibited the total expression of ARGs and VFs and decreased the number of pathogenic microorganisms expressing these genes. Azoxystrobin increased the total expression of ARGs and VFs, as well as the number of pathogens expressing VFs, but concomitantly reduced the number of pathogens expressing ARGs. Two tested pollutants dramatically changed the expression profiles of ARGs and VFs, with distinct patterns: AgNPs displayed a negative effect, while azoxystrobin showed a positive effect on their expression profiles. Our findings provided a systematical insight to demonstrate that non-antibiotic antimicrobial agents with different mechanisms of action showed various effects on ARGs and VFs, and therefore represented different ecological risks.
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Affiliation(s)
- Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Kepin Ni
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Bingfeng Chen
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou 510006, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
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20
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Li J, Daniell TJ, Jin MK, Chang RY, Wang T, Zhang J, Yang XR, Zhu YG. Phyllosphere antibiotic resistome in a natural primary vegetation across a successional sequence after glacier retreat. ENVIRONMENT INTERNATIONAL 2023; 174:107903. [PMID: 37058975 DOI: 10.1016/j.envint.2023.107903] [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: 01/25/2023] [Revised: 03/17/2023] [Accepted: 03/24/2023] [Indexed: 06/19/2023]
Abstract
The spread of antibiotic-resistance genes (ARGs) has posed a significant threat to human health over the past decades. Despite the fact that the phyllosphere represents a crucial pool of microorganisms, little is known about the profile and drivers of ARGs in less human interference natural habitats. In order to minimize the influence of environmental factors, here we collected leaf samples from the early-, middle- and late-successional stages across a primary vegetation successional sequence within 2 km, to investigate how the phyllosphere ARGs develop in natural habitats. Phyllosphere ARGs were determined using high-throughput quantitative PCR. Bacterial community and leaf nutrient content were also measured to assess their contribution to the phyllosphere ARGs. A total of 151 unique ARGs were identified, covering almost all recognized major antibiotic classes. We further found that there was some stochastic and a core set of the phyllosphere ARGs during the plant community succession process, due to the fluctuant phyllosphere habitat and specific selection effect of plant individuals. The ARG abundance significantly decreased due to the reduction of the phyllosphere bacterial diversity, community complexity, and leaf nutrient content during the plant community succession process. While the closer links between soil and fallen leaf resulted in a higher ARG abundance in leaf litter than in fresh leaf. In summary, our study reveals that the phyllosphere harbors a broad spectrum of ARGs in the natural environment. These phyllosphere ARGs are driven by various environmental factors, including the plant community composition, host leaf properties, and the phyllosphere microbiome.
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Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Tim J Daniell
- Plants, Photosynthesis and Soil, School of Biosciences, The University of Sheffield, Sheffield, UK
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China
| | - Rui-Ying Chang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Tao Wang
- CAS Key Laboratory of Mountain Surface Processes and Ecological Regulation, Institute of Mountain Hazards and Environment, Chinese Academy of Sciences, Chengdu 610041, China
| | - Jing Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, 1799 Jimei Road, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, C.A.S. Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China.
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21
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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22
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Zhang F, Xu N, Zhang Z, Zhang Q, Yang Y, Yu Z, Sun L, Lu T, Qian H. Shaping effects of rice, wheat, maize, and soybean seedlings on their rhizosphere microbial community. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:35972-35984. [PMID: 36539666 DOI: 10.1007/s11356-022-24835-3] [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: 09/08/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
The rhizosphere microbiome plays critical roles in plant growth and is an important interface for resource exchange between plants and the soil environment. Crops at various growing stages, especially the seedling stage, have strong shaping effects on the rhizosphere microbial community, and such community reconstruction will positively feed back to the plant growth. In the present study, we analyzed the variations of bacterial and fungal communities in the rhizosphere of four crop species: rice, soybean, maize, and wheat during successive cultivations (three repeats for the seedling stages) using 16S rRNA gene and internal transcribed spacer (ITS) high-throughput sequencing. We found that the relative abundances of specific microorganisms decreased after different cultivation times, e.g., Sphingomonas, Pseudomonas, Rhodanobacter, and Caulobacter, which have been reported as plant-growth beneficial bacteria. The relative abundances of potential plant pathogenic fungi Myrothecium and Ascochyta increased with the successive cultivation times. The co-occurrence network analysis showed that the bacterial and fungal communities under maize were much more stable than those under rice, soybean, and wheat. The present study explored the characteristics of bacteria and fungi in crop seedling rhizosphere and indicated that the characteristics of indigenous soil flora might determine the plant growth status. Further study will focus on the use of the critical microorganisms to control the growth and yield of specific crops.
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Affiliation(s)
- Fan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Yaohui Yang
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Zhitao Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China.
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, 310014, People's Republic of China
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23
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Diurnal Variation of Epiphytic Microbiota: an Unignorable Factor Affecting the Anaerobic Fermentation Characteristics of Sorghum-Sudangrass Hybrid Silage. Microbiol Spectr 2023; 11:e0340422. [PMID: 36519845 PMCID: PMC9927590 DOI: 10.1128/spectrum.03404-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Forage epiphytic microbiota exhibits pronounced changes in composition and function throughout the day. However, the effects of these changes on silage fermentation are rarely explored. Here, we transplanted the epiphytic microbiota of sorghum-sudangrass hybrid (SSG) harvested at 7:00 h (AM), 12:00 h (M), and 17:00 h (PM) to sterilized SSG to evaluate the effects of diurnal variation of epiphytic microbiota on fermentation characteristics. During fermentation, remarkable differences in bacterial community successions were observed between silages inoculated with AM and M microbiota. Compared to AM microbiota, M microbiota inoculation increased the proportions of Pantoea dispersa, Leuconostoc lactis, Enterobacter, and Klebsiella variicola, whereas it decreased the proportions of Weissella cibaria and Lactobacillus plantarum during fermentation. This led to the most rapid pH declines and organic acid production in AM silage and the slowest in M silage. Both M and PM microbiota affected the bacterial cooccurrence patterns, indicated by decreased complexity and stability in the community structures of M and PM silages compared to that of AM silage. The predicted functions indicated that some key carbohydrate metabolism pathways related to lactic acid synthesis were downregulated, while some competing pathways (ascorbate and aldarate metabolism and C5-branched dibasic acid metabolism) were upregulated in M silage compared to AM silage after 3 days of fermentation. Correlation analysis revealed positive correlations between competing pathways and enterobacterial species. The current study highlights the importance of diurnal variation of epiphytic microbiota in affecting the silage bacterial community, potentially providing an effective strategy to improve silage quality by optimizing harvest time. IMPORTANCE Ensiling is a way to preserve wet biomass for animal and bioenergy production worldwide. The fermentation quality of silage is largely dependent on the epiphytic microbiota of the material. Plant epiphytic microbiota exhibit diurnal changes in composition and function. However, the effects of these changes on silage fermentation are rarely explored. The results presented here demonstrated that diurnal variation of epiphytic microbiota could affect the fermentation characteristics and bacterial community during SSG fermentation. Marked bacterial community differences were observed between AM and M silages during the initial 3 days of fermentation. The dominance rate of Lactobacillus plantarum was highest in AM silage, whereas enterobacterial species were more abundant in M silage. The predicted function revealed downregulated lactic acid synthesis pathways and upregulated competing pathways in M silage compared to those in AM silage. This study provides clues for technological-parameter optimization of the fermentation process by the selection of harvest time.
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24
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Li JH, Muhammad Aslam M, Gao YY, Dai L, Hao GF, Wei Z, Chen MX, Dini-Andreote F. Microbiome-mediated signal transduction within the plant holobiont. Trends Microbiol 2023; 31:616-628. [PMID: 36702670 DOI: 10.1016/j.tim.2022.12.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 01/26/2023]
Abstract
Microorganisms colonizing the plant rhizosphere and phyllosphere play crucial roles in plant growth and health. Recent studies provide new insights into long-distance communication from plant roots to shoots in association with their commensal microbiome. In brief, these recent advances suggest that specific plant-associated microbial taxa can contribute to systemic plant responses associated with the enhancement of plant health and performance in face of a variety of biotic and abiotic stresses. However, most of the mechanisms associated with microbiome-mediated signal transduction in plants remain poorly understood. In this review, we provide an overview of long-distance signaling mechanisms within plants mediated by the commensal plant-associated microbiomes. We advocate the view of plants and microbes as a holobiont and explore key molecules and mechanisms associated with plant-microbe interactions and changes in plant physiology activated by signal transduction.
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Affiliation(s)
- Jian-Hong Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Mehtab Muhammad Aslam
- State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong
| | - Yang-Yang Gao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China
| | - Ge-Fei Hao
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Zhong Wei
- Jiangsu Provincial Key Lab for Organic Solid Waste Utilization, National Engineering Research Center for Organic Fertilizers, Jiangsu Collaborative Innovation Center for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Mo-Xian Chen
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, 550025, China.
| | - Francisco Dini-Andreote
- Department of Plant Science & Huck Institutes of the Life Sciences, The Pennsylvania State University, University Park, PA, USA
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25
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Hoffmann A, Posirca AR, Lewin S, Verch G, Büttner C, Müller MEH. Environmental Filtering Drives Fungal Phyllosphere Community in Regional Agricultural Landscapes. PLANTS (BASEL, SWITZERLAND) 2023; 12:507. [PMID: 36771591 PMCID: PMC9919219 DOI: 10.3390/plants12030507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
To adapt to climate change, several agricultural strategies are currently being explored, including a shift in land use areas. Regional differences in microbiome composition and associated phytopathogens need to be considered. However, most empirical studies on differences in the crop microbiome focused on soil communities, with insufficient attention to the phyllosphere. In this study, we focused on wheat ears in three regions in northeastern Germany (Magdeburger Börde (MBB), Müncheberger Sander (MSA), Uckermärkisches Hügelland (UKH)) with different yield potentials, soil, and climatic conditions. To gain insight into the fungal community at different sites, we used a metabarcoding approach (ITS-NGS). Further, we examined the diversity and abundance of Fusarium and Alternaria using culture-dependent and culture-independent techniques. For each region, the prevalence of different orders rich in phytopathogenic fungi was determined: Sporidiobolales in MBB, Capnodiales and Pleosporales in MSA, and Hypocreales in UKH were identified as taxonomic biomarkers. Additionally, F. graminearum was found predominantly in UKH, whereas F. poae was more abundant in the other two regions. Environmental filters seem to be strong drivers of these differences, but we also discuss the possible effects of dispersal and interaction filters. Our results can guide shifting cultivation regions to be selected in the future concerning their phytopathogenic infection potential.
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Affiliation(s)
- Annika Hoffmann
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
- Phytomedicine, Albrecht Daniel Thaer Institute, Faculty of Life Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Alexandra-Raluca Posirca
- Phytomedicine, Albrecht Daniel Thaer Institute, Faculty of Life Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
- State Office for Rural Development, Agriculture and Land Reorganization (LELF) Brandenburg, Division P, 15236 Frankfurt (Oder), Germany
| | - Simon Lewin
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Gernot Verch
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
| | - Carmen Büttner
- Phytomedicine, Albrecht Daniel Thaer Institute, Faculty of Life Science, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Marina E. H. Müller
- Leibniz Centre for Agricultural Landscape Research (ZALF), 15374 Müncheberg, Germany
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Wang Z, Fu C, Tian J, Wang W, Peng D, Dai X, Tian H, Zhou X, Li L, Yin H. Responses of the bacterial community of tobacco phyllosphere to summer climate and wildfire disease. FRONTIERS IN PLANT SCIENCE 2022; 13:1050967. [PMID: 36618666 PMCID: PMC9811124 DOI: 10.3389/fpls.2022.1050967] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Accepted: 11/08/2022] [Indexed: 06/17/2023]
Abstract
Both biotic and abiotic factors continually affect the phyllospheric ecology of plants. A better understanding of the drivers of phyllospheric community structure and multitrophic interactions is vital for developing plant protection strategies. In this study, 16S rRNA high-throughput sequencing was applied to study how summer climatic factors and bacterial wildfire disease have affected the composition and assembly of the bacterial community of tobacco (Nicotiana tabacum L.) phyllosphere. Our results indicated that three time series groups (T1, T2 and T3) formed significantly distinct clusters. The neutral community model (NCM) and beta nearest taxon index (betaNTI) demonstrated that the overall bacterial community assembly was predominantly driven by stochastic processes. Variance partitioning analysis (VPA) further showed that the complete set of the morbidity and climatic variables together could explain 35.7% of the variation of bacterial communities. The node numbers of the molecular ecological networks (MENs) showed an overall uptrend from T1 to T3. Besides, Pseudomonas is the keystone taxa in the MENs from T1 to T3. PICRUSt2 predictions revealed significantly more abundant genes of osmoprotectant biosynthesis/transport in T2, and more genes for pathogenicity and metabolizing organic substrate in T3. Together, this study provides insights into spatiotemporal patterns, processes and response mechanisms underlying the phyllospheric bacterial community.
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Affiliation(s)
- Zhenhua Wang
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Changwu Fu
- 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
| | - Deyuan Peng
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xi Dai
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Hui Tian
- Zhangjiajie Tobacco Company of Hunan Province, Zhangjiajie, China
| | - Xiangping Zhou
- Yongzhou Tobacco Company of Hunan Province, Yongzhou, 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
| | - 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
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27
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Qiu D, Ke M, Zhang Q, Zhang F, Lu T, Sun L, Qian H. Response of microbial antibiotic resistance to pesticides: An emerging health threat. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 850:158057. [PMID: 35977623 DOI: 10.1016/j.scitotenv.2022.158057] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2022] [Revised: 08/09/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The spread of microbial antibiotic resistance has seriously threatened public health globally. Non-antibiotic stressors have significantly contributed to the evolution of bacterial antibiotic resistance. Although numerous studies have been conducted on the potential risk of pesticide pollution for bacterial antibiotic resistance, a systematic review of these concerns is still lacking. In the present study, we elaborate the mechanism underlying the effects of pesticides on bacterial antibiotic resistance acquisition as well as the propagation of antimicrobial resistance. Pesticide stress enhanced the acquisition of antibiotic resistance in bacteria via various mechanisms, including the activation of efflux pumps, inhibition of outer membrane pores for resistance to antibiotics, and gene mutation induction. Horizontal gene transfer is a major mechanism whereby pesticides influence the transmission of antibiotic resistance genes (ARGs) in bacteria. Pesticides promoted the conjugation transfer of ARGs by increasing cell membrane permeability and increased the proportion of bacterial mobile gene elements, which facilitate the spread of ARGs. This review can improve our understanding regarding the pesticide-induced generation and spread of ARGs and antibiotic resistant bacteria. Moreover, it can be applied to reduce the ecological risks of ARGs in the future.
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Affiliation(s)
- Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Fan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Liwei Sun
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, PR China.
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28
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Xiang LG, Wang HC, Cai LT, Guo T, Luo F, Hsiang T, Yu ZH. Variations in leaf phyllosphere microbial communities and development of tobacco brown spot before and after fungicide application. Front Microbiol 2022; 13:1068158. [PMID: 36466663 PMCID: PMC9714265 DOI: 10.3389/fmicb.2022.1068158] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 10/31/2022] [Indexed: 10/17/2023] Open
Abstract
In recent years, STROBY (50% Kresoxim-methyl) has been widely used to control tobacco brown spot in Guizhou Province, China. As a broad-spectrum fungicide, STROBY targets not only phytopathogens, but also affects many other microorganisms including those pathogenic, beneficial, or neutral to the plant hosts. To understand the effects of STROBY on the phyllosphere microbial communities of tobacco leaves during the development of tobacco brown spot, the fungal and bacterial communities of symptomatic and asymptomatic leaves at four time points, before spraying (August 29) and after spraying (September 3, 8, and 13), were investigated using the Illumina high-throughput sequencing. The results showed that STROBY had significant effects on the phyllosphere microbial communities of tobacco leaves. Microbial communities in asymptomatic leaves were more greatly affected than their counterparts in symptomatic leaves, and fungal communities were more sensitive than bacterial communities. Throughout the experiment, the most common genera in symptomatic leaves were Alternaria, Pseudomonas, Pantoea, and Sphingomonas, and in asymptomatic leaves, these were Golubevia and Pantoea. After spraying, the alpha diversity of fungal communities increased in symptomatic leaves and decreased in asymptomatic leaves, while the alpha diversity of bacteria increased in both types of leaves. Beta diversity showed that in asymptomatic leaves, the fungal communities in the first stage was significantly different from the remaining three stages. In contrast, the fungal communities in symptomatic leaves and the bacterial communities in all leaves did not fluctuate significantly during the four stages. Before spraying (August 29), the dominant functions of the fungal community were animal pathogen, endophyte, plant pathogen, and wood saprotroph. Whereas after spraying (September 3, 8, and 13), the proportion of the above fungal functions decreased and the unassigned functions increased, especially in asymptomatic leaves. This study describes the effects of STROBY application and tobacco brown spot presence in shaping the leaf phyllosphere microbial communities, and provides insights into the microbial community effects on tobacco leaves of a strobilurin fungicide.
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Affiliation(s)
- Li-Gang Xiang
- College of Agriculture, Yangtze University, Jingzhou, Hubei, China
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou,China
| | - Han-Cheng Wang
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou,China
| | - Liu-Ti Cai
- Guizhou Provincial Academician Workstation of Microbiology and Health, Guizhou Academy of Tobacco Science, Guiyang, Guizhou,China
| | - Tao Guo
- College of Life Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Fei Luo
- College of Life Sciences, Yangtze University, Jingzhou, Hubei, China
| | - Tom Hsiang
- School of Environmental Sciences, University of Guelph, Guelph, ON, Canada
| | - Zhi-He Yu
- College of Life Sciences, Yangtze University, Jingzhou, Hubei, China
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Xu N, Zhang Z, Shen Y, Zhang Q, Liu Z, Yu Y, Wang Y, Lei C, Ke M, Qiu D, Lu T, Chen Y, Xiong J, Qian H. Compare the performance of multiple binary classification models in microbial high-throughput sequencing datasets. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 837:155807. [PMID: 35537509 DOI: 10.1016/j.scitotenv.2022.155807] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 05/04/2022] [Accepted: 05/05/2022] [Indexed: 06/14/2023]
Abstract
The development of machine learning and deep learning provided solutions for predicting microbiota response on environmental change based on microbial high-throughput sequencing. However, there were few studies specifically clarifying the performance and practical of two types of binary classification models to find a better algorithm for the microbiota data analysis. Here, for the first time, we evaluated the performance, accuracy and running time of the binary classification models built by three machine learning methods - random forest (RF), support vector machine (SVM), logistic regression (LR), and one deep learning method - back propagation neural network (BPNN). The built models were based on the microbiota datasets that removed low-quality variables and solved the class imbalance problem. Additionally, we optimized the models by tuning. Our study demonstrated that dataset pre-processing was a necessary process for model construction. Among these 4 binary classification models, BPNN and RF were the most suitable methods for constructing microbiota binary classification models. Using these 4 models to predict multiple microbial datasets, BPNN showed the highest accuracy and the most robust performance, while the RF method was ranked second. We also constructed the optimal models by adjusting the epochs of BPNN and the n_estimators of RF for six times. The evaluation related to performances of models provided a road map for the application of artificial intelligence to assess microbial ecology.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Yechao Shen
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Zhen Liu
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, PR China
| | - Yitian Yu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Chaotang Lei
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China
| | - Yiling Chen
- Institute of Environmental and Ecological Engineering, Guangdong University of Technology, Guangzhou, 510006, PR China
| | - Juntao Xiong
- College of Mathematics and Informatics, South China Agricultural University, Guangzhou, 510642, PR China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, PR China.
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