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Sivaprakasam N, Vaithiyanathan S, Gandhi K, Narayanan S, Kavitha PS, Rajasekaran R, Muthurajan R. Metagenomics approaches in unveiling the dynamics of Plant Growth-Promoting Microorganisms (PGPM) vis-à-vis Phytophthora sp. suppression in various crop ecological systems. Res Microbiol 2024:104217. [PMID: 38857835 DOI: 10.1016/j.resmic.2024.104217] [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: 02/29/2024] [Revised: 05/02/2024] [Accepted: 06/04/2024] [Indexed: 06/12/2024]
Abstract
Phytophthora species are destructive pathogens causing yield losses in different ecological systems, such as potato, black pepper, pepper, avocado, citrus, and tobacco. The diversity of plant growth-promoting microorganisms (PGPM) plays a crucial role in disease suppression. Knowledge of metagenomics approaches is essential for assessing the dynamics of PGPM and Phytophthora species across various ecosystems, facilitating effective management strategies for better crop protection. This review discusses the dynamic interplay between PGPM and Phytophthora sp. using metagenomics approaches that sheds light on the potential of PGPM strains tailored to specific crop ecosystems to bolster pathogen suppressiveness.
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Affiliation(s)
- Navarasu Sivaprakasam
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | | | - Karthikeyan Gandhi
- Department of Plant Pathology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Swarnakumari Narayanan
- Department of Nematology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - P S Kavitha
- School of Post Graduate Studies, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raghu Rajasekaran
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
| | - Raveendran Muthurajan
- Centre for Plant Molecular Biology & Biotechnology, Tamil Nadu Agricultural University, Coimbatore, Tamil Nadu, India
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Wang P, Zhang H, Hu X, Xu L, An X, Jin T, Ma R, Li Z, Chen S, Du S, Wei G, Chen C. Comparing the Potential of Silicon Nanoparticles and Conventional Silicon for Salinity Stress Alleviation in Soybean ( Glycine max L.): Growth and Physiological Traits and Rhizosphere/Endophytic Bacterial Communities. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:10781-10793. [PMID: 38709780 DOI: 10.1021/acs.jafc.4c00154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
Abstract
In this study, 20-day-old soybean plants were watered with 100 mL of 100 mM NaCl solution and sprayed with silica nanoparticles (SiO2 NPs) or potassium silicate every 3 days over 15 days, with a final dosage of 12 mg of SiO2 per plant. We assessed the alterations in the plant's growth and physiological traits, and the responses of bacterial microbiome within the leaf endosphere, rhizosphere, and root endosphere. The result showed that the type of silicon did not significantly impact most of the plant parameters. However, the bacterial communities within the leaf and root endospheres had a stronger response to SiO2 NPs treatment, showing enrichment of 24 and 13 microbial taxa, respectively, compared with the silicate treatment, which led to the enrichment of 9 and 8 taxonomic taxa, respectively. The rhizosphere bacterial communities were less sensitive to SiO2 NPs, enriching only 2 microbial clades, compared to the 8 clades enriched by silicate treatment. Furthermore, SiO2 NPs treatment enriched beneficial genera, such as Pseudomonas, Bacillus, and Variovorax in the leaf and root endosphere, likely enhancing plant growth and salinity stress resistance. These findings highlight the potential of SiO2 NPs for foliar application in sustainable farming by enhancing plant-microbe interactions to improve salinity tolerance.
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Affiliation(s)
- Pan Wang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Hui Zhang
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xiao Hu
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Leilei Xu
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Xin An
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | | | - Ruixue Ma
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Zhefei Li
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Sanfeng Chen
- State Key Laboratory for Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Sen Du
- National Agro-Tech Extension and Service Center, Beijing 100125, China
| | - Gehong Wei
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
| | - Chun Chen
- State Key Laboratory of Crop Stress Resistance and High-Efficiency Production, Shaanxi Key Laboratory of Agricultural and Environmental Microbiology, College of Life Sciences, Northwest A&F University, Yangling 712100, Shaanxi, China
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Zhao B, Yan Y, Cao D, Xia Y. Germinating rice seeds shape rhizospheric bacteria via releasing benzaldehyde. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108632. [PMID: 38657546 DOI: 10.1016/j.plaphy.2024.108632] [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: 01/03/2024] [Revised: 03/23/2024] [Accepted: 04/14/2024] [Indexed: 04/26/2024]
Abstract
Plants are not passively exposed to microbes during their life cycles, but rather shape the microbiome in their own way. However, little information is available about when and how plants recruit their microbes in the life cycles. We scrutinized the recruitment of soil microbes by rice (Oryza sativa) at the seed germination stage. Bacteria of Enterobacteria and Weeksellaceae were the most preferentially recruited by the germinating seeds, despite of many other bacteria in the soil. The seedlings that recruited Enterobacteria and Weeksellaceae bacteria notably outperformed those without these microbes in leaf length (by 54.21%), root length (by 188.11%) and biomass (by 88.65%). Further, we detected benzaldehyde, a plant-specific volatile metabolite, in the exudates of germinating seeds. Addition of benzaldehyde to the soil resulted in enrichment of Enterobacteria bacteria, suggesting that seed-released benzaldehyde could be a cue to recruit beneficial bacteria. Taken together, our results demonstrated that plants could recruit beneficial bacteria from the soil at the very early life stage of seed germination via releasing specific metabolites.
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Affiliation(s)
- Bixi Zhao
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Yuxi Yan
- School of Environment, Harbin Institute of Technology, Harbin, 150001, China; School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Dechang Cao
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, Yunnan, 650201, China.
| | - Yu Xia
- School of Environmental Science and Engineering, College of Engineering, Southern University of Science and Technology, Shenzhen, 518055, China.
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Xiong C, K. Singh B, Zhu YG, Hu HW, Li PP, Han YL, Han LL, Zhang QB, Wang JT, Liu SY, Wu CF, Ge AH, Zhang LM, He JZ. Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development. mSystems 2024; 9:e0105523. [PMID: 38501864 PMCID: PMC11019923 DOI: 10.1128/msystems.01055-23] [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: 02/28/2024] [Indexed: 03/20/2024] Open
Abstract
Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.
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Affiliation(s)
- Chao Xiong
- 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
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
| | - Brajesh K. Singh
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - 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
| | - Hang-Wei Hu
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
| | - Pei-Pei Li
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Yan-Lai Han
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - Li-Li Han
- 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
| | - Qin-Bing Zhang
- Soil and Fertilizer Station of Qilin District, Qujing, Yunnan Province, China
| | - Jun-Tao Wang
- Hawkesbury Institute for the Environment, Western Sydney University, Penrith, New South Wales, Australia
- Global Centre for Land-Based Innovation, Western Sydney University, Penrith, New South Wales, Australia
| | - Si-Yi Liu
- 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
| | - Chuan-Fa Wu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- College of Resource and Environmental Sciences, Henan Agricultural University, Zhengzhou, China
| | - An-Hui Ge
- 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
| | - Li-Mei Zhang
- 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
| | - Ji-Zheng He
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria, Australia
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Zhang Y, Du Y, Zhang Z, Islam W, Zeng F. Unveiling the diversity, composition, and dynamics of phyllosphere microbial communities in Alhagi sparsifolia across desert basins and seasons in Xinjiang, China. Front Microbiol 2024; 15:1361756. [PMID: 38591034 PMCID: PMC10999668 DOI: 10.3389/fmicb.2024.1361756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 03/07/2024] [Indexed: 04/10/2024] Open
Abstract
Phyllosphere microbes residing on plant leaf surfaces for maintaining plant health have gained increasing recognition. However, in desert ecosystems, knowledge about the variety, composition, and coexistence patterns of microbial communities in the phyllosphere remains limited. This study, conducted across three basins (Turpan-TLF, Tarim-CL, and Dzungaria-MSW) and three seasons (spring, summer, and autumn) in Xinjiang, China, aimed to explore the diversity and composition of microbial communities in the phyllosphere, encompassing both bacteria and fungi in Alhagi sparsifolia. We also investigated the co-occurrence patterns, influencing factors, and underlying mechanisms driving these dynamics. Results indicate that phyllosphere bacteria exhibited lower diversity indices (ACE, Shannon, Simpson, Fisher phylogenetic diversity, and Richness) in spring compared to summer and autumn, while the Goods Coverage Index (GCI) was higher in spring. Conversely, diversity indices and GCI of phyllosphere fungi showed an opposite trend. Interestingly, the lowest level of multi-functionality and niche width in phyllosphere bacteria occurred in spring, while the highest level was observed in phyllosphere fungi. Furthermore, the study revealed that no significant differences in multi-functionality were found among the regions (CL, MSW, and TLF). Network analysis highlighted that during spring, phyllosphere bacteria exhibited the lowest number of nodes, edges, and average degree, while phyllosphere fungi had the highest. Surprisingly, the multi-functionality of both phyllosphere bacteria and fungi showed no significant correlation with climatic and environmental factors but displayed a significant association with the morphological characteristics and physicochemical properties of leaves. Structural Equation Model indicated that the morphological characteristics of leaves significantly influenced the multi-functionality of phyllosphere bacteria and fungi. However, the indirect and total effects of climate on multi-functionality were greater than the effects of physicochemical properties and morphological characteristics of leaves. These findings offer new insights into leaf phyllosphere microbial community structure, laying a theoretical foundation for vegetation restoration and rational plant resource utilization in desert ecosystems.
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Affiliation(s)
- Yulin Zhang
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Yi Du
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhihao Zhang
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Waqar Islam
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
| | - Fanjiang Zeng
- College of Ecology and Environmental, Xinjiang University, Urumqi, China
- State Key Laboratory of Desert and Oasis Ecology, Key Laboratory of Ecological Safety and Sustainable Development in Arid Lands, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Xinjiang Key Laboratory of Desert Plant Roots Ecology and Vegetation Restoration, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
- Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, China
- University of Chinese Academy of Sciences, Beijing, China
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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
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Muneer MA, Chen X, Wang H, Munir MZ, Afridi MS, Yan X, Ji B, Li W, Wu L, Zheng C. Unraveling two decades of phyllosphere endophytes: tracing research trends and insights through visualized knowledge maps, with emphasis on microbial interactions as emerging frontiers. STRESS BIOLOGY 2024; 4:12. [PMID: 38319560 PMCID: PMC10847081 DOI: 10.1007/s44154-024-00148-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 01/07/2024] [Indexed: 02/07/2024]
Abstract
Phyllosphere endophytes play a critical role in a myriad of biological functions, such as maintaining plant health and overall fitness. They play a determinative role in crop yield and quality by regulating vital processes, such as leaf functionality and longevity, seed mass, apical growth, flowering, and fruit development. This study conducted a comprehensive bibliometric analysis aiming to review the prevailing research trajectories in phyllosphere endophytes and harness both primary areas of interest and emerging challenges. A total of 156 research articles on phyllosphere endophytes, published between 2002 and 2022, were retrieved from the Web of Science Core Collection (WoSCC). A systematic analysis was conducted using CiteSpace to visualize the evolution of publication frequency, the collaboration network, the co-citation network, and keywords co-occurrence. The findings indicated that initially, there were few publications on the topic of phyllosphere endophytes. However, from 2011 onwards, there was a notable increase in the number of publications on phyllosphere endophytes, gaining worldwide attention. Among authors, Arnold, A Elizabeth is widely recognized as a leading author in this research area. In terms of countries, the USA and China hold the highest rankings. As for institutional ranking, the University of Arizona is the most prevalent and leading institute in this particular subject. Collaborative efforts among the authors and institutions tend to be confined to small groups, and a large-scale collaborative network needs to be established. This study identified the influential journals, literature, and hot research topics. These findings also highlight the interconnected nature of key themes, e.g., phyllosphere endophyte research revolves around the four pillars: diversity, fungal endophytes, growth, and endophytic fungi. This study provides an in-depth perspective on phyllosphere endophytes studies, revealing the identification of biodiversity and microbial interaction of phyllosphere endophytes as the principal research frontiers. These analytical findings not only elucidate the recent trajectory of phyllosphere endophyte research but also provide invaluable insights for similar studies and their potential applications on a global scale.
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Affiliation(s)
- Muhammad Atif Muneer
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xiaohui Chen
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention; Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Hexin Wang
- Anhui Province Key Lab of Farmland Ecological Conservation and Pollution Prevention; Anhui Province Engineering and Technology Research Center of Intelligent Manufacture and Efficient Utilization of Green Phosphorus Fertilizer, College of Resources and Environment, Anhui Agricultural University, Hefei, 230036, China
| | - Muhammad Zeeshan Munir
- School of Environment and Energy, Peking University Shenzhen Graduate School, 2199, Lishui Rd, Shenzhen, 518055, China
| | - Muhammad Siddique Afridi
- Department of Plant Pathology, Federal University of Lavras (UFLA), Lavras, MG, CEP 37200-900, Brazil
| | - Xiaojun Yan
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Baoming Ji
- College of Grassland Science, Beijing Forestry University, Beijing, China
| | - Wenqing Li
- Fujian Institute of Tobacco Sciences, Fuzhou, 350013, China
| | - Liangquan Wu
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chaoyuan Zheng
- International Magnesium Institute, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Jing J, Garbeva P, Raaijmakers JM, Medema MH. Strategies for tailoring functional microbial synthetic communities. THE ISME JOURNAL 2024; 18:wrae049. [PMID: 38537571 PMCID: PMC11008692 DOI: 10.1093/ismejo/wrae049] [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: 01/08/2024] [Revised: 02/26/2024] [Indexed: 04/12/2024]
Abstract
Natural ecosystems harbor a huge reservoir of taxonomically diverse microbes that are important for plant growth and health. The vast diversity of soil microorganisms and their complex interactions make it challenging to pinpoint the main players important for the life support functions microbes can provide to plants, including enhanced tolerance to (a)biotic stress factors. Designing simplified microbial synthetic communities (SynComs) helps reduce this complexity to unravel the molecular and chemical basis and interplay of specific microbiome functions. While SynComs have been successfully employed to dissect microbial interactions or reproduce microbiome-associated phenotypes, the assembly and reconstitution of these communities have often been based on generic abundance patterns or taxonomic identities and co-occurrences but have only rarely been informed by functional traits. Here, we review recent studies on designing functional SynComs to reveal common principles and discuss multidimensional approaches for community design. We propose a strategy for tailoring the design of functional SynComs based on integration of high-throughput experimental assays with microbial strains and computational genomic analyses of their functional capabilities.
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Affiliation(s)
- Jiayi Jing
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Paolina Garbeva
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Jos M Raaijmakers
- Department of Microbial Ecology, Netherlands Institute of Ecology (NIOO-KNAW), Droevendaalsesteeg 10, 6708 PB Wageningen, The Netherlands
| | - Marnix H Medema
- Bioinformatics Group, Department of Plant Science, Wageningen University & Research, Droevendaalsesteeg 1, 6708PB Wageningen, The Netherlands
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Shao Q, Ran Q, Li X, Dong C, Huang J, Han Y. Deciphering the effect of phytohormones on the phyllosphere microbiota of Eucommia ulmoides. Microbiol Res 2024; 278:127513. [PMID: 37837828 DOI: 10.1016/j.micres.2023.127513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/30/2023] [Accepted: 10/06/2023] [Indexed: 10/16/2023]
Abstract
Phytohormones are key signals mediating plant-microbe molecular communication. However, their roles in driving phyllosphere microbiota assembly remain unclear. Here, high throughput target assays for 12 phytohormones and microbial amplicon sequencing techniques were used to reveal the effects of hormone components on phyllosphere microbiota of Eucommia ulmoides. Most of the phytohormone components in old leaves were lower than in tender leaves, such as indole-3-acetic acid (IAA), salicylic acid (SA), and jasmonic acid (JA), but the phyllosphere microbial community diversity in the older leaves was significantly higher than in the tender leaves, with more complex and aggregated microbial cooccurrence network. The E. ulmoides phyllosphere microbiota at tender and older leaf stage were dominated by the same dominant taxa at the phylum level, with Ascomycota and Basidiomycota as the main fungal taxa and Actinobacteriota, Bacteroidota, Firmicutes and Proteobacteria as the main bacterial taxa. FUNGuild and FAPROTAX functional predictions revealed that the high abundance functional groups of the E. ulmoides phyllosphere microbes were similar at tender and old leaf stages, with fungal functions mainly involving in plant pathogen, undefined saprotroph and endophyte, and bacterial functions mainly involving in chemoheterotrophy, fermentation and aerobic_chemoheterotrophy. Additionally, mantel test and variance partitioning analysis showed that IAA and N6-(delta 2-isopentenyl)-adenine (IP) were key phytohormones impacting the E. ulmoides phyllosphere microbiota, and their effects were largely interdependent. Our results improve the understanding of composition, diversity, function and influencing factors of phyllosphere microbiota, which might provide cue for sustainable agriculture and forestry management via precise regulation of the phyllosphere microbiota.
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Affiliation(s)
- Qiuyu Shao
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Qingsong Ran
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Xu Li
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Chunbo Dong
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China
| | - Jianzhong Huang
- Engineering Research Center of Industrial Microbiology, Ministry of Education, Fujian Normal University, Fuzhou 350108, Fujian, China
| | - Yanfeng Han
- Institute of Fungus Resources, Department of Ecology/Key laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Guizhou University, Guiyang 5 50025, Guizhou, China.
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10
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Si H, Cui B, Liu F, Zhao M. Microbial community and chemical composition of cigar tobacco ( Nicotiana tabacum L.) leaves altered by tobacco wildfire disease. PLANT DIRECT 2023; 7:e551. [PMID: 38099080 PMCID: PMC10719477 DOI: 10.1002/pld3.551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 11/08/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023]
Abstract
Tobacco wildfire disease caused by Pseudomonas syringae pv. tabaci is one of the most destructive foliar bacterial diseases occurring worldwide. However, the effect of wildfire disease on cigar tobacco leaves has not been clarified in detail. In this study, the differences in microbiota and chemical factors between wildfire disease-infected leaves and healthy leaves were characterized using high-throughput Illumina sequencing and a continuous-flow analytical system, respectively. The results demonstrated significant alterations in the structure of the phyllosphere microbial community in response to wildfire disease, and the infection of P. syringae pv. tabaci led to a decrease in bacterial richness and diversity. Furthermore, the content of nicotine, protein, total nitrogen, and Cl- in diseased leaves significantly increased by 47.86%, 17.46%, 20.08%, and 72.77% in comparison to healthy leaves, while the levels of total sugar and reducing sugar decreased by 59.59% and 70.0%, respectively. Notably, the wildfire disease had little effect on the content of starch and K+. Redundancy analysis revealed that Pseudomonas, Staphylococcus, Cladosporium, and Wallemia displayed positive correlations with nicotine, protein, total nitrogen, Cl- and K+ contents, while Pantoea, Erwinia, Sphingomonas, Terrisporobacter, Aspergillus, Alternaria, Sampaiozyma, and Didymella displayed positive correlations with total sugar and reducing sugar contents. Brevibacterium, Brachybacterium, and Janibacter were found to be enriched in diseased leaves, suggesting their potential role in disease suppression. Co-occurrence network analysis indicated that positive correlations were prevalent in microbial networks, and the bacterial network of healthy tobacco leaves exhibited greater complexity compared to diseased tobacco leaves. This study revealed the impact of wildfire disease on the microbial community and chemical compositions of tobacco leaves and provides new insights for the biological control of tobacco wildfire disease.
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Affiliation(s)
- Hongyang Si
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Bing Cui
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Fang Liu
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Mingqin Zhao
- Flavors and Fragrance Engineering and Technology Research Center of Henan Province, College of Tobacco ScienceHenan Agricultural UniversityZhengzhouHenanChina
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11
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Zhu YG, Peng J, Chen C, Xiong C, Li S, Ge A, Wang E, Liesack W. Harnessing biological nitrogen fixation in plant leaves. TRENDS IN PLANT SCIENCE 2023; 28:1391-1405. [PMID: 37270352 DOI: 10.1016/j.tplants.2023.05.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/05/2023]
Abstract
The importance of biological nitrogen fixation (BNF) in securing food production for the growing world population with minimal environmental cost has been increasingly acknowledged. Leaf surfaces are one of the biggest microbial habitats on Earth, harboring diverse free-living N2-fixers. These microbes inhabit the epiphytic and endophytic phyllosphere and contribute significantly to plant N supply and growth. Here, we summarize the contribution of phyllosphere-BNF to global N cycling, evaluate the diversity of leaf-associated N2-fixers across plant hosts and ecosystems, illustrate the ecological adaptation of N2-fixers to the phyllosphere, and identify the environmental factors driving BNF. Finally, we discuss potential BNF engineering strategies to improve the nitrogen uptake in plant leaves and thus sustainable food production.
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Affiliation(s)
- Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China.
| | - Jingjing Peng
- State Key Laboratory of Nutrient Use and Management, College of Resources and Environmental Sciences, National Academy of Agriculture Green Development, China Agricultural University, Beijing, 100193, China
| | - Cai Chen
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Chao Xiong
- College of Urban and Environmental Sciences, Peking University, Beijing, 100871, China
| | - Shule Li
- Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, China
| | - Anhui Ge
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Ertao Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, SIBS, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Werner Liesack
- Max Planck Institute for Terrestrial Microbiology, Marburg, 35043, Germany
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12
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Xiong Q, Yang J, Ni S. Microbiome-Mediated Protection against Pathogens in Woody Plants. Int J Mol Sci 2023; 24:16118. [PMID: 38003306 PMCID: PMC10671361 DOI: 10.3390/ijms242216118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/23/2023] [Accepted: 10/31/2023] [Indexed: 11/26/2023] Open
Abstract
Pathogens, especially invasive species, have caused significant global ecological, economic, and social losses in forests. Plant disease research has traditionally focused on direct interactions between plants and pathogens in an appropriate environment. However, recent research indicates that the microbiome can interact with the plant host and pathogens to modulate plant resistance or pathogen pathogenicity, thereby altering the outcome of plant-pathogen interactions. Thus, this presents new opportunities for studying the microbial management of forest diseases. Compared to parallel studies on human and crop microbiomes, research into the forest tree microbiome and its critical role in forest disease progression has lagged. The rapid development of microbiome sequencing and analysis technologies has resulted in the rapid accumulation of a large body of evidence regarding the association between forest microbiomes and diseases. These data will aid the development of innovative, effective, and environmentally sustainable methods for the microbial management of forest diseases. Herein, we summarize the most recent findings on the dynamic structure and composition of forest tree microbiomes in belowground and aboveground plant tissues (i.e., rhizosphere, endosphere, and phyllosphere), as well as their pleiotropic impact on plant immunity and pathogen pathogenicity, highlighting representative examples of biological control agents used to modulate relevant tree microbiomes. Lastly, we discuss the potential application of forest tree microbiomes in disease control as well as their future prospects and challenges.
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Affiliation(s)
- Qin Xiong
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Life Science, Nanjing Forestry University, Nanjing 210037, China; (J.Y.); (S.N.)
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13
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Wang Z, Jiang Y, Zhang M, Chu C, Chen Y, Fang S, Jin G, Jiang M, Lian JY, Li Y, Liu Y, Ma K, Mi X, Qiao X, Wang X, Wang X, Xu H, Ye W, Zhu L, Zhu Y, He F, Kembel SW. Diversity and biogeography of plant phyllosphere bacteria are governed by latitude-dependent mechanisms. THE NEW PHYTOLOGIST 2023; 240:1534-1547. [PMID: 37649282 DOI: 10.1111/nph.19235] [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: 07/04/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023]
Abstract
Predicting and managing the structure and function of plant microbiomes requires quantitative understanding of community assembly and predictive models of spatial distributions at broad geographic scales. Here, we quantified the relative contribution of abiotic and biotic factors to the assembly of phyllosphere bacterial communities, and developed spatial distribution models for keystone bacterial taxa along a latitudinal gradient, by analyzing 16S rRNA gene sequences from 1453 leaf samples taken from 329 plant species in China. We demonstrated a latitudinal gradient in phyllosphere bacterial diversity and community composition, which was mostly explained by climate and host plant factors. We found that host-related factors were increasingly important in explaining bacterial assembly at higher latitudes while nonhost factors including abiotic environments, spatial proximity and plant neighbors were more important at lower latitudes. We further showed that local plant-bacteria associations were interconnected by hub bacteria taxa to form metacommunity-level networks, and the spatial distribution of these hub taxa was controlled by hosts and spatial factors with varying importance across latitudes. For the first time, we documented a latitude-dependent importance in the driving factors of phyllosphere bacteria assembly and distribution, serving as a baseline for predicting future changes in plant phyllosphere microbiomes under global change and human activities.
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Affiliation(s)
- Zihui Wang
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, H2X 1Y4, Canada
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Yuan Jiang
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Minhua Zhang
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Chengjin Chu
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Yongfa Chen
- State Key Laboratory of Biocontrol, School of Ecology, Sun Yat-sen University, Guangzhou, 510275, China
| | - Shuai Fang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Guangze Jin
- Center for Ecological Research, Northeast Forestry University, Harbin, 150040, China
| | - Mingxi Jiang
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Ju-Yu Lian
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Yanpeng Li
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Yu Liu
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Keping Ma
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiangcheng Mi
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Xiujuan Qiao
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Xihua Wang
- Zhejiang Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
| | - Xugao Wang
- CAS Key Laboratory of Forest Ecology and Management, Institute of Applied Ecology, Chinese Academy of Sciences, Shenyang, 110016, China
| | - Han Xu
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, 510520, China
| | - Wanhui Ye
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Li Zhu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yan Zhu
- State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Fangliang He
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
- Department of Renewable Resources, University of Alberta, Edmonton, AB, T6G 2H1, Canada
| | - Steven W Kembel
- Département des Sciences Biologiques, Université du Québec à Montréal, Montréal, Québec, H2X 1Y4, Canada
- ECNU-Alberta Joint Lab for Biodiversity Study, Tiantong Forest Ecosystem National Observation and Research Station, School of Ecology and Environmental Sciences, East China Normal University, Shanghai, 200241, China
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14
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Dong X, Jiang F, Duan D, Tian Z, Liu H, Zhang Y, Hou F, Nan Z, Chen T. Contrasting Effects of Grazing in Shaping the Seasonal Trajectory of Foliar Fungal Endophyte Communities on Two Semiarid Grassland Species. J Fungi (Basel) 2023; 9:1016. [PMID: 37888272 PMCID: PMC10608051 DOI: 10.3390/jof9101016] [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: 09/14/2023] [Revised: 10/03/2023] [Accepted: 10/10/2023] [Indexed: 10/28/2023] Open
Abstract
Fungal endophytes are harboured in the leaves of every individual plant host and contribute to plant health, leaf senescence, and early decomposition. In grasslands, fungal endophytes and their hosts often coexist with large herbivores. However, the influence of grazing by large herbivores on foliar fungal endophyte communities remains largely unexplored. We conducted a long-term (18 yr) grazing experiment to explore the effects of grazing on the community composition and diversity of the foliar fungal endophytes of two perennial grassland species (i.e., Artemisia capillaris and Stipa bungeana) across one growing season. Grazing significantly increased the mean fungal alpha diversity of A. capillaris in the early season. In contrast, grazing significantly reduced the mean fungal alpha diversity of endophytic fungi of S. bungeana in the late season. Grazing, growing season, and their interactions concurrently structured the community composition of the foliar fungal endophytes of both plant species. However, growing season consistently outperformed grazing and environmental factors in shaping the community composition and diversity of both plant species. Overall, our findings demonstrate that the foliar endophytic fungal community diversity and composition differed in response to grazing between A. capillaris and S. bungeana during one growing season. The focus on this difference will enhance our understanding of grazing's impact on ecological systems and improve land management practices in grazing regions. This variation in the effects of leaf nutrients and plant community characteristics on foliar endophytic fungal community diversity and composition may have a pronounced impact on plant health and plant-fungal interactions.
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Affiliation(s)
- Xin Dong
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Feifei Jiang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Dongdong Duan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
- Sichuan Zoige Alpine Wetland Ecosystem National Observation and Research Station, Institute of Qinghai-Tibetan Plateau, Southwest Minzu University, Chengdu 610041, China
| | - Zhen Tian
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Huining Liu
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Yinan Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Fujiang Hou
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Zhibiao Nan
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
| | - Tao Chen
- State Key Laboratory of Herbage Improvement and Grassland Agro-Ecosystems, Center for Grassland Microbiome, College of Pastoral Agricultural Science and Technology, Lanzhou University, Lanzhou 730000, China; (X.D.); (F.J.); (D.D.); (Z.T.); (H.L.); (Y.Z.); (F.H.); (Z.N.)
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15
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Guo B, Zhang H, Liu Y, Chen J, Li J. Drought-resistant trait of different crop genotypes determines assembly patterns of soil and phyllosphere microbial communities. Microbiol Spectr 2023; 11:e0006823. [PMID: 37754752 PMCID: PMC10581042 DOI: 10.1128/spectrum.00068-23] [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: 01/10/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023] Open
Abstract
Crop microbiomes are widely recognized to play a role in crop stress resistance, but the ecological processes that shape crop microbiomes under water stress are unclear. Therefore, we investigated the bacterial communities of two oat (Avena sativa) and two wheat (Triticum aestivum) genotypes under different water stress conditions. Our results show that the microbial assemblage was determined by the crop compartment niche. Host selection pressure on the bacterial community increased progressively from soil to epiphyte to endophyte pathways, leading to a decrease in bacterial community diversity and network complexity. Source tracing shows that soil is the primary source of crop microbial communities and that bulk soil is the main potential source of crop microbiota. It filters gradually through the different compartment niches of the crop. We found that the phyla Actinobacteria, Proteobacteria, Gemmatimonadota, and Myxococcota were significantly enriched in bacterial communities associated with crop-resistance enzyme activity. Crop genotype influenced the composition of the rhizosphere soil microbial community, and the composition of the phylloplane microbial community was affected by water stress. IMPORTANCE In this paper, we investigated the assembly of the plant microbiome in response to water stress. We found that the determinant of microbiome assembly under water stress was the host type and that microbial communities were progressively filtered and enriched as they moved from soil to epiphyte to endophyte communities, with the main potential source being bulk soil. We also screened for bacterial communities that were significantly associated with crop enzyme activity. Our research provides insights into the manipulation of microbes in response to crop resistance to water stress.
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Affiliation(s)
- Baobei Guo
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
- Pomology Institute, Shanxi Agricultural University, Taiyuan, Shanxi, China
| | - Hong Zhang
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Yong Liu
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Jianwen Chen
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
| | - Junjian Li
- Institute of Loess Plateau, Shanxi University, Taiyuan, Shanxi, China
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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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Saati-Santamaría Z, Vicentefranqueira R, Kolařik M, Rivas R, García-Fraile P. Microbiome specificity and fluxes between two distant plant taxa in Iberian forests. ENVIRONMENTAL MICROBIOME 2023; 18:64. [PMID: 37481564 PMCID: PMC10363313 DOI: 10.1186/s40793-023-00520-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 07/14/2023] [Indexed: 07/24/2023]
Abstract
BACKGROUND Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant-microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model. RESULTS Although the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry. CONCLUSIONS There are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere-rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant-microbial interactions in natural ecosystems and the microbiome features of plants.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain.
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain.
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic.
| | - Rocío Vicentefranqueira
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
| | - Miroslav Kolařik
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská 1083, 142 20, Prague, Czech Republic
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), 37008, Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, 37007, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, 37185, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), 37008, Salamanca, Spain
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Yin X, Martineau C, Samad A, Fenton NJ. Out of site, out of mind: Changes in feather moss phyllosphere microbiota in mine offsite boreal landscapes. Front Microbiol 2023; 14:1148157. [PMID: 37089542 PMCID: PMC10113616 DOI: 10.3389/fmicb.2023.1148157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 03/14/2023] [Indexed: 04/07/2023] Open
Abstract
Plant-microbe interactions play a crucial role in maintaining biodiversity and ecological services in boreal forest biomes. Mining for minerals, and especially the emission of heavy metal-enriched dust from mine sites, is a potential threat to biodiversity in offsite landscapes. Understanding the impacts of mining on surrounding phyllosphere microbiota is especially lacking. To investigate this, we characterized bacterial and fungal communities in the phyllosphere of feather moss Pleurozium schreberi (Brid). Mitt in boreal landscapes near six gold mine sites at different stages of the mine lifecycle. We found that (1) both mining stage and ecosystem type are drivers of the phyllosphere microbial community structure in mine offsite landscapes; (2) Bacterial alpha diversity is more sensitive than fungal alpha diversity to mining stage, while beta diversity of both groups is impacted; (3) mixed and deciduous forests have a higher alpha diversity and a distinct microbial community structure when compared to coniferous and open canopy ecosystems; (4) the strongest effects are detectable within 0.2 km from operating mines. These results confirmed the presence of offsite effects of mine sites on the phyllosphere microbiota in boreal forests, as well as identified mining stage and ecosystem type as drivers of these effects. Furthermore, the footprint was quantified at 0.2 km, providing a reference distance within which mining companies and policy makers should pay more attention during ecological assessment and for the development of mitigation strategies. Further studies are needed to assess how these offsite effects of mines affect the functioning of boreal ecosystems.
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Affiliation(s)
- Xiangbo Yin
- NSERC-UQAT Industrial Chair in Northern Biodiversity in a Mining Context, Rouyn-Noranda, QC, Canada
- Centre d’Étude de la Forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, QC, Canada
- *Correspondence: Xiangbo Yin,
| | - Christine Martineau
- NSERC-UQAT Industrial Chair in Northern Biodiversity in a Mining Context, Rouyn-Noranda, QC, Canada
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Abdul Samad
- Natural Resources Canada, Canadian Forest Service, Laurentian Forestry Centre, Quebec City, QC, Canada
| | - Nicole J. Fenton
- NSERC-UQAT Industrial Chair in Northern Biodiversity in a Mining Context, Rouyn-Noranda, QC, Canada
- Centre d’Étude de la Forêt, Institut de Recherche sur les Forêts (IRF), Université du Québec en Abitibi-Témiscamingue (UQAT), Rouyn-Noranda, QC, Canada
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19
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Li J, Jin MK, Neilson R, Hu SL, Tang YJ, Zhang Z, Huang FY, Zhang J, Yang XR. Plant identity shapes phyllosphere microbiome structure and abundance of genes involved in nutrient cycling. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161245. [PMID: 36587661 DOI: 10.1016/j.scitotenv.2022.161245] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/03/2022] [Accepted: 12/24/2022] [Indexed: 06/17/2023]
Abstract
The phyllosphere is a fluctuant micro-environment habitat that harbors diverse microbial communities that have the potential to influence plant growth through their effect on host fitness. However, we know little about the driving factors of phyllosphere microbial functional traits, e.g., genes related to nutrient cycling and microbial community structure under anthropic disturbance. Here, we characterized phyllosphere microbial communities and the abundance of genes related to nutrient cycling from diverse plant species between urban and natural habitats. We measured leaf functional traits to investigate the potential drivers of the phyllosphere microbial profile. Results indicated that phyllosphere microbial communities differed significantly between urban and natural habitats, and that this variation was dependent upon plant species. Host plant species had a greater influence on the abundance of genes involved in nutrient cycling in the phyllosphere than habitat. In addition, phyllosphere microbial diversity and functional gene abundance were significantly correlated. Furthermore, host leaf functional traits (e.g., specific leaf area and nutrient content) were potential driving factors of both phyllosphere microbial community structure and the abundance of genes involved in nutrient cycling. These findings contribute to a better understanding of the phyllosphere microbiome and its biotic and abiotic controlling factors, which improves our understanding of plant-microbe interactions and their ecosystem functions under anthropic disturbance.
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Affiliation(s)
- Jian Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R, China
| | - Ming-Kang Jin
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Roy Neilson
- Ecological Sciences, The James Hutton Institute, Dundee DD2 5DA, Scotland, UK
| | - Shi-Lin Hu
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Yi-Jia Tang
- School of Life and Environmental Sciences, the University of Sydney, NSW 2015, Australia; Sydney Institute of Agriculture, NSW 2006, Australia
| | - Zhao Zhang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Fu-Yi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Jing Zhang
- Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Xiao-Ru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, Peoples R, China.
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20
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Zhu Y, Zhu D, Rillig MC, Yang Y, Chu H, Chen Q, Penuelas J, Cui H, Gillings M. Ecosystem Microbiome Science. MLIFE 2023; 2:2-10. [PMID: 38818334 PMCID: PMC10989922 DOI: 10.1002/mlf2.12054] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Revised: 12/11/2022] [Accepted: 12/15/2022] [Indexed: 06/01/2024]
Abstract
The microbiome contributes to multiple ecosystem functions and services through its interactions with a complex environment and other organisms. To date, however, most microbiome studies have been carried out on individual hosts or particular environmental compartments. This greatly limits a comprehensive understanding of the processes and functions performed by the microbiome and its dynamics at an ecosystem level. We propose that the theory and tools of ecosystem ecology be used to investigate the connectivity of microorganisms and their interactions with the biotic and abiotic environment within entire ecosystems and to examine their contributions to ecosystem services. Impacts of natural and anthropogenic stressors on ecosystems will likely cause cascading effects on the microbiome and lead to unpredictable outcomes, such as outbreaks of emerging infectious diseases or changes in mutualistic interactions. Despite enormous advances in microbial ecology, we are yet to study microbiomes of ecosystems as a whole. Doing so would establish a new framework for microbiome study: Ecosystem Microbiome Science. The advent and application of molecular and genomic technologies, together with data science and modeling, will accelerate progress in this field.
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Affiliation(s)
- Yong‐Guan Zhu
- Key Laboratory of Urban Environment and Health, Institute of Urban EnvironmentChinese Academy of SciencesXiamenChina
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco‐environmental SciencesChinese Academy of SciencesBeijingChina
| | - Dong Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco‐environmental SciencesChinese Academy of SciencesBeijingChina
| | - Matthias C. Rillig
- Institute of BiologyFreie Universität BerlinBerlinGermany
- Berlin‐Brandenburg Institute of Advanced Biodiversity Research (BBIB)BerlinGermany
| | - Yunfeng Yang
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of EnvironmentTsinghua UniversityBeijingChina
| | - Haiyan Chu
- State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil ScienceChinese Academy of SciencesNanjingChina
| | - Qing‐Lin Chen
- Faculty of Veterinary and Agricultural SciencesThe University of MelbourneMelbourneVictoriaAustralia
| | - Josep Penuelas
- CSIC, Global Ecology Unit CREAF‐CSIC‐UABBellaterraCataloniaSpain
- CREAFCerdanyola del VallèsCataloniaSpain
| | - Hui‐Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Centre for Eco‐environmental SciencesChinese Academy of SciencesBeijingChina
| | - Michael Gillings
- ARC Centre of Excellence for Synthetic Biology, and Department of Biological SciencesMacquarie UniversitySydneyNew South WalesAustralia
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Šigutová H, Šigut M, Pyszko P, Kostovčík M, Kolařík M, Drozd P. Seasonal Shifts in Bacterial and Fungal Microbiomes of Leaves and Associated Leaf-Mining Larvae Reveal Persistence of Core Taxa Regardless of Diet. Microbiol Spectr 2023; 11:e0316022. [PMID: 36629441 PMCID: PMC9927363 DOI: 10.1128/spectrum.03160-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 12/16/2022] [Indexed: 01/12/2023] Open
Abstract
Microorganisms are key mediators of interactions between insect herbivores and their host plants. Despite a substantial interest in studying various aspects of these interactions, temporal variations in microbiomes of woody plants and their consumers remain understudied. In this study, we investigated shifts in the microbiomes of leaf-mining larvae (Insecta: Lepidoptera) and their host trees over one growing season in a deciduous temperate forest. We used 16S and ITS2 rRNA gene metabarcoding to profile the bacterial and fungal microbiomes of leaves and larvae. We found pronounced shifts in the leaf and larval microbiota composition and richness as the season progressed, and bacteria and fungi showed consistent patterns. The quantitative similarity between leaf and larval microbiota was very low for bacteria (~9%) and decreased throughout the season, whereas fungal similarity increased and was relatively high (~27%). In both leaves and larvae, seasonality, along with host taxonomy, was the most important factor shaping microbial communities. We identified frequently occurring microbial taxa with significant seasonal trends, including those more prevalent in larvae (Streptococcus, Candida sake, Debaryomyces prosopidis, and Neoascochyta europaea), more prevalent in leaves (Erwinia, Seimatosporium quercinum, Curvibasidium cygneicollum, Curtobacterium, Ceramothyrium carniolicum, and Mycosphaerelloides madeirae), and frequent in both leaves and larvae (bacterial strain P3OB-42, Methylobacterium/Methylorubrum, Bacillus, Acinetobacter, Cutibacterium, and Botrytis cinerea). Our results highlight the importance of considering seasonality when studying the interactions between plants, herbivorous insects, and their respective microbiomes, and illustrate a range of microbial taxa persistent in larvae, regardless of their occurrence in the diet. IMPORTANCE Leaf miners are endophagous insect herbivores that feed on plant tissues and develop and live enclosed between the epidermis layers of a single leaf for their entire life cycle. Such close association is a precondition for the evolution of more intimate host-microbe relationships than those found in free-feeding herbivores. Simultaneous comparison of bacterial and fungal microbiomes of leaves and their tightly linked consumers over time represents an interesting study system that could fundamentally contribute to the ongoing debate on the microbial residence of insect gut. Furthermore, leaf miners are ideal model organisms for interpreting the ecological and evolutionary roles of microbiota in host plant specialization. In this study, the larvae harbored specific microbial communities consisting of core microbiome members. Observed patterns suggest that microbes, especially bacteria, may play more important roles in the caterpillar holobiont than generally presumed.
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Affiliation(s)
- Hana Šigutová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Šigut
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Petr Pyszko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Kostovčík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Miroslav Kolařík
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Pavel Drozd
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
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22
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Zhang Y, Li X, Lu L, Huang F, Liu H, Zhang Y, Yang L, Usman M, Li S. Urbanization Reduces Phyllosphere Microbial Network Complexity and Species Richness of Camphor Trees. Microorganisms 2023; 11:microorganisms11020233. [PMID: 36838198 PMCID: PMC9966171 DOI: 10.3390/microorganisms11020233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 12/31/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Studies on microbial communities associated with foliage in natural ecosystems have grown in number in recent years yet have rarely focused on urban ecosystems. With urbanization, phyllosphere microorganisms in the urban environment have come under pressures from increasing human activities. To explore the effects of urbanization on the phyllosphere microbial communities of urban ecosystems, we investigated the phyllosphere microbial structure and the diversity of camphor trees in eight parks along a suburban-to-urban gradient. The results showed that the number of ASVs (amplicon sequence variants), unique on the phyllosphere microbial communities of three different urbanization gradients, was 4.54 to 17.99 times higher than that of the shared ASVs. Specific microbial biomarkers were also found for leaf samples from each urbanization gradient. Moreover, significant differences (R2 = 0.133, p = 0.005) were observed in the phyllosphere microbial structure among the three urbanization gradients. Alpha diversity and co-occurrence patterns of bacterial communities showed that urbanization can strongly reduce the complexity and species richness of the phyllosphere microbial network of camphor trees. Correlation analysis with environmental factors showed that leaf total carbon (C), nitrogen (N), and sulfur (S), as well as leaf C/N, soil pH, and artificial light intensity at night (ALIAN) were the important drivers in determining the divergence of phyllosphere microbial communities across the urbanization gradient. Together, we found that urbanization can affect the composition of the phyllosphere bacterial community of camphor trees, and that the interplay between human activities and plant microbial communities may contribute to shaping the urban microbiome.
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Affiliation(s)
- Yifang Zhang
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Xiaomin Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Lu Lu
- College of Environmental Science and Engineering, China West Normal University, Nanchong 637009, China
- Correspondence: (L.L.); (S.L.)
| | - Fuyi Huang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Hao Liu
- Department of Health and Environmental Sciences, Xi’an Jiaotong-Liverpool University, 111 Ren’ai Road, Suzhou 215123, China
| | - Yu Zhang
- State Key Lab of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Luhua Yang
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
| | - Muhammad Usman
- PEIE Research Chair for the Development of Industrial Estates and Free Zones, Center for Environmental Studies and Research, Sultan Qaboos University, Al-Khoud, Muscat 123, Oman
| | - Shun Li
- Key Laboratory of Urban Environment and Health, Ningbo Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China
- Correspondence: (L.L.); (S.L.)
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23
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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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24
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Jiang W, Chen R, Zhao L, Qin L, Fan H, Chen X, Wang Y, Yin C, Mao Z. Chemical fumigants control apple replant disease: Microbial community structure-mediated inhibition of Fusarium and degradation of phenolic acids. JOURNAL OF HAZARDOUS MATERIALS 2022; 440:129786. [PMID: 36007363 DOI: 10.1016/j.jhazmat.2022.129786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/31/2022] [Accepted: 08/13/2022] [Indexed: 06/15/2023]
Abstract
Fusarium and phenolic acids in apple replant soil have deleterious effects on soil, which affects the growth of young replanted apple trees. Here, we studied the effects of different chemical fumigants (metham sodium, dazomet, calcium cyanamide, 1,3-dichloropropene, and methyl bromide) on Fusarium and phenolic acids in soil. The chemical fumigants disturbed the apple replant soil microbial community to different degrees in the order from highest to the lowest as methyl bromide > 1,3-dichloropropene > dazomet > metham sodium > calcium cyanamide. Compared with the control, the total numbers of Operational Taxonomic Unit (OTU) were 104.63 % and 9.38 % lower in the methyl bromide and calcium cyanamide treatments, respectively while the average contents of Fusarium were 88.04 % and 59.18% lower in these treatments, respectively. Higher disturbance degrees resulted in a slower recovery rate of the soil microbial community, which facilitated the transformation of the soil into a disease-suppressing state. During the recovery process, the roots recruited Streptomyces OTU2796 and Bacillus OTU2243, which alleviated Fusarium-induced stress via the synthesis of polyketones and macrolides. The roots also recruited Sphingomonas OTU3488, OTU5572, and OTU8147, which alleviated phenolic acid-induced stress through the degradation of benzoate and polycyclic aromatic hydrocarbons.
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Affiliation(s)
- Weitao Jiang
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Ran Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Zhao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Lei Qin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Hai Fan
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Xuesen Chen
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Yanfang Wang
- College of Chemistry and Material Science Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Chengmiao Yin
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China
| | - Zhiquan Mao
- State Key Laboratory of Crop Biology College of Horticulture Science and Engineering Shandong Agricultural University Tai'an, Shandong 271018, PR China.
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25
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Li K, Cheng K, Wang H, Zhang Q, Yang Y, Jin Y, He X, Wu R. Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping. FRONTIERS IN PLANT SCIENCE 2022; 13:996121. [PMID: 36275601 PMCID: PMC9583167 DOI: 10.3389/fpls.2022.996121] [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: 07/17/2022] [Accepted: 08/26/2022] [Indexed: 06/16/2023]
Abstract
The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few have systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions - mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140-728 SNPs (Single nucleotide polymorphisms) responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22-43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the "endophenotype" role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.
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Affiliation(s)
- Kaihang Li
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Kexin Cheng
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Haochen Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Qi Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yan Yang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yi Jin
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Xiaoqing He
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
| | - Rongling Wu
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- National Engineering Research Center of Tree Breeding and Ecological Restoration, Beijing Forestry University, Beijing, China
- Departments of Public Health Sciences and Statistics, Center for Statistical Genetics, The Pennsylvania State University, Hershey, PA, United States
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26
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Hasanuzzaman M, Raihan MRH, Nowroz F, Fujita M. Insight into the Mechanism of Salt-Induced Oxidative Stress Tolerance in Soybean by the Application of Bacillus subtilis: Coordinated Actions of Osmoregulation, Ion Homeostasis, Antioxidant Defense, and Methylglyoxal Detoxification. Antioxidants (Basel) 2022; 11:antiox11101856. [PMID: 36290578 PMCID: PMC9598349 DOI: 10.3390/antiox11101856] [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: 08/19/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/16/2022] Open
Abstract
Considering the growth-promoting potential and other regulatory roles of bacteria, we investigated the possible mechanism of the role of Bacillus subtilis in conferring salt tolerance in soybean. Soybean (Glycine max cv. BARI Soybean-5) seeds were inoculated with B. subtilis, either through a presoaking with seeds or a direct application with pot soil. After 20 days of sowing, both the seed- and soil-inoculated plants were exposed to 50, 100, and 150 mM of NaCl for 30 days. A clear sign of oxidative stress was evident through a remarkable increase in lipid peroxidation, hydrogen peroxide, methylglyoxal, and electrolyte leakage in the salt treated plants. Moreover, the efficiency of the ascorbate (AsA)–glutathione (GSH) pathways was declined. Consequently, the plant growth, biomass accumulation, water relations, and content of the photosynthetic pigments were decreased. Salt stress also caused an increased Na+/K+ ratio and decreased Ca2+. On the contrary, the B. subtilis inoculated plants showed increased levels of AsA and GSH, their redox balance, and the activities of the AsA–GSH pathway enzymes, superoxide dismutase, catalase, glutathione peroxidase, glutathione S-transferase, and peroxidase. The B. subtilis inoculated plants also enhanced the activities of glyoxalase enzymes, which mitigated methylglyoxal toxicity in coordination with ROS homeostasis. Besides this, the accumulation of K+ and Ca2+ was increased to maintain the ion homeostasis in the B. subtilis inoculated plants under salinity. Furthermore, the plant water status was uplifted in the salt treated soybean plants with B. subtilis inoculation. This investigation reveals the potential of B. subtilis in mitigating salt-induced oxidative stress in soybean plants through modulating the antioxidant defense and glyoxalase systems along with maintaining ion homeostasis and osmotic adjustments. In addition, it was evident that the soil inoculation performed better than the seed inoculation in mitigating salt-induced oxidative damages in soybean.
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Affiliation(s)
- Mirza Hasanuzzaman
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
- Correspondence:
| | - Md. Rakib Hossain Raihan
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Farzana Nowroz
- Department of Agronomy, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Dhaka 1207, Bangladesh
| | - Masayuki Fujita
- Laboratory of Plant Stress Responses, Faculty of Agriculture, Kagawa University, Miki-cho, Kita-gun, Takamatsu 761-0795, Japan
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27
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Dundas CM, Dinneny JR. Genetic Circuit Design in Rhizobacteria. BIODESIGN RESEARCH 2022; 2022:9858049. [PMID: 37850138 PMCID: PMC10521742 DOI: 10.34133/2022/9858049] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/31/2022] [Indexed: 10/19/2023] Open
Abstract
Genetically engineered plants hold enormous promise for tackling global food security and agricultural sustainability challenges. However, construction of plant-based genetic circuitry is constrained by a lack of well-characterized genetic parts and circuit design rules. In contrast, advances in bacterial synthetic biology have yielded a wealth of sensors, actuators, and other tools that can be used to build bacterial circuitry. As root-colonizing bacteria (rhizobacteria) exert substantial influence over plant health and growth, genetic circuit design in these microorganisms can be used to indirectly engineer plants and accelerate the design-build-test-learn cycle. Here, we outline genetic parts and best practices for designing rhizobacterial circuits, with an emphasis on sensors, actuators, and chassis species that can be used to monitor/control rhizosphere and plant processes.
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Affiliation(s)
| | - José R. Dinneny
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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Rabiey M, Welch T, Sanchez-Lucas R, Stevens K, Raw M, Kettles GJ, Catoni M, McDonald MC, Jackson RW, Luna E. Scaling-up to understand tree-pathogen interactions: A steep, tough climb or a walk in the park? CURRENT OPINION IN PLANT BIOLOGY 2022; 68:102229. [PMID: 35567925 DOI: 10.1016/j.pbi.2022.102229] [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: 02/04/2022] [Revised: 03/15/2022] [Accepted: 04/04/2022] [Indexed: 06/15/2023]
Abstract
Plants have proficient tools that allow them to survive interactions with pathogens. Upon attack, they respond with specific countermeasures, which are controlled by the immune system. However, defences can fail and this failure exposes plants to fast-spreading devastation. Trees face similar challenges to other plants and their immune system allows them to mount defences against pathogens. However, their slow growth, longevity, woodiness, and size can make trees a challenging system to study. Here, we review scientific successes in plant systems, highlight the key challenges and describe the enormous opportunities for pathology research in trees. We discuss the benefits that scaling-up our understanding on tree-pathogen interactions can provide in the fight against plant pathogenic threats.
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Affiliation(s)
- Mojgan Rabiey
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Thomas Welch
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Rosa Sanchez-Lucas
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Katie Stevens
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Mark Raw
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Graeme J Kettles
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Marco Catoni
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Megan C McDonald
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Robert W Jackson
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK
| | - Estrella Luna
- The Birmingham Institute of Forest Research, School of Biosciences, University of Birmingham, Edgbaston Campus, Birmingham, B15 2TT, UK.
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Masocha VF, Liu H, Zhan P, Wang K, Zeng A, Shen S, Schneider H. Bacterial Microbiome in the Phyllo-Endosphere of Highly Specialized Rock Spleenwort. FRONTIERS IN PLANT SCIENCE 2022; 13:891155. [PMID: 35874023 PMCID: PMC9302946 DOI: 10.3389/fpls.2022.891155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Bacteria communities associated with plants have been given increasing consideration because they are arguably beneficial to their host plants. To understand the ecological and evolutionary impact of these mutualistic associations, it is important to explore the vast unknown territory of bacterial genomic diversity and their functional contributions associated with the major branches of the tree-of-life. Arguably, this aim can be achieved by profiling bacterial communities by applying high throughput sequencing approaches, besides establishing model plant organisms to test key predictions. This study utilized the Illumina Miseq reads of bacterial 16S rRNA sequences to determine the bacterial diversity associated with the endosphere of the leaves of the highly specialized rock spleenwort Asplenium delavayi (Aspleniaceae). By documenting the bacterial communities associated with ferns collected in natural occurrence and cultivation, this study discovered the most species-rich bacterial communities associated with terrestrial ferns reported until now. Despite the substantial variations of species diversity and composition among accessions, a set of 28 bacterial OTUs was found to be shared among all accessions. Functional analyses recovered evidence to support the predictions that changes in bacterial community compositions correspond to functional differentiation. Given the ease of cultivating this species, Asplenium delavayi is introduced here as a model organism to explore the ecological and evolutionary benefits created by mutualistic associations between bacteria and ferns.
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Affiliation(s)
- Valerie F. Masocha
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Hongmei Liu
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Pingshan Zhan
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
| | - Kaikai Wang
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ao Zeng
- School of Biological and Chemical Sciences, Pu’er University, Pu’er, China
| | - Sike Shen
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Harald Schneider
- Centre for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Beijing, China
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Dea HI, Urban A, Kazarina A, Houseman GR, Thomas SG, Loecke T, Greer MJ, Platt TG, Lee S, Jumpponen A. Precipitation, Not Land Use, Primarily Determines the Composition of Both Plant and Phyllosphere Fungal Communities. FRONTIERS IN FUNGAL BIOLOGY 2022; 3:805225. [PMID: 37746168 PMCID: PMC10512219 DOI: 10.3389/ffunb.2022.805225] [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: 10/30/2021] [Accepted: 06/10/2022] [Indexed: 09/26/2023]
Abstract
Plant communities and fungi inhabiting their phyllospheres change along precipitation gradients and often respond to changes in land use. Many studies have focused on the changes in foliar fungal communities on specific plant species, however, few have addressed the association between whole plant communities and their phyllosphere fungi. We sampled plant communities and associated phyllosphere fungal communities in native prairie remnants and post-agricultural sites across the steep precipitation gradient in the central plains in Kansas, USA. Plant community cover data and MiSeq ITS2 metabarcode data of the phyllosphere fungal communities indicated that both plant and fungal community composition respond strongly to mean annual precipitation (MAP), but less so to land use (native prairie remnants vs. post-agricultural sites). However, plant and fungal diversity were greater in the native remnant prairies than in post-agricultural sites. Overall, both plant and fungal diversity increased with MAP and the communities in the arid and mesic parts of the gradient were distinct. Analyses of the linkages between plant and fungal communities (Mantel and Procrustes tests) identified strong correlations between the composition of the two. However, despite the strong correlations, regression models with plant richness, diversity, or composition (ordination axis scores) and land use as explanatory variables for fungal diversity and evenness did not improve the models compared to those with precipitation and land use (ΔAIC < 2), even though the explanatory power of some plant variables was greater than that of MAP as measured by R2. Indicator taxon analyses suggest that grass species are the primary taxa that differ in the plant communities. Similar analyses of the phyllosphere fungi indicated that many plant pathogens are disproportionately abundant either in the arid or mesic environments. Although decoupling the drivers of fungal communities and their composition - whether abiotic or host-dependent - remains a challenge, our study highlights the distinct community responses to precipitation and the tight tracking of the plant communities by their associated fungal symbionts.
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Affiliation(s)
- Hannah I. Dea
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Abigail Urban
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Anna Kazarina
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Gregory R. Houseman
- Department of Biological Sciences, Wichita State University, Wichita, KS, United States
| | - Samantha G. Thomas
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, United States
| | - Terry Loecke
- Kansas Biological Survey and Center for Ecological Research, University of Kansas, Lawrence, KS, United States
- Environmental Studies Program, University of Kansas, Lawrence, KS, United States
| | - Mitchell J. Greer
- Department of Agriculture and Nutrition Science, Southern Utah University, Cedar City, UT, United States
| | - Thomas G. Platt
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Sonny Lee
- Division of Biology, Kansas State University, Manhattan, KS, United States
| | - Ari Jumpponen
- Division of Biology, Kansas State University, Manhattan, KS, United States
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Francioli D, Cid G, Hajirezaei MR, Kolb S. Leaf bacterial microbiota response to flooding is controlled by plant phenology in wheat (Triticum aestivum L.). Sci Rep 2022; 12:11197. [PMID: 35778470 PMCID: PMC9249782 DOI: 10.1038/s41598-022-15133-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 11/09/2022] Open
Abstract
Leaf microbiota mediates foliar functional traits, influences plant fitness, and contributes to various ecosystem functions, including nutrient and water cycling. Plant phenology and harsh environmental conditions have been described as the main determinants of leaf microbiota assembly. How climate change may modulate the leaf microbiota is unresolved and thus, we have a limited understanding on how environmental stresses associated with climate change driven weather events affect composition and functions of the microbes inhabiting the phyllosphere. Thus, we conducted a pot experiment to determine the effects of flooding stress on the wheat leaf microbiota. Since plant phenology might be an important factor in the response to hydrological stress, flooding was induced at different plant growth stages (tillering, booting and flowering). Using a metabarcoding approach, we monitored the response of leaf bacteria to flooding, while key soil and plant traits were measured to correlate physiological plant and edaphic factor changes with shifts in the bacterial leaf microbiota assembly. In our study, plant growth stage represented the main driver in leaf microbiota composition, as early and late plants showed distinct bacterial communities. Overall, flooding had a differential effect on leaf microbiota dynamics depending at which developmental stage it was induced, as a more pronounced disruption in community assembly was observed in younger plants.
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Affiliation(s)
- Davide Francioli
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.
| | - Geeisy Cid
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Mohammad-Reza Hajirezaei
- Department of Physiology and Cell Biology, Leibniz Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany
| | - Steffen Kolb
- Microbial Biogeochemistry, Research Area Landscape Functioning, Leibniz Center for Agricultural Landscape Research E.V. (ZALF), Müncheberg, Germany.,Thaer Institute, Faculty of Life Sciences, Humboldt University of Berlin, Berlin, Germany
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Pan S, Zhang W, Li Y, Zhou P, Zhang H, Niu L, Wang L. Understanding the ecological processes governing hydrophyte-associated bacterial communities involved in hydrophyte growth and development. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2022; 312:114952. [PMID: 35339791 DOI: 10.1016/j.jenvman.2022.114952] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/11/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Maintaining hydrophyte growth has been a major focus of aquatic ecological research. The hydrophyte microbiome plays a key role in the growth and health of hydrophytes, but the ecological processes regulating the assembly and function of hydrophyte microbial communities remain unclear. This knowledge gap limits the efficacy of managing microbiomes to enhance the capacity of hydrophytes to restore the aquatic environment. Here, we sampled three typical hydrophytes (Ceratophyllum demersum, Nymphoides peltatum, and Potamogeton crispus) to study the ecological process governing hydrophyte-associated bacterial communities. The results demonstrated that hydrophyte-associated bacterial communities were affected more by the hydrophyte host species (HEEI = 2.40) than by the environment (HEEI = 1.00). The hydrophyte host species not only affected bacterial community assembly, but reduced the diversity and network complexity of the bacterial community relative to that of the environment. Furthermore, the core taxa of two hydrophytes were identified. Chryseobacterium was the core taxon of N. peltatum, and Burkholderia-Caballeronia-Paraburkholderia, Pseudolabrys, and Pajaroellobacter were the core taxa of P. crispus. The core taxa of P. crispus were closely related to potential denitrification-related functions of bacteria and revealed that P. crispus played a role in denitrification during aquatic ecological restoration. Overall, the results of this study highlight the need to develop approaches employing hydrophyte-associated bacteria to promote the development of hydrophytes, which will be essential for increasing the utility of hydrophyte microbiomes in the future and enhancing aquatic ecological restoration.
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Affiliation(s)
- Shenyang Pan
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Wenlong Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China.
| | - Yi Li
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Pengcheng Zhou
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Huanjun Zhang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Lihua Niu
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
| | - Longfei Wang
- Key Laboratory of Integrated Regulation and Resource Development on Shallow Lakes, Ministry of Education, College of Environment, Hohai University, Nanjing, 210098, PR China
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Fu WQ, Xu M, Zhang AY, Sun K, Dai CC, Jia Y. Remediation of phenanthrene phytotoxicity by the interaction of rice and endophytic fungus P. liquidambaris in practice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2022; 235:113415. [PMID: 35306213 DOI: 10.1016/j.ecoenv.2022.113415] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 03/07/2022] [Accepted: 03/10/2022] [Indexed: 06/14/2023]
Abstract
Phenanthrene cannot be effectively degraded in the agricultural production systems and it is greatly hazardous for food safety and human health. In our study, the remediation ability and mechanism of rice and endophytic fungus Phomopsis liquidambaris interaction on phenanthrene in the rice-growing environment were explored using laboratory and pot experiments. The results showed that plant-endophyte interaction had the potential to enhance remediation on phenanthrene contamination in the rice-growing environment. The content of phenanthrene in soil and rice (including leaves, roots, and grains) of the plant-endophyte interaction system was about 42% and 27% lower than of the non-inoculated treatment under 100 mg kg-1 treatment. The mechanism may be related to the improvement of plant growth, root activity, chlorophyll content, ATP energy supply, and antagonistic ability of rice to promote the absorption of phenanthrene in the rice-growing environment, and then the phenanthrene absorbed into the rice was degraded by improving the phenanthrene degrading enzyme activities and gene relative expression levels of P. liquidambaris during plant-endophyte interaction. Moreover, the plant-endophyte interaction system could also promote rice growth and increase rice yield by over 20% more than the control under 50 mg kg-1 treatment. This study indicated a promising potential of the plant-endophyte interaction system for pollution remediation in agriculture.
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Affiliation(s)
- Wan-Qiu Fu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Man Xu
- Nanjing Institute of Environmental Science, Ministry of Ecology and Environmental of China, Nanjing 210042, China
| | - Ai-Yue Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
| | - Yong Jia
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China.
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Unlocking the Changes of Phyllosphere Fungal Communities of Fishscale Bamboo (Phyllachora heterocladae) under Rhombic-Spot Disease Stressed Conditions. FORESTS 2022. [DOI: 10.3390/f13020185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
As an important nonwood bioresource, fishscale bamboo (Phyllachora heterocladae Oliver) is widely distributed in the subtropical region of China. Rhombic-spot disease, caused by Neostagonosporella sichuanensis, is one of the most serious diseases that threatens fishscale bamboo health. However, there is limited knowledge about how rhombic-spot disease influences the diversity and structures of phyllosphere fungal communities. In this study, we investigated the phyllosphere fungal communities from stems, branches, and leaves of fishscale bamboo during a rhombic-spot disease outbreak using 18S rRNA sequencing. We found that only the phyllosphere fungal community from stems was significantly affected by pathogen invasion in terms of community richness, diversity, and structure. FUNGuild analysis revealed that the major classifications of phyllosphere fungi based on trophic modes in stems, branches, and leaves changed from symbiotroph-pathotroph, no obvious dominant trophic mode, and symbiotroph to saprotroph, saprotroph–pathotroph–symbiotroph, and saprotroph–symbiotroph, respectively, after pathogen invasion. The fungal community composition of the three tissues displayed significant differences at the genus level between healthy and diseased plants. The associations among fungal species in diseased samples showed more complex co-occurrence network structures than those of healthy samples. Taken together, our results highlight the importance of plant pathological conditions for the assembly of phyllosphere fungal communities in different tissues.
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