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Vidal-Villarejo M, Dößelmann B, Kogler B, Hammerschmidt M, Oppliger B, Oppliger H, Schmid K. Regional diversity and leaf microbiome interactions of the fungal maize pathogen Exserohilum turcicum in Switzerland: A metagenomic analysis. Mol Ecol 2024; 33:e17482. [PMID: 39082382 DOI: 10.1111/mec.17482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/01/2024] [Accepted: 07/12/2024] [Indexed: 08/28/2024]
Abstract
The spread and adaptation of fungal plant pathogens in agroecosystems are facilitated by environmental homogeneity. Metagenomic sequencing of infected tissues allowed us to monitor eco-evolutionary dynamics and interactions between host, pathogen and plant microbiome. Exserohilum turcicum, the causal agent of northern corn leaf blight (NCLB) in maize, is distributed in multiple clonal lineages throughout Europe. To characterize regional pathogen diversity, we conducted metagenomic DNA sequencing on 241 infected leaf samples from the highly susceptible Swiss maize landrace Rheintaler Ribelmais, collected over 3 years (2016-2018) from an average of 14 agricultural farms within the Swiss Rhine Valley. All major European clonal lineages of E. turcicum were identified. Lineages differ by their mating types which indicates potential for sexual recombination and rapid evolution of new pathogen strains, although we found no evidence of recent recombination. The associated eukaryotic and prokaryotic leaf microbiome exhibited variation in taxonomic diversity between years and locations and is likely influenced by local weather conditions. A network analysis revealed distinct clusters of eukaryotic and prokaryotic taxa that correlates with the frequency of E. turcicum sequencing reads, suggesting causal interactions. Notably, the yeast genus Metschnikowia exhibited a strongly negative association with E. turcicum, supporting its known potential as biological control agent against fungal pathogens. Our findings show that metagenomic sequencing is a useful tool for analysing the role of environmental factors and potential pathogen-microbiome interactions in shaping pathogen dynamics and evolution, suggesting their potential for effective pathogen management strategies.
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Affiliation(s)
- Mireia Vidal-Villarejo
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | - Bianca Dößelmann
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
| | | | | | - Barbara Oppliger
- Rhytop GmbH, Salez, Switzerland
- Landwirtschaftliches Zentrum Sankt Gallen, Salez, Switzerland
- Verein Rheintaler Ribelmais e.V, Salez, Switzerland
| | - Hans Oppliger
- Rhytop GmbH, Salez, Switzerland
- Landwirtschaftliches Zentrum Sankt Gallen, Salez, Switzerland
- Verein Rheintaler Ribelmais e.V, Salez, Switzerland
| | - Karl Schmid
- Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Stuttgart, Germany
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Hoefle D, Sommer M, Wassermann B, Faticov M, Serra D, Berg G, Tack AJM, Abdelfattah A. Oak seedling microbiome assembly under climate warming and drought. ENVIRONMENTAL MICROBIOME 2024; 19:62. [PMID: 39198873 PMCID: PMC11360865 DOI: 10.1186/s40793-024-00602-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2024] [Accepted: 08/11/2024] [Indexed: 09/01/2024]
Abstract
Despite that climate change is currently one of the most pervasive challenges, its effects on the plant-associated microbiome is still poorly studied. The aim of this study was to evaluate the impact of the independent and combinatory effect of climate warming and drought on the microbiome assembly of oak from seed to seedling. In a multifactorial experimental set up, acorns were subjected to different temperatures (15 °C, 20 °C, and 25 °C) and soil moisture levels (drought (15%) and control (60%)) from germination until the seedling stage, after which the bacterial and fungal communities associated to the rhizosphere and phyllosphere were characterized by amplicon sequencing and qPCR. The results showed a stronger effect of temperature on fungal than on bacterial diversity and the effect was more pronounced in the phyllosphere. Under drought condition, temperature had a significantly negative effect on phyllosphere fungal diversity. In the rhizosphere, temperature had a significant effect on the fungal community composition which was primarily caused by species turnover. Regardless of temperature, Actinobacteriota was significantly enriched in drought, a group of bacteria known to increase plant drought tolerance. This study provides new insights into the effect of climate change on the plant microbiome in natural ecosystems.
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Affiliation(s)
- Daniel Hoefle
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
| | - Milena Sommer
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Birgit Wassermann
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
| | - Maria Faticov
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Département de biologie, Université de Sherbrooke, Sherbrooke, QC, J1K 2R1, Canada
| | - Demetrio Serra
- Fondazione Mediterranea Terina Onlus, Zona industriale Benedetto XVI, 88046, Ficarella, CZ, Italy
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam OT, Golm, Germany
| | - Ayco J M Tack
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
- Department of Ecology, Environment and Plant Sciences, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany.
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, Graz, 8010, Austria.
- Bolin Centre for Climate Research, Stockholm University, Svante Arrhenius väg 20A, Stockholm, SE-106 91, Sweden.
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Liu B, Li C, Zhao X, Zhang C, He X, Qu L, Zhang N. Contrasting Patterns of Fungal and Bacterial Endophytes Inhabiting Temperate Tree Leaves in Response to Thinning. J Fungi (Basel) 2024; 10:470. [PMID: 39057355 PMCID: PMC11277613 DOI: 10.3390/jof10070470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Revised: 06/30/2024] [Accepted: 07/04/2024] [Indexed: 07/28/2024] Open
Abstract
The phyllosphere is an important but underestimated habitat for a variety of microorganisms, with limited knowledge about leaf endophytes as a crucial component of the phyllosphere microbiome. In this study, we investigated the mechanisms of communities and co-occurrence networks of leaf endophytes in response to forest thinning in a temperate forest. As we expected, contrasting responses of fungal and bacterial endophytes were observed. Specifically, the diversity of leaf endophytic fungi and the complexity of their co-occurrence networks increased significantly with thinning intensity, whereas the complexity of endophytic bacterial co-occurrence networks decreased. In particular, microbiota inhabiting damaged leaves seem to be more intensively interacting, showing an evident fungi-bacteria trade-off under forest thinning. In damaged leaves, besides the direct effects of thinning, thinning-induced changes in neighbor tree diversity indirectly altered the diversity of leaf fungal and bacterial endophytes via modifying leaf functional traits such as leaf dry matter content and specific leaf area. These findings provide new experimental evidence for the trade-offs between leaf endophytic fungi and bacteria under the different magnitudes of deforestation, highlighting their dependence on the presence or absence of leaf damage.
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Affiliation(s)
- Beiping Liu
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Chunhuan Li
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Xiuhai Zhao
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China; (X.Z.); (C.Z.)
| | - Chunyu Zhang
- Research Center of Forest Management Engineering of State Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China; (X.Z.); (C.Z.)
| | - Xinyi He
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
| | - Laiye Qu
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China;
| | - Naili Zhang
- State Key Laboratory of Efficient Production of Forest Resources, College of Forestry, Beijing Forestry University, Beijing 100083, China; (B.L.); (C.L.); (X.H.)
- The Key Laboratory for Silviculture and Conservation of Ministry of Education, College of Forestry, Beijing Forestry University, Beijing 100083, China
- Ecological Observation and Research Station of Heilongjiang Sanjiang Plain Wetlands, National Forestry and Grassland Administration, Shuangyashan 518000, 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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Hao X, Gu Y, Zhang H, Wang X, Liu X, Chen C, Wang C, Zhang X, Liu X, Shen X. Synthetic Microbial Community Promotes Bacterial Communities Leading to Soil Multifunctionality in Desertified Land. Microorganisms 2024; 12:1117. [PMID: 38930499 PMCID: PMC11205429 DOI: 10.3390/microorganisms12061117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2024] [Revised: 05/28/2024] [Accepted: 05/28/2024] [Indexed: 06/28/2024] Open
Abstract
Soil desertification is an important challenge in global soil management, and effectively and stably restoring soil function is an urgent problem. Using synthetic microbial communities (SynComs) is a burgeoning microbial strategy aimed at enhancing soil nutrients through functional synergies among diverse microorganisms; nevertheless, their effectiveness in restoring desertified soils remains unknown. In this study, we conducted a two-year field experiment using a SynCom constructed by in situ probiotic bacteria and set up control, chemical fertilizer, and combined SynCom-chemical fertilizer (combined fertilizer) treatments to investigate the linkage between microbial communities and soil multifunctionality in the soil surface layer (0-10 cm). Both the bacterial and fungal communities differed the most under the combined fertilizer treatment compared to the control. The bacterial communities differed more under treatments of the SynCom than the chemical fertilizer, while the fungal communities differed more under the chemical fertilizer treatment than the SynCom treatment. Regarding soil function, the SynCom strengthened the correlation between enzyme activities and both bacterial communities and functional properties. pH and available potassium were the main influencing factors under the chemical fertilizer and combined fertilizer treatments. The beta-diversity of the bacterial communities was significantly correlated with soil multifunctionality. Random forest analyses showed that the SynCom significantly enhanced the bacterial communities, driving soil multifunctionality, and that some potential microbial taxa drove multiple nutrient cycles simultaneously. In summary, the SynCom effectively increased the abundance of most carbon, nitrogen, and phosphorus functional genes as well as soil enzyme activities. The bacterial community composition contributed significantly to soil multifunctionality. Hence, the development of novel microbial agents holds significant potential for improving soil functionality and managing desertification.
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Affiliation(s)
- Xinwei Hao
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Yazhou Gu
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd., Qingyang 745000, China; (Y.G.); (H.Z.)
| | - Hongzhi Zhang
- Qingyang Longfeng Sponge City Construction Management and Operation Co., Ltd., Qingyang 745000, China; (Y.G.); (H.Z.)
| | - Xiao Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Xiaozhen Liu
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010013, China; (X.L.); (X.Z.)
| | - Chunlei Chen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Congcong Wang
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
| | - Xiaoqing Zhang
- Institute of Grassland Research, Chinese Academy of Agricultural Sciences, Hohhot 010013, China; (X.L.); (X.Z.)
| | - Xingyu Liu
- State Key Laboratory of Geological Processes and Mineral Resources, Institute of Earth Sciences, China University of Geosciences, Beijing 100083, China;
| | - Xihui Shen
- State Key Laboratory for Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Xianyang 712100, China; (X.H.); (X.W.); (C.C.); (C.W.)
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6
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Bechtold EK, Wanek W, Nuesslein B, DaCosta M, Nüsslein K. Successional changes in bacterial phyllosphere communities are plant-host species dependent. Appl Environ Microbiol 2024; 90:e0175023. [PMID: 38349147 PMCID: PMC11206175 DOI: 10.1128/aem.01750-23] [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: 10/02/2023] [Accepted: 01/17/2024] [Indexed: 03/21/2024] Open
Abstract
Phyllosphere microbial communities are increasingly experiencing intense pulse disturbance events such as drought. It is currently unknown how phyllosphere communities respond to such disturbances and if they are able to recover. We explored the stability of phyllosphere communities over time, in response to drought stress, and under recovery from drought on temperate forage grasses. Compositional or functional changes were observed during the disturbance period and whether communities returned to non-stressed levels following recovery. Here, we found that phyllosphere community composition shifts as a result of simulated drought but does not fully recover after irrigation is resumed and that the degree of community response to drought is host species dependent. However, while community composition had changed, we found a high level of functional stability (resistance) over time and in the water deficit treatment. Ecological modeling enabled us to understand community assembly processes over a growing season and to determine if they were disrupted during a disturbance event. Phyllosphere community succession was characterized by a strong level of ecological drift, but drought disturbance resulted in variable selection, or, in other words, communities were diverging due to differences in selective pressures. This successional divergence of communities with drought was unique for each host species. Understanding phyllosphere responses to environmental stresses is important as climate change-induced stresses are expected to reduce crop productivity and phyllosphere functioning. IMPORTANCE Leaf surface microbiomes have the potential to influence agricultural and ecosystem productivity. We assessed their stability by determining composition, functional resistance, and resilience. Resistance is the degree to which communities remain unchanged as a result of disturbance, and resilience is the ability of a community to recover to pre-disturbance conditions. By understanding the mechanisms of community assembly and how they relate to the resistance and resilience of microbial communities under common environmental stresses such as drought, we can better understand how communities will adapt to a changing environment and how we can promote healthy agricultural microbiomes. In this study, phyllosphere compositional stability was highly related to plant host species phylogeny and, to a lesser extent, known stress tolerances. Phyllosphere community assembly and stability are a result of complex interactions of ecological processes that are differentially imposed by host species.
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Affiliation(s)
- Emily K. Bechtold
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Wolfgang Wanek
- Division of Terrestrial Ecosystem Research, Center of Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Benedikt Nuesslein
- Department of Biology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Michelle DaCosta
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Klaus Nüsslein
- Department of Microbiology, University of Massachusetts Amherst, Amherst, Massachusetts, USA
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Zhao J, Xie X, Jiang Y, Li J, Fu Q, Qiu Y, Fu X, Yao Z, Dai Z, Qiu Y, Chen H. Effects of simulated warming on soil microbial community diversity and composition across diverse ecosystems. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 911:168793. [PMID: 37996030 DOI: 10.1016/j.scitotenv.2023.168793] [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: 09/27/2023] [Revised: 11/20/2023] [Accepted: 11/20/2023] [Indexed: 11/25/2023]
Abstract
Soil warming can directly affect the microbial community, or indirectly affect the microbial community by affecting soil moisture, nutrient availability, vegetation growth, etc. However, the response of microorganisms to soil warming is complex, and there is no uniform conclusion on the impact and mechanism of warming on microbial diversity. As the global climate gradually warms, a comprehensive assessment of warming on soil microbial community changes is essential to understand and predict the response of microbial geochemical processes to soil warming. Here, we perform a meta-analysis of studies to investigate changes in soil microbial communities along soil warming gradients and the response of soil microbes to elevated temperature in different ecosystems. We found that the α diversity index of soil microorganisms decreased significantly with the increase in temperature, and the β diversity altered with the increase in soil temperature and the shifts in ecosystem. Most bacteria only alter when the temperature rises higher. Compared to the non-warming condition, the relative abundance of Acidobacteria, Proteobacteria, Bacteroidetes, Planctomycetes and Verrucomicrobia decreased by 19 %, 11 %, 19 %, 8 % and 6 %, respectively, and the relative abundance of Firmicutes increased by 34 %. Compared to farmland, forest, grassland and tundra ecosystems, soil microorganisms in wetland ecosystems were more sensitive to temperature increase, and the changes in bacteria were consistent with the overall alterations. This meta-analysis revealed significant changes in the composition of microbial communities on soil warming. With the decrease in biodiversity under increasing temperature conditions, these dominant microbiomes, which can grow well under high-temperature conditions, will play a stronger role in regulating nutrient and energy flow. Our analysis adds a global perspective to the temperature response of soil microbes, which is critical to improving our understanding of the mechanisms of how soil microbes change in response to climate warming.
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Affiliation(s)
- Jiayi Zhao
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xuan Xie
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yuying Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jiaxin Li
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Qi Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yingbo Qiu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xianheng Fu
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zhiyuan Yao
- School of Civil and Environmental Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Zhongmin Dai
- Institute of Soil and Water Resources and Environmental Science, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Yunpeng Qiu
- College of Resources and Environmental Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Huaihai Chen
- State Key Laboratory of Biocontrol, School of Ecology, Shenzhen Campus of Sun Yat-sen University, Shenzhen, Guangdong 518107, China.
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Yu Y, Zhou Y, Janssens IA, Deng Y, He X, Liu L, Yi Y, Xiao N, Wang X, Li C, Xiao C. Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation. GLOBAL CHANGE BIOLOGY 2024; 30:e17111. [PMID: 38273581 DOI: 10.1111/gcb.17111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 11/12/2023] [Accepted: 12/01/2023] [Indexed: 01/27/2024]
Abstract
While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.
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Affiliation(s)
- Yang Yu
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Yong Zhou
- Department of Wildland Resources, Utah State University, Logan, Utah, USA
- Ecology Center, Utah State University, Logan, Utah, USA
| | - Ivan A Janssens
- Research Group of Plant and Vegetation Ecology, Department of Biology, University of Antwerp, Wilrijk, Belgium
| | - Ye Deng
- CAS Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Xiaojia He
- The Administrative Center for China's Agenda 21, Beijing, China
| | - Lingli Liu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yin Yi
- School of Life Sciences, Guizhou Normal University, Guiyang, China
| | - Nengwen Xiao
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, Beijing, China
| | - Xiaodong Wang
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Chao Li
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
| | - Chunwang Xiao
- Key Laboratory of Ecology and Environment in Minority Areas (Minzu University of China), National Ethnic Affairs Commission, Beijing, China
- College of Life and Environmental Sciences, Minzu University of China, Beijing, China
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Yang Q, Yan Y, Huang J, Wang Z, Feng M, Cheng H, Zhang P, Zhang H, Xu J, Zhang M. The Impact of Warming on Assembly Processes and Diversity Patterns of Bacterial Communities in Mesocosms. Microorganisms 2023; 11:2807. [PMID: 38004818 PMCID: PMC10672829 DOI: 10.3390/microorganisms11112807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 11/14/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria in lake water bodies and sediments play crucial roles in various biogeochemical processes. In this study, we conducted a comprehensive analysis of bacterioplankton and sedimentary bacteria community composition and assembly processes across multiple seasons in 18 outdoor mesocosms exposed to three temperature scenarios. Our findings reveal that warming and seasonal changes play a vital role in shaping microbial diversity, species interactions, and community assembly disparities in water and sediment ecosystems. We observed that the bacterioplankton networks were more fragile, potentially making them susceptible to disturbances, whereas sedimentary bacteria exhibited increased stability. Constant warming and heatwaves had contrasting effects: heatwaves increased stability in both planktonic and sedimentary bacteria communities, but planktonic bacterial networks became more fragile under constant warming. Regarding bacterial assembly, stochastic processes primarily influenced the composition of planktonic and sedimentary bacteria. Constant warming intensified the stochasticity of bacterioplankton year-round, while heatwaves caused a slight shift from stochastic to deterministic in spring and autumn. In contrast, sedimentary bacteria assembly is mainly dominated by drift and remained unaffected by warming. Our study enhances our understanding of how bacterioplankton and sedimentary bacteria communities respond to global warming across multiple seasons, shedding light on the complex dynamics of microbial ecosystems in lakes.
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Affiliation(s)
- Qian Yang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Yifeng Yan
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Jinhe Huang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Zhaolei Wang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Mingjun Feng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Haowu Cheng
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
| | - Peiyu Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Huan Zhang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Jun Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (P.Z.); (H.Z.); (J.X.)
| | - Min Zhang
- Hubei Provincial Engineering Laboratory for Pond Aquaculture, Engineering Research Center of Green Development for Conventional Aquatic Biological Industry in the Yangtze River Economic Belt, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China; (Q.Y.); (Y.Y.); (J.H.); (Z.W.); (M.F.); (H.C.)
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10
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Cambon MC, Trillat M, Lesur-Kupin I, Burlett R, Chancerel E, Guichoux E, Piouceau L, Castagneyrol B, Le Provost G, Robin S, Ritter Y, Van Halder I, Delzon S, Bohan DA, Vacher C. Microbial biomarkers of tree water status for next-generation biomonitoring of forest ecosystems. Mol Ecol 2023; 32:5944-5958. [PMID: 37815414 DOI: 10.1111/mec.17149] [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: 03/08/2023] [Revised: 09/14/2023] [Accepted: 09/19/2023] [Indexed: 10/11/2023]
Abstract
Next-generation biomonitoring proposes to combine machine-learning algorithms with environmental DNA data to automate the monitoring of the Earth's major ecosystems. In the present study, we searched for molecular biomarkers of tree water status to develop next-generation biomonitoring of forest ecosystems. Because phyllosphere microbial communities respond to both tree physiology and climate change, we investigated whether environmental DNA data from tree phyllosphere could be used as molecular biomarkers of tree water status in forest ecosystems. Using an amplicon sequencing approach, we analysed phyllosphere microbial communities of four tree species (Quercus ilex, Quercus robur, Pinus pinaster and Betula pendula) in a forest experiment composed of irrigated and non-irrigated plots. We used these microbial community data to train a machine-learning algorithm (Random Forest) to classify irrigated and non-irrigated trees. The Random Forest algorithm detected tree water status from phyllosphere microbial community composition with more than 90% accuracy for oak species, and more than 75% for pine and birch. Phyllosphere fungal communities were more informative than phyllosphere bacterial communities in all tree species. Seven fungal amplicon sequence variants were identified as candidates for the development of molecular biomarkers of water status in oak trees. Altogether, our results show that microbial community data from tree phyllosphere provides information on tree water status in forest ecosystems and could be included in next-generation biomonitoring programmes that would use in situ, real-time sequencing of environmental DNA to help monitor the health of European temperate forest ecosystems.
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Affiliation(s)
- Marine C Cambon
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
- School of Natural Sciences, Bangor University, Bangor, UK
| | | | - Isabelle Lesur-Kupin
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
- HelixVenture, Mérignac, France
| | - Régis Burlett
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
| | | | | | | | | | | | | | - Yves Ritter
- INRAE, University of Bordeaux, BIOGECO, Pessac, France
| | | | | | - David A Bohan
- Agroécologie, INRAE, Université Bourgogne Franche-Comté, Dijon, France
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11
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Wang W, Hu C, Chang Y, Wang L, Bi Q, Lu X, Zheng Z, Zheng X, Wu D, Niu B. Differentiated responses of the phyllosphere bacterial community of the yellowhorn tree to precipitation and temperature regimes across Northern China. FRONTIERS IN PLANT SCIENCE 2023; 14:1265362. [PMID: 37954985 PMCID: PMC10634255 DOI: 10.3389/fpls.2023.1265362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 10/10/2023] [Indexed: 11/14/2023]
Abstract
Introduction As an ephemeral and oligotrophic environment, the phyllosphere harbors many highly diverse microorganisms. Importantly, it is known that their colonization of plant leaf surfaces is considerably influenced by a few abiotic factors related to climatic conditions. Yet how the dynamics of phyllosphere bacterial community assembly are shaped by detailed climatological elements, such as various bioclimatic variables, remains poorly understood. Methods Using high-throughput 16S rRNA gene amplicon sequencing technology, we analyzed the bacterial communities inhabiting the leaf surfaces of an oilseed tree, yellowhorn (Xanthoceras sorbifolium), grown at four sites (Yinchuan, Otogqianqi, Tongliao, and Zhangwu) whose climatic status differs in northern China. Results and Discussion We found that the yellowhorn phyllosphere's bacterial community was generally dominated by four phyla: Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Nevertheless, bacterial community composition differed significantly among the four sampled site regions, indicating the possible impact of climatological factors upon the phyllosphere microbiome. Interestingly, we also noted that the α-diversities of phyllosphere microbiota showed strong positive or negative correlation with 13 bioclimatic factors (including 7 precipitation factors and 6 temperature factors). Furthermore, the relative abundances of 55 amplicon sequence variants (ASVs), including three ASVs representing two keystone taxa (the genera Curtobacterium and Streptomyces), exhibited significant yet contrary responses to the precipitation and temperature climatic variables. That pattern was consistent with all ASVs' trends of possessing opposite correlations to those two parameter classes. In addition, the total number of links and nodes, which conveys community network complexity, increased with rising values of most temperature variables. Besides that, remarkably positive relevance was found between average clustering coefficient and most precipitation variables. Altogether, these results suggest the yellowhorn phyllosphere bacterial community is capable of responding to variation in rainfall and temperature regimes in distinctive ways.
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Affiliation(s)
- Weixiong Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Congcong Hu
- Department of Mathematics, Shanghai Normal University, Shanghai, China
| | - Yu Chang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Libing Wang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Quanxin Bi
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xin Lu
- Chifeng Research Institute of Forestry Science, Chifeng, China
- National Forestry and Grassland Shiny-Leaved Yellowhorn Engineering and Technology Research Center, Chifeng, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
| | - Xiaoqi Zheng
- Center for Single-Cell Omics, School of Public Health, Shanghai Jiao Tong University, School of Medicine, Shanghai, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- The Center for Basic Forestry Research, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
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12
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Gómez-Pérez D, Schmid M, Chaudhry V, Hu Y, Velic A, Maček B, Ruhe J, Kemen A, Kemen E. Proteins released into the plant apoplast by the obligate parasitic protist Albugo selectively repress phyllosphere-associated bacteria. THE NEW PHYTOLOGIST 2023; 239:2320-2334. [PMID: 37222268 DOI: 10.1111/nph.18995] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Accepted: 04/11/2023] [Indexed: 05/25/2023]
Abstract
Biotic and abiotic interactions shape natural microbial communities. The mechanisms behind microbe-microbe interactions, particularly those protein based, are not well understood. We hypothesize that released proteins with antimicrobial activity are a powerful and highly specific toolset to shape and defend plant niches. We have studied Albugo candida, an obligate plant parasite from the protist Oomycota phylum, for its potential to modulate the growth of bacteria through release of antimicrobial proteins into the apoplast. Amplicon sequencing and network analysis of Albugo-infected and uninfected wild Arabidopsis thaliana samples revealed an abundance of negative correlations between Albugo and other phyllosphere microbes. Analysis of the apoplastic proteome of Albugo-colonized leaves combined with machine learning predictors enabled the selection of antimicrobial candidates for heterologous expression and study of their inhibitory function. We found for three candidate proteins selective antimicrobial activity against Gram-positive bacteria isolated from A. thaliana and demonstrate that these inhibited bacteria are precisely important for the stability of the community structure. We could ascribe the antibacterial activity of the candidates to intrinsically disordered regions and positively correlate it with their net charge. This is the first report of protist proteins with antimicrobial activity under apoplastic conditions that therefore are potential biocontrol tools for targeted manipulation of the microbiome.
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Affiliation(s)
- Daniel Gómez-Pérez
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Monja Schmid
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Vasvi Chaudhry
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Yiheng Hu
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Ana Velic
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Boris Maček
- Department of Biology, Quantitative Proteomics Group, Interfaculty Institute of Cell Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Jonas Ruhe
- Max Planck Institute for Plant Breeding Research, 50829, Cologne, Germany
| | - Ariane Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
| | - Eric Kemen
- Microbial Interactions in Plant Ecosystems, Center for Plant Molecular Biology, University of Tübingen, 72076, Tübingen, Germany
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13
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Smets W, Chock MK, Walsh CM, Vanderburgh CQ, Kau E, Lindow SE, Fierer N, Koskella B. Leaf side determines the relative importance of dispersal versus host filtering in the phyllosphere microbiome. mBio 2023; 14:e0111123. [PMID: 37436063 PMCID: PMC10470611 DOI: 10.1128/mbio.01111-23] [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: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 07/13/2023] Open
Abstract
Leaves harbor distinct microbial communities that can have an important impact on plant health and microbial ecosystems worldwide. Nevertheless, the ecological processes that shape the composition of leaf microbial communities remain unclear, with previous studies reporting contradictory results regarding the importance of bacterial dispersal versus host selection. This discrepancy could be driven in part because leaf microbiome studies typically consider the upper and lower leaf surfaces as a single entity despite these habitats possessing considerable anatomical differences. We characterized the composition of bacterial phyllosphere communities from the upper and lower leaf surfaces across 24 plant species. Leaf surface pH and stomatal density were found to shape phyllosphere community composition, and the underside of leaves had lower richness and higher abundances of core community members than upper leaf surfaces. We found fewer endemic bacteria on the upper leaf surfaces, suggesting that dispersal is more important in shaping these communities, with host selection being a more important force in microbiome assembly on lower leaf surfaces. Our study illustrates how changing the scale in which we observe microbial communities can impact our ability to resolve and predict microbial community assembly patterns on leaf surfaces. IMPORTANCE Leaves can harbor hundreds of different bacterial species that form unique communities for every plant species. Bacterial communities on leaves are really important because they can, for example, protect their host against plant diseases. Usually, bacteria from the whole leaf are considered when trying to understand these communities; however, this study shows that the upper and lower sides of a leaf have a very different impact on how these communities are shaped. It seems that the bacteria on the lower leaf side are more closely associated with the plant host, and communities on the upper leaf side are more impacted by immigrating bacteria. This can be really important when we want to treat, for example, crops in the field with beneficial bacteria or when trying to understand host-microbe interactions on the leaves.
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Affiliation(s)
- Wenke Smets
- Department of Integrative Biology, University of California, Berkeley, California, USA
- Department of Bioscience Engineering, University of Antwerp, Antwerpen, Belgium
| | - Mason K. Chock
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Corinne M. Walsh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Caihong Qiu Vanderburgh
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
| | - Ethan Kau
- Department of Integrative Biology, University of California, Berkeley, California, USA
| | - Steven E. Lindow
- Department of Plant and Microbial Biology, University of California, Berkeley, California, USA
| | - Noah Fierer
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado, USA
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Colorado, USA
| | - Britt Koskella
- Department of Integrative Biology, University of California, Berkeley, California, USA
- Chan Zuckerberg Biohub, San Francisco, California, USA
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14
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Huang S, Zha X, Fu G. Affecting Factors of Plant Phyllosphere Microbial Community and Their Responses to Climatic Warming-A Review. PLANTS (BASEL, SWITZERLAND) 2023; 12:2891. [PMID: 37631103 PMCID: PMC10458011 DOI: 10.3390/plants12162891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 08/02/2023] [Accepted: 08/06/2023] [Indexed: 08/27/2023]
Abstract
Phyllosphere microorganisms are not only an important part of plants, but also an important part of microorganisms. In this review, the function of phyllosphere microorganisms, the assembly mechanism of phyllosphere microorganisms, the driving factors of phyllosphere microbial community structure, and the effects of climate warming on phyllosphere microbial community structure were reviewed. Generally, phyllosphere microorganisms have a variety of functions (e.g., fixing nitrogen, promoting plant growth). Although selection and dispersal processes together regulate the assembly of phyllospheric microbial communities, which one of the ecological processes is dominant and how external disturbances alter the relative contributions of each ecological process remains controversial. Abiotic factors (e.g., climatic conditions, geographical location and physical and chemical properties of soil) and biological factors (e.g., phyllosphere morphological structure, physiological and biochemical characteristics, and plant species and varieties) can affect phyllosphere microbial community structure. However, the predominant factors affecting phyllosphere microbial community structure are controversial. Moreover, how climate warming affects the phyllosphere microbial community structure and its driving mechanism have not been fully resolved, and further relevant studies are needed.
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Affiliation(s)
- Shaolin Huang
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
| | - Xinjie Zha
- Xi’an University of Finance and Economics, Xi’an 710100, China;
| | - Gang Fu
- Lhasa Plateau Ecosystem Research Station, Key Laboratory of Ecosystem Network Observation and Modeling, Institute of Geographic Sciences and Natural Resources Research, Chinese Academy of Sciences, Beijing 100101, China;
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15
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Chau KD, Samad-Zada F, Kelemen EP, Rehan SM. Integrative population genetics and metagenomics reveals urbanization increases pathogen loads and decreases connectivity in a wild bee. GLOBAL CHANGE BIOLOGY 2023; 29:4193-4211. [PMID: 37173859 DOI: 10.1111/gcb.16757] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Revised: 04/27/2023] [Accepted: 04/30/2023] [Indexed: 05/15/2023]
Abstract
As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural landscapes, threatening wildlife including economically important species such as bees. In this study, we employ whole genome sequencing to characterize the population genetics, metagenome and microbiome, and environmental stressors of a common wild bee, Ceratina calcarata. Population genomic analyses revealed the presence of low genetic diversity and elevated levels of inbreeding. Through analyses of isolation by distance, resistance, and environment across urban landscapes, we found that green spaces including shrubs and scrub were the most optimal pathways for bee dispersal, and conservation efforts should focus on preserving these land traits to maintain high connectivity across sites for wild bees. Metagenomic analyses revealed landscape sites exhibiting urban heat island effects, such as high temperatures and development but low precipitation and green space, had the highest taxa alpha diversity across all domains even when isolating for potential pathogens. Notably, the integration of population and metagenomic data showed that reduced connectivity in urban areas is not only correlated with lower relatedness among individuals but is also associated with increased pathogen diversity, exposing vulnerable urban bees to more pathogens. Overall, our combined population and metagenomic approach found significant environmental variation in bee microbiomes and nutritional resources even in the absence of genetic differentiation, as well as enabled the potential early detection of stressors to bee health.
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16
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Lv T, Zhan C, Pan Q, Xu H, Fang H, Wang M, Matsumoto H. Plant pathogenesis: Toward multidimensional understanding of the microbiome. IMETA 2023; 2:e129. [PMID: 38867927 PMCID: PMC10989765 DOI: 10.1002/imt2.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/26/2023] [Indexed: 06/14/2024]
Abstract
Single pathogen-targeted disease management measure has shown drawbacks in field efficacy under the scenario of global change. An in-depth understanding of plant pathogenesis will provide a promising solution but faces the challenges of the emerging paradigm involving the plant microbiome. While the beneficial impact of the plant microbiome is well characterized, their potential role in facilitating pathological processes has so far remained largely overlooked. To address these unsolved controversies and emerging challenges, we hereby highlight the pathobiome, the disease-assisting portion hidden in the plant microbiome, in the plant pathogenesis paradigm. We review the detrimental actions mediated by the pathobiome at multiple scales and further discuss how natural and human triggers result in the prevalence of the plant pathobiome, which would probably provide a clue to the mitigation of plant disease epidemics. Collectively, the article would advance the current insight into plant pathogenesis and also pave a new way to cope with the upward trends of plant disease by designing the pathobiome-targeted measure.
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Affiliation(s)
- Tianxing Lv
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Qianqian Pan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Haorong Xu
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Hongda Fang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
- Global Education Program for AgriScience Frontiers, Graduate School of AgricultureHokkaido UniversitySapporoJapan
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and InsectsZhejiang UniversityHangzhouChina
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and BiotechnologyZhejiang UniversityHangzhouChina
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17
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Yang LN, Ren M, Zhan J. Modeling plant diseases under climate change: evolutionary perspectives. TRENDS IN PLANT SCIENCE 2023; 28:519-526. [PMID: 36593138 DOI: 10.1016/j.tplants.2022.12.011] [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: 07/29/2022] [Revised: 12/07/2022] [Accepted: 12/15/2022] [Indexed: 05/22/2023]
Abstract
Infectious plant diseases are a major threat to global agricultural productivity, economic development, and ecological integrity. There is widespread concern that these social and natural disasters caused by infectious plant diseases may escalate with climate change and computer modeling offers a unique opportunity to address this concern. Here, we analyze the intrinsic problems associated with current modeling strategies and highlight the need to integrate evolutionary principles into polytrophic, eco-evolutionary frameworks to improve predictions. We particularly discuss how evolutionary shifts in functional trade-offs, relative adaptability between plants and pathogens, ecosystems, and climate preferences induced by climate change may feedback to future plant disease epidemics and how technological advances can facilitate the generation and integration of this relevant knowledge for better modeling predictions.
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Affiliation(s)
- Li-Na Yang
- Fujian Key Laboratory on Conservation and Sustainable Utilization of Marine Biodiversity, Fuzhou Institute of Oceanography, Minjiang University, Fuzhou, 350108, China
| | - Maozhi Ren
- Institute of Urban Agriculture, Chinese Academy of Agricultural Sciences, Chengdu National Agricultural Science and Technology Center, Chengdu, China.
| | - Jiasui Zhan
- Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
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18
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Elyamine AM, Wang H, Oummu-Kulthum MAH, Raissa S, Nahdhoit AR, Meng S, Tao P, Hu Z. Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105920. [PMID: 36931048 DOI: 10.1016/j.marenvres.2023.105920] [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: 07/12/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r2 = 0.904), nitrogen (r2 = 0.72), phosphorus content (r2 = 0.62) and the water factor (r2 = 0.93). It was however highly and negatively correlated with the canopy cover (r2 = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China; Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Han Wang
- Huanhuai University, Zhumadian, 46000, China
| | | | - Sailine Raissa
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Ahamada Rachid Nahdhoit
- Institute of Graduate Studies, Fundamental and Industrial Microbiology, Istanbul University, 34134, Vezneciler Faith, Istanbul, Turkey
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China.
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19
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Chesters D, Liu X, Bell KL, Orr MC, Xie T, Zhou Q, Zhu C. An integrative bioinformatics pipeline shows that honeybee-associated microbiomes are driven primarily by pollen composition. INSECT SCIENCE 2023; 30:555-568. [PMID: 36001735 DOI: 10.1111/1744-7917.13104] [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: 02/08/2022] [Revised: 07/11/2022] [Accepted: 07/24/2022] [Indexed: 06/15/2023]
Abstract
The microbiomes associated with bee nests influence colony health through various mechanisms, although it is not yet clear how honeybee congeners differ in microbiome assembly processes, in particular the degrees to which floral visitations and the environment contribute to different aspects of diversity. We used DNA metabarcoding to sequence bacterial 16S rRNA from honey and stored pollen from nests of 4 honeybee species (Apis cerana, A. dorsata, A. florea, and A. laboriosa) sampled throughout Yunnan, China, a global biodiversity hotspot. We developed a computational pipeline integrating multiple databases for quantifying key facets of diversity, including compositional, taxonomic, phylogenetic, and functional ones. Further, we assessed candidate drivers of observed microbiome dissimilarity, particularly differences in floral visitations, habitat disturbance, and other key environmental variables. Analyses revealed that microbiome alpha diversity was broadly equivalent across the study sites and between bee species, apart from functional diversity which was very low in nests of the reclusive A. laboriosa. Turnover in microbiome composition across Yunnan was driven predominantly by pollen composition. Human disturbance negatively impacted both compositional and phylogenetic alpha diversity of nest microbiomes, but did not correlate with microbial turnover. We herein make progress in understanding microbiome diversity associated with key pollinators in a biodiversity hotspot, and provide a model for the use of a comprehensive informatics framework in assessing pattern and drivers of diversity, which enables the inclusion of explanatory variables both subtly and fundamentally different and enables elucidation of emergent or unexpected drivers.
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Affiliation(s)
- Douglas Chesters
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Xiuwei Liu
- Institute of Agro-Products Processing, Yunnan Province Academy of Agricultural Science, Kunming, China
| | - Karen L Bell
- School of Biological Sciences, University of Western Australia, Crawley, WA, Australia
- CSIRO Health & Biosecurity, Floreat, WA, Australia
| | - Michael C Orr
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
| | - Tingting Xie
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Life Sciences, Anhui Normal University, Wuhu, Anhui Province, China
| | - Qingsong Zhou
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Chaodong Zhu
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- International College, University of Chinese Academy of Sciences, Beijing, China
- State Key Laboratory of Integrated Pest Management, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
- College of Biological Sciences, University of Chinese Academy of Sciences, Beijing, China
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20
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Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
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Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
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21
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Zhou R, Duan GL, García-Palacios P, Yang G, Cui HL, Yan M, Yin Y, Yi XY, Li L, Delgado-Baquerizo M, Zhu YG. Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China. Front Microbiol 2023; 14:1065302. [PMID: 36992926 PMCID: PMC10041966 DOI: 10.3389/fmicb.2023.1065302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionThe microbiome inhabiting plant leaves is critical for plant health and productivity. Wild soybean (Glycine soja), which originated in China, is the progenitor of cultivated soybean (Glycine max). So far, the community structure and assembly mechanism of phyllosphere microbial community on G. soja were poorly understood.MethodsHere, we combined a national-scale survey with high-throughput sequencing and microsatellite data to evaluate the contribution of host genotype vs. climate in explaining the foliar microbiome of G. soja, and the core foliar microbiota of G. soja were identified.ResultsOur findings revealed that both the host genotype and environmental factors (i.e., geographic location and climatic conditions) were important factors regulating foliar community assembly of G. soja. Host genotypes explained 0.4% and 3.6% variations of the foliar bacterial and fungal community composition, respectively, while environmental factors explained 25.8% and 19.9% variations, respectively. We further identified a core microbiome thriving on the foliage of all G. soja populations, including bacterial (dominated by Methylobacterium-Methylorubrum, Pantoea, Quadrisphaera, Pseudomonas, and Sphingomonas) and fungal (dominated by Cladosporium, Alternaria, and Penicillium) taxa.ConclusionOur study revealed the significant role of host genetic distance as a driver of the foliar microbiome of the wild progenitor of soya, as well as the effects of climatic changes on foliar microbiomes. These findings would increase our knowledge of assembly mechanisms in the phyllosphere of wild soybeans and suggest the potential to manage the phyllosphere of soya plantations by plant breeding and selecting specific genotypes under climate change.
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Affiliation(s)
- Rui Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Yan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Yun Yi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- *Correspondence: Yong-Guan Zhu,
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22
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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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23
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Do TT, Smyth C, Crispie F, Burgess C, Brennan F, Walsh F. Comparison of soil and grass microbiomes and resistomes reveals grass as a greater antimicrobial resistance reservoir than soil. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 857:159179. [PMID: 36191722 DOI: 10.1016/j.scitotenv.2022.159179] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/09/2022] [Accepted: 09/28/2022] [Indexed: 06/16/2023]
Abstract
Grasslands cover a large proportion of global agricultural landmass used to feed herbivores and ruminants and link the environment to the food chain via animals onto humans. However, most scientific studies of antimicrobial resistance and microbiomes at the environmental - animal nexus have focused on soil or vegetables rather than grasslands. Based on previous microbiome phyllosphere-soil studies we hypothesised that the microbiome and resistomes across soil and grass would have a core of shared taxa and antimicrobial resistance genes (ARGs), but that in addition each would also have a minority of unique signatures. Our data indicated grass contained a wider variety and higher relative abundance of ARGs and mobile genetic elements (MGEs) than soil with or without slurry amendments. The microbiomes of soil and grass were similar in content but varied in the composition proportionality. While there were commonalities across many of the ARGs present in soil and on grass their correlations with MGEs and bacteria differed, suggesting a source other than soil is also relevant for the resistome of grass. The variations in the relative abundances of ARGs in soil and on grass also indicated that either the MGEs or the bacteria carrying the ARGs comprised a higher relative abundance on grass than in soil. We conclude that while soil may be a source of some of these genes it cannot be the source for all ARGs and MGEs. Our data identifies grass as a more diverse and abundant reservoir of ARGs and MGEs in the environment than soil, which is significant to human and animal health when viewed in the context of grazing food animals.
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Affiliation(s)
- Thi Thuy Do
- Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland
| | - Cian Smyth
- Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland
| | - Fiona Crispie
- Teagasc Food Research Centre, Moorepark, Fermoy, Co. Cork P61 C996, Ireland
| | | | - Fiona Brennan
- Teagasc, Crops, Environment and Land-Use Programme, Johnstown Castle, Co. Wexford Y35 Y521, Ireland
| | - Fiona Walsh
- Department of Biology, Maynooth University, Maynooth, Co. Kildare W23 F2H6, Ireland; Kathleen Lonsdale Institute for Human Health Research, Maynooth University, Maynooth, Co. Kildare, Ireland.
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24
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Li J, Bates KA, Hoang KL, Hector TE, Knowles SCL, King KC. Experimental temperatures shape host microbiome diversity and composition. GLOBAL CHANGE BIOLOGY 2023; 29:41-56. [PMID: 36251487 PMCID: PMC10092218 DOI: 10.1111/gcb.16429] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 07/20/2022] [Indexed: 05/10/2023]
Abstract
Global climate change has led to more extreme thermal events. Plants and animals harbour diverse microbial communities, which may be vital for their physiological performance and help them survive stressful climatic conditions. The extent to which microbiome communities change in response to warming or cooling may be important for predicting host performance under global change. Using a meta-analysis of 1377 microbiomes from 43 terrestrial and aquatic species, we found a decrease in the amplicon sequence variant-level microbiome phylogenetic diversity and alteration of microbiome composition under both experimental warming and cooling. Microbiome beta dispersion was not affected by temperature changes. We showed that the host habitat and experimental factors affected microbiome diversity and composition more than host biological traits. In particular, aquatic organisms-especially in marine habitats-experienced a greater depletion in microbiome diversity under cold conditions, compared to terrestrial hosts. Exposure involving a sudden long and static temperature shift was associated with microbiome diversity loss, but this reduction was attenuated by prior-experimental lab acclimation or when a ramped regime (i.e., warming) was used. Microbial differential abundance and co-occurrence network analyses revealed several potential indicator bacterial classes for hosts in heated environments and on different biome levels. Overall, our findings improve our understanding on the impact of global temperature changes on animal and plant microbiome structures across a diverse range of habitats. The next step is to link these changes to measures of host fitness, as well as microbial community functions, to determine whether microbiomes can buffer some species against a more thermally variable and extreme world.
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Affiliation(s)
- Jingdi Li
- Department of BiologyUniversity of OxfordOxfordUK
| | | | - Kim L. Hoang
- Department of BiologyUniversity of OxfordOxfordUK
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25
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Smith TP, Mombrikotb S, Ransome E, Kontopoulos DG, Pawar S, Bell T. Latent functional diversity may accelerate microbial community responses to temperature fluctuations. eLife 2022; 11:e80867. [PMID: 36444646 PMCID: PMC9708066 DOI: 10.7554/elife.80867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 10/26/2022] [Indexed: 11/30/2022] Open
Abstract
How complex microbial communities respond to climatic fluctuations remains an open question. Due to their relatively short generation times and high functional diversity, microbial populations harbor great potential to respond as a community through a combination of strain-level phenotypic plasticity, adaptation, and species sorting. However, the relative importance of these mechanisms remains unclear. We conducted a laboratory experiment to investigate the degree to which bacterial communities can respond to changes in environmental temperature through a combination of phenotypic plasticity and species sorting alone. We grew replicate soil communities from a single location at six temperatures between 4°C and 50°C. We found that phylogenetically and functionally distinct communities emerge at each of these temperatures, with K-strategist taxa favored under cooler conditions and r-strategist taxa under warmer conditions. We show that this dynamic emergence of distinct communities across a wide range of temperatures (in essence, community-level adaptation) is driven by the resuscitation of latent functional diversity: the parent community harbors multiple strains pre-adapted to different temperatures that are able to 'switch on' at their preferred temperature without immigration or adaptation. Our findings suggest that microbial community function in nature is likely to respond rapidly to climatic temperature fluctuations through shifts in species composition by resuscitation of latent functional diversity.
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Affiliation(s)
- Thomas P Smith
- The Georgina Mace Centre for the Living Planet, Imperial College LondonAscotUnited Kingdom
| | - Shorok Mombrikotb
- The Georgina Mace Centre for the Living Planet, Imperial College LondonAscotUnited Kingdom
| | - Emma Ransome
- The Georgina Mace Centre for the Living Planet, Imperial College LondonAscotUnited Kingdom
| | | | - Samraat Pawar
- The Georgina Mace Centre for the Living Planet, Imperial College LondonAscotUnited Kingdom
| | - Thomas Bell
- The Georgina Mace Centre for the Living Planet, Imperial College LondonAscotUnited Kingdom
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26
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Zhang M, Peng C, Sun W, Dong R, Hao J. Effects of Variety, Plant Location, and Season on the Phyllosphere Bacterial Community Structure of Alfalfa (Medicago sativa L.). Microorganisms 2022; 10:microorganisms10102023. [PMID: 36296299 PMCID: PMC9610643 DOI: 10.3390/microorganisms10102023] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 10/05/2022] [Accepted: 10/11/2022] [Indexed: 11/16/2022] Open
Abstract
Plant phyllosphere bacteria are vital for plant health and productivity and are affected by both abiotic and biotic factors. In this study, we surveyed the structure of the phyllosphere bacterial community associated with alfalfa. For two varieties of alfalfa, forty-eight samples of phyllosphere communities were collected at two locations over four seasons in 2020. Proteobacteria and actinobacteria were associated with the dominating phylum in the bacterial communities of the alfalfa phyllosphere. Sphingomonas was the most abundant genus-level bacteria, followed by Methylobacterium, Burkholderia-Caballeronia-Paraburkholderia, and Pseudomonas. Sampling time had a greater affect than site and variety on alfalfa surface microorganisms. The variation in phyllosphere bacterial community assembly was mostly explained by the season–site interaction (43%), season–variety interaction (35%), and season (28%). Variety, site–variety interaction, and season–site–variety interactions did not have a meaningful effect on phyllosphere bacterial diversity and community structure. The bacterial community in the phyllosphere of alfalfa showed seasonal changes over time. The environmental factors that contributed most to the phyllosphere bacterial community of alfalfa were temperature and sunshine duration, which were significantly positively correlated with most of the dominant bacterial genera in the alfalfa phyllosphere.
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27
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Muyshondt B, Wuyts K, Van Mensel A, Smets W, Lebeer S, Aleixo C, Alós Ortí M, Casanelles-Abella J, Chiron F, Giacomo P, Laanisto L, Moretti M, Niinemets Ü, Pinho P, Tryjanowski P, Woszczyło P, Samson R. Phyllosphere bacterial communities in urban green areas throughout Europe relate to urban intensity. FEMS Microbiol Ecol 2022; 98:6695091. [PMID: 36085374 DOI: 10.1093/femsec/fiac106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/25/2022] [Accepted: 09/07/2022] [Indexed: 12/14/2022] Open
Abstract
The phyllosphere harbours a diverse and specific bacterial community, which influences plant health and ecosystem functioning. In this study, we investigated the impact of urban green areas connectivity and size on the composition and diversity of phyllosphere bacterial communities. Hereto, we evaluated the diversity and composition of phyllosphere bacterial communities of 233 Platanus x acerifolia and Acer pseudoplatanus trees in 77 urban green areas throughout 6 European cities. The community composition and diversity significantly differed between cities but only to a limited extent between tree species. We could show that urban intensity correlated significantly with the community composition of phyllosphere bacteria. In particular, a significant correlation was found between the relative abundances for 29 out of the 50 most abundant families and the urban intensity: the abundances of classic phyllosphere families, such as Acetobacteraceae, Planctomycetes, and Beijerinkiaceae, decreased with urban intensity (i.e. more abundant in areas with more green, lower air pollution, and lower temperature), while those related to human activities, such as Enterobacteriaceae and Bacillaceae, increased with urban intensity. The results of this study suggest that phyllosphere bacterial communities in European cities are associated with urban intensity and that effect is mediated by several combined stress factors.
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Affiliation(s)
- Babette Muyshondt
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Karen Wuyts
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Anskje Van Mensel
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Wenke Smets
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Sarah Lebeer
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
| | - Cristiana Aleixo
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Marta Alós Ortí
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Joan Casanelles-Abella
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland.,Landscape Ecology, Institute of Terrestrial Ecosystems, ETH Zurich, CH-8092, Zurich, Switzerland
| | - François Chiron
- CNRS, AgroParisTech, Ecologie Systématique Evolution, Université Paris-Saclay, 91405 Orsay, France
| | - Puglielli Giacomo
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Lauri Laanisto
- Chair of Biodiversity and Nature Tourism, Estonian University of Life Sciences, 51005, Tartu, Estonia
| | - Marco Moretti
- Biodiversity and Conservation Biology, Swiss Federal Research Institute WSL, CH-8903, Birmensdorf, Switzerland
| | - Ülo Niinemets
- Chair of Crop Science and Plant Biology, Estonian University of Life Sciences, 51006, Tartu, Estonia
| | - Pedro Pinho
- Centre for Ecology, Evolution and Environmental Changes, Faculdade de Ciências da Universidade de Lisboa, 3810-135, Lisbon, Portugal
| | - Piotr Tryjanowski
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Patrycja Woszczyło
- Department of Zoology, Poznan University of Life Sciences, 60-637, Poland
| | - Roeland Samson
- Environmental Ecology and Applied Microbiology (ENdEMIC), Department of Bioscience Engineering, University of Antwerp, 2000, Antwerp, Belgium
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Wei X, Yu L, Han B, Liu K, Shao X, Jia S. Spatial variations of root-associated bacterial communities of alpine plants in the Qinghai-Tibet Plateau. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 839:156086. [PMID: 35605870 DOI: 10.1016/j.scitotenv.2022.156086] [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: 03/08/2022] [Revised: 05/13/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Exploring the geospatial variation of root-associated microbiomes is critical for understanding plant-microbe-environment interactions and plant environmental adaptability. Root-associated bacterial communities from the three compartments [rhizosphere surrounding soil (RSS), rhizosphere soil (rhizosphere), and root endosphere (endophytic)] are influenced by multiple factors, including plant species and geographical locations. Nonetheless, these communities remain poorly understood under harsh conditions. In this study, we selected four dominant alpine plants on the Qinghai-Tibet Plateau (i.e., Elymus nutans, Festuca sinensis, Kobresia pygmaea, and Kobresia humilis) to investigate their root-associated bacterial communities across 11 geographical locations and determine the factors driving spatial variation. The results showed that the microbiota of the three compartments had significantly different community compositions, with more Pseudomonadaceae and Enterobacteriaceae present in the endosphere. Spatial variations in root endophytic microbiota were mainly governed by stochastic processes, which were different from the deterministic processes in the other two compartments. Meanwhile, the geographical location had greater effects on bacterial communities than plant species, and the spatial variation of α-diversity in the endosphere was much higher than that in the RSS and rhizosphere. We further found that the differentiation of bacterial diversity in the endosphere among sympatric plant species was enhanced by higher annual precipitation, lower soil nutrients (carbon and nitrogen), and pH. For example, the coefficient of variation of endosphere Pseudomonadaceae abundance was positively correlated with annual mean precipitation, whereas that of Enterobacteriaceae abundance was negatively correlated with soil pH. The co-occurrence network analysis identified a higher proportion of bacterial coexistence in the endosphere (70.9%) than in the RSS (49.5%) and rhizosphere soil (50.9%). Finally, we revealed the relative convergence of endophytic communities among sympatric plant species in the alpine grasslands.
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Affiliation(s)
- Xiaoting Wei
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Lu Yu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Bing Han
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Kesi Liu
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xinqing Shao
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing 100193, China.
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29
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Nottingham AT, Scott JJ, Saltonstall K, Broders K, Montero-Sanchez M, Püspök J, Bååth E, Meir P. Microbial diversity declines in warmed tropical soil and respiration rise exceed predictions as communities adapt. Nat Microbiol 2022; 7:1650-1660. [PMID: 36065063 DOI: 10.1038/s41564-022-01200-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 07/12/2022] [Indexed: 01/04/2023]
Abstract
Perturbation of soil microbial communities by rising temperatures could have important consequences for biodiversity and future climate, particularly in tropical forests where high biological diversity coincides with a vast store of soil carbon. We carried out a 2-year in situ soil warming experiment in a tropical forest in Panama and found large changes in the soil microbial community and its growth sensitivity, which did not fully explain observed large increases in CO2 emission. Microbial diversity, especially of bacteria, declined markedly with 3 to 8 °C warming, demonstrating a breakdown in the positive temperature-diversity relationship observed elsewhere. The microbial community composition shifted with warming, with many taxa no longer detected and others enriched, including thermophilic taxa. This community shift resulted in community adaptation of growth to warmer temperatures, which we used to predict changes in soil CO2 emissions. However, the in situ CO2 emissions exceeded our model predictions threefold, potentially driven by abiotic acceleration of enzymatic activity. Our results suggest that warming of tropical forests will have rapid, detrimental consequences both for soil microbial biodiversity and future climate.
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Affiliation(s)
- Andrew T Nottingham
- School of Geography, University of Leeds, Leeds, UK. .,School of Geosciences, University of Edinburgh, Edinburgh, UK. .,Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.
| | - Jarrod J Scott
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | | | - Kirk Broders
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama.,Mycotoxin Prevention and Applied Microbiology Research Unit, National Center for Agricultural Utilization Research, Agricultural Research Service USDA, Peoria, IL, USA
| | | | - Johann Püspök
- Smithsonian Tropical Research Institute, Balboa, Ancon, Republic of Panama
| | - Erland Bååth
- Section of Microbial Ecology, Department of Biology, Lund University, Lund, Sweden
| | - Patrick Meir
- School of Geosciences, University of Edinburgh, Edinburgh, UK.,Research School of Biology, Australian National University, Canberra, Australia
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30
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Zhu Y, Xiong C, Wei Z, Chen Q, Ma B, Zhou S, Tan J, Zhang L, Cui H, Duan G. Impacts of global change on the phyllosphere microbiome. THE NEW PHYTOLOGIST 2022; 234:1977-1986. [PMID: 34921429 PMCID: PMC9306672 DOI: 10.1111/nph.17928] [Citation(s) in RCA: 54] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2021] [Indexed: 05/21/2023]
Abstract
Plants form complex interaction networks with diverse microbiomes in the environment, and the intricate interplay between plants and their associated microbiomes can greatly influence ecosystem processes and functions. The phyllosphere, the aerial part of the plant, provides a unique habitat for diverse microbes, and in return the phyllosphere microbiome greatly affects plant performance. As an open system, the phyllosphere is subjected to environmental perturbations, including global change, which will impact the crosstalk between plants and their microbiomes. In this review, we aim to provide a synthesis of current knowledge of the complex interactions between plants and the phyllosphere microbiome under global changes and to identify future priority areas of research on this topic.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Chao Xiong
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Zhong Wei
- Key Laboratory of Plant ImmunityJiangsu Provincial Key Laboratory for Organic Solid Waste UtilizationJiangsu Collaborative Innovation Center for Solid Organic Waste Resource UtilizationNational Engineering Research Center for Organic‐Based FertilizersNanjing Agricultural UniversityWeigang, Nanjing210095China
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneParkvilleVic3010Australia
| | - Bin Ma
- Zhejiang Provincial Key Laboratory of Agricultural Resources and EnvironmentCollege of Environmental and Natural Resource SciencesZhejiang UniversityHangzhou310058China
- Hangzhou Innovation CenterZhejiang UniversityHangzhou311200China
| | - Shu‐Yi‐Dan Zhou
- Key Laboratory of Urban Environment and HealthInstitute of Urban EnvironmentChinese Academy of SciencesXiamen361021China
| | - Jiaqi Tan
- Department of Biological SciencesLouisiana State UniversityBaton RougeLA70803USA
| | - Li‐Mei Zhang
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
| | - Gui‐Lan Duan
- State Key Laboratory of Urban and Regional EcologyResearch Center for Eco‐Environmental SciencesChinese Academy of SciencesBeijing100085China
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31
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Xu N, Zhao Q, Zhang Z, Zhang Q, Wang Y, Qin G, Ke M, Qiu D, Peijnenburg WJGM, Lu T, Qian H. Phyllosphere Microorganisms: Sources, Drivers, and Their Interactions with Plant Hosts. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:4860-4870. [PMID: 35435673 DOI: 10.1021/acs.jafc.2c01113] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The leaves of plants are colonized by various microorganisms. In comparison to the rhizosphere, less is known about the characteristics and ecological functions of phyllosphere microorganisms. Phyllosphere microorganisms mainly originate from soil, air, and seeds. The composition of phyllosphere microorganisms is mainly affected by ecological and abiotic factors. Phyllosphere microorganisms execute multiple ecological functions by influencing leaf functions and longevity, seed mass, fruit development, and homeostasis of host growth. A plant can respond to phyllosphere microorganisms by secondary metabolite secretion and its immune system. Meanwhile, phyllosphere microorganisms play an important role in ecological stability and environmental safety assessment. However, as a result of the instability of the phyllosphere environment and the poor cultivability of phyllosphere microorganisms in the current research, there are still many limitations, such as the lack of insight into the mechanisms of plant-microorganism interactions, the roles of phyllosphere microorganisms in plant growth processes, the responses of phyllosphere microorganisms to plant metabolites, etc. This review summarizes the latest progress made in the research of the phyllosphere in recent years. This is beneficial for deepening our understanding of phyllosphere microorganisms and promoting the research of plant-atmosphere interactions, plant pathogens, and plant biological control.
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Affiliation(s)
- Nuohan Xu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Science, Urumqi, Xinjiang 830011, People's Republic of China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Qi Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Yan Wang
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Guoyan Qin
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Danyan Qiu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - W J G M Peijnenburg
- Institute of Environmental Sciences (CML), Leiden University, 2300 RA Leiden, Netherlands
- National Institute of Public Health and the Environment (RIVM), Center for Safety of Substances and Products, Post Office Box 1, 3720 BA Bilthoven, Netherlands
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
| | - Haifeng Qian
- College of Environment, Zhejiang University of Technology, Hangzhou, Zhejiang 310032, People's Republic of China
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32
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Mu Z, Dong S, Li Y, Li S, Shen H, Zhang J, Han Y, Xu Y, Zhao Z. Soil Bacterial Community Responses to N Application and Warming in a Qinghai-Tibetan Plateau Alpine Steppe. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.709518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nitrogen deposition and climate warming can alter soil bacterial communities. However, the response of soil bacteria in an alpine steppe to these changes is largely unknown. In this study, a field experiment was performed on the northeastern Qinghai-Tibetan Plateau to determine the changes in soil bacterial communities of alpine steppes in response to nitrogen application and warming. The experiment consisted of four treatments, namely no-N application with no-warming (CK), N application (8 kg N ha−1 year−1) with no-warming (N), warming with no-N application (W), and N application (8 kg N ha−1 year−1) with warming (W&N). This study aimed to investigate (1) the changes in soil bacterial diversity and community structure under simulated nitrogen deposition and warming conditions, and (2) the key environmental factors responsible for these changes. Based on the results, soil bacterial diversity and community composition did not change significantly in the short term. Warming had a significant effect on overall bacterial composition, rare species composition, and individual bacterial taxa. Besides, the interaction between nitrogen application and warming had a significant effect on community β-diversity. Above-ground plant variables were highly correlated with bacterial community characteristics. Nitrogen application and warming did not significantly alter the distribution range of the bacterial community. Overall, this study suggests that soil bacterial communities can remain relatively stable at the level of simulated nitrogen application and warming and that short-term climatic changes may have no significant impacts on soil bacterial communities.
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33
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Phyllosphere Community Assembly and Response to Drought Stress on Common Tropical and Temperate Forage Grasses. Appl Environ Microbiol 2021; 87:e0089521. [PMID: 34161142 DOI: 10.1128/aem.00895-21] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Grasslands represent a critical ecosystem important for global food production, soil carbon storage, and water regulation. Current intensification and expansion practices add to the degradation of grasslands and dramatically increase greenhouse gas emissions and pollution. Thus, new ways to sustain and improve their productivity are needed. Research efforts focus on the plant-leaf microbiome, or phyllosphere, because its microbial members impact ecosystem function by influencing pathogen resistance, plant hormone production, and nutrient availability through processes including nitrogen fixation. However, little is known about grassland phyllospheres and their response to environmental stress. In this study, globally dominant temperate and tropical forage grass species were grown in a greenhouse under current climate conditions and drought conditions that mimic future climate predictions to understand if (i) plant host taxa influence microbial community assembly, (ii) microbial communities respond to drought stress, and (iii) phyllosphere community changes correlate to changes in plant host traits and stress-response strategies. Community analysis using high-resolution sequencing revealed Gammaproteobacteria as the dominant bacterial class, which increased under severe drought stress on both temperate and tropical grasses while overall bacterial community diversity declined. Bacterial community diversity, structure, and response to drought were significantly different between grass species. This community dependence on plant host species correlated with differences in grass species traits, which became more defined under drought stress conditions, suggesting symbiotic evolutionary relationships between plant hosts and their associated microbial community. Further understanding these strategies and the functions microbes provide to plants will help us utilize microbes to promote agricultural and ecosystem productivity in the future. IMPORTANCE Globally important grassland ecosystems are at risk of degradation due to poor management practices compounded by predicted increases in severity and duration of drought over the next century. Finding new ways to support grassland productivity is critical to maintaining their ecological and agricultural benefits. Discerning how grassland microbial communities change in response to climate stress will help us understand how plant-microbe relationships may be useful to sustainably support grasslands in the future. In this study, phyllosphere community diversity and composition were significantly altered under drought conditions. The significance of our research is demonstrating how severe climate stress reduces bacterial community diversity, which previously was directly associated with decreased plant productivity. These findings guide future questions about functional plant-microbe interactions under stress conditions, greatly enhancing our understanding of how bacteria can increase food security by promoting grassland growth and resilience.
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34
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Lajoie G, Kembel SW. Host neighborhood shapes bacterial community assembly and specialization on tree species across a latitudinal gradient. ECOL MONOGR 2021. [DOI: 10.1002/ecm.1443] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Geneviève Lajoie
- Département des sciences biologiques Université du Québec à Montréal 141, Avenue du Président‐Kennedy Montréal QuébecH2X 1Y4Canada
| | - Steven W. Kembel
- Département des sciences biologiques Université du Québec à Montréal 141, Avenue du Président‐Kennedy Montréal QuébecH2X 1Y4Canada
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35
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Klarenberg IJ, Keuschnig C, Warshan D, Jónsdóttir IS, Vilhelmsson O. The Total and Active Bacterial Community of the Chlorolichen Cetraria islandica and Its Response to Long-Term Warming in Sub-Arctic Tundra. Front Microbiol 2020; 11:540404. [PMID: 33391192 PMCID: PMC7775390 DOI: 10.3389/fmicb.2020.540404] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 11/30/2020] [Indexed: 01/04/2023] Open
Abstract
Lichens are traditionally defined as a symbiosis between a fungus and a green alga and or a cyanobacterium. This idea has been challenged by the discovery of bacterial communities inhabiting the lichen thalli. These bacteria are thought to contribute to the survival of lichens under extreme and changing environmental conditions. How these changing environmental conditions affect the lichen-associated bacterial community composition remains unclear. We describe the total (rDNA-based) and potentially metabolically active (rRNA-based) bacterial community of the lichen Cetaria islandica and its response to long-term warming using a 20-year warming experiment in an Icelandic sub-Arctic tundra. 16S rRNA and rDNA amplicon sequencing showed that the orders Acetobacterales (of the class Alphaproteobacteria) and Acidobacteriales (of the phylum Acidobacteria) dominated the bacterial community. Numerous amplicon sequence variants (ASVs) could only be detected in the potentially active community but not in the total community. Long-term warming led to increases in relative abundance of bacterial taxa on class, order and ASV level. Warming altered the relative abundance of ASVs of the most common bacterial genera, such as Granulicella and Endobacter. The potentially metabolically active bacterial community was also more responsive to warming than the total community. Our results suggest that the bacterial community of the lichen C. islandica is dominated by acidophilic taxa and harbors disproportionally active rare taxa. We also show for the first time that climate warming can lead to shifts in lichen-associated bacterial community composition.
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Affiliation(s)
- Ingeborg J. Klarenberg
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | - Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, CNRS, École Centrale de Lyon, Écully, France
| | - Denis Warshan
- Faculty of Life and Environmental Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Oddur Vilhelmsson
- Natural Resource Sciences, University of Akureyri, Akureyri, Iceland
- BioMedical Center, University of Iceland, Reykjavík, Iceland
- School of Biological Sciences, University of Reading, Reading, United Kingdom
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36
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Shakir S, Zaidi SSEA, de Vries FT, Mansoor S. Plant Genetic Networks Shaping Phyllosphere Microbial Community. Trends Genet 2020; 37:306-316. [PMID: 33036802 DOI: 10.1016/j.tig.2020.09.010] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 09/04/2020] [Accepted: 09/10/2020] [Indexed: 12/14/2022]
Abstract
Phyllosphere microbial communities inhabit the aerial plant parts, such as leaves and flowers, where they form complex molecular interactions with the host plant. Contrary to the relatively well-studied rhizosphere microbiome, scientists are just starting to understand, and potentially utilize, the phyllosphere microbiome. In this article, we summarize the recent studies that have provided novel insights into the mechanism of the host genotype shaping the phyllosphere microbiome and the possibility to select a stable and well-adapted microbiome. We also discuss the most pressing gaps in our knowledge and identify the most promising research directions and tools for understanding the assembly and function of phyllosphere microbiomes - this understanding is necessary if we are to harness phyllosphere microbiomes for improving plant growth and health in managed systems.
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Affiliation(s)
- Sara Shakir
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Syed Shan-E-Ali Zaidi
- Plant Genetics, TERRA Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Franciska T de Vries
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, The Netherlands
| | - Shahid Mansoor
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering, Faisalabad, Pakistan.
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37
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Dew RM, McFrederick QS, Rehan SM. Diverse Diets with Consistent Core Microbiome in Wild Bee Pollen Provisions. INSECTS 2020; 11:insects11080499. [PMID: 32759653 PMCID: PMC7469187 DOI: 10.3390/insects11080499] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 07/26/2020] [Accepted: 07/29/2020] [Indexed: 12/13/2022]
Abstract
Bees collect pollen from flowers for their offspring, and by doing so contribute critical pollination services for our crops and ecosystems. Unlike many managed bee species, wild bees are thought to obtain much of their microbiome from the environment. However, we know surprisingly little about what plant species bees visit and the microbes associated with the collected pollen. Here, we addressed the hypothesis that the pollen and microbial components of bee diets would change across the range of the bee, by amplicon sequencing pollen provisions of a widespread small carpenter bee, Ceratina calcarata, across three populations. Ceratina calcarata was found to use a diversity of floral resources across its range, but the bacterial genera associated with pollen provisions were very consistent. Acinetobacter, Erwinia, Lactobacillus, Sodalis, Sphingomonas and Wolbachia were among the top ten bacterial genera across all sites. Ceratina calcarata uses both raspberry (Rubus) and sumac (Rhus) stems as nesting substrates, however nests within these plants showed no preference for host plant pollen. Significant correlations in plant and bacterial co-occurrence differed between sites, indicating that many of the most common bacterial genera have either regional or transitory floral associations. This range-wide study suggests microbes present in brood provisions are conserved within a bee species, rather than mediated by climate or pollen composition. Moving forward, this has important implications for how these core bacteria affect larval health and whether these functions vary across space and diet. These data increase our understanding of how pollinators interact with and adjust to their changing environment.
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Affiliation(s)
- Rebecca M. Dew
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada;
| | - Quinn S. McFrederick
- Department of Entomology, University of California Riverside, Riverside, CA 92521, USA;
| | - Sandra M. Rehan
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada;
- Correspondence: ; Tel.: +1-416-736-2100
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The gut and feed residue microbiota changing during the rearing of Hermetia illucens larvae. Antonie van Leeuwenhoek 2020; 113:1323-1344. [PMID: 32638136 DOI: 10.1007/s10482-020-01443-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/24/2020] [Indexed: 12/19/2022]
Abstract
Larvae of Hermetia illucens, commonly known as black soldier fly, efficiently convert organic waste into nutrient-rich supplements for different applications. Here we performed a preliminary experiment to investigate the dynamics of the H. illucens gut microbiota and changes in the composition of the bacterial community in the residue of the larval feed during rearing. We furthermore quantified the presence of antibiotic resistance and disinfectant genes in the gut and feed microbiota during the rearing process to elucidate if rearing leads to a reduction, increase, and/or transfer of resistance genes from the feed to larvae and vice versa. We found that the gut and feed residue bacterial communities were distinct throughout the rearing process. The gut microbiome remained more stable compared to the feed residue microbiome varying in both bacterial abundance and community structure during rearing. Antibiotic-resistance genes were present in both, gut and feed residues, with a significant increase in pupae and residue samples taken at the end of the rearing process. Disinfectant-resistance genes were present in the feed residue and even increased during the rearing process but were not transferred to the gut microbiome. We conclude that H. illucens larvae have a stable gut microbiome that does not change significantly over the course of larval development, whereas bacterial communities in the feed residue are strongly affected by rearing. If the presence of antibiotics and disinfectants during rearing, can promote the spread of antibiotic/disinfectant-resistance genes among feed and larvae needs to be evaluated in further experiments.
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Zhao Q, Liu W, Li Y, Ke M, Qu Q, Yuan W, Pan X, Qian H. Enantioselective effects of imazethapyr residues on Arabidopsis thaliana metabolic profile and phyllosphere microbial communities. J Environ Sci (China) 2020; 93:57-65. [PMID: 32446460 DOI: 10.1016/j.jes.2020.03.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/04/2020] [Accepted: 03/04/2020] [Indexed: 06/11/2023]
Abstract
Imazethapyr (IM) is a widely used acetolactate synthase-inhibiting chiral herbicide. It has long-term residuals that may be absorbed by the human body through the edible parts of plants, such as vegetable leaves or fruits. Here, we selected a model plant, Arabidopsis thaliana, to determine the effects of R-IM and S-IM on its leaf structure, photosynthetic efficiency, and metabolites, as well as the structures of microorganisms in the phyllosphere, after 7 days of exposure. Our results indicated enantiomeric differences in plant growth between R-IM and S-IM; 133 µg/kg R-IM showed heavier inhibition of photosynthetic efficiency and greater changes to subcellular structure than S-IM. R-IM and S-IM also had different effects on metabolism and leaf microorganisms. S-IM mainly increased lipid compounds and decreased amino acids, while R-IM increased sugar accumulation. The relative abundance of Moraxellaceae human pathogenic bacteria was increased by R-IM treatment, indicating that R-IM treatment may increase leaf surface pathogenic bacteria. Our research provides a new perspective for evaluating the harmfulness of pesticide residues in soil, phyllosphere microbiome changes via the regulation of plant metabolism, and induced pathogenic bacterial accumulation risks.
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Affiliation(s)
- Qianqiu Zhao
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wanyue Liu
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Qian Qu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Wenting Yuan
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Xiangliang Pan
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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40
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Longley R, Noel ZA, Benucci GMN, Chilvers MI, Trail F, Bonito G. Crop Management Impacts the Soybean ( Glycine max) Microbiome. Front Microbiol 2020; 11:1116. [PMID: 32582080 PMCID: PMC7283522 DOI: 10.3389/fmicb.2020.01116] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/21/2022] Open
Abstract
Soybean (Glycine max) is an important leguminous crop that is grown throughout the United States and around the world. In 2016, soybean was valued at $41 billion USD in the United States alone. Increasingly, soybean farmers are adopting alternative management strategies to improve the sustainability and profitability of their crop. Various benefits have been demonstrated for alternative management systems, but their effects on soybean-associated microbial communities are not well-understood. In order to better understand the impact of crop management systems on the soybean-associated microbiome, we employed DNA amplicon sequencing of the Internal Transcribed Spacer (ITS) region and 16S rRNA genes to analyze fungal and prokaryotic communities associated with soil, roots, stems, and leaves. Soybean plants were sampled from replicated fields under long-term conventional, no-till, and organic management systems at three time points throughout the growing season. Results indicated that sample origin was the main driver of beta diversity in soybean-associated microbial communities, but management regime and plant growth stage were also significant factors. Similarly, differences in alpha diversity are driven by compartment and sample origin. Overall, the organic management system had lower fungal and bacterial Shannon diversity. In prokaryotic communities, aboveground tissues were dominated by Sphingomonas and Methylobacterium while belowground samples were dominated by Bradyrhizobium and Sphingomonas. Aboveground fungal communities were dominated by Davidiella across all management systems, while belowground samples were dominated by Fusarium and Mortierella. Specific taxa including potential plant beneficials such as Mortierella were indicator species of the conventional and organic management systems. No-till management increased the abundance of groups known to contain plant beneficial organisms such as Bradyrhizobium and Glomeromycotina. Network analyses show different highly connected hub taxa were present in each management system. Overall, this research demonstrates how specific long-term cropping management systems alter microbial communities and how those communities change throughout the growth of soybean.
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Affiliation(s)
- Reid Longley
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States
| | - Zachary A Noel
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Gian Maria Niccolò Benucci
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
| | - Martin I Chilvers
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Genetics and Genomic Sciences Program, Michigan State University, East Lansing, MI, United States
| | - Frances Trail
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States.,Department of Plant Biology, Michigan State University, East Lansing, MI, United States
| | - Gregory Bonito
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, MI, United States.,Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, United States
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Ulrich K, Becker R, Behrendt U, Kube M, Ulrich A. A Comparative Analysis of Ash Leaf-Colonizing Bacterial Communities Identifies Putative Antagonists of Hymenoscyphus fraxineus. Front Microbiol 2020; 11:966. [PMID: 32547506 PMCID: PMC7273808 DOI: 10.3389/fmicb.2020.00966] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 04/22/2020] [Indexed: 12/13/2022] Open
Abstract
In the last few years, the alarming spread of Hymenoscyphus fraxineus, the causal agent of ash dieback, has resulted in a substantial threat to native ash stands in central and northern Europe. Since leaves and leaf petioles are the primary infection sites, phyllosphere microorganisms are presumed to interact with the pathogen and are discussed as a source of biocontrol agents. We studied compound leaves from susceptible and visible infection-free trees in four ash stands with a high likelihood of infection to assess a possible variation in the bacterial microbiota, depending on the health status of the trees. The bacterial community was analyzed by culture-independent 16S rRNA gene amplicon sequencing and through the isolation and taxonomic classification of 2,589 isolates using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). The bacterial community structure did not show significant differences. However, a set of amplicon sequence variants (ASVs) and MALDI groups belonging to Luteimonas, Aureimonas, Pseudomonas, Bacillus, and Paenibacillus were distinctly increased in tolerant trees, which may be associated with the ability of the tree to resist the pathogen. The most obvious differences were observed for Luteimonas, a genus that is also exclusively present in the healthy core microbiome. In a first in vitro screen of antagonists, approximately 11% of total isolates suppressed the growth of H. fraxineus, but a statistical test with two different H. fraxineus strains confirmed only the antagonistic activity of 8% of these isolates. The antagonistic isolates were assigned to Bacillus velezensis, Pantoea vagans, and Pseudomonas caspiana. Overall, our study provides a set of isolates or phylogenetic groups that might be involved in the process that prevents the penetration and spread of H. fraxineus. In the next step, in planta experiments are required with a longer period of exposure to H. fraxineus to evaluate effective isolates or consortia of isolates acting through direct antagonism or competition or indirectly by inducing resistance.
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Affiliation(s)
- Kristina Ulrich
- Institute of Forest Genetics, Johann Heinrich von Thünen Institute, Waldsieversdorf, Germany
| | - Regina Becker
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Undine Behrendt
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Michael Kube
- Integrative Infection Biology Crops-Livestock, University of Hohenheim, Stuttgart, Germany
| | - Andreas Ulrich
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
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42
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Aydogan EL, Budich O, Hardt M, Choi YH, Jansen-Willems AB, Moser G, Müller C, Kämpfer P, Glaeser SP. Global warming shifts the composition of the abundant bacterial phyllosphere microbiota as indicated by a cultivation-dependent and -independent study of the grassland phyllosphere of a long-term warming field experiment. FEMS Microbiol Ecol 2020; 96:5835220. [DOI: 10.1093/femsec/fiaa087] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 05/08/2020] [Indexed: 02/06/2023] Open
Abstract
ABSTRACT
The leaf-colonizing bacterial microbiota was studied in a long-term warming experiment on a permanent grassland, which had been continuously exposed to increased surface temperature (+2°C) for more than six years. Two abundant plant species, Arrhenatherum elatius and Galium album, were studied. Surface warming reduced stomata opening and changed leaf metabolite profiles. Leaf surface colonization and the concentration of leaf-associated bacterial cells were not affected. However, bacterial 16S ribosomal RNA (rRNA) gene amplicon Illumina sequencing showed significant temperature effects on the plant species-specific phyllosphere microbiota. Warming partially affected the concentrations of cultured bacteria and had a significant effect on the composition of most abundant cultured plant species-specific bacteria. The abundance of Sphingomonas was significantly reduced. Sphingomonas isolates from warmed plots represented different phylotypes, had different physiological traits and were better adapted to higher temperatures. Among Methylobacterium isolates, a novel phylotype with a specific mxaFtype was cultured from plants of warmed plots while the most abundant phylotype cultured from control plots was strongly reduced. This study clearly showed a correlation of long-term surface warming with changes in the plant physiology and the development of a physiologically and genetically adapted phyllosphere microbiota.
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Affiliation(s)
- Ebru L Aydogan
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Olga Budich
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Martin Hardt
- Biomedical Research Center Seltersberg – Imaging Unit, Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Young Hae Choi
- Natural Products Laboratory, Institute of Biology, Leiden University, Sylviusweg 72, 2333 BE Leiden, The Netherlands
| | - Anne B Jansen-Willems
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Gerald Moser
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
| | - Christoph Müller
- Institute of Plant Ecology (IFZ), Justus Liebig University Giessen, D-39392 Giessen, Germany
- School of Biology and Environmental Science and Earth Institute, University College Dublin, Belfield, D04V1W8 Dublin, Ireland
| | - Peter Kämpfer
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
| | - Stefanie P Glaeser
- Institute of Applied Microbiology (IFZ), Justus Liebig University Giessen, D-35392 Giessen, Germany
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Leveau JH. A brief from the leaf: latest research to inform our understanding of the phyllosphere microbiome. Curr Opin Microbiol 2019; 49:41-49. [PMID: 31707206 DOI: 10.1016/j.mib.2019.10.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/03/2019] [Accepted: 10/04/2019] [Indexed: 01/05/2023]
Abstract
The plant leaf surface, or phyllosphere, represents a unique and challenging microbial biome with a diverse and dynamic community of commensal, parasitic, and mutualistic agents of microscopic proportions. This mini-review offers a digest of recently published research dedicated to the study of phyllosphere microbiota, framed in the context of processes and outcomes of microbial community assembly, structure, and (inter)activity in the phyllosphere, with particular focus on the contributions of environment, plant, and microbe, and on the potential benefits of interrogating those contributions at finer resolutions.
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Affiliation(s)
- Johan Hj Leveau
- Department of Plant Pathology, University of California, Davis, CA 95616, USA.
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Liu W, Ke M, Zhang Z, Lu T, Zhu Y, Li Y, Pan X, Qian H. Effects of imazethapyr spraying on plant growth and leaf surface microbial communities in Arabidopsis thaliana. J Environ Sci (China) 2019; 85:35-45. [PMID: 31471029 DOI: 10.1016/j.jes.2019.04.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Revised: 04/11/2019] [Accepted: 04/12/2019] [Indexed: 06/10/2023]
Abstract
Imazethapyr (IM) is an acetolactate synthase (ALS)-inhibiting herbicide that has been widely used in recent years. However, IM spraying can lead to the accumulation of herbicide residues in leaves. Here, we determined the effects of IM spraying on the plant growth and leaf surface microbial communities of Arabidopsis thaliana after 7 and 14 days of exposure. The results suggested that IM spraying inhibited plant growth. Fresh weight decreased to 48% and 26% of the control value after 7 and 14 days, respectively, of 0.035 kg/ha IM exposure. In addition, anthocyanin content increased 9.2-fold and 37.2-fold relative to the control content after 7 and 14 days of treatment, respectively. Furthermore, IM spraying destroyed the cell structures of the leaves, as evidenced by increases in the number of starch granules and the stomatal closure rate. Reductions in photosynthetic efficiency and antioxidant enzyme activity were observed after IM spraying, especially after 14 days of exposure. The diversity and evenness of the leaf microbiota were not affected by IM treatment, but the composition of community structure at the genus level was altered by IM spraying. Imazethapyr application increased the abundance of Pseudomonas, a genus that includes species pathogenic to plants and humans, indicating that IM potentially increased the abundance of pathogenic bacteria on leaves. Our findings increase our understanding of the relationships between herbicide application and the microbial community structures on plant leaves, and they provide a new perspective for studying the ecological safety of herbicide usage.
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Affiliation(s)
- Wanyue Liu
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China
| | - Mingjing Ke
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Zhenyan Zhang
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Tao Lu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Youchao Zhu
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Yan Li
- College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Xiangliang Pan
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; College of Environment, Zhejiang University of Technology, Hangzhou 310032, China
| | - Haifeng Qian
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi 830011, China; College of Environment, Zhejiang University of Technology, Hangzhou 310032, China.
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45
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Janakiev T, Dimkić I, Bojić S, Fira D, Stanković S, Berić T. Bacterial communities of plum phyllosphere and characterization of indigenous antagonistic Bacillus thuringiensis R3/3 isolate. J Appl Microbiol 2019; 128:528-543. [PMID: 31606926 DOI: 10.1111/jam.14488] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 09/30/2019] [Accepted: 10/08/2019] [Indexed: 12/01/2022]
Abstract
AIMS The characterization of bacterial communities diversity on four local plum cultivars in two phenological stages using culture-dependent and culture-independent methods and screening among culturable plum community for indigenous bacteria active against phytopathogens. METHODS AND RESULTS The bacterial communities associated with leaves and fruits of four local Serbian plum cultivars (Požegača, Ranka, Čačanska Lepotica and Čačanska Rodna) were investigated in two phenological stages during early (May) and late (July) fruit maturation. Metagenomic approach revealed Methylobacterium, Sphingomonas and Hymenobacter as dominant genera. The most frequently isolated representatives with cultivable approach were pseudomonads with Pseudomonas syringae and Pseudomonas graminis, the most likely resident species of plum community. Antagonistic Bacillus thuringiensis R3/3 isolate from plum phyllosphere had ability to produce exoenzymes, reduce the growth of phytopathogenic bacteria in co-culture environment and show quorum quenching activity. CONCLUSIONS Plum cultivar and growth season contribute to the structure of the bacterial community associated with plum. Plum phyllosphere is good source of antagonists effective against phytopathogens. SIGNIFICANCE AND IMPACT OF STUDY Knowledge of bacterial communities on plum will have an impact on studies related to phyllosphere ecology and biocontrol. The indigenous antagonistic isolate, B. thuringiensis R3/3, from plum could be further investigated for its potential use in biological control of plum diseases.
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Affiliation(s)
- T Janakiev
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - I Dimkić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Bojić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - D Fira
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - S Stanković
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
| | - T Berić
- University of Belgrade - Faculty of Biology, Belgrade, Serbia
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46
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Zhang Z, Kong X, Jin D, Yu H, Zhu X, Su X, Wang P, Zhang R, Jia M, Deng Y. Euonymus japonicus phyllosphere microbiome is significantly changed by powdery mildew. Arch Microbiol 2019; 201:1099-1109. [PMID: 31147747 DOI: 10.1007/s00203-019-01683-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 05/06/2019] [Accepted: 05/21/2019] [Indexed: 12/24/2022]
Abstract
Euonymus japonicus Thunb. is a woody and ornamental plant popular in China, Europe and North America. Powdery mildew is one of the most serious diseases that affect E. japonicus growth. In this study, the diseased and apparently healthy leaves were collected from E. japonicus planted in a greenbelt in Beijing, and the effect of powdery mildew on the epiphytic microbial community was investigated by using Illumina sequencing. The results showed that the healthy leaves (HL) harbored greater bacterial and fungal diversity than diseased leaves (DL). Furthermore, both bacterial and fungal communities in DL exhibited significantly different structures from those in HL. The relative abundance of several bacterial phyla (Proteobacteria and Firmicutes) and fungal phyla (Ascomycota and Basidiomycota) were altered by powdery mildew. At the genus level, most genera decreased as powdery mildew pathogen Erysiphe increased, while the genera Kocuria and Exiguobacterium markedly increased. Leaf properties, especially protein content was found to significantly affect beta-diversity of the bacterial and fungal community. Network analysis revealed that positive bacterial interactions in DL were stronger than those in HL samples. Insights into the underlying the indigenous microbial phyllosphere populations of E. japonicus response to powdery mildew will help in the development of methods for controlling plant diseases.
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Affiliation(s)
- Zhuo Zhang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.,Key Laboratory of Pest Management of Horticultural Crops of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Xiao Kong
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Decai Jin
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China.
| | - Hao Yu
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
| | - Xun Zhu
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Xiaofeng Su
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Pei Wang
- College of Plant Protection, Hunan Agricultural University, Changsha, 410128, China.,Key Laboratory of Pest Management of Horticultural Crops of Hunan Province, Hunan Plant Protection Institute, Hunan Academy of Agricultural Science, Changsha, 410125, China
| | - Ruiyong Zhang
- Federal Institute for Geosciences and Natural Resources (BGR), Hannover, 30655, Germany
| | - Minghong Jia
- Beijing Key Laboratory of Detection and Control of Spoilage Organisms and Pesticide Residues in Agricultural Products, Beijing University of Agriculture, Beijing, 102206, China
| | - Ye Deng
- Key Laboratory of Environmental Biotechnology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China
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