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Li C, Han Y, Zou X, Zhang X, Ran Q, Dong C. A systematic discussion and comparison of the construction methods of synthetic microbial community. Synth Syst Biotechnol 2024; 9:775-783. [PMID: 39021362 PMCID: PMC11253132 DOI: 10.1016/j.synbio.2024.06.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2024] [Revised: 06/15/2024] [Accepted: 06/18/2024] [Indexed: 07/20/2024] Open
Abstract
Synthetic microbial community has widely concerned in the fields of agriculture, food and environment over the past few years. However, there is little consensus on the method to synthetic microbial community from construction to functional verification. Here, we review the concept, characteristics, history and applications of synthetic microbial community, summarizing several methods for synthetic microbial community construction, such as isolation culture, core microbiome mining, automated design, and gene editing. In addition, we also systematically summarized the design concepts, technological thresholds, and applicable scenarios of various construction methods, and highlighted their advantages and limitations. Ultimately, this review provides four efficient, detailed, easy-to-understand and -follow steps for synthetic microbial community construction, with major implications for agricultural practices, food production, and environmental governance.
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Affiliation(s)
- Chenglong 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, 550025, Guizhou, 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, 550025, Guizhou, China
| | - Xiao Zou
- 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, 550025, Guizhou, China
| | - Xueqian Zhang
- 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, 550025, 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, 550025, 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, 550025, Guizhou, China
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Ramakrishnan DK, Jauernegger F, Hoefle D, Berg C, Berg G, Abdelfattah A. Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems. BMC Microbiol 2024; 24:417. [PMID: 39425049 PMCID: PMC11490174 DOI: 10.1186/s12866-024-03574-0] [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: 04/29/2024] [Accepted: 10/08/2024] [Indexed: 10/21/2024] Open
Abstract
BACKGROUND While substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors. METHODS We investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450-2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed. RESULTS Our study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers. CONCLUSION This study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant-microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures.
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Affiliation(s)
- Dinesh Kumar Ramakrishnan
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Franziska Jauernegger
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
| | - Daniel Hoefle
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Christian Berg
- Institute of Biology, Department of Plant Sciences, NAWI Graz, University of Graz, 8010, Graz, Austria
| | - Gabriele Berg
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12, 8010, Graz, Austria
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Ahmed Abdelfattah
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Max-Eyth Allee 100, 14469, Potsdam, Germany.
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Li J, Li XC, Gan HY, Zhang Y, Guo ZX, Liu YX, Lin YQ, Guo LD. Plant diversity increases diversity and network complexity rather than alters community assembly processes of leaf-associated fungi in a subtropical forest. SCIENCE CHINA. LIFE SCIENCES 2024:10.1007/s11427-024-2630-6. [PMID: 39432205 DOI: 10.1007/s11427-024-2630-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Accepted: 05/23/2024] [Indexed: 10/22/2024]
Abstract
Plant diversity significantly impacts ecosystem processes and functions, yet its influence on the community assembly of leaf fungi remains poorly understood. In this study, we investigated leaf epiphytic and endophytic fungal communities in a Chinese subtropical tree species richness experiment, ranging from 1 to 16 species, using amplicon sequencing to target the internal transcribed spacer 1 region of the rDNA. We found that the community assembly of epiphytic and endophytic fungi was predominantly governed by stochastic processes, with a higher contribution of dispersal limitation on epiphytic than on endophytic fungal communities but a higher contribution of selection on endophytic than on epiphytic fungal communities. The plant-epiphytic fungus interaction network was more complex (e.g., more highly connected and strongly nested but less specialized and modularized) than the plant-endophytic fungus interaction network. Additionally, tree species richness was positively correlated with the network complexity and diversity of epiphytic (α-, β- and γ-diversity) and endophytic (β- and γ-diversity) fungi, but was not associated with the contribution of the stochastic and deterministic processes on the community assembly of epiphytic and endophytic fungi. This study highlights that tree species diversity enhances the diversity and network complexity, rather than alters the ecological processes in community assembly of leaf-associated fungi.
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Affiliation(s)
- Jie Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Xing-Chun Li
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hui-Yun Gan
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yue Zhang
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zi-Xuan Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yu-Xuan Liu
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yong-Qing Lin
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Liang-Dong Guo
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Abdelsattar M, Soliman MS, Mohamed RA, Radwan KH, El-Mahdy MM, Mousa KH, Khalil SRM, Osman E, Alameldin HF, Hussein A, Hassanein SE, Abdallah NA, Alsamman AM, Osama O. Transcriptomic insights into mycorrhizal interactions with tomato root: a comparative study of short- and long-term post-inoculation responses. Front Genet 2024; 15:1434761. [PMID: 39440244 PMCID: PMC11493745 DOI: 10.3389/fgene.2024.1434761] [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: 05/18/2024] [Accepted: 08/29/2024] [Indexed: 10/25/2024] Open
Abstract
Background Arbuscular mycorrhiza (AM) refers to a symbiotic association between plant roots and fungi that enhances the uptake of mineral nutrients from the soil and enables the plant to tolerate abiotic and biotic stresses. Although previously reported RNA-seq analyses have identified large numbers of AM-responsive genes in model plants, such as Solanum lycopersicum L., further studies are underway to comprehensively understand the complex interactions between plant roots and AM, especially in terms of the short- and long-term responses after inoculation. Results Herein, we used RNA-seq technology to obtain the transcriptomes of tomato roots inoculated with the fungus Rhizophagus irregularis at 7 and 30 days post inoculation (dpi). Of the 1,019 differentially expressed genes (DEGs) in tomato roots, 635 genes showed differential expressions between mycorrhizal and non-mycorrhizal associations at the two time points. The number of upregulated DEGs far exceeded the number of downregulated ones at 7 dpi, and this difference decreased at 30 dpi. Several notable genes were particularly involved in the plant defense, plant growth and development, ion transport, and biological processes, namely, GABAT, AGP, POD, NQO1, MT4, MTA, and AROGP3. In addition, the Kyoto encyclopedia of genes and genomes pathway enrichment analysis revealed that some of the genes were involved in different pathways, including those of ascorbic acid (AFRR, GME1, and APX), metabolism (CYP, GAPC2, and CAM2), and sterols (CYC1 and HMGR), as well as genes related to cell division and cell cycle (CDKB2 and PCNA). Conclusion These findings provide valuable new data on AM-responsive genes in tomato roots at both short- and long-term postinoculation stages, enabling the deciphering of biological interactions between tomato roots and symbiotic fungi.
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Affiliation(s)
- Mohamed Abdelsattar
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Maali S. Soliman
- Plant Pathology Research Institute, Agricultural Research Center, Giza, Egypt
- The Central Laboratory for Phytosanitary and Food Safety, United Integrated Laboratories, Barka, Oman
| | - Rasha A. Mohamed
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Radwan
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- National Biotechnology Network of Expertise, ASRT, Cairo, Egypt
| | - Mohamed M. El-Mahdy
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Khaled H. Mousa
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Shaimaa R. M. Khalil
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Engy Osman
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hussien F. Alameldin
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- Sugarbeet and Bean Research Unit, U.S. Department of Agriculture - Agriculture Research Service (USDA-ARS), East Lansing, MI, United States
| | - Ahmed Hussein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Sameh E. Hassanein
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
| | - Naglaa A. Abdallah
- National Biotechnology Network of Expertise, ASRT, Cairo, Egypt
- Department of Genetics, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Alsamman M. Alsamman
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
- International Center for Agriculture Research in the Dry Areas (ICARD), Giza, Egypt
| | - Omnia Osama
- Agricultural Genetic Engineering Research Institute (AGERI), Agricultural Research Center (ARC), Giza, Egypt
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Maitra P, Hrynkiewicz K, Szuba A, Niestrawska A, Mucha J. The effects of Pinus sylvestris L. geographical origin on the community and co-occurrence of fungal and bacterial endophytes in a common garden experiment. Microbiol Spectr 2024; 12:e0080724. [PMID: 39248476 PMCID: PMC11448405 DOI: 10.1128/spectrum.00807-24] [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: 03/28/2024] [Accepted: 08/12/2024] [Indexed: 09/10/2024] Open
Abstract
Below-ground microorganisms, particularly endophytes, are pivotal for plant establishment and functioning through nutrient acquisition and enhancing resistance to abiotic and biotic stresses. The impact of host plant origin within a species on the composition and interaction networks of root endophytic fungi and bacteria has been less explored compared with plant phylogeny and biological distance. This study investigates the effect of geographic origin on the fungal and bacterial microbiomes of Pinus sylvestris L. root endophytes. Roots from plants grown in a common garden, originating from six locations, were harvested in two distinct seasons. Fungal and bacterial microbiomes were analyzed using Illumina MiSeq sequencing. The operational taxonomic unit (OTU) richness of endophytic fungi and bacteria showed no significant variation due to tree origin or season. However, the Shannon diversity index for endophytic fungi was seasonally influenced. The composition of endophytic fungal and bacterial communities was affected by both tree origin and season, correlating with host root biochemical parameters, such as starch, total non-structural carbohydrates, carbon, nitrogen, and climatic factors, such as mean annual precipitation and temperature. Moreover, the abundance of specific endophytic fungi and bacteria varied across different P. sylvestris origins, depending on the season. The complexity of the co-occurrence networks of fungal and bacterial endophytes within P. sylvestris also differed by geographical origin and season. This study highlights the significant role of biochemical and climatic factors associated with tree origin in shaping interactions with endophytic communities, potentially affecting plant health and adaptability across diverse environments. IMPORTANCE This study advances our understanding of how plant ecotype and seasonal changes influence root endophytic communities in Scots pine (Pinus sylvestris). By examining trees from various origins grown in a common garden, it highlights the role of tree origin and season in shaping fungal and bacterial community and co-occurrence networks. Importantly, this research demonstrates that tree origin impacts the composition and interaction networks of root endophytes and depends on the season. The study's findings suggest that root biochemical traits and climatic conditions (e.g., temperature, precipitation) associated with tree origin are crucial in determining the assembly of endophytic communities. This understanding could lead to innovative strategies for enhancing plant health and adaptability across different environments, contributing to forestry and conservation efforts. The research underscores the complexity of plant-microbe interactions and the need for a comprehensive approach to studying them, highlighting the interplay between tree origin and microbial ecology in forest ecosystems.
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Affiliation(s)
- Pulak Maitra
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
- W.K. Kellogg Biological Station, Michigan State University, Hickory Corners, Michigan, USA
| | - Katarzyna Hrynkiewicz
- Department of Microbiology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University in Toruń, Toruń, Poland
| | - Agnieszka Szuba
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
| | | | - Joanna Mucha
- Institute of Dendrology, Polish Academy of Sciences, Kórnik, Poland
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Nakagami S, Wang Z, Han X, Tsuda K. Regulation of Bacterial Growth and Behavior by Host Plant. ANNUAL REVIEW OF PHYTOPATHOLOGY 2024; 62:69-96. [PMID: 38857544 DOI: 10.1146/annurev-phyto-010824-023359] [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: 06/12/2024]
Abstract
Plants are associated with diverse bacteria in nature. Some bacteria are pathogens that decrease plant fitness, and others are beneficial bacteria that promote plant growth and stress resistance. Emerging evidence also suggests that plant-associated commensal bacteria collectively contribute to plant health and are essential for plant survival in nature. Bacteria with different characteristics simultaneously colonize plant tissues. Thus, plants need to accommodate bacteria that provide service to the host plants, but they need to defend against pathogens at the same time. How do plants achieve this? In this review, we summarize how plants use physical barriers, control common goods such as water and nutrients, and produce antibacterial molecules to regulate bacterial growth and behavior. Furthermore, we highlight that plants use specialized metabolites that support or inhibit specific bacteria, thereby selectively recruiting plant-associated bacterial communities and regulating their function. We also raise important questions that need to be addressed to improve our understanding of plant-bacteria interactions.
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Affiliation(s)
- Satoru Nakagami
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Zhe Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Xiaowei Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
| | - Kenichi Tsuda
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, China
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, China;
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Huang F, Ling J, Cui Y, Guo B, Song X. Profiling of the Citrus Leaf Endophytic Mycobiota Reveals Abundant Pathogen-Related Fungal Groups. J Fungi (Basel) 2024; 10:596. [PMID: 39330356 PMCID: PMC11433070 DOI: 10.3390/jof10090596] [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: 07/24/2024] [Revised: 08/16/2024] [Accepted: 08/21/2024] [Indexed: 09/28/2024] Open
Abstract
Plant endophytic microbial communities consist of many latent plant pathogens and, also, many pathogen-related species with reduced virulence. Though with a long history of co-evolution, the diversity and composition of the endophytic mycobiota, especially the pathogen-related fungal groups, has been under-investigated in Citrus (C.). Based on the amplicon sequencing of fungal internal transcribed spacer (ITS), the leaf endophytic mycobiota were profiled on citrus varieties from different citrus-producing regions. The pomelo variety shared significantly distinctive leaf mycobiota when compared to the mandarin and sweet orange; these conform to their host genetic relationships. In addition, a data set of 241 citrus-related fungi, including 171 (71%) pathogens and potential pathogens, was summarized from previous studies. Under the criteria of local BLAST (covered ITS nucleotide ≥ 150 bp, sequence identity ≥ 99%), a total of 935 fungal operational taxonomic units (OTUs) were assigned to 62 pathogen-related fungal groups, representing 14.9% of the relative abundance in the whole community. Of which, the top groups consisted of Colletotrichum gloeosporioides (mean relative abundance, 4.3%), Co. citricola and Co. karstii (2.7%), Zasmidium citri-griseum (2.4%), and Z. fructigenum (1.4%). At the genus level, the ratio of the pathogen-related fungal groups in 64% of fungal genera (16 out of 25) exceeded 50%, which are the solely or mainly occurring fungi of their genus in citrus. Our study suggests that the leaf endophytic compartment may be an important place for the growth of latent pathogens.
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Affiliation(s)
- Feng Huang
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Jinfeng Ling
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Yiping Cui
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Bin Guo
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
| | - Xiaobing Song
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China Ministry of Agriculture and Rural Affairs, Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou 510640, China
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Thomas G, Kay WT, Fones HN. Life on a leaf: the epiphyte to pathogen continuum and interplay in the phyllosphere. BMC Biol 2024; 22:168. [PMID: 39113027 PMCID: PMC11304629 DOI: 10.1186/s12915-024-01967-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 08/01/2024] [Indexed: 08/11/2024] Open
Abstract
Epiphytic microbes are those that live for some or all of their life cycle on the surface of plant leaves. Leaf surfaces are a topologically complex, physicochemically heterogeneous habitat that is home to extensive, mixed communities of resident and transient inhabitants from all three domains of life. In this review, we discuss the origins of leaf surface microbes and how different biotic and abiotic factors shape their communities. We discuss the leaf surface as a habitat and microbial adaptations which allow some species to thrive there, with particular emphasis on microbes that occupy the continuum between epiphytic specialists and phytopathogens, groups which have considerable overlap in terms of adapting to the leaf surface and between which a single virulence determinant can move a microbial strain. Finally, we discuss the recent findings that the wheat pathogenic fungus Zymoseptoria tritici spends a considerable amount of time on the leaf surface, and ask what insights other epiphytic organisms might provide into this pathogen, as well as how Z. tritici might serve as a model system for investigating plant-microbe-microbe interactions on the leaf surface.
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Affiliation(s)
| | - William T Kay
- Department of Plant Sciences, University of Oxford, Oxford, UK
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Beattie GA, Bayliss KL, Jacobson DA, Broglie R, Burkett-Cadena M, Sessitsch A, Kankanala P, Stein J, Eversole K, Lichens-Park A. From Microbes to Microbiomes: Applications for Plant Health and Sustainable Agriculture. PHYTOPATHOLOGY 2024; 114:1742-1752. [PMID: 38776137 DOI: 10.1094/phyto-02-24-0054-kc] [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: 08/22/2024]
Abstract
Plant-microbe interaction research has had a transformative trajectory, from individual microbial isolate studies to comprehensive analyses of plant microbiomes within the broader phytobiome framework. Acknowledging the indispensable role of plant microbiomes in shaping plant health, agriculture, and ecosystem resilience, we underscore the urgent need for sustainable crop production strategies in the face of contemporary challenges. We discuss how the synergies between advancements in 'omics technologies and artificial intelligence can help advance the profound potential of plant microbiomes. Furthermore, we propose a multifaceted approach encompassing translational considerations, transdisciplinary research initiatives, public-private partnerships, regulatory policy development, and pragmatic expectations for the practical application of plant microbiome knowledge across diverse agricultural landscapes. We advocate for strategic collaboration and intentional transdisciplinary efforts to unlock the benefits offered by plant microbiomes and address pressing global issues in food security. By emphasizing a nuanced understanding of plant microbiome complexities and fostering realistic expectations, we encourage the scientific community to navigate the transformative journey from discoveries in the laboratory to field applications. As companies specializing in agricultural microbes and microbiomes undergo shifts, we highlight the necessity of understanding how to approach sustainable agriculture with site-specific management solutions. While cautioning against overpromising, we underscore the excitement of exploring the many impacts of microbiome-plant interactions. We emphasize the importance of collaborative endeavors with societal partners to accelerate our collective capacity to harness the diverse and yet-to-be-discovered beneficial activities of plant microbiomes.
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Affiliation(s)
- Gwyn A Beattie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Department of Plant Pathology, Entomology and Microbiology, Iowa State University, Ames, IA 50014, U.S.A
| | - Kirsty L Bayliss
- Food Futures Institute, Murdoch University, Murdoch, Western Australia 6150, Australia
| | - Daniel A Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN 37830, U.S.A
| | - Richard Broglie
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
| | | | - Angela Sessitsch
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Bioresources Unit, AIT Austrian Institute of Technology, 3430 Tulln, Austria
| | | | - Joshua Stein
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Kellye Eversole
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
- Eversole Associates, Arlington, MA 02476, U.S.A
| | - Ann Lichens-Park
- International Alliance for Phytobiomes Research, Eau Claire, WI 54701, U.S.A
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10
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Huang Y, Zhai L, Chai X, Liu Y, Lv J, Pi Y, Gao B, Wang X, Wu T, Zhang X, Han Z, Wang Y. Bacillus B2 promotes root growth and enhances phosphorus absorption in apple rootstocks by affecting MhMYB15. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:1880-1899. [PMID: 38924231 DOI: 10.1111/tpj.16893] [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: 02/17/2024] [Revised: 05/13/2024] [Accepted: 06/11/2024] [Indexed: 06/28/2024]
Abstract
Due to the chelation of phosphorus in the soil, it becomes unavailable for plant growth and development. The mechanisms by which phosphorus-solubilizing bacteria activate immobilized phosphorus to promote the growth and development of woody plants, as well as the intrinsic molecular mechanisms, are not clear. Through the analysis of microbial communities in the rhizosphere 16S V3-V4 and a homologous gene encoding microbial alkaline phosphomonoesterase (phoD) in phosphate-efficient (PE) and phosphate-inefficient apple rootstocks, it was found that PE significantly enriched beneficial rhizobacteria. The best phosphorus-solubilizing bacteria, Bacillus sp. strain 7DB1 (B2), was isolated, purified, and identified from the rhizosphere soil of PE rootstocks. Incubating with Bacillus B2 into the rhizosphere of apple rootstocks significantly increased the soluble phosphorus and flavonoid content in the rhizosphere soil. Simultaneously, this process stimulates the root development of the rootstocks and enhances plant phosphorus uptake. After root transcriptome sequencing, candidate transcription factor MhMYB15, responsive to Bacillus B2, was identified through heatmap and co-expression network analysis. Yeast one-hybrid, electrophoretic mobility shift assay, and LUC assay confirmed that MhMYB15 can directly bind to the promoter regions of downstream functional genes, including chalcone synthase MhCHS2 and phosphate transporter MhPHT1;15. Transgenic experiments with MhMYB15 revealed that RNAi-MhMYB15 silenced lines failed to induce an increase in flavonoid content and phosphorus levels in the roots under the treatment of Bacillus B2, and plant growth was slower than the control. In conclusion, MhMYB15 actively responds to Bacillus B2, regulating the accumulation of flavonoids and the uptake of phosphorus, thereby influencing plant growth and development.
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Affiliation(s)
- Yimei Huang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Longmei Zhai
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xiaofen Chai
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Yao Liu
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Jiahong Lv
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Ying Pi
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Beibei Gao
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xiaona Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Ting Wu
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Xinzhong Zhang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Zhenhai Han
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
| | - Yi Wang
- College of Horticulture, China Agricultural University, Beijing, 100193, P.R. China
- Key Laboratory of Biology and Genetic Improvement of Horticultural (Nutrition and Physiology), The Ministry of Agriculture and Rural Affairs, Beijing, P.R. China
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11
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de Matos JP, Ribeiro DF, da Silva AK, de Paula CH, Cordeiro IF, Lemes CGDC, Sanchez AB, Rocha LCM, Garcia CCM, Almeida NF, Alves RM, de Abreu VAC, Varani AM, Moreira LM. Diversity and potential functional role of phyllosphere-associated actinomycetota isolated from cupuassu (Theobroma grandiflorum) leaves: implications for ecosystem dynamics and plant defense strategies. Mol Genet Genomics 2024; 299:73. [PMID: 39066857 DOI: 10.1007/s00438-024-02162-1] [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: 11/07/2023] [Accepted: 06/25/2024] [Indexed: 07/30/2024]
Abstract
Exploring the intricate relationships between plants and their resident microorganisms is crucial not only for developing new methods to improve disease resistance and crop yields but also for understanding their co-evolutionary dynamics. Our research delves into the role of the phyllosphere-associated microbiome, especially Actinomycetota species, in enhancing pathogen resistance in Theobroma grandiflorum, or cupuassu, an agriculturally valuable Amazonian fruit tree vulnerable to witches' broom disease caused by Moniliophthora perniciosa. While breeding resistant cupuassu genotypes is a possible solution, the capacity of the Actinomycetota phylum to produce beneficial metabolites offers an alternative approach yet to be explored in this context. Utilizing advanced long-read sequencing and metagenomic analysis, we examined Actinomycetota from the phyllosphere of a disease-resistant cupuassu genotype, identifying 11 Metagenome-Assembled Genomes across eight genera. Our comparative genomic analysis uncovered 54 Biosynthetic Gene Clusters related to antitumor, antimicrobial, and plant growth-promoting activities, alongside cutinases and type VII secretion system-associated genes. These results indicate the potential of phyllosphere-associated Actinomycetota in cupuassu for inducing resistance or antagonism against pathogens. By integrating our genomic discoveries with the existing knowledge of cupuassu's defense mechanisms, we developed a model hypothesizing the synergistic or antagonistic interactions between plant and identified Actinomycetota during plant-pathogen interactions. This model offers a framework for understanding the intricate dynamics of microbial influence on plant health. In conclusion, this study underscores the significance of the phyllosphere microbiome, particularly Actinomycetota, in the broader context of harnessing microbial interactions for plant health. These findings offer valuable insights for enhancing agricultural productivity and sustainability.
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Affiliation(s)
- Jéssica Pereira de Matos
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Dilson Fagundes Ribeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Ana Karla da Silva
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Camila Henriques de Paula
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Isabella Ferreira Cordeiro
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Angélica Bianchini Sanchez
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | | | - Camila Carrião Machado Garcia
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil
| | - Nalvo F Almeida
- Faculdade de Computação, Universidade Federal de Mato Grosso do Sul, Campo Grande, MS, Brazil
| | | | | | - Alessandro M Varani
- Departamento de Biotecnologia Agropecuária e Ambiental, Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal, SP, Brazil.
| | - Leandro Marcio Moreira
- Núcleo de Pesquisas em Ciências Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
- Departamento de Ciências Biológicas, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto, Ouro Preto, MG, 35400-000, Brazil.
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12
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Zhang H, Li S, Zhou S, Guo W, Chen P, Li Y, Wu W. Divergence of Phyllosphere Microbial Community Assemblies and Components of Volatile Organic Compounds between the Invasive Sphagneticola trilobata, the Native Sphagneticola calendulacea and Their Hybrids, and Its Implications for Invasiveness. Genes (Basel) 2024; 15:955. [PMID: 39062734 PMCID: PMC11275861 DOI: 10.3390/genes15070955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2024] [Revised: 07/18/2024] [Accepted: 07/18/2024] [Indexed: 07/28/2024] Open
Abstract
Closely-related plant groups with distinct microbiomes, chemistries and ecological characteristics represent tractable models to explore mechanisms shaping species spread, competitive dynamics and community assembly at the interface of native and introduced ranges. We investigated phyllosphere microbial communities, volatile organic compound (VOC) compositions, and potential interactions among introduced S. trilobata, native S. calendulacea and their hybrid in South China. S. trilobata exhibited higher α diversity but significantly different community composition compared to the native and hybrid groups. However, S. calendulacea and the hybrid shared certain microbial taxa, suggesting potential gene flow or co-existence. The potent antimicrobial VOC profile of S. trilobata, including unique compounds like p-cymene (13.33%), likely contributes to its invasion success. The hybrid's intermediate microbial and VOC profiles suggest possible consequences for species distribution, genetic exchange, and community assembly in heterogeneous environments. This hybrid deserves further study as both an opportunity for and threat to diversity maintenance. These differentiating yet connected plant groups provide insight into ecological and evolutionary dynamics shaping microbiome structure, species co-occurrence and competitive outcomes during biological exchange and habitat transformation. An interdisciplinary approach combining chemical and microbial ecology may reveal mechanisms underlying community stability and change, informing management of species spread in a globalized world.
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Affiliation(s)
| | | | | | | | | | | | - Wei Wu
- Scarce and Quality Economic Forest Engineering Technology Research Center, College of Horticulture and Landscape Architecture, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China; (H.Z.); (S.L.); (S.Z.); (W.G.); (P.C.); (Y.L.)
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13
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Boyle JA, Frederickson ME, Stinchcombe JR. Genetic architecture of heritable leaf microbes. Microbiol Spectr 2024; 12:e0061024. [PMID: 38842309 PMCID: PMC11218475 DOI: 10.1128/spectrum.00610-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Accepted: 05/02/2024] [Indexed: 06/07/2024] Open
Abstract
Host-associated microbiomes are shaped by both their environment and host genetics, and often impact host performance. The scale of host genetic variation important to microbes is largely unknown yet fundamental to the community assembly of host-associated microbiomes, with implications for the eco-evolutionary dynamics of microbes and hosts. Using Ipomoea hederacea, ivyleaf morning glory, we generated matrilines differing in quantitative genetic variation and leaf shape, which is controlled by a single Mendelian locus. We then investigated the relative roles of Mendelian and quantitative genetic variation in structuring the leaf microbiome and how these two sources of genetic variation contributed to microbe heritability. We found that despite large effects of the environment, both Mendelian and quantitative genetic host variation contribute to microbe heritability and that the cumulative small effect genomic differences due to matriline explained as much or more microbial variation than a single large effect Mendelian locus. Furthermore, our results are the first to suggest that leaf shape itself contributes to variation in the abundances of some phyllosphere microbes.IMPORTANCEWe investigated how host genetic variation affects the assembly of Ipomoea hederacea's natural microbiome. We found that the genetic architecture of leaf-associated microbiomes involves both quantitative genetic variation and Mendelian traits, with similar contributions to microbe heritability. The existence of Mendelian and quantitative genetic variation for host-associated microbes means that plant evolution at the leaf shape locus or other quantitative genetic loci has the potential to shape microbial abundance and community composition.
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Affiliation(s)
- Julia A Boyle
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - Megan E Frederickson
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
| | - John R Stinchcombe
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada
- Swedish Collegium for Advanced Study, Uppsala, Sweden
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14
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Jorrin B, Haskett TL, Knights HE, Martyn A, Underwood TJ, Dolliver J, Ledermann R, Poole PS. Stable, fluorescent markers for tracking synthetic communities and assembly dynamics. MICROBIOME 2024; 12:81. [PMID: 38715147 PMCID: PMC11075435 DOI: 10.1186/s40168-024-01792-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 03/09/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND After two decades of extensive microbiome research, the current forefront of scientific exploration involves moving beyond description and classification to uncovering the intricate mechanisms underlying the coalescence of microbial communities. Deciphering microbiome assembly has been technically challenging due to their vast microbial diversity but establishing a synthetic community (SynCom) serves as a key strategy in unravelling this process. Achieving absolute quantification is crucial for establishing causality in assembly dynamics. However, existing approaches are primarily designed to differentiate a specific group of microorganisms within a particular SynCom. RESULTS To address this issue, we have developed the differential fluorescent marking (DFM) strategy, employing three distinguishable fluorescent proteins in single and double combinations. Building on the mini-Tn7 transposon, DFM capitalises on enhanced stability and broad applicability across diverse Proteobacteria species. The various DFM constructions are built using the pTn7-SCOUT plasmid family, enabling modular assembly, and facilitating the interchangeability of expression and antibiotic cassettes in a single reaction. DFM has no detrimental effects on fitness or community assembly dynamics, and through the application of flow cytometry, we successfully differentiated, quantified, and tracked a diverse six-member SynCom under various complex conditions like root rhizosphere showing a different colonisation assembly dynamic between pea and barley roots. CONCLUSIONS DFM represents a powerful resource that eliminates dependence on sequencing and/or culturing, thereby opening new avenues for studying microbiome assembly. Video Abstract.
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Affiliation(s)
- Beatriz Jorrin
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK.
| | - Timothy L Haskett
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Hayley E Knights
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Anna Martyn
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Thomas J Underwood
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Jessica Dolliver
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Raphael Ledermann
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
| | - Philip S Poole
- Molecular Plant Sciences Section, Department of Biology, University of Oxford, Oxford, OX1 3RB, UK
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15
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Kunzler M, Schlechter RO, Schreiber L, Remus-Emsermann MNP. Hitching a Ride in the Phyllosphere: Surfactant Production of Pseudomonas spp. Causes Co-swarming of Pantoea eucalypti 299R. MICROBIAL ECOLOGY 2024; 87:62. [PMID: 38683223 PMCID: PMC11058625 DOI: 10.1007/s00248-024-02381-4] [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: 02/12/2024] [Accepted: 04/17/2024] [Indexed: 05/01/2024]
Abstract
Here, we demonstrate the beneficial effect of surfactant-producing pseudomonads on Pantoea eucalypti 299R. We conducted a series of experiments in environments of increasing complexity. P. eucalypti 299R (Pe299R), and Pseudomonas sp. FF1 (Pff1) or Pe299R and surfactant-production deficient Pseudomonas sp. FF1::ΔviscB (Pff1ΔviscB) were co-inoculated in broth, on swarming agar plates, and on plants. In broth, there were no differences in the growth dynamics of Pe299R when growing in the presence of Pff1 or Pff1ΔviscB. By contrast, on swarming agar plates, Pe299R was able to co-swarm with Pff1 which led to a significant increase in Pe299R biomass compared to Pe299R growing with Pff1ΔviscB or in monoculture. Finally in planta, and using the single-cell bioreporter for reproductive success (CUSPER), we found a temporally distinct beneficial effect of Pff1 on co-inoculated Pe299R subpopulations that did not occur in the presence of Pff1ΔviscB. We tested three additional surfactant-producing pseudomonads and their respective surfactant knockout mutants on PE299R on swarming agar showing similar results. This led us to propose a model for the positive effect of surfactant production during leaf colonization. Our results indicate that co-motility might be common during leaf colonization and adds yet another facet to the already manyfold roles of surfactants.
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Affiliation(s)
- Michael Kunzler
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany
| | - Rudolf O Schlechter
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany
| | - Lukas Schreiber
- Institute for Cellular and Molecular Botany, Bonn University, Kirschallee 1-3, 53115, Bonn, Germany
| | - Mitja N P Remus-Emsermann
- Institute for Biology - Microbiology, Freie Universität Berlin, Königin-Luise Straße 12-16, 14195, Berlin, Germany.
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16
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Zhao C, Onyino J, Gao X. Current Advances in the Functional Diversity and Mechanisms Underlying Endophyte-Plant Interactions. Microorganisms 2024; 12:779. [PMID: 38674723 PMCID: PMC11052469 DOI: 10.3390/microorganisms12040779] [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: 03/02/2024] [Revised: 04/06/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Plant phenotype is a complex entity largely controlled by the genotype and various environmental factors. Importantly, co-evolution has allowed plants to coexist with the biotic factors in their surroundings. Recently, plant endophytes as an external plant phenotype, forming part of the complex plethora of the plant microbial assemblage, have gained immense attention from plant scientists. Functionally, endophytes impact the plant in many ways, including increasing nutrient availability, enhancing the ability of plants to cope with both abiotic and biotic stress, and enhancing the accumulation of important plant secondary metabolites. The current state of research has been devoted to evaluating the phenotypic impacts of endophytes on host plants, including their direct influence on plant metabolite accumulation and stress response. However, there is a knowledge gap in how genetic factors influence the interaction of endophytes with host plants, pathogens, and other plant microbial communities, eventually controlling the extended microbial plant phenotype. This review will summarize how host genetic factors can impact the abundance and functional diversity of the endophytic microbial community, how endophytes influence host gene expression, and the host-endophyte-pathogen disease triangle. This information will provide novel insights into how breeders could specifically target the plant-endophyte extended phenotype for crop improvement.
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Affiliation(s)
- Caihong Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Johnmark Onyino
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiquan Gao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Nanjing Agricultural University, Nanjing 210095, China; (C.Z.); (J.O.)
- Collaborative Innovation Center for Modern Crop Production Co-Sponsored by Province and Ministry, Nanjing 210095, China
- College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
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17
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Pacheco-Moreno A, Bollmann-Giolai A, Chandra G, Brett P, Davies J, Thornton O, Poole P, Ramachandran V, Brown JKM, Nicholson P, Ridout C, DeVos S, Malone JG. The genotype of barley cultivars influences multiple aspects of their associated microbiota via differential root exudate secretion. PLoS Biol 2024; 22:e3002232. [PMID: 38662644 PMCID: PMC11045101 DOI: 10.1371/journal.pbio.3002232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Accepted: 03/19/2024] [Indexed: 04/28/2024] Open
Abstract
Plant-associated microbes play vital roles in promoting plant growth and health, with plants secreting root exudates into the rhizosphere to attract beneficial microbes. Exudate composition defines the nature of microbial recruitment, with different plant species attracting distinct microbiota to enable optimal adaptation to the soil environment. To more closely examine the relationship between plant genotype and microbial recruitment, we analysed the rhizosphere microbiomes of landrace (Chevallier) and modern (NFC Tipple) barley (Hordeum vulgare) cultivars. Distinct differences were observed between the plant-associated microbiomes of the 2 cultivars, with the plant-growth promoting rhizobacterial genus Pseudomonas substantially more abundant in the Tipple rhizosphere. Striking differences were also observed between the phenotypes of recruited Pseudomonas populations, alongside distinct genotypic clustering by cultivar. Cultivar-driven Pseudomonas selection was driven by root exudate composition, with the greater abundance of hexose sugars secreted from Tipple roots attracting microbes better adapted to growth on these metabolites and vice versa. Cultivar-driven selection also operates at the molecular level, with both gene expression and the abundance of ecologically relevant loci differing between Tipple and Chevallier Pseudomonas isolates. Finally, cultivar-driven selection is important for plant health, with both cultivars showing a distinct preference for microbes selected by their genetic siblings in rhizosphere transplantation assays.
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Affiliation(s)
- Alba Pacheco-Moreno
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | | | - Govind Chandra
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Brett
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Jack Davies
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Owen Thornton
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Philip Poole
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - Vinoy Ramachandran
- Department of Biology, University of Oxford, South Parks Road, Oxford, United Kingdom
| | - James K. M. Brown
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Paul Nicholson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
| | - Chris Ridout
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Sarah DeVos
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- New Heritage Barley, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, United Kingdom
- School of Biological Sciences, University of East Anglia, Norwich, United Kingdom
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18
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Dang N, Xing W, Gai X, Chen G. Modulating phyllosphere microbiome structure and function in Loropetalum chinense and Osmanthus fragrans: The impact of foliar dust and heavy metals. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 916:170250. [PMID: 38253107 DOI: 10.1016/j.scitotenv.2024.170250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Trees can effectively capture airborne particles and improve air quality. However, the specific response of phyllosphere microbiome (PMo) in different plant species to particulate matter (PM) and the heavy metals it contains are not yet fully understood. In this study, we investigated the impact of PM on the diversity and function of PMo in Loropetalum chinense and Osmanthus fragrans trees grown in industrial and clean zones with varying levels of PM pollution. Our findings revealed that leaf dust had a significant negative effect on microbial richness, with O. fragrans exhibiting higher microbial diversity than L. chinense. The dominant phylum of phyllosphere bacteria in all samples was Proteobacteria, and the dominant genera were Stenotrophomonas and Delftia. The relative abundance of these genera varied significantly among plant species and regions. Our results showed that PM had a significant impact on the community composition of PMo, with the presence of heavy metals exerting a greater effect than particle size. Moreover, the foliar microbial community of plants grown in industrial zones exhibited significantly higher metabolic functions related to stress resistance and disease resistance compared to plants in control zones. These findings highlight the structural and functional responses of PMo to PM and indicate their potential for enhancing plant adaptation to environmental stress.
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Affiliation(s)
- Ning Dang
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Wenli Xing
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Xu Gai
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China
| | - Guangcai Chen
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311400, China.
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19
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Smee MR, Herr KL, Abdul-Khaliq S, Cadet CEA, Hendry TA. Draft genome sequences of eight bacterial isolates from Pisum sativum leaf surfaces. Microbiol Resour Announc 2024; 13:e0081323. [PMID: 38117066 DOI: 10.1128/mra.00813-23] [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: 09/08/2023] [Accepted: 11/29/2023] [Indexed: 12/21/2023] Open
Abstract
Bacterial communities in the phyllosphere, the above-ground parts of plants, are diverse yet understudied. These bacteria are important for plant health and also for inter-kingdom interactions with beneficial and pest insect species. Here, we present draft genomes of eight culturable bacterial isolates from leaf surfaces in the Pisum sativum phyllosphere.
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Affiliation(s)
- Melanie R Smee
- Department of Microbiology, Cornell University , Ithaca, New York, USA
| | - Kathryn L Herr
- Department of Microbiology, Cornell University , Ithaca, New York, USA
| | | | - Chris E A Cadet
- Department of Microbiology, Cornell University , Ithaca, New York, USA
| | - Tory A Hendry
- Department of Microbiology, Cornell University , Ithaca, New York, USA
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Parnell JJ, Vintila S, Tang C, Wagner MR, Kleiner M. Evaluation of ready-to-use freezer stocks of a synthetic microbial community for maize root colonization. Microbiol Spectr 2024; 12:e0240123. [PMID: 38084978 PMCID: PMC10783020 DOI: 10.1128/spectrum.02401-23] [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: 06/07/2023] [Accepted: 11/06/2023] [Indexed: 01/13/2024] Open
Abstract
IMPORTANCE Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs.
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Affiliation(s)
- J. Jacob Parnell
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Simina Vintila
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Clara Tang
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
| | - Maggie R. Wagner
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, USA
- Kansas Biological Survey & Center for Ecological Research, University of Kansas, Lawrence, Kansas, USA
| | - Manuel Kleiner
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
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21
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He C, Zhang M, Li X, He X. Seasonal dynamics of phyllosphere epiphytic microbial communities of medicinal plants in farmland environment. FRONTIERS IN PLANT SCIENCE 2024; 14:1328586. [PMID: 38239215 PMCID: PMC10794659 DOI: 10.3389/fpls.2023.1328586] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 12/11/2023] [Indexed: 01/22/2024]
Abstract
Introduction The phyllosphere of plants is inhabited by various microorganisms, which play a crucial role in plant physiological metabolism. Currently, there is limited research on the dynamic effects of species and seasons on plant phyllosphere microbial community diversity and microbial interactions. Methods In this study, high-throughput sequencing technology was used to sequence the leaf surface parasitic microorganisms of five medicinal plants (Bupleurum chinense, Atractylodes lancea, Salvia miltiorrhiza, Astragalus membranaceus, and Lonicera japonica). Results The results showed that bacteria and fungi clustered into 3,898 and 1,572 operational taxonomic units (OTUs), respectively. Compared to host species, seasons had a more significant impact on the a diversity of bacteria and fungi. The heterogeneity of phyllosphere microbial communities was greater in winter compared to summer. Key species analysis at the OTU level and Spearman correlation analysis demonstrated significant preferences in microbial interactions under plant and seasonal backgrounds. The network connections between bacterial and fungal communities significantly increased during seasonal transitions compared to connections with plants. Discussion This study enhances our understanding of the composition and ecological roles of plant-associated microbial communities in small-scale agricultural environments. Additionally, it provides valuable insights for assessing the biodiversity of medicinal plants.
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Affiliation(s)
- Chao He
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Man Zhang
- College of Life Sciences, Hebei University, Baoding, China
| | - Xianen Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Xueli He
- College of Life Sciences, Hebei University, Baoding, China
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22
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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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23
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Huang WF, Li J, Huang JA, Liu ZH, Xiong LG. Review: Research progress on seasonal succession of phyllosphere microorganisms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111898. [PMID: 37879538 DOI: 10.1016/j.plantsci.2023.111898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/15/2023] [Revised: 09/15/2023] [Accepted: 10/12/2023] [Indexed: 10/27/2023]
Abstract
Phyllosphere microorganisms have recently attracted the attention of scientists studying plant microbiomes. The origin, diversity, functions, and interactions of phyllosphere microorganisms have been extensively explored. Many experiments have demonstrated seasonal cycles of phyllosphere microbes. However, a comprehensive comparison of these separate investigations to characterize seasonal trends in phyllosphere microbes of woody and herbaceous plants has not been conducted. In this review, we explored the dynamic changes of phyllosphere microorganisms in woody and non-woody plants with the passage of the season, sought to find the driving factors, summarized these texts, and thought about future research trends regarding the application of phyllosphere microorganisms in agricultural production. Seasonal trends in phyllosphere microorganisms of herbaceous and woody plants have similarities and differences, but extensive experimental validation is needed. Climate, insects, hosts, microbial interactions, and anthropogenic activities are the diverse factors that influence seasonal variation in phyllosphere microorganisms.
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Affiliation(s)
- Wen-Feng Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Juan Li
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Jian-An Huang
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Zhong-Hua Liu
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China
| | - Li-Gui Xiong
- Key Laboratory of Tea Science of Ministry of Education, Hunan Agricultural University, Changsha, Hunan, China; National Research Center of Engineering and Technology for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Co-Innovation Center of Education Ministry for Utilization of Botanical Functional Ingredients, Hunan Agricultural University, Changsha, Hunan, China; Key Laboratory for Evaluation and Utilization of Gene Resources of Horticultural Crops, Ministry of Agriculture and Rural Affairs of China, Hunan Agricultural University, Changsha, Hunan, China.
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24
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Mehlferber EC, Debray R, Conover AE, Sherman JK, Kaulbach G, Reed R, McCue KF, Ferrel JE, Khanna R, Koskella B. Phyllosphere microbial associations improve plant reproductive success. FRONTIERS IN PLANT SCIENCE 2023; 14:1273330. [PMID: 38143578 PMCID: PMC10739325 DOI: 10.3389/fpls.2023.1273330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Accepted: 11/09/2023] [Indexed: 12/26/2023]
Abstract
The above-ground (phyllosphere) plant microbiome is increasingly recognized as an important component of plant health. We hypothesized that phyllosphere bacterial recruitment may be disrupted in a greenhouse setting, and that adding a bacterial amendment would therefore benefit the health and growth of host plants. Using a newly developed synthetic phyllosphere bacterial microbiome for tomato (Solanum lycopersicum), we tested this hypothesis across multiple trials by manipulating microbial inoculation of leaves and measuring subsequent plant growth and reproductive success, comparing results from plants grown in both greenhouse and field settings. We confirmed that greenhouse-grown plants have a relatively depauperate phyllosphere bacterial microbiome, which both makes them an ideal system for testing the impact of phyllosphere communities on plant health and important targets for microbial amendments as we move towards increased agricultural sustainability. We find that the addition of the synthetic microbial community early in greenhouse growth leads to an increase in fruit production in this setting, implicating the phyllosphere microbiome as a key component of plant fitness and emphasizing the role that these bacterial microbiomes likely play in the ecology and evolution of plant communities.
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Affiliation(s)
- Elijah C. Mehlferber
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Reena Debray
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Asa E. Conover
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Julia K. Sherman
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
| | - Griffin Kaulbach
- Department of Environmental Studies, Haverford College, PA, United States
| | - Robert Reed
- i-Cultiver, Inc., Manteca, CA, United States
| | - Kent F. McCue
- Crop Improvement and Genetics Research Unit, Agricultural Research Service, Western Regional Research Center, United States Department of Agriculture, Albany, CA, United States
| | - Jon E. Ferrel
- i-Cultiver, Inc., Manteca, CA, United States
- Azomite Mineral Products, Inc., Nephi, UT, United States
| | - Rajnish Khanna
- i-Cultiver, Inc., Manteca, CA, United States
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA, United States
| | - Britt Koskella
- Koskella Lab, University of California, Department of Integrative Biology, Berkeley, CA, United States
- Chan Zuckerberg Biohub, San Francisco, CA, United States
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Shankar N, Shetty P, Melo TC, Kesseli R. Multi-Generation Ecosystem Selection of Rhizosphere Microbial Communities Associated with Plant Genotype and Biomass in Arabidopsis thaliana. Microorganisms 2023; 11:2932. [PMID: 38138075 PMCID: PMC10745315 DOI: 10.3390/microorganisms11122932] [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: 11/02/2023] [Revised: 12/01/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The role of the microbiome in shaping the host's phenotype has emerged as a critical area of investigation, with implications in ecology, evolution, and host health. The complex and dynamic interactions involving plants and their diverse rhizospheres' microbial communities are influenced by a multitude of factors, including but not limited to soil type, environment, and plant genotype. Understanding the impact of these factors on microbial community assembly is key to yielding host-specific and robust benefits for plants, yet it remains challenging. Here, we conducted an artificial ecosystem selection experiment for eight generations of Arabidopsis thaliana Ler and Cvi to select soil microbiomes associated with a higher or lower biomass of the host. This resulted in divergent microbial communities shaped by a complex interplay between random environmental variations, plant genotypes, and biomass selection pressures. In the initial phases of the experiment, the genotype and the biomass selection treatment had modest but significant impacts. Over time, the plant genotype and biomass treatments gained more influence, explaining ~40% of the variation in the microbial community's composition. Furthermore, a genotype-specific association of plant-growth-promoting rhizobacterial taxa, Labraceae with Ler and Rhizobiaceae with Cvi, was observed under selection for high biomass.
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Affiliation(s)
- Nachiket Shankar
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Prateek Shetty
- Institute of Plant Biology, Biological Research Centre, 6726 Szeged, Hungary;
| | - Tatiana C. Melo
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
| | - Rick Kesseli
- Department of Biology, University of Massachusetts, Boston, MA 02125, USA (R.K.)
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26
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Oldstone-Jackson C, Huang F, Bergelson J. Microbe-associated molecular pattern recognition receptors have little effect on endophytic Arabidopsis thaliana microbiome assembly in the field. FRONTIERS IN PLANT SCIENCE 2023; 14:1276472. [PMID: 38023837 PMCID: PMC10663345 DOI: 10.3389/fpls.2023.1276472] [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: 08/12/2023] [Accepted: 10/06/2023] [Indexed: 12/01/2023]
Abstract
Plant microbiome structure affects plant health and productivity. A limited subset of environmental microbes successfully establishes within plant tissues, but the forces underlying this selectivity remain poorly characterized. Transmembrane pattern recognition receptors (PRRs), used by plants to detect microbe-associated molecular patterns (MAMPs), are strong candidates for achieving this selectivity because PRRs can potentially interact with many members of the microbiome. Indeed, MAMPs found in many microbial taxa, including beneficials and commensals, can instigate a robust immune response that affects microbial growth. Surprisingly, we found that MAMP-detecting PRRs have little effect on endophytic bacterial and fungal microbiome structure in the field. We compared the microbiomes of four PRR knockout lines of Arabidopsis thaliana to wild-type plants in multiple tissue types over several developmental stages and detected only subtle shifts in fungal, but not bacterial, β-diversity in one of the four PRR mutants. In one developmental stage, lore mutants had slightly altered fungal β-diversity, indicating that LORE may be involved in plant-fungal interactions in addition to its known role in detecting certain bacterial lipids. No other effects of PRRs on α-diversity, microbiome variability, within-individual homogeneity, or microbial load were found. The general lack of effect suggests that individual MAMP-detecting PRRs are not critical in shaping the endophytic plant microbiome. Rather, we suggest that MAMP-detecting PRRs must either act in concert and/or are individually maintained through pleiotropic effects or interactions with coevolved mutualists or pathogens. Although unexpected, these results offer insights into the role of MAMP-detecting PRRs in plant-microbe interactions and help direct future efforts to uncover host genetic elements that control plant microbiome assembly.
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Affiliation(s)
| | - Feng Huang
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Plant Protection Research Institute, Guangdong Academy of Agricultural Sciences, Guangzhou, Guangdong, China
| | - Joy Bergelson
- Department of Ecology and Evolution, The University of Chicago, Chicago, IL, United States
- Center for Genomics and Systems Biology, Department of Biology, College of Arts and Science, New York University, New York, NY, United States
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Hakobyan A, Velte S, Sickel W, Quandt D, Stoll A, Knief C. Tillandsia landbeckii phyllosphere and laimosphere as refugia for bacterial life in a hyperarid desert environment. MICROBIOME 2023; 11:246. [PMID: 37936139 PMCID: PMC10631034 DOI: 10.1186/s40168-023-01684-x] [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: 06/15/2023] [Accepted: 09/28/2023] [Indexed: 11/09/2023]
Abstract
BACKGROUND The lack of water is a major constraint for microbial life in hyperarid deserts. Consequently, the abundance and diversity of microorganisms in common habitats such as soil are strongly reduced, and colonization occurs primarily by specifically adapted microorganisms that thrive in particular refugia to escape the harsh conditions that prevail in these deserts. We suggest that plants provide another refugium for microbial life in hyperarid deserts. We studied the bacterial colonization of Tillandsia landbeckii (Bromeliaceae) plants, which occur in the hyperarid regions of the Atacama Desert in Chile, one of the driest and oldest deserts on Earth. RESULTS We detected clear differences between the bacterial communities being plant associated to those of the bare soil surface (PERMANOVA, R2 = 0.187, p = 0.001), indicating that Tillandsia plants host a specific bacterial community, not only dust-deposited cells. Moreover, the bacterial communities in the phyllosphere were distinct from those in the laimosphere, i.e., on buried shoots (R2 = 0.108, p = 0.001), indicating further habitat differentiation within plant individuals. The bacterial taxa detected in the phyllosphere are partly well-known phyllosphere colonizers, but in addition, some rather unusual taxa (subgroup2 Acidobacteriae, Acidiphilum) and insect endosymbionts (Wolbachia, "Candidatus Uzinura") were found. The laimosphere hosted phyllosphere-associated as well as soil-derived taxa. The phyllosphere bacterial communities showed biogeographic patterns across the desert (R2 = 0.331, p = 0.001). These patterns were different and even more pronounced in the laimosphere (R2 = 0.467, p = 0.001), indicating that different factors determine community assembly in the two plant compartments. Furthermore, the phyllosphere microbiota underwent temporal changes (R2 = 0.064, p = 0.001). CONCLUSIONS Our data demonstrate that T. landbeckii plants host specific bacterial communities in the phyllosphere as well as in the laimosphere. Therewith, these plants provide compartment-specific refugia for microbial life in hyperarid desert environments. The bacterial communities show biogeographic patterns and temporal variation, as known from other plant microbiomes, demonstrating environmental responsiveness and suggesting that bacteria inhabit these plants as viable microorganisms. Video Abstract.
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Affiliation(s)
- Anna Hakobyan
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Stefanie Velte
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
| | - Wiebke Sickel
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany
- Institute of Biodiversity, Johann Heinrich Von Thünen Institute, Brunswick, Germany
| | - Dietmar Quandt
- Nees Institute for Biodiversity of Plants, University of Bonn, Bonn, Germany
| | - Alexandra Stoll
- Centro de Estudios Avanzados en Zonas Áridas Ceaza, La Serena, Chile
- Instituto de Investigación Multidisciplinar en Ciencia y Tecnología, Universidad de La Serena, La Serena, Chile
| | - Claudia Knief
- Molecular Biology of the Rhizosphere, Institute for Crop Science and Resource Conservation (INRES), University of Bonn, 53115, Bonn, Germany.
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Fang K, Yang AL, Li YX, Zeng ZY, Wang RF, Li T, Zhao ZW, Zhang HB. Native plants change the endophyte assembly and growth of an invasive plant in response to climatic factors. Appl Environ Microbiol 2023; 89:e0109323. [PMID: 37815356 PMCID: PMC10617555 DOI: 10.1128/aem.01093-23] [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: 06/28/2023] [Accepted: 08/08/2023] [Indexed: 10/11/2023] Open
Abstract
Climate change, microbial endophytes, and local plants can affect the establishment and expansion of invasive species, yet no study has been performed to assess these interactions. Using a growth chamber, we integrated the belowground (rhizosphere soils) and aboveground (mixture of mature leaf and leaf litter) microbiota into an experimental framework to evaluate the impacts of four native plants acting as microbial inoculation sources on endophyte assembly and growth of the invasive plant Ageratina adenophora in response to drought stress and temperature change. We found that fungal and bacterial enrichment in the leaves and roots of A. adenophora exhibited distinct patterns in response to climatic factors. Many fungi were enriched in roots in response to high temperature and drought stress; in contrast, many bacteria were enriched in leaves in response to low temperature and drought stress. Inoculation of microbiota from phylogenetically close native plant species (i.e., Asteraceae Artemisia atrovirens) causes the recipient plant A. adenophora (Asteraceae) to enrich dominant microbial species from inoculation sources, which commonly results in a lower dissimilar endophytic microbiota and thus produces more negative growth effects when compared to non-Asteraceae inoculations. Drought, microbial inoculation source, and temperature directly impacted the growth of A. adenophora. Both drought and inoculation also indirectly impacted the growth of A. adenophora by changing the root endophytic fungal assembly. Our data indicate that native plant identity can greatly impact the endophyte assembly and host growth of invasive plants, which is regulated by drought and temperature.IMPORTANCEThere has been increasing interest in the interactions between global changes and plant invasions; however, it remains to quantify the role of microbial endophytes in plant invasion with a consideration of their variation in the root vs leaf of hosts, as well as the linkages between microbial inoculations, such as native plant species, and climatic factors, such as temperature and drought. Our study found that local plants acting as microbial inoculants can impact fungal and bacterial enrichment in the leaves and roots of the invasive plant Ageratina adenophora and thus produce distinct growth effects in response to climatic factors; endophyte-mediated invasion of A. adenophora is expected to operate more effectively under favorable moisture. Our study is important for understanding the interactions between climate change, microbial endophytes, and local plant identity in the establishment and expansion of invasive species.
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Affiliation(s)
- Kai Fang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Ai-Ling Yang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Yu-Xuan Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhao-Ying Zeng
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, China
| | - Rui-Fang Wang
- College of Agriculture and Forestry, Puer University, Puer, Yunnan, China
| | - Tao Li
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Zhi-Wei Zhao
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
| | - Han-Bo Zhang
- State Key Laboratory for Conservation and Utilization of Bioresources in Yunnan, Yunnan University, Kunming, China
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Bosorogan A, Cardenas-Poire E, Gonzales-Vigil E. Tomato defences modulate not only insect performance but also their gut microbial composition. Sci Rep 2023; 13:18139. [PMID: 37875520 PMCID: PMC10598054 DOI: 10.1038/s41598-023-44938-2] [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: 08/04/2023] [Accepted: 10/13/2023] [Indexed: 10/26/2023] Open
Abstract
Plants protect their tissues from insect herbivory with specialized structures and chemicals, such as cuticles, trichomes, and metabolites contained therein. Bacteria inside the insect gut are also exposed to plant defences and can potentially modify the outcome of plant-insect interactions. To disentangle this complex multi-organism system, we used tomato mutants impaired in the production of plant defences (odorless-2 and jasmonic acid-insensitive1) and two cultivars (Ailsa Craig and Castlemart), exposed them to herbivory by the cabbage looper (Trichoplusia ni H.) and collected the insect frass for bacterial community analysis. While the epicuticular wax and terpene profiles were variable, the leaf fatty acid composition remained consistent among genotypes. Moreover, larval weight confirmed the negative association between plant defences and insect performance. The distinctive frass fatty acid profiles indicated that plant genotype also influences the lipid digestive metabolism of insects. Additionally, comparisons of leaf and insect-gut bacterial communities revealed a limited overlap in bacterial species between the two sample types. Insect bacterial community abundance and diversity were notably reduced in insects fed on the mutants, with Enterobacteriaceae being the predominant group, whereas putatively pathogenic taxa were found in wildtype genotypes. Altogether, these results indicate that plant defences can modulate insect-associated bacterial community composition.
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Affiliation(s)
- Andreea Bosorogan
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, M1C 1A4, Canada
- Department of Cell and Systems Biology, University of Toronto, Toronto, M5S 3G5, Canada
| | | | - Eliana Gonzales-Vigil
- Department of Biological Sciences, University of Toronto Scarborough, Toronto, M1C 1A4, Canada.
- Department of Cell and Systems Biology, University of Toronto, Toronto, M5S 3G5, Canada.
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Wang Y, Yang ZN, Luo SQ. An assembled bacterial community associated with Artemisia annua L. causes plant protection against a pathogenic fungus. Front Microbiol 2023; 14:1218474. [PMID: 37876787 PMCID: PMC10591200 DOI: 10.3389/fmicb.2023.1218474] [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: 05/07/2023] [Accepted: 09/12/2023] [Indexed: 10/26/2023] Open
Abstract
The microorganisms associated with a plant influence its growth and fitness. These microorganisms accumulate on the aerial and root surfaces of plants, as well as within the plants, as endophytes, although how the interaction between microorganisms protects the plant from pathogens is still little understood. In the current study, the impact of assembled the bacterial communities against the pathogenic fungus to promote Artemisia annua L. growths was investigated. We established a model of bacterium-fungus-plant system. Eight bacterial strains and a fungal pathogen Globisporangium ultimum (Glo) were isolated from wild A. annua roots and leaves, respectively. We assembled the six-bacteria community (C6: Rhizobium pusense, Paracoccus sp., Flavobacterium sp., Brevundimonas sp., Stenotrophomonas sp., and Bacillus sp.) with inhibition, and eight-bacteria community (C8) composing of C6 plus another two bacteria (Brevibacillus nitrificans and Cupriavidus sp.) without inhibition against Glo in individually dual culture assays. Inoculation of seedlings with C8 significantly reduced impact of Glo. The growth and disease suppression of A. annua seedlings inoculated with C8 + Glo were significantly better than those of seedlings inoculated with only Glo. C8 had more inhibitory effects on Glo, and also enhanced the contents of four metabolites in seedling roots compared to Glo treatment only. Additionally, the inhibitory effects of root extracts from A. annua seedlings showed that Glo was most sensitive, the degree of eight bacteria sensitivity were various with different concentrations. Our findings suggested that the non-inhibitory bacteria played a vital role in the bacterial community composition and that some bacterial taxa were associated with disease suppression. The construction of a defined assembled bacterial community could be used as a biological fungicide, promoting biological disease control of plants.
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Affiliation(s)
- Yu Wang
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
| | - Zhan-nan Yang
- Key Laboratory for Information System of Mountainous Areas and Protection of Ecological Environment of Guizhou Province, Guizhou Normal University, Guiyang, Guizhou, China
| | - Shi-qiong Luo
- School of Life Sciences, Guizhou Normal University, Guiyang, Guizhou, China
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31
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De Mandal S, Jeon J. Phyllosphere Microbiome in Plant Health and Disease. PLANTS (BASEL, SWITZERLAND) 2023; 12:3481. [PMID: 37836221 PMCID: PMC10575124 DOI: 10.3390/plants12193481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 09/24/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023]
Abstract
The phyllosphere refers to the aboveground surface of plants colonized by diverse microorganisms. Microbes inhabiting this environment play an important role in enhancing the host's genomic and metabolic capabilities, including defense against pathogens. Compared to the large volume of studies on rhizosphere microbiome for plant health and defense, our understanding of phyllosphere microbiome remains in its infancy. In this review, we aim to explore the mechanisms that govern the phyllosphere assembly and their function in host defence, as well as highlight the knowledge gaps. These efforts will help develop strategies to harness the phyllosphere microbiome toward sustainable crop production.
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Affiliation(s)
| | - Junhyun Jeon
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea;
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Mesny F, Hacquard S, Thomma BPHJ. Co-evolution within the plant holobiont drives host performance. EMBO Rep 2023; 24:e57455. [PMID: 37471099 PMCID: PMC10481671 DOI: 10.15252/embr.202357455] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 06/28/2023] [Accepted: 07/06/2023] [Indexed: 07/21/2023] Open
Abstract
Plants interact with a diversity of microorganisms that influence their growth and resilience, and they can therefore be considered as ecological entities, namely "plant holobionts," rather than as singular organisms. In a plant holobiont, the assembly of above- and belowground microbiota is ruled by host, microbial, and environmental factors. Upon microorganism perception, plants activate immune signaling resulting in the secretion of factors that modulate microbiota composition. Additionally, metabolic interdependencies and antagonism between microbes are driving forces for community assemblies. We argue that complex plant-microbe and intermicrobial interactions have been selected for during evolution and may promote the survival and fitness of plants and their associated microorganisms as holobionts. As part of this process, plants evolved metabolite-mediated strategies to selectively recruit beneficial microorganisms in their microbiota. Some of these microbiota members show host-adaptation, from which mutualism may rapidly arise. In the holobiont, microbiota members also co-evolved antagonistic activities that restrict proliferation of microbes with high pathogenic potential and can therefore prevent disease development. Co-evolution within holobionts thus ultimately drives plant performance.
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Affiliation(s)
- Fantin Mesny
- Institute for Plant SciencesUniversity of CologneCologneGermany
| | - Stéphane Hacquard
- Department of Plant Microbe InteractionsMax Planck Institute for Plant Breeding ResearchCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
| | - Bart PHJ Thomma
- Institute for Plant SciencesUniversity of CologneCologneGermany
- Cluster of Excellence on Plant Sciences (CEPLAS)CologneGermany
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33
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Escudero-Martinez C, Bulgarelli D. Engineering the Crop Microbiota Through Host Genetics. ANNUAL REVIEW OF PHYTOPATHOLOGY 2023; 61:257-277. [PMID: 37196364 DOI: 10.1146/annurev-phyto-021621-121447] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
The microbiota populating the plant-soil continuum defines an untapped resource for sustainable crop production. The host plant is a driver for the taxonomic composition and function of these microbial communities. In this review, we illustrate how the host genetic determinants of the microbiota have been shaped by plant domestication and crop diversification. We discuss how the heritable component of microbiota recruitment may represent, at least partially, a selection for microbial functions underpinning the growth, development, and health of their host plants and how the magnitude of this heritability is influenced by the environment. We illustrate how host-microbiota interactions can be treated as an external quantitative trait and review recent studies associating crop genetics with microbiota-based quantitative traits. We also explore the results of reductionist approaches, including synthetic microbial communities, to establish causal relationships between microbiota and plant phenotypes. Lastly, we propose strategies to integrate microbiota manipulation into crop selection programs. Although a detailed understanding of when and how heritability for microbiota composition can be deployed for breeding purposes is still lacking, we argue that advances in crop genomics are likely to accelerate wider applications of plant-microbiota interactions in agriculture.
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Affiliation(s)
| | - Davide Bulgarelli
- Plant Sciences, School of Life Sciences, University of Dundee, Dundee, United Kingdom; ,
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34
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Schlechter RO, Kear EJ, Bernach M, Remus DM, Remus-Emsermann MNP. Metabolic resource overlap impacts competition among phyllosphere bacteria. THE ISME JOURNAL 2023; 17:1445-1454. [PMID: 37355740 PMCID: PMC10432529 DOI: 10.1038/s41396-023-01459-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 06/12/2023] [Accepted: 06/13/2023] [Indexed: 06/26/2023]
Abstract
The phyllosphere is densely colonised by microbial communities, despite sparse and heterogeneously distributed resources. The limitation of resources is expected to drive bacterial competition resulting in exclusion or coexistence based on fitness differences and resource overlap between individual colonisers. We studied the impact of resource competition by determining the effects of different bacterial colonisers on the growth of the model epiphyte Pantoea eucalypti 299R (Pe299R). Resource overlap was predicted based on genome-scale metabolic modelling. By combining results of metabolic modelling and pairwise competitions in the Arabidopsis thaliana phyllosphere and in vitro, we found that ten resources sufficed to explain fitness of Pe299R. An effect of both resource overlap and phylogenetic relationships was found on competition outcomes in vitro as well as in the phyllosphere. However, effects of resource competition were much weaker in the phyllosphere when compared to in vitro experiments. When investigating growth dynamics and reproductive success at the single-cell resolution, resource overlap and phylogenetic relationships are only weakly correlated with epiphytic Pe299R reproductive success, indicating that the leaf's spatial heterogeneity mitigates resource competition. Although the correlation is weak, the presence of competitors led to the development of Pe299R subpopulations that experienced different life histories and cell divisions. In some in planta competitions, Pe299R benefitted from the presence of epiphytes despite high resource overlap to the competitor strain suggesting other factors having stronger effects than resource competition. This study provides fundamental insights into how bacterial communities are shaped in heterogeneous environments and a framework to predict competition outcomes.
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Affiliation(s)
- Rudolf O Schlechter
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand.
- Bioprotection Research Core, University of Canterbury, Christchurch, 8011, New Zealand.
| | - Evan J Kear
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
| | - Michał Bernach
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand
- Department of Electrical and Computer Engineering, University of Canterbury, Christchurch, 8011, New Zealand
| | - Daniela M Remus
- Protein Science and Engineering, Callaghan Innovation, School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Mitja N P Remus-Emsermann
- Institute of Microbiology and Dahlem Centre of Plant Sciences, Department of Biology, Chemistry, Pharmacy, Freie Universität Berlin, Berlin, Germany.
- School of Biological Sciences, University of Canterbury, Christchurch, 8011, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, 8011, New Zealand.
- Bioprotection Research Core, University of Canterbury, Christchurch, 8011, New Zealand.
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35
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Wei TL, Zheng YP, Wang ZH, Shang YX, Pei MS, Liu HN, Yu YH, Shi QF, Jiang DM, Guo DL. Comparative microbiome analysis reveals the variation in microbial communities between 'Kyoho' grape and its bud mutant variety. PLoS One 2023; 18:e0290853. [PMID: 37647311 PMCID: PMC10468054 DOI: 10.1371/journal.pone.0290853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 08/17/2023] [Indexed: 09/01/2023] Open
Abstract
Microbes are an important part of the vineyard ecosystem, which significantly influence the quality of grapes. Previously, we identified a bud mutant variety (named 'Fengzao') from 'Kyoho' grapes. The variation of microbial communities in grape and its bud mutant variety has not been studied yet. So, in this study, with the samples of both 'Fengzao' and 'Kyoho', we conducted high-throughput microbiome sequencing and investigated their microbial communities in different tissues. Obvious differences were observed in the microbial communities between 'Fengzao' and 'Kyoho'. The fruit and the stem are the tissues with relatively higher abundance of microbes, while the leaves contained less microbes. The fruit and the stem of 'Kyoho' and the stem of 'Fengzao' had relatively higher species diversity based on the alpha diversity analysis. Proteobacteria, Enterobacteriaceae and Rhodobacteraceae had significantly high abundance in 'Fengzao'. Firmicutes and Pseudomonas were highly abundant in the stems of 'Kyoho', and family of Spirochaetaceae, Anaplasmataceae, Chlorobiaceae, and Sphingomonadaceae, and genera of Spirochaeta, Sphingomonas, Chlorobaculum and Wolbachia were abundant in the fruits of 'Kyoho'. These identified microbes are main components of the microbial communities, and could be important regulators of grapevine growth and development. This study revealed the differences in the microbial compositions between 'Kyoho' and its bud mutant, and these identified microbes will be significant resources for the future researches on the quality regulation and disease control of grapevines.
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Affiliation(s)
- Tong-Lu Wei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Yu-Ping Zheng
- Library, Henan University of Science and Technology, Luoyang, 471023, China
| | - Ze-Hang Wang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Ya-Xin Shang
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Mao-Song Pei
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Hai-Nan Liu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Yi-He Yu
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Qiao-Fang Shi
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Dong-Ming Jiang
- Jiangsu Red Sun Wine Industry Limited Company, Xuzhou, 221000, China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China
- Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
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36
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Luo K, Zhao G, Chen M, Tian X. Effects of maize resistance and leaf chemical substances on the structure of phyllosphere fungal communities. FRONTIERS IN PLANT SCIENCE 2023; 14:1241055. [PMID: 37645458 PMCID: PMC10461017 DOI: 10.3389/fpls.2023.1241055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 07/25/2023] [Indexed: 08/31/2023]
Abstract
It is well known that plant genotype can regulate phyllosphere fungi at the species level. However, little is known about how plant varieties shape the fungal communities in the phyllosphere. In this study, four types of maize varieties with various levels of resistances to Exserohilum turcicum were subjected to high-throughput sequencing to reveal the properties that influences the composition of phyllosphere fungal communities. The dominant fungi genera for all four maize varieties were Alternaria at different relative abundances, followed by Nigrospora. Hierarchical clustering analysis, non-metric multidimensional scaling and similarity analysis confirmed that the fungal communities in the phyllosphere of the four varieties were significantly different and clustered into the respective maize variety they inhabited. The findings from Redundancy Analysis (RDA) indicated that both maize resistance and leaf chemical constituents, including nitrogen, phosphorus, tannins, and flavonoids, were the major drivers in determining the composition of phyllosphere fungal communities. Among these factors, maize resistance was found to be the most influential, followed by phosphorus. The co-occurrence network of the fungal communities in the phyllosphere of highly resistant variety had higher complexity, integrity and stability compared to others maize varieties. In a conclusion, maize variety resistance and leaf chemical constituents play a major role in shaping the phyllosphere fungal community. The work proposes a link between the assembled fungal communities within the phyllosphere with maize variety that is resistant to pathogenic fungi infection.
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Affiliation(s)
- Kun Luo
- Hunan Agricultural University, Changsha, Hunan, China
| | - Gonghua Zhao
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Mengfei Chen
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
| | - Xueliang Tian
- Henan Engineering Research Center of Biological Pesticide & Fertilizer Development and Synergistic Application, Henan Institute of Science and Technology, Xinxiang, Henan, China
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37
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Martins SJ, Pasche J, Silva HAO, Selten G, Savastano N, Abreu LM, Bais HP, Garrett KA, Kraisitudomsook N, Pieterse CMJ, Cernava T. The Use of Synthetic Microbial Communities to Improve Plant Health. PHYTOPATHOLOGY 2023; 113:1369-1379. [PMID: 36858028 DOI: 10.1094/phyto-01-23-0016-ia] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Despite the numerous benefits plants receive from probiotics, maintaining consistent results across applications is still a challenge. Cultivation-independent methods associated with reduced sequencing costs have considerably improved the overall understanding of microbial ecology in the plant environment. As a result, now, it is possible to engineer a consortium of microbes aiming for improved plant health. Such synthetic microbial communities (SynComs) contain carefully chosen microbial species to produce the desired microbiome function. Microbial biofilm formation, production of secondary metabolites, and ability to induce plant resistance are some of the microbial traits to consider when designing SynComs. Plant-associated microbial communities are not assembled randomly. Ecological theories suggest that these communities have a defined phylogenetic organization structured by general community assembly rules. Using machine learning, we can study these rules and target microbial functions that generate desired plant phenotypes. Well-structured assemblages are more likely to lead to a stable SynCom that thrives under environmental stressors as compared with the classical selection of single microbial activities or taxonomy. However, ensuring microbial colonization and long-term plant phenotype stability is still one of the challenges to overcome with SynComs, as the synthetic community may change over time with microbial horizontal gene transfer and retained mutations. Here, we explored the advances made in SynCom research regarding plant health, focusing on bacteria, as they are the most dominant microbial form compared with other members of the microbiome and the most commonly found in SynCom studies.
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Affiliation(s)
- Samuel J Martins
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Josephine Pasche
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | - Hiago Antonio O Silva
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Gijs Selten
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Noah Savastano
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Lucas Magalhães Abreu
- Departamento de Fitopatologia, Universidade Federal de Viçosa, Viçosa, MG 36570-900, Brazil
| | - Harsh P Bais
- Department of Plant and Soil Sciences, 311 AP Biopharma, University of Delaware, Newark, DE 19713, U.S.A
| | - Karen A Garrett
- Department of Plant Pathology, University of Florida, Gainesville, FL, 32611, U.S.A
| | | | - Corné M J Pieterse
- Plant-Microbe Interactions, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8020, Austria
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, U.K
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38
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Henry LP, Bergelson J. Evolutionary implications of host genetic control for engineering beneficial microbiomes. CURRENT OPINION IN SYSTEMS BIOLOGY 2023; 34:None. [PMID: 37287906 PMCID: PMC10242548 DOI: 10.1016/j.coisb.2023.100455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Engineering new functions in the microbiome requires understanding how host genetic control and microbe-microbe interactions shape the microbiome. One key genetic mechanism underlying host control is the immune system. The immune system can promote stability in the composition of the microbiome by reshaping the ecological dynamics of its members, but the degree of stability will depend on the interplay between ecological context, immune system development, and higher-order microbe-microbe interactions. The eco-evolutionary interplay affecting composition and stability should inform the strategies used to engineer new functions in the microbiome. We conclude with recent methodological developments that provide an important path forward for both engineering new functionality in the microbiome and broadly understanding how ecological interactions shape evolutionary processes in complex biological systems.
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Addison S, Armstrong C, Wigley K, Hartley R, Wakelin S. What matters most? Assessment of within-canopy factors influencing the needle microbiome of the model conifer, Pinus radiata. ENVIRONMENTAL MICROBIOME 2023; 18:45. [PMID: 37254222 DOI: 10.1186/s40793-023-00507-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 05/22/2023] [Indexed: 06/01/2023]
Abstract
The assembly and function of the phyllosphere microbiome is important to the overall fitness of plants and, thereby, the ecosystems they inhabit. Presently, model systems for tree phyllosphere microbiome studies are lacking, yet forests resilient to pests, diseases, and climate change are important to support a myriad of ecosystem services impacting from local to global levels. In this study, we extend the development of model microbiome systems for trees species, particularly coniferous gymnosperms, by undertaking a structured approach assessing the phyllosphere microbiome of Pinus radiata. Canopy sampling height was the single most important factor influencing both alpha- and beta-diversity of bacterial and fungal communities (p < 0.005). Bacterial and fungal phyllosphere microbiome richness was lowest in samples from the top of the canopy, subsequently increasing in the middle and then bottom canopy samples. These differences maybe driven by either by (1) exchange of microbiomes with the forest floor and soil with the lower foliage, (2) strong ecological filtering in the upper canopy via environmental exposure (e.g., UV), (3) canopy density, (4) or combinations of factors. Most taxa present in the top canopy were also present lower in tree; as such, sampling strategies focussing on lower canopy sampling should provide good overall phyllosphere microbiome coverage for the tree. The dominant phyllosphere bacteria were Alpha-proteobacteria (Rhizobiales and Sphingomonas) along with Acidobacteria Gp1. However, the P. radiata phyllosphere microbiome samples were fungal dominated. From the top canopy samples, Arthoniomycetes and Dothideomycetes were highly represented, with abundances of Arthoniomycetes then reducing in lower canopy samples whilst abundances of Ascomycota increased. The most abundant fungal taxa were Phaeococcomyces (14.4% of total reads) and Phaeotheca spp. (10.38%). A second-order effect of canopy sampling direction was evident in bacterial community composition (p = 0.01); these directional influences were not evident for fungal communities. However, sterilisation of needles did impact fungal community composition (p = 0.025), indicating potential for community differences in the endosphere versus leaf surface compartments. Needle age was only important in relation to bacterial communities, but was canopy height dependant (interaction p = 0.008). By building an understanding of the primary and secondary factors related to intra-canopy phyllosphere microbiome variation, we provide a sampling framework to either explicitly minimise or capture variation in needle collection to enable ongoing ecological studies targeted at inter-canopy or other experimental levels.
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Affiliation(s)
| | | | | | | | - Steven Wakelin
- Scion, P.O. Box 29237, Riccarton, Christchurch, 8440, New Zealand.
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40
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Xu L, Wang R, Jin B, Chen J, Jiang T, Ali W, Tian S, Lu L. Cadmium inhibits powdery mildew colonization and reconstructs microbial community in leaves of the hyperaccumulator plant Sedum alfredii. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2023; 260:115076. [PMID: 37257346 DOI: 10.1016/j.ecoenv.2023.115076] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/27/2023] [Accepted: 05/24/2023] [Indexed: 06/02/2023]
Abstract
Understanding the influence of the heavy metal cadmium (Cd) on the phyllosphere microbiome of hyperaccumulator plants is crucial for enhancing phytoremediation. The characteristics of the phyllosphere of Sedum alfredii Hance, a hyperaccumulator plant, were investigated using 16S rRNA and internal transcribed spacer amplicon sequencing of powdery mildew-infected leaves treated or untreated with Cd. The results showed that the colonization of powdery mildew caused severe chlorosis and necrosis in S. alfredii leaves, and the relative abundance of Leotiomycetes in infected leaves increased dramatically and significantly decreased phyllosphere microbiome diversity. However, S. alfredii preferentially accumulated higher concentrations of Cd in the leaves of infected plants than in uninfected plants by powdery mildew, which in turn significantly inhibited powdery mildew colonization in leaves; the relative abundance of the fungal class Leotiomycetes in infected leaves decreased, and alpha and beta diversities of the phyllosphere microbiome significantly increased with Cd treatment in the infected plants. In addition, the inter-kingdom networks in the microbiota of the infected leaves treated with Cd presented many nodes and edges, and the highest inter-kingdom modularity compared to the untreated infected leaves, indicating a highly connected microbial community. These results suggest that Cd significantly inhibits powdery mildew colonization by altering the composition of the phyllosphere microbiome in S. alfredii leaves, paving the way for efficient heavy metal phytoremediation and providing a new perspective on defense strategies against heavy metals.
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Affiliation(s)
- Lingling Xu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Runze Wang
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Bingjie Jin
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiuzhou Chen
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Tianchi Jiang
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Waqar Ali
- State Key Laboratory of Environmental Geochemistry, Institute of Geochemistry, Chinese Academy of Science's, Guiyang 550081, China
| | - Shengke Tian
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Lingli Lu
- MOE Key Laboratory of Environment Remediation and Ecological Health, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Agricultural Resource and Environment of Zhejiang Province, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China.
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41
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Jing J, Wang W, Deng L, Yi L, Zeng K. A core epiphytic bacterial consortia synergistically protect citrus from postharvest disease. Food Chem 2023; 407:135103. [PMID: 36493476 DOI: 10.1016/j.foodchem.2022.135103] [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: 09/27/2022] [Revised: 11/03/2022] [Accepted: 11/25/2022] [Indexed: 12/02/2022]
Abstract
Biological antagonists are a series of microbes that can control pathogens to reduce the incidence of disease or reduce symptoms. Herein, four varieties of citrus fruit were selected to perform an amplicon sequencing on their epiphytic microbiota to get a systematic understanding of them. Co-occurrence network, Venn, and LefSe analysis were performed to filter to 24 genera which represent the universality, specificity, and correlation among samples. Functional analysis hinted that the genes related to chitinase, which most of these 24 bacteria carry, might lead to a disease-suppressive phenotype. 115 strains of epiphytic bacteria were isolated, and the bacterial synthetic community was constructed by 8 strains. The in vivo test results indicated they were able to reduce pathogen development for a longer time than separate inoculation. Collectively, this study showed the disease control potential provided by native epiphytic bacteria of fruit and give a new strategy to sustainable agriculture.
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Affiliation(s)
- Jiayi Jing
- College of Food Science, Southwest University, Chongqing 400715, PR China.
| | - Wenjun Wang
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China.
| | - Lili Deng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China.
| | - Lanhua Yi
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China.
| | - Kaifang Zeng
- College of Food Science, Southwest University, Chongqing 400715, PR China; Food Storage and Logistics Research Center, Southwest University, Chongqing 400715, PR China; National Citrus Engineering Research Center, Chongqing 400712, PR China.
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Elyamine AM, Wang H, Oummu-Kulthum MAH, Raissa S, Nahdhoit AR, Meng S, Tao P, Hu Z. Mangroves leaves phyllosphere bacteria community and its ability to survive under pyrene stress during the acclimation process. MARINE ENVIRONMENTAL RESEARCH 2023; 187:105920. [PMID: 36931048 DOI: 10.1016/j.marenvres.2023.105920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 02/12/2023] [Accepted: 02/14/2023] [Indexed: 06/18/2023]
Abstract
Plants in general and mangroves in particular can harbor hyper-diverse microorganisms in their different compartments including the phyllosphere area. This study used the leaves of three mangrove species; black mangrove (Avicenia germinans), red mangrove (Rhizophora mangle) and mangrove apple (Sonneratia alba) in order to evaluate the phyllosphere epiphytic bacterial community on their leaves surface and assess the ability of some epiphytic bacteria to tolerate and survive under pyrene stress. Through the 16S rRNA genes sequencing, 380203, 405203 and 344863 OTUs were identified respectively in the leaves of mangroves apple, black and red mangroves. The identified OTUs was positively correlated with leaves-wax (p < 0.05, r2 = 0.904), nitrogen (r2 = 0.72), phosphorus content (r2 = 0.62) and the water factor (r2 = 0.93). It was however highly and negatively correlated with the canopy cover (r2 = 0.93). The pyrene degradation rate in the mineral salt medium (MSM) containing pyrene as external stress was different in each mangrove species and varied depending on various factors. Therefore, through the succession culture in MSM, several bacteria strain belonging to Rhizobiales and Enterobacteres were found to be abundant in red mangroves. Bacteria belonging to Bacilliales and Sphingobacteriales were more abundant in mangroves apples and bacteria from Xanthomonadales and Sphingomonadales were more presents in back mangroves. The important finding was to reveal that the black mangrove at the non-submerged substrate, recorded the highest number of OTU, coinciding with its highest leaf's nitrogen and phosphorus content and most importantly, its highest rate of pyrene degradation. The general result of this study join previous research results and get place in the mangrove agenda, as part of a better understanding insight into the role of plant identity in driving the phyllosphere epiphytic microbial community structures in mangrove ecosystems.
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Affiliation(s)
- Ali Mohamed Elyamine
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China; Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Han Wang
- Huanhuai University, Zhumadian, 46000, China
| | | | - Sailine Raissa
- Department of Life Science, Faculty of Science and Technology, University of Comoros, Moroni, 269, Comoros
| | - Ahamada Rachid Nahdhoit
- Institute of Graduate Studies, Fundamental and Industrial Microbiology, Istanbul University, 34134, Vezneciler Faith, Istanbul, Turkey
| | - Shanshan Meng
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Peng Tao
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China
| | - Zhong Hu
- Key Laboratory of Resources and Environmental Microbiology, Department of Biology, Shantou University, Shantou City, Guangdong, 515063, China.
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Abdelsattar AM, Elsayed A, El-Esawi MA, Heikal YM. Enhancing Stevia rebaudiana growth and yield through exploring beneficial plant-microbe interactions and their impact on the underlying mechanisms and crop sustainability. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 198:107673. [PMID: 37030249 DOI: 10.1016/j.plaphy.2023.107673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 03/22/2023] [Accepted: 03/27/2023] [Indexed: 05/07/2023]
Abstract
Stevia rebaudiana is an important medicinal plant which represents the most important sugar substitute in many countries. Poor seed germination of this plant is a critical problem that affects the final yield and the availability of the products in the market. Continuous cropping without supplying soil nutrients is also a serious issue as it results in declining soil fertility. This review highlights the important use of beneficial bacteria for the enhancement of Stevia rebaudiana growth and its dynamic interactions in the phyllosphere, rhizosphere, and endosphere. Fertilizers can increase crop yield and preserve and improve soil fertility. There is a rising concern that prolonged usage of chemical fertilizers may have negative impacts on the ecosystem of the soil. On the other hand, soil health and fertility are improved by plant growth-promoting bacteria which could eventually increase plant growth and productivity. Accordingly, a biocompatible strategy involving beneficial microorganisms inoculation is applied to boost plant growth and reduce the negative effects of chemical fertilizers. Plants benefit extensively from endophytic bacteria, which promote growth and induce resistance to pathogens and stresses. Additionally, several plant growth-promoting bacteria are able to produce amino acids, polyamines, and hormones that can be used as alternatives to chemicals. Therefore, understanding the dynamic interactions between bacteria and Stevia can help make the favorable bacterial bio-formulations, use them more effectively, and apply them to Stevia to improve yield and quality.
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Affiliation(s)
- Amal M Abdelsattar
- Botany Department, Faculty of Science, Mansoura University, 35516, Mansoura, Egypt.
| | - Ashraf Elsayed
- Botany Department, Faculty of Science, Mansoura University, 35516, Mansoura, Egypt
| | - Mohamed A El-Esawi
- Botany Department, Faculty of Science, Tanta University, 31527, Tanta, Egypt; Photobiology Research Group, Sorbonne Université CNRS, 75005, Paris, France
| | - Yasmin M Heikal
- Botany Department, Faculty of Science, Mansoura University, 35516, Mansoura, Egypt
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Wicaksono WA, Morauf C, Müller H, Abdelfattah A, Donat C, Berg G. The mature phyllosphere microbiome of grapevine is associated with resistance against Plasmopara viticola. Front Microbiol 2023; 14:1149307. [PMID: 37113228 PMCID: PMC10127535 DOI: 10.3389/fmicb.2023.1149307] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Accepted: 03/15/2023] [Indexed: 04/29/2023] Open
Abstract
Phyllosphere microbiota represents a substantial but hardly explored reservoir for disease resistance mechanisms. The goal of our study was to understand the link between grapevine cultivars susceptibility to Plasmopara viticola, one of the most devastating leaf pathogens in viticulture, and the phyllosphere microbiota. Therefore, we analyzed a 16S rRNA gene library for the dominant phyllosphere bacterial phyla Alphaproteobacteria of seven Vitis genotypes at different developmental stages, i.e., flowering and harvesting, via amplicon sequencing. Young leaves had significantly higher Alphaproteobacterial richness and diversity without significant host-specificity. In contrast, the microbial communities of mature leaves were structurally distinct in accordance with P. viticola resistance levels. This statistically significant link between mature bacterial phyllosphere communities and resistant phenotypes was corroborated by beta diversity metrics and network analysis. Beyond direct host-driven effects via the provision of microhabitats, we found evidence that plants recruit for specific bacterial taxa that were likely playing a fundamental role in mediating microbe-microbe interactions and structuring clusters within mature communities. Our results on grape-microbiota interaction provide insights for targeted biocontrol and breeding strategies.
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Affiliation(s)
- Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
| | | | - Henry Müller
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Ahmed Abdelfattah
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | | | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Austrian Centre of Industrial Biotechnology (ACIB GmbH), Graz, Austria
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Ayilara MS, Adeleke BS, Babalola OO. Bioprospecting and Challenges of Plant Microbiome Research for Sustainable Agriculture, a Review on Soybean Endophytic Bacteria. MICROBIAL ECOLOGY 2023; 85:1113-1135. [PMID: 36319743 PMCID: PMC10156819 DOI: 10.1007/s00248-022-02136-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 10/24/2022] [Indexed: 05/04/2023]
Abstract
This review evaluates oilseed crop soybean endophytic bacteria, their prospects, and challenges for sustainable agriculture. Soybean is one of the most important oilseed crops with about 20-25% protein content and 20% edible oil production. The ability of soybean root-associated microbes to restore soil nutrients enhances crop yield. Naturally, the soybean root endosphere harbors root nodule bacteria, and endophytic bacteria, which help increase the nitrogen pool and reclamation of another nutrient loss in the soil for plant nutrition. Endophytic bacteria can sustain plant growth and health by exhibiting antibiosis against phytopathogens, production of enzymes, phytohormone biosynthesis, organic acids, and secondary metabolite secretions. Considerable effort in the agricultural industry is focused on multifunctional concepts and bioprospecting on the use of bioinput from endophytic microbes to ensure a stable ecosystem. Bioprospecting in the case of this review is a systemic overview of the biorational approach to harness beneficial plant-associated microbes to ensure food security in the future. Progress in this endeavor is limited by available techniques. The use of molecular techniques in unraveling the functions of soybean endophytic bacteria can explore their use in integrated organic farming. Our review brings to light the endophytic microbial dynamics of soybeans and current status of plant microbiome research for sustainable agriculture.
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Affiliation(s)
- Modupe Stella Ayilara
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
| | - Bartholomew Saanu Adeleke
- Department of Biological Sciences, Microbiology Unit, Faculty of Science, Olusegun Agagu University of Science and Technology, PMB 353, Okitipupa, Nigeria
| | - Olubukola Oluranti Babalola
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
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Zhang J, Liu W, Bu J, Lin Y, Bai Y. Host genetics regulate the plant microbiome. Curr Opin Microbiol 2023; 72:102268. [PMID: 36708613 DOI: 10.1016/j.mib.2023.102268] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 12/20/2022] [Accepted: 01/05/2023] [Indexed: 01/27/2023]
Abstract
Plants recruit a taxonomically diverse microbial community, collectively termed the plant microbiome, that includes mutualists, pathogens, and commensals. These myriad microorganisms are robustly intertwined with their hosts and can determine plant fate by influencing fitness and growth or offering protection from detrimental bacteria, fungi, and herbivores. Recent studies have revealed significant effects of host genome diversity on plant-microbiome assembly and how host genetics determine microbiome composition, which is crucial for beneficial functions. The few host loci identified through genome-wide association studies suggest that genes involved in plant development, immunity, nutrient uptake, and root exudates regulate plant-microbiome community structure. Elucidating the role of host genetics in plant-microbiome assembly is key to understanding how plant-microbiome interactions are evolving and how to unlock the breeding and engineering potential of the microbiome for sustainable agriculture.
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Affiliation(s)
- Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Weidong Liu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Jingshu Bu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China; College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yanbing Lin
- College of Life Sciences, Northwest A&F University, 712100 Shaanxi, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China; CAS center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, 100049 Beijing, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China.
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Lan G, Wei Y, Li Y, Wu Z. Diversity and assembly of root-associated microbiomes of rubber trees. FRONTIERS IN PLANT SCIENCE 2023; 14:1136418. [PMID: 37063173 PMCID: PMC10102524 DOI: 10.3389/fpls.2023.1136418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION Understanding the diversity and assembly of the microbiomes of plant roots is crucial to manipulate them for sustainable ecosystem functioning. However, there are few reports about microbial communities at a continuous fine-scale of roots for rubber trees. METHODS We investigate the structure, diversity, and assembly of bacterial and fungal communities for the soil (non-rhizosphere), rhizosphere, and rhizoplane as well as root endosphere of rubber trees using the amplicon sequencing of 16S ribosomal ribonucleic acid (rRNA) and Internally Transcribed Spacer (ITS) genes. RESULTS We show that 18.69% of bacterial and 20.20% of fungal operational taxonomic units (OTUs) in the rhizoplane derived from the endosphere and 20.64% of bacterial and 20.60% of fungal OTUs from the soil. This suggests that the rhizoplane microbial community was a mixed community of soil and endosphere microbial communities and that microorganisms can disperse bidirectionally across different compartments of the plant root. On the other hand, in the absence of an enrichment or depletion of core bacterial and fungal OTUs in the rhizosphere, little differences in microbial composition as well as a more shared microbial network structure between the soil and the rhizosphere support the theory that the rhizosphere microbial community is a subset of the soil community. A large number of functional genes (such as nitrogen fixation and nitrite reduction) and more enriched core OTUs as well as a less stable but more complex network structure were observed in the rhizoplane of rubber tree roots. This demonstrated that the rhizoplane is the most active root compartment and a hotspot for plant-soil-environment interactions. In addition, bacterial and fungal communities in the rhizoplane were more stochastic compared to the rhizosphere and soil. DISCUSSION Our study expands our understanding of root-associated microbial community structure and function, which may provide the scientific basis for sustainable agriculture through biological process management.
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Affiliation(s)
- Guoyu Lan
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
| | - Yaqing Wei
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- College of Ecology and Environment, Hainan University, Haikou, Hainan, China
| | - Yuwu Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, Shandong, China
| | - Zhixiang Wu
- Rubber Research Institute, Chinese Academy of Tropical Agricultural Sciences, Haikou, Hainan, China
- Tropical Forestry Ecology Group, Hainan Danzhou Tropical Agro-ecosystem National Observation and Research Station, Danzhou, Hainan, China
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Liu J, Zhang W, Liu Y, Zhu W, Yuan Z, Su X, Ding C. Differences in phyllosphere microbiomes among different Populus spp. in the same habitat. FRONTIERS IN PLANT SCIENCE 2023; 14:1143878. [PMID: 37063209 PMCID: PMC10098339 DOI: 10.3389/fpls.2023.1143878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
INTRODUCTION The above-ground parts of terrestrial plants are collectively known as the phyllosphere. The surface of the leaf blade is a unique and extensive habitat for microbial communities. Phyllosphere bacteria are the second most closely associated microbial group with plants after fungi and viruses, and are the most abundant, occupying a dominant position in the phyllosphere microbial community. Host species are a major factor influencing the community diversity and structure of phyllosphere microorganisms. METHODS In this study, six Populus spp. were selected for study under the same site conditions and their phyllosphere bacterial community DNA fragments were paired-end sequenced using 16S ribosomal RNA (rRNA) gene amplicon sequencing. Based on the distribution of the amplicon sequence variants (ASVs), we assessed the alpha-diversity level of each sample and further measured the differences in species abundance composition among the samples, and predicted the metabolic function of the community based on the gene sequencing results. RESULTS The results revealed that different Populus spp. under the same stand conditions resulted in different phyllosphere bacterial communities. The bacterial community structure was mainly affected by the carbon and soluble sugar content of the leaves, and the leaf nitrogen, phosphorus and carbon/nitrogen were the main factors affecting the relative abundance of phyllosphere bacteria. DISCUSSION Previous studies have shown that a large proportion of the variation in the composition of phyllosphere microbial communities was explained by the hosts themselves. In contrast, leaf-borne nutrients were an available resource for bacteria living on the leaf surface, thus influencing the community structure of phyllosphere bacteria. These were similar to the conclusions obtained in this study. This study provides theoretical support for the study of the composition and structure of phyllosphere bacterial communities in woody plants and the factors influencing them.
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Affiliation(s)
- Jiaying Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Weixi Zhang
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Yuting Liu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
| | - Wenxu Zhu
- College of Forestry, Shenyang Agriculture University, Shenyang, China
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Research Station of Liaohe-River Plain Forest Ecosystem, Chinese Forest Ecosystem Research Network (CFERN), College of Forestry, Shenyang Agricultural University, Tieling, China
| | - Zhengsai Yuan
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Xiaohua Su
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
| | - Changjun Ding
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
- Key Laboratory of Tree Breeding and Cultivation of State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, China
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Du XD, Wang J, Shen C, Wang J, Jing Z, Huang LN, Luo ZH, Ge Y. Increased Leaf Bacterial Network Complexity along the Native Plant Diversity Gradient Facilitates Plant Invasion? PLANTS (BASEL, SWITZERLAND) 2023; 12:1406. [PMID: 36987094 PMCID: PMC10052042 DOI: 10.3390/plants12061406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/28/2023] [Revised: 03/18/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Understanding the mechanisms of biological invasion is critical to biodiversity protection. Previous studies have produced inconsistent relationships between native species richness and invasibility, referred to as the invasion paradox. Although facilitative interactions among species have been proposed to explain the non-negative diversity-invasibility relationship, little is known about the facilitation of plant-associated microbes in invasions. We established a two-year field biodiversity experiment with a native plant species richness gradient (1, 2, 4, or 8 species) and analyzed the effects of community structure and network complexity of leaf bacteria on invasion success. Our results indicated a positive relationship between invasibility and network complexity of leaf bacteria of the invader. Consistent with previous studies, we also found that native plant species richness increased the leaf bacterial diversity and network complexity. Moreover, the results of the leaf bacteria community assembly of the invader suggested that the complex bacteria community resulted from higher native diversity rather than higher invader biomass. We concluded that increased leaf bacterial network complexity along the native plant diversity gradient likely facilitated plant invasion. Our findings provided evidence of a potential mechanism by which microbes may affect the plant community invasibility, hopefully helping to explain the non-negative relationship between native diversity and invasibility.
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Affiliation(s)
- Xiang-Deng Du
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiang Wang
- School of Life Science, Taizhou University, Taizhou 318000, China
| | - Congcong Shen
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jichen Wang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhongwang Jing
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li-Nan Huang
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Zhen-Hao Luo
- School of Life Sciences, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuan Ge
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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50
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Zhou R, Duan GL, García-Palacios P, Yang G, Cui HL, Yan M, Yin Y, Yi XY, Li L, Delgado-Baquerizo M, Zhu YG. Environmental factors and host genotype control foliar epiphytic microbial community of wild soybeans across China. Front Microbiol 2023; 14:1065302. [PMID: 36992926 PMCID: PMC10041966 DOI: 10.3389/fmicb.2023.1065302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 02/16/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionThe microbiome inhabiting plant leaves is critical for plant health and productivity. Wild soybean (Glycine soja), which originated in China, is the progenitor of cultivated soybean (Glycine max). So far, the community structure and assembly mechanism of phyllosphere microbial community on G. soja were poorly understood.MethodsHere, we combined a national-scale survey with high-throughput sequencing and microsatellite data to evaluate the contribution of host genotype vs. climate in explaining the foliar microbiome of G. soja, and the core foliar microbiota of G. soja were identified.ResultsOur findings revealed that both the host genotype and environmental factors (i.e., geographic location and climatic conditions) were important factors regulating foliar community assembly of G. soja. Host genotypes explained 0.4% and 3.6% variations of the foliar bacterial and fungal community composition, respectively, while environmental factors explained 25.8% and 19.9% variations, respectively. We further identified a core microbiome thriving on the foliage of all G. soja populations, including bacterial (dominated by Methylobacterium-Methylorubrum, Pantoea, Quadrisphaera, Pseudomonas, and Sphingomonas) and fungal (dominated by Cladosporium, Alternaria, and Penicillium) taxa.ConclusionOur study revealed the significant role of host genetic distance as a driver of the foliar microbiome of the wild progenitor of soya, as well as the effects of climatic changes on foliar microbiomes. These findings would increase our knowledge of assembly mechanisms in the phyllosphere of wild soybeans and suggest the potential to manage the phyllosphere of soya plantations by plant breeding and selecting specific genotypes under climate change.
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Affiliation(s)
- Rui Zhou
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Gui-Lan Duan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Pablo García-Palacios
- Instituto de Ciencias Agrarias, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | - Guang Yang
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
| | - Hui-Ling Cui
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Ming Yan
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yue Yin
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xing-Yun Yi
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Lv Li
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Manuel Delgado-Baquerizo
- Laboratorio de Biodiversidad y Funcionamiento Ecosistémico, Instituto de Recursos Naturales y Agrobiología de Sevilla (IRNAS), CSIC, Sevilla, Spain
- Unidad Asociada CSIC-UPO (BioFun), Universidad Pablo de Olavide, Sevilla, Spain
| | - Yong-Guan Zhu
- State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
- *Correspondence: Yong-Guan Zhu,
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