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Tao K, Jensen IT, Zhang S, Villa-Rodríguez E, Blahovska Z, Salomonsen CL, Martyn A, Björgvinsdóttir ÞN, Kelly S, Janss L, Glasius M, Waagepetersen R, Radutoiu S. Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly. Nat Commun 2024; 15:3436. [PMID: 38653767 DOI: 10.1038/s41467-024-47752-0] [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: 05/31/2023] [Accepted: 04/09/2024] [Indexed: 04/25/2024] Open
Abstract
Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia impacts the remaining microbiota and whether it depends on nitrogen nutrition. Here, we use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We find that Nod factors are produced by symbionts to activate Nod factor signaling in the host and that this modulates the root exudate profile and the assembly of a symbiotic root microbiota. Lotus plants with different symbiotic abilities, grown in unfertilized or nitrate-supplemented soils, display three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We find that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrate that selected bacterial genera characterizing state-dependent microbiomes have a high level of accurate prediction.
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Affiliation(s)
- Ke Tao
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ib T Jensen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Mathematical Sciences, Aalborg University, Aarhus, Denmark
| | - Sha Zhang
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Eber Villa-Rodríguez
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Zuzana Blahovska
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anna Martyn
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Department of Plant-Microbe Interactions, Max-Planck-Institute for Plant Breeding Research, Cologne, Germany
| | | | - Simon Kelly
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- Biotechnology, Lincoln Agritech, Canterbury, New Zealand
| | - Luc Janss
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, Denmark
| | | | | | - Simona Radutoiu
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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2
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Shi H, Li W, Chen H, Meng Y, Wu H, Wang J, Shen S. Synthetic Microbial Community Members Interact to Metabolize Caproic Acid to Inhibit Potato Dry Rot Disease. Int J Mol Sci 2024; 25:4437. [PMID: 38674022 PMCID: PMC11050339 DOI: 10.3390/ijms25084437] [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: 03/12/2024] [Revised: 04/07/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
The potato dry rot disease caused by Fusarium spp. seriously reduces potato yield and threatens human health. However, potential biocontrol agents cannot guarantee the stability and activity of biocontrol. Here, 18 synthetic microbial communities of different scales were constructed, and the synthetic microbial communities with the best biocontrol effect on potato dry rot disease were screened through in vitro and in vivo experiments. The results show that the synthetic community composed of Paenibacillus amylolyticus, Pseudomonas putida, Acinetobacter calcoaceticus, Serratia proteamaculans, Actinomycetia bacterium and Bacillus subtilis has the best biocontrol activity. Metabolomics results show that Serratia protoamaculans interacts with other member strains to produce caproic acid and reduce the disease index to 38.01%. Furthermore, the mycelial growth inhibition after treatment with caproic acid was 77.54%, and flow cytometry analysis showed that the living conidia rate after treatment with caproic acid was 11.2%. This study provides potential value for the application of synthetic microbial communities in potatoes, as well as the interaction mechanisms between member strains of synthetic microbial communities.
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Affiliation(s)
- Huiqin Shi
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Wei Li
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Hongyu Chen
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Yao Meng
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Huifang Wu
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Jian Wang
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
| | - Shuo Shen
- Academy of Agriculture and Forestry Sciences, Qinghai University, Xining 810016, China; (H.S.); (W.L.); (H.C.); (Y.M.); (H.W.); (J.W.)
- Key Laboratory of Potato Breeding of Qinghai Province, Xining 810016, China
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
- Key Laboratory of Qinghai Tibet Plateau Biotechnology, Ministry of Education, Xining 810016, China
- Northwest Potato Engineering Research Center, Ministry of Education, Xining 810016, China
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3
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Daniel BBJ, Steiger Y, Sintsova A, Field CM, Nguyen BD, Schubert C, Cherrak Y, Sunagawa S, Hardt WD, Vorholt JA. Assessing microbiome population dynamics using wild-type isogenic standardized hybrid (WISH)-tags. Nat Microbiol 2024; 9:1103-1116. [PMID: 38503975 PMCID: PMC10994841 DOI: 10.1038/s41564-024-01634-9] [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: 09/19/2023] [Accepted: 02/09/2024] [Indexed: 03/21/2024]
Abstract
Microbiomes feature recurrent compositional structures under given environmental conditions. However, these patterns may conceal diverse underlying population dynamics that require intrastrain resolution. Here we developed a genomic tagging system, termed wild-type isogenic standardized hybrid (WISH)-tags, that can be combined with quantitative polymerase chain reaction and next-generation sequencing for microbial strain enumeration. We experimentally validated the performance of 62 tags and showed that they can be differentiated with high precision. WISH-tags were introduced into model and non-model bacterial members of the mouse and plant microbiota. Intrastrain priority effects were tested using one species of isogenic barcoded bacteria in the murine gut and the Arabidopsis phyllosphere, both with and without microbiota context. We observed colonization resistance against late-arriving strains of Salmonella Typhimurium in the mouse gut, whereas the phyllosphere accommodated Sphingomonas latecomers in a manner proportional to their presence at the late inoculation timepoint. This demonstrates that WISH-tags are a resource for deciphering population dynamics underlying microbiome assembly across biological systems.
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Affiliation(s)
| | - Yves Steiger
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Anna Sintsova
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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4
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Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L. Data-driven prediction of colonization outcomes for complex microbial communities. Nat Commun 2024; 15:2406. [PMID: 38493186 PMCID: PMC10944475 DOI: 10.1038/s41467-024-46766-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 03/08/2024] [Indexed: 03/18/2024] Open
Abstract
Microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse mechanisms governing microbial dynamics. Here, we propose a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validate this approach using synthetic data, finding that machine learning models can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conduct colonization experiments for commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approaches can predict the colonization outcomes in experiments. Furthermore, we find that while most resident species are predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., Enterococcus faecalis inhibits the invasion of E. faecium invasion. The presented results suggest that the data-driven approaches are powerful tools to inform the ecology and management of microbial communities.
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Affiliation(s)
- Lu Wu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Xu-Wen Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Zining Tao
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- Shandong Agricultural University, Tai'an, China
| | - Tong Wang
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wenlong Zuo
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yu Zeng
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Yang-Yu Liu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Center for Artificial Intelligence and Modeling, The Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL, USA.
| | - Lei Dai
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China.
- University of Chinese Academy of Sciences, Beijing, China.
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5
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Zhao P, Hong S, Li Y, Chen H, Gao H, Wang C. From phyllosphere to insect cuticles: silkworms gather antifungal bacteria from mulberry leaves to battle fungal parasite attacks. MICROBIOME 2024; 12:40. [PMID: 38409012 PMCID: PMC10895815 DOI: 10.1186/s40168-024-01764-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 01/11/2024] [Indexed: 02/28/2024]
Abstract
BACKGROUND Bacterial transfers from plants to insect herbivore guts have been well investigated. However, bacterial exchanges between plant phyllospheres and insect cuticles remain unclear, as does their related biological function. RESULTS Here, we report that the cuticular bacterial loads of silkworm larvae quickly increased after molting and feeding on the white mulberry (Morus alba) leaves. The isolation and examination of silkworm cuticular bacteria identified one bacterium Mammaliicoccus sciuri that could completely inhibit the spore germination of fungal entomopathogens Metarhizium robertsii and Beauveria bassiana. Interestingly, Ma. sciuri was evident originally from mulberry leaves, which could produce a secreted chitinolytic lysozyme (termed Msp1) to damage fungal cell walls. In consistency, the deletion of Msp1 substantially impaired bacterial antifungal activity. Pretreating silkworm larvae with Ma. sciuri cells followed by fungal topical infections revealed that this bacterium could help defend silkworms against fungal infections. Unsurprisingly, the protective efficacy of ΔMsp1 was considerably reduced when compared with that of wild-type bacterium. Administration of bacterium-treated diets had no negative effect on silkworm development; instead, bacterial supplementation could protect the artificial diet from Aspergillus contamination. CONCLUSIONS The results of this study evidence that the cross-kingdom transfer of bacteria from plant phyllospheres to insect herbivore cuticles can help protect insects against fungal parasite attacks. Video Abstract.
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Affiliation(s)
- Pengfei Zhao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Song Hong
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yuekun Li
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haimin Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Hanchun Gao
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
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Cui Y, Zhao H, Zhang C. Zinc oxide nanoparticles enhance plasmid transfer among growth-promoting endophytes in Arabidopsis thaliana. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169682. [PMID: 38163607 DOI: 10.1016/j.scitotenv.2023.169682] [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: 11/19/2023] [Revised: 12/23/2023] [Accepted: 12/23/2023] [Indexed: 01/03/2024]
Abstract
Nanoparticles (NPs) hold great promise for agricultural applications, yet their potential impact on exogenous gene transfer within plant remains poorly understood. In this study, we utilized the non-conjugative plasmid pCAMBIA1300, harboring the bialaphos resistance (bar) gene expressed in plant and the kanamycin resistance (kanR) gene as selectable marker in bacteria. Our results revealed a significant increase in the transfer of plasmid (via carrier Escherichia coli DH5α), both intra- and inter-species within the endophyte, when Arabidopsis thaliana was exposed to environmentally relevant level of zinc oxide (ZnO) NPs at a concentration of 0.7 μg/mL throughout its lifespan. Intriguingly, the plasmid exhibited selective transfer to growth-promoting endophytes, such as Enterobacter, Serratia, and Achromobacter, with the presence of ZnO NPs expanding the pool of potential recipients. This result is due to the facilitation of an endophytic and mutualistic lifestyle of invasive E. coli DH5α and the enrichment of beneficial bacteria aided by ZnO NPs. The plant's descendant generations did not express the bar gene, and the endophytes carrying the exogenous plasmid did not transmit it to sub sequent generation. This research provides crucial insights for assessing the potential risks associated with gene contamination and ensuring the safe and sustainable use of NPs in agriculture.
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Affiliation(s)
- Yueting Cui
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Huiru Zhao
- School of Environment, Beijing Normal University, Beijing 100857, China
| | - Chengdong Zhang
- School of Environment, Beijing Normal University, Beijing 100857, China.
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7
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Rangel LI, Leveau JHJ. Applied microbiology of the phyllosphere. Appl Microbiol Biotechnol 2024; 108:211. [PMID: 38358509 PMCID: PMC10869387 DOI: 10.1007/s00253-024-13042-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 01/24/2024] [Accepted: 01/29/2024] [Indexed: 02/16/2024]
Abstract
The phyllosphere, or plant leaf surface, represents a microbial ecosystem of considerable size, holding extraordinary biodiversity and enormous potential for the discovery of new products, tools, and applications in biotechnology, agriculture, medicine, and elsewhere. This mini-review highlights the applied microbiology of the phyllosphere as an original field of study concerning itself with the genes, gene products, natural compounds, and traits that underlie phyllosphere-specific adaptations and services that have commercial and economic value for current or future innovation. Examples include plant-growth-promoting and disease-suppressive phyllobacteria, probiotics and fermented foods that support human health, as well as microbials that remedy foliar contamination with airborne pollutants, residual pesticides, or plastics. Phyllosphere microbes promote plant biomass conversion into compost, renewable energy, animal feed, or fiber. They produce foodstuffs such as thickening agents and sugar substitutes, industrial-grade biosurfactants, novel antibiotics and cancer drugs, as well as enzymes used as food additives or freezing agents. Furthermore, new developments in DNA sequence-based profiling of leaf-associated microbial communities allow for surveillance approaches in the context of food safety and security, for example, to detect enteric human pathogens on leafy greens, predict plant disease outbreaks, and intercept plant pathogens and pests on internationally traded goods. KEY POINTS: • Applied phyllosphere microbiology concerns leaf-specific adaptations for economic value • Phyllobioprospecting searches the phyllosphere microbiome for product development • Phyllobiomonitoring tracks phyllosphere microbial profiles for early risk detection.
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Affiliation(s)
- Lorena I Rangel
- Cell & Molecular Sciences, The James Hutton Institute, Dundee, Scotland, UK.
- Department of Plant Pathology, University of California, Davis, CA, USA.
| | - Johan H J Leveau
- Department of Plant Pathology, University of California, Davis, CA, USA.
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8
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Thomas GA, Paradell Gil T, Müller CT, Rogers HJ, Berger CN. From field to plate: How do bacterial enteric pathogens interact with ready-to-eat fruit and vegetables, causing disease outbreaks? Food Microbiol 2024; 117:104389. [PMID: 37919001 DOI: 10.1016/j.fm.2023.104389] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/11/2023] [Accepted: 09/17/2023] [Indexed: 11/04/2023]
Abstract
Ready-to-eat fruit and vegetables are a convenient source of nutrients and fibre for consumers, and are generally safe to eat, but are vulnerable to contamination with human enteric bacterial pathogens. Over the last decade, Salmonella spp., pathogenic Escherichia coli, and Listeria monocytogenes have been linked to most of the bacterial outbreaks of foodborne illness associated with fresh produce. The origins of these outbreaks have been traced to multiple sources of contamination from pre-harvest (soil, seeds, irrigation water, domestic and wild animal faecal matter) or post-harvest operations (storage, preparation and packaging). These pathogens have developed multiple processes for successful attachment, survival and colonization conferring them the ability to adapt to multiple environments. However, these processes differ across bacterial strains from the same species, and across different plant species or cultivars. In a competitive environment, additional risk factors are the plant microbiome phyllosphere and the plant responses; both factors directly modulate the survival of the pathogens on the leaf's surface. Understanding the mechanisms involved in bacterial attachment to, colonization of, and proliferation, on fresh produce and the role of the plant in resisting bacterial contamination is therefore crucial to reducing future outbreaks.
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Affiliation(s)
- Gareth A Thomas
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Teresa Paradell Gil
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Carsten T Müller
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK
| | - Cedric N Berger
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AX, UK.
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Entila F, Han X, Mine A, Schulze-Lefert P, Tsuda K. Commensal lifestyle regulated by a negative feedback loop between Arabidopsis ROS and the bacterial T2SS. Nat Commun 2024; 15:456. [PMID: 38212332 PMCID: PMC10784570 DOI: 10.1038/s41467-024-44724-2] [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: 05/09/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024] Open
Abstract
Despite the plant health-promoting effects of plant microbiota, these assemblages also comprise potentially detrimental microbes. How plant immunity controls its microbiota to promote plant health under these conditions remains largely unknown. We find that commensal bacteria isolated from healthy Arabidopsis plants trigger diverse patterns of reactive oxygen species (ROS) production dependent on the immune receptors and completely on the NADPH oxidase RBOHD that selectively inhibited specific commensals, notably Xanthomonas L148. Through random mutagenesis, we find that L148 gspE, encoding a type II secretion system (T2SS) component, is required for the damaging effects of Xanthomonas L148 on rbohD mutant plants. In planta bacterial transcriptomics reveals that RBOHD suppresses most T2SS gene expression including gspE. L148 colonization protected plants against a bacterial pathogen, when gspE was inhibited by ROS or mutation. Thus, a negative feedback loop between Arabidopsis ROS and the bacterial T2SS tames a potentially detrimental leaf commensal and turns it into a microbe beneficial to the host.
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Affiliation(s)
- Frederickson Entila
- 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, 430070, China
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, 50829, Germany
| | - Xiaowei Han
- 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, 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China
- 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, 518120, China
| | - Akira Mine
- JST PRESTO, Kawaguchi-shi, Saitama, 332-0012, Japan
- Laboratory of Plant Pathology, Graduate School of Agriculture, Kyoto University, Kyoto, 606-8502, Japan
| | - Paul Schulze-Lefert
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, 50829, Germany
| | - Kenichi Tsuda
- 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, 430070, China.
- Department of Plant Microbe Interactions, Max Planck Institute for Plant Breeding Research, Carl-von-Linne-Weg 10, Cologne, 50829, Germany.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan, 430070, China.
- 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, 518120, China.
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10
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Su P, Kang H, Peng Q, Wicaksono WA, Berg G, Liu Z, Ma J, Zhang D, Cernava T, Liu Y. Microbiome homeostasis on rice leaves is regulated by a precursor molecule of lignin biosynthesis. Nat Commun 2024; 15:23. [PMID: 38167850 PMCID: PMC10762202 DOI: 10.1038/s41467-023-44335-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 12/08/2023] [Indexed: 01/05/2024] Open
Abstract
In terrestrial ecosystems, plant leaves provide the largest biological habitat for highly diverse microbial communities, known as the phyllosphere microbiota. However, the underlying mechanisms of host-driven assembly of these ubiquitous communities remain largely elusive. Here, we conduct a large-scale and in-depth assessment of the rice phyllosphere microbiome aimed at identifying specific host-microbe links. A genome-wide association study reveals a strong association between the plant genotype and members of four bacterial orders, Pseudomonadales, Burkholderiales, Enterobacterales and Xanthomonadales. Some of the associations are specific to a distinct host genomic locus, pathway or even gene. The compound 4-hydroxycinnamic acid (4-HCA) is identified as the main driver for enrichment of bacteria belonging to Pseudomonadales. 4-HCA can be synthesized by the host plant's OsPAL02 from the phenylpropanoid biosynthesis pathway. A knockout mutant of OsPAL02 results in reduced Pseudomonadales abundance, dysbiosis of the phyllosphere microbiota and consequently higher susceptibility of rice plants to disease. Our study provides a direct link between a specific plant metabolite and rice phyllosphere homeostasis opening possibilities for new breeding strategies.
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Affiliation(s)
- Pin Su
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Houxiang Kang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qianze Peng
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China
- College of Tropical Crops, Hainan University, Haikou, 570228, China
| | - Wisnu Adi Wicaksono
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
| | - Gabriele Berg
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, 14469, Germany
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, 14476, Germany
| | - Zhuoxin Liu
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Jiejia Ma
- Longping Branch, College of Biology, Hunan University, Changsha, 410082, China
| | - Deyong Zhang
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
- National Center of Technology Innovation for Saline-Alkali Tolerant Rice in Sanya City, Sanya, 572024, China.
- College of Tropical Crops, Hainan University, Haikou, 570228, China.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Graz, 8010, Austria.
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, Southampton, SO17 1BJ, UK.
| | - Yong Liu
- State Key Laboratory of Hybrid Rice and Institute of Plant Protection, Hunan Academy of Agricultural Sciences, Changsha, 410125, China.
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11
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Carper DL, Lawrence TJ, Quiroz D, Kueppers LM, Frank AC. Needle bacterial community structure across the species range of limber pine. ISME COMMUNICATIONS 2024; 4:ycae062. [PMID: 38800125 PMCID: PMC11128189 DOI: 10.1093/ismeco/ycae062] [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: 09/30/2023] [Revised: 04/12/2024] [Accepted: 04/23/2024] [Indexed: 05/29/2024]
Abstract
Bacteria on and inside leaves can influence forest tree health and resilience. The distribution and limits of a tree species' range can be influenced by various factors, with biological interactions among the most significant. We investigated the processes shaping the bacterial needle community across the species distribution of limber pine, a widespread Western conifer inhabiting a range of extreme habitats. We tested four hypotheses: (i) Needle community structure varies across sites, with site-specific factors more important to microbial assembly than host species selection; (ii) dispersal limitation structures foliar communities across the range of limber pine; (iii) the relative significance of dispersal and selection differs across sites in the tree species range; and (iv) needle age structures bacterial communities. We characterized needle communities from the needle surface and tissue of limber pine and co-occurring conifers across 16 sites in the limber pine distribution. Our findings confirmed that site characteristics shape the assembly of bacterial communities across the host species range and showed that these patterns are not driven by dispersal limitation. Furthermore, the strength of selection by the host varied by site, possibly due to differences in available microbes. Our study, by focusing on trees in their natural setting, reveals real needle bacterial dynamics in forests, which is key to understanding the balance between stochastic and deterministic processes in shaping forest tree-microbe interactions. Such understanding will be necessary to predict or manipulate these interactions to support forest ecosystem productivity or assist plant migration and adaptation in the face of global change.
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Affiliation(s)
- Dana L Carper
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
- Quantitative and Systems Biology Program, University of California, Merced, Merced, CA 95343, United States
| | - Travis J Lawrence
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37831, United States
| | - Dianne Quiroz
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
| | - Lara M Kueppers
- Energy & Resources Group, University of California, Berkeley, Berkeley, CA 94720, United States
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Climate and Ecosystem Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, United States
| | - A Carolin Frank
- Sierra Nevada Research Institute, University of California, Merced, Merced, CA 95353, United States
- Life and Environmental Sciences Department, School of Natural Sciences, University of California, Merced, 5200 Lake Rd, Merced, CA 95343, United States
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12
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Pfeilmeier S, Werz A, Ote M, Bortfeld-Miller M, Kirner P, Keppler A, Hemmerle L, Gäbelein CG, Petti GC, Wolf S, Pestalozzi CM, Vorholt JA. Leaf microbiome dysbiosis triggered by T2SS-dependent enzyme secretion from opportunistic Xanthomonas pathogens. Nat Microbiol 2024; 9:136-149. [PMID: 38172620 PMCID: PMC10769872 DOI: 10.1038/s41564-023-01555-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 11/13/2023] [Indexed: 01/05/2024]
Abstract
In healthy plants, the innate immune system contributes to maintenance of microbiota homoeostasis, while disease can be associated with microbiome perturbation or dysbiosis, and enrichment of opportunistic plant pathogens like Xanthomonas. It is currently unclear whether the microbiota change occurs independently of the opportunistic pathogens or is caused by the latter. Here we tested if protein export through the type-2 secretion system (T2SS) by Xanthomonas causes microbiome dysbiosis in Arabidopsis thaliana in immunocompromised plants. We found that Xanthomonas strains secrete a cocktail of plant cell wall-degrading enzymes that promote Xanthomonas growth during infection. Disease severity and leaf tissue degradation were increased in A. thaliana mutants lacking the NADPH oxidase RBOHD. Experiments with gnotobiotic plants, synthetic bacterial communities and wild-type or T2SS-mutant Xanthomonas revealed that virulence and leaf microbiome composition are controlled by the T2SS. Overall, a compromised immune system in plants can enrich opportunistic pathogens, which damage leaf tissues and ultimately cause microbiome dysbiosis by facilitating growth of specific commensal bacteria.
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Affiliation(s)
- Sebastian Pfeilmeier
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
- Molecular Plant Pathology, Swammerdam Institute of Life Sciences, University of Amsterdam, Amsterdam, the Netherlands.
| | - Anja Werz
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Marine Ote
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Pascal Kirner
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | - Lucas Hemmerle
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | | | - Sarah Wolf
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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13
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Jian Y, Gong D, Wang Z, Liu L, He J, Han X, Tsuda K. How plants manage pathogen infection. EMBO Rep 2024; 25:31-44. [PMID: 38177909 PMCID: PMC10897293 DOI: 10.1038/s44319-023-00023-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/27/2023] [Accepted: 11/27/2023] [Indexed: 01/06/2024] Open
Abstract
To combat microbial pathogens, plants have evolved specific immune responses that can be divided into three essential steps: microbial recognition by immune receptors, signal transduction within plant cells, and immune execution directly suppressing pathogens. During the past three decades, many plant immune receptors and signaling components and their mode of action have been revealed, markedly advancing our understanding of the first two steps. Activation of immune signaling results in physical and chemical actions that actually stop pathogen infection. Nevertheless, this third step of plant immunity is under explored. In addition to immune execution by plants, recent evidence suggests that the plant microbiota, which is considered an additional layer of the plant immune system, also plays a critical role in direct pathogen suppression. In this review, we summarize the current understanding of how plant immunity as well as microbiota control pathogen growth and behavior and highlight outstanding questions that need to be answered.
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Affiliation(s)
- Yinan Jian
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Dianming Gong
- National Key Laboratory of Crop Genetic Improvement, Hubei Hongshan Laboratory, Huazhong Agricultural University, 430070, Wuhan, China
| | - Zhe Wang
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Lijun Liu
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Jingjing He
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Xiaowei Han
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Kenichi Tsuda
- National Key Laboratory of Agricultural Microbiology, Hubei Hongshan Laboratory, Hubei Key Laboratory of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China.
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, 430070, Wuhan, China.
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China.
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14
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Emmenegger B, Massoni J, Pestalozzi CM, Bortfeld-Miller M, Maier BA, Vorholt JA. Identifying microbiota community patterns important for plant protection using synthetic communities and machine learning. Nat Commun 2023; 14:7983. [PMID: 38042924 PMCID: PMC10693592 DOI: 10.1038/s41467-023-43793-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 11/20/2023] [Indexed: 12/04/2023] Open
Abstract
Plant-associated microbiomes contribute to important ecosystem functions such as host resistance to biotic and abiotic stresses. The factors that determine such community outcomes are inherently difficult to identify under complex environmental conditions. In this study, we present an experimental and analytical approach to explore microbiota properties relevant for a microbiota-conferred host phenotype, here plant protection, in a reductionist system. We screened 136 randomly assembled synthetic communities (SynComs) of five bacterial strains each, followed by classification and regression analyses as well as empirical validation to test potential explanatory factors of community structure and composition, including evenness, total commensal colonization, phylogenetic diversity, and strain identity. We find strain identity to be the most important predictor of pathogen reduction, with machine learning algorithms improving performances compared to random classifications (94-100% versus 32% recall) and non-modelled predictions (0.79-1.06 versus 1.5 RMSE). Further experimental validation confirms three strains as the main drivers of pathogen reduction and two additional strains that confer protection in combination. Beyond the specific application presented in our study, we provide a framework that can be adapted to help determine features relevant for microbiota function in other biological systems.
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Affiliation(s)
| | - Julien Massoni
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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15
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Wang X, Zhang J, Lu X, Bai Y, Wang G. Two diversities meet in the rhizosphere: root specialized metabolites and microbiome. J Genet Genomics 2023:S1673-8527(23)00212-6. [PMID: 37879496 DOI: 10.1016/j.jgg.2023.10.004] [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: 06/15/2023] [Revised: 10/15/2023] [Accepted: 10/15/2023] [Indexed: 10/27/2023]
Abstract
Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites (SMs). These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.
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Affiliation(s)
- Xiaochen Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Jingying Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Xinjun Lu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China
| | - Yang Bai
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan 572025, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
| | - Guodong Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, The Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agricultural Sciences, Chinese Academy of Sciences, Beijing 100049, China.
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16
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Russ D, Fitzpatrick CR, Teixeira PJPL, Dangl JL. Deep discovery informs difficult deployment in plant microbiome science. Cell 2023; 186:4496-4513. [PMID: 37832524 DOI: 10.1016/j.cell.2023.08.035] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 08/28/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023]
Abstract
Plant-associated microbiota can extend plant immune system function, improve nutrient acquisition and availability, and alleviate abiotic stresses. Thus, naturally beneficial microbial therapeutics are enticing tools to improve plant productivity. The basic definition of plant microbiota across species and ecosystems, combined with the development of reductionist experimental models and the manipulation of plant phenotypes with microbes, has fueled interest in its translation to agriculture. However, the great majority of microbes exhibiting plant-productivity traits in the lab and greenhouse fail in the field. Therapeutic microbes must reach détente, the establishment of uneasy homeostasis, with the plant immune system, invade heterogeneous pre-established plant-associated communities, and persist in a new and potentially remodeled community. Environmental conditions can alter community structure and thus impact the engraftment of therapeutic microbes. We survey recent breakthroughs, challenges, and opportunities in translating beneficial microbes from the lab to the field.
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Affiliation(s)
- Dor Russ
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Connor R Fitzpatrick
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Jeffery L Dangl
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Howard Hughes Medical Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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17
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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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18
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Beiralas R, Ozer N, Segev E. Abundant Sulfitobacter marine bacteria protect Emiliania huxleyi algae from pathogenic bacteria. ISME COMMUNICATIONS 2023; 3:100. [PMID: 37740057 PMCID: PMC10517135 DOI: 10.1038/s43705-023-00311-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 09/10/2023] [Accepted: 09/13/2023] [Indexed: 09/24/2023]
Abstract
Emiliania huxleyi is a unicellular micro-alga that forms massive oceanic blooms and plays key roles in global biogeochemical cycles. Mounting studies demonstrate various stimulatory and inhibitory influences that bacteria have on the E. huxleyi physiology. To investigate these algal-bacterial interactions, laboratory co-cultures have been established by us and by others. Owing to these co-cultures, various mechanisms of algal-bacterial interactions have been revealed, many involving bacterial pathogenicity towards algae. However, co-cultures represent a significantly simplified system, lacking the complexity of bacterial communities. In order to investigate bacterial pathogenicity within an ecologically relevant context, it becomes imperative to enhance the microbial complexity of co-culture setups. Phaeobacter inhibens bacteria are known pathogens that cause the death of E. huxleyi algae in laboratory co-culture systems. The bacteria depend on algal exudates for growth, but when algae senesce, bacteria switch to a pathogenic state and induce algal death. Here we investigate whether P. inhibens bacteria can induce algal death in the presence of a complex bacterial community. We show that an E. huxleyi-associated bacterial community protects the alga from the pathogen, although the pathogen occurs within the community. To study how the bacterial community regulates pathogenicity, we reduced the complex bacterial community to a five-member synthetic community (syncom). The syncom is comprised of a single algal host and five isolated bacterial species, which represent major bacterial groups that are naturally associated with E. huxleyi. We discovered that a single bacterial species in the reduced community, Sulfitobacter pontiacus, protects the alga from the pathogen. We further found that algal protection from P. inhibens pathogenicity is a shared trait among several Sulfitobacter species. Algal protection by bacteria might be a common phenomenon with ecological significance, which is overlooked in reduced co-culture systems.
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Affiliation(s)
- Roni Beiralas
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Noy Ozer
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel
| | - Einat Segev
- Department of Plant and Environmental Sciences, The Weizmann Institute of Science, Rehovot, Israel.
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19
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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: 6] [Impact Index Per Article: 6.0] [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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20
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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: 1] [Impact Index Per Article: 1.0] [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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21
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Janda M, Rybak K, Krassini L, Meng C, Feitosa-Junior O, Stigliano E, Szulc B, Sklenar J, Menke FL, Malone JG, Brachmann A, Klingl A, Ludwig C, Robatzek S. Biophysical and proteomic analyses of Pseudomonas syringae pv. tomato DC3000 extracellular vesicles suggest adaptive functions during plant infection. mBio 2023; 14:e0358922. [PMID: 37366628 PMCID: PMC10470744 DOI: 10.1128/mbio.03589-22] [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: 01/06/2023] [Accepted: 05/03/2023] [Indexed: 06/28/2023] Open
Abstract
Vesiculation is a process employed by Gram-negative bacteria to release extracellular vesicles (EVs) into the environment. EVs from pathogenic bacteria play functions in host immune modulation, elimination of host defenses, and acquisition of nutrients from the host. Here, we observed EV production of the bacterial speck disease causal agent, Pseudomonas syringae pv. tomato (Pto) DC3000, as outer membrane vesicle release. Mass spectrometry identified 369 proteins enriched in Pto DC3000 EVs. The EV samples contained known immunomodulatory proteins and could induce plant immune responses mediated by bacterial flagellin. Having identified two biomarkers for EV detection, we provide evidence for Pto DC3000 releasing EVs during plant infection. Bioinformatic analysis of the EV-enriched proteins suggests a role for EVs in antibiotic defense and iron acquisition. Thus, our data provide insights into the strategies this pathogen may use to develop in a plant environment. IMPORTANCE The release of extracellular vesicles (EVs) into the environment is ubiquitous among bacteria. Vesiculation has been recognized as an important mechanism of bacterial pathogenesis and human disease but is poorly understood in phytopathogenic bacteria. Our research addresses the role of bacterial EVs in plant infection. In this work, we show that the causal agent of bacterial speck disease, Pseudomonas syringae pv. tomato, produces EVs during plant infection. Our data suggest that EVs may help the bacteria to adapt to environments, e.g., when iron could be limiting such as the plant apoplast, laying the foundation for studying the factors that phytopathogenic bacteria use to thrive in the plant environment.
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Affiliation(s)
- Martin Janda
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
- Department of Biochemistry and Microbiology, University of Chemistry and Technology Prague, Prague, Czechia
- Faculty of Science, University of South Bohemia in České Budějovice, České Budějovice, Czechia
| | - Katarzyna Rybak
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Laura Krassini
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Chen Meng
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Strasse, Freising, United Kingdom
| | | | - Egidio Stigliano
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
| | - Beata Szulc
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Jan Sklenar
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Frank L.H. Menke
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
| | - Jacob G. Malone
- John Innes Centre, Norwich Research Park, Norwich, United Kingdom
- University of East Anglia, Norwich Research Park, Norwich, United Kingdom
| | - Andreas Brachmann
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Andreas Klingl
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
| | - Christina Ludwig
- Bavarian Center for Biomolecular Mass Spectrometry (BayBioMS), Technical University of Munich, Gregor-Mendel-Strasse, Freising, United Kingdom
| | - Silke Robatzek
- LMU Munich Biocenter, Ludwig-Maximilian-University of Munich, Munich, Germany
- The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom
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22
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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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23
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Thomazella DPDT, Teixeira PJPL. Microbiome-mediated metabolic defence. NATURE PLANTS 2023; 9:1174-1175. [PMID: 37433973 DOI: 10.1038/s41477-023-01470-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/13/2023]
Affiliation(s)
| | - Paulo José Pereira Lima Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, Brazil.
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24
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Sun Y, Zheng C, Zhou J, Zhen M, Wei X, Yan X, Guo X, Zheng L, Shao M, Li C, Qin D, Zhang J, Xiong L, Xing J, Huang B, Dong Z, Cheng P, Yu G. Pathogen Profile of Klebsiella variicola, the Causative Agent of Banana Sheath Rot. PLANT DISEASE 2023; 107:2325-2334. [PMID: 37596715 DOI: 10.1094/pdis-09-22-2018-re] [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: 08/20/2023]
Abstract
Banana (Musa spp.) is an important fruit and food crop worldwide. In recent years, banana sheath rot has become a major problem in banana cultivation, causing plant death and substantial economic losses. Nevertheless, the pathogen profile of this disease has not been fully characterized. Klebsiella variicola is a versatile bacterium capable of colonizing different hosts, such as plants, humans, insects, and animals, and is recognized as an emerging pathogen in various hosts. In this study, we obtained 12 bacterial isolates from 12 different banana samples showing banana sheath rot in Guangdong and Guangxi Provinces, China. Phylogenetic analysis based on 16S rRNA sequences confirmed that all 12 isolates were K. variicola strains. We sequenced the genomes of these strains, performed comparative genomic analysis with other sequenced K. variicola strains, and found a lack of consistency in accessory gene content among these K. variicola strains. However, prediction based on the pan-genome of K. variicola revealed 22 unique virulence factors carried by the 12 pathogenic K. variicola isolates. Microbiome and microbial interaction network analysis of endophytes between the healthy tissues of diseased plants and healthy plants of two cultivars showed that Methanobacterium negatively interacts with Klebsiella in banana plants and that Herbaspirillum might indirectly inhibit Methanobacterium to promote Klebsiella growth. These results suggest that banana sheath rot is caused by the imbalance of plant endophytes and opportunistic pathogenic bacteria, providing an important basis for research and control of this disease.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Yunhao Sun
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chuanyuan Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jianuan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Center, South China Agricultural University, Guangzhou 510642, China
| | - Meng Zhen
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xingying Wei
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xun Yan
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Xiaojian Guo
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Li Zheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Mingwei Shao
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Chunji Li
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Di Qin
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Jie Zhang
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Resources and Environment, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Lina Xiong
- School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, China
| | - Juejun Xing
- Laboratory and Equipment Management Department, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Bingzhi Huang
- Institute of Fruit Tree Research, Guangdong Academy of Agricultural Sciences, Guangzhou 510000, China
| | - Zhangyong Dong
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
| | - Ping Cheng
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
| | - Guohui Yu
- Innovative Institute for Plant Health, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
- Key Laboratory of Green Prevention and Control on Fruits and Vegetables in South China, Ministry of Agriculture and Rural Affairs, Beijing, China
- Guangdong University Key Laboratory for Sustainable Control of Fruit and Vegetable Diseases and Pests, Guangzhou 510225, China
- College of Agriculture and Biology, Zhongkai University of Agriculture and Engineering, Guangzhou 510225, China
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25
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Zhu Q, Fei YJ, Wu YB, Luo DL, Chen M, Sun K, Zhang W, Dai CC. Endophytic Fungus Reshapes Spikelet Microbiome to Reduce Mycotoxin Produced by Fusarium proliferatum through Altering Rice Metabolites. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023. [PMID: 37466504 DOI: 10.1021/acs.jafc.3c02616] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2023]
Abstract
Rice spikelet rot disease (RSRD) caused by Fusarium proliferatum seriously reduces rice yield and produces mycotoxins that threaten human health. The root symbiotic endophytic fungus Phomopsis liquidambaris reduces RSRD incidence and fumonisins accumulation in grain by 21.5 and 9.3%, respectively, while the mechanism of disease resistance remains largely elusive. Here, we found that B3 significantly reduced the abundance of pathogen from 79.91 to 2.84% and considerably enriched resistant microbes Pseudomonas and Proteobacteria in the spikelet microbial community. Further study revealed that B3 altered the metabolites of spikelets, especially hordenine and l-aspartic acid, which played a key role in reshaping the microbiome and supporting the growth of the functional core microbe Pseudomonas, and inhibited the pathogen growth and mycotoxin production. This study provided a feasibility of regulating the function of aboveground microbial communities by manipulating plant subsurface tissues to control disease and mycotoxin pollutants in agricultural production.
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Affiliation(s)
- Qiang Zhu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yan-Jun Fei
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Yi-Bo Wu
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - De-Lin Luo
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Man Chen
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Kai Sun
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Wei Zhang
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
| | - Chuan-Chao Dai
- Jiangsu Key Laboratory for Microbes and Functional Genomics, Jiangsu Engineering and Technology Research Center for Industrialization of Microbial Resources, College of Life Sciences, Nanjing Normal University, Nanjing, Jiangsu 210023, China
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26
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Schäfer M, Pacheco AR, Künzler R, Bortfeld-Miller M, Field CM, Vayena E, Hatzimanikatis V, Vorholt JA. Metabolic interaction models recapitulate leaf microbiota ecology. Science 2023; 381:eadf5121. [PMID: 37410834 DOI: 10.1126/science.adf5121] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Accepted: 05/18/2023] [Indexed: 07/08/2023]
Abstract
Resource allocation affects the structure of microbiomes, including those associated with living hosts. Understanding the degree to which this dependency determines interspecies interactions may advance efforts to control host-microbiome relationships. We combined synthetic community experiments with computational models to predict interaction outcomes between plant-associated bacteria. We mapped the metabolic capabilities of 224 leaf isolates from Arabidopsis thaliana by assessing the growth of each strain on 45 environmentally relevant carbon sources in vitro. We used these data to build curated genome-scale metabolic models for all strains, which we combined to simulate >17,500 interactions. The models recapitulated outcomes observed in planta with >89% accuracy, highlighting the role of carbon utilization and the contributions of niche partitioning and cross-feeding in the assembly of leaf microbiomes.
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Affiliation(s)
- Martin Schäfer
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Alan R Pacheco
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | - Rahel Künzler
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
| | | | | | - Evangelia Vayena
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
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27
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Kaneko H, Miyata F, Kurokawa M, Hashimoto K, Kuchitsu K, Furuya T. Diversity and characteristics of plant immunity-activating bacteria from Brassicaceae plants. BMC Microbiol 2023; 23:175. [PMID: 37407947 DOI: 10.1186/s12866-023-02920-y] [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: 03/23/2023] [Accepted: 06/28/2023] [Indexed: 07/07/2023] Open
Abstract
BACKGROUND Microorganisms that activate plant immune responses are useful for application as biocontrol agents in agriculture to minimize crop losses. The present study was conducted to identify and characterize plant immunity-activating microorganisms in Brassicaceae plants. RESULTS A total of 25 bacterial strains were isolated from the interior of a Brassicaceae plant, Raphanus sativus var. hortensis. Ten different genera of bacteria were identified: Pseudomonas, Leclercia, Enterobacter, Xanthomonas, Rhizobium, Agrobacterium, Pantoea, Rhodococcus, Microbacterium, and Plantibacter. The isolated strains were analyzed using a method to detect plant immunity-activating microorganisms that involves incubation of the microorganism with tobacco BY-2 cells, followed by treatment with cryptogein, a proteinaceous elicitor of tobacco immune responses. In this method, cryptogein-induced production of reactive oxygen species (ROS) in BY-2 cells serves as a marker of immune activation. Among the 25 strains examined, 6 strains markedly enhanced cryptogein-induced ROS production in BY-2 cells. These 6 strains colonized the interior of Arabidopsis plants, and Pseudomonas sp. RS3R-1 and Rhodococcus sp. RS1R-6 selectively enhanced plant resistance to the bacterial pathogens Pseudomonas syringae pv. tomato DC3000 and Pectobacterium carotovorum subsp. carotovorum NBRC 14082, respectively. In addition, Pseudomonas sp. RS1P-1 effectively enhanced resistance to both pathogens. We also comprehensively investigated the localization (i.e., cellular or extracellular) of the plant immunity-activating components produced by the bacteria derived from R. sativus var. hortensis and the components produced by previously isolated bacteria derived from another Brassicaceae plant species, Brassica rapa var. perviridis. Most gram-negative strains enhanced cryptogein-induced ROS production in BY-2 cells via the presence of cells themselves rather than via extracellular components, whereas many gram-positive strains enhanced ROS production via extracellular components. Comparative genomic analyses supported the hypothesis that the structure of lipopolysaccharides in the outer cell envelope plays an important role in the ROS-enhancing activity of gram-negative Pseudomonas strains. CONCLUSIONS The assay method described here based on elicitor-induced ROS production in cultured plant cells enabled the discovery of novel plant immunity-activating bacteria from R. sativus var. hortensis. The results in this study also suggest that components involved in the ROS-enhancing activity of the bacteria may differ depending largely on genus and species.
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Affiliation(s)
- Hiroki Kaneko
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan
| | - Fuma Miyata
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan
| | - Mari Kurokawa
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan
| | - Kenji Hashimoto
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan
| | - Kazuyuki Kuchitsu
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan
| | - Toshiki Furuya
- Department of Applied Biological Science, Faculty of Science and Technology, Tokyo University of Science, Yamazaki, Noda, 2641, 278-8510, Chiba, Japan.
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28
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González-García MP, Conesa CM, Lozano-Enguita A, Baca-González V, Simancas B, Navarro-Neila S, Sánchez-Bermúdez M, Salas-González I, Caro E, Castrillo G, Del Pozo JC. Temperature changes in the root ecosystem affect plant functionality. PLANT COMMUNICATIONS 2023; 4:100514. [PMID: 36585788 DOI: 10.1016/j.xplc.2022.100514] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Revised: 12/22/2022] [Accepted: 12/29/2022] [Indexed: 05/11/2023]
Abstract
Climate change is increasing the frequency of extreme heat events that aggravate its negative impact on plant development and agricultural yield. Most experiments designed to study plant adaption to heat stress apply homogeneous high temperatures to both shoot and root. However, this treatment does not mimic the conditions in natural fields, where roots grow in a dark environment with a descending temperature gradient. Excessively high temperatures severely decrease cell division in the root meristem, compromising root growth, while increasing the division of quiescent center cells, likely in an attempt to maintain the stem cell niche under such harsh conditions. Here, we engineered the TGRooZ, a device that generates a temperature gradient for in vitro or greenhouse growth assays. The root systems of plants exposed to high shoot temperatures but cultivated in the TGRooZ grow efficiently and maintain their functionality to sustain proper shoot growth and development. Furthermore, gene expression and rhizosphere or root microbiome composition are significantly less affected in TGRooZ-grown roots than in high-temperature-grown roots, correlating with higher root functionality. Our data indicate that use of the TGRooZ in heat-stress studies can improve our knowledge of plant response to high temperatures, demonstrating its applicability from laboratory studies to the field.
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Affiliation(s)
- Mary Paz González-García
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Carlos M Conesa
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Alberto Lozano-Enguita
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Victoria Baca-González
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Bárbara Simancas
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Sara Navarro-Neila
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - María Sánchez-Bermúdez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Isai Salas-González
- Undergraduate Program in Genomic Sciences, Center for Genomics Sciences, Universidad Nacional Autonóma de México, Av. Universidad s/n. Col. Chamilpa, Cuernavaca 62210, Morelos, México
| | - Elena Caro
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain; Departamento de Biotecnología-Biología Vegetal, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid (UPM), 28040 Madrid, Spain
| | - Gabriel Castrillo
- Future Food Beacon of Excellence & School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | - Juan C Del Pozo
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA/CSIC), Universidad Politécnica de Madrid (UPM) - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria-CSIC (INIA/CSIC), Campus Montegancedo, 28223 Pozuelo de Alarcón (Madrid), Spain.
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De Sousa BFS, Domingo-Serrano L, Salinero-Lanzarote A, Palacios JM, Rey L. The T6SS-Dependent Effector Re78 of Rhizobium etli Mim1 Benefits Bacterial Competition. BIOLOGY 2023; 12:678. [PMID: 37237492 PMCID: PMC10215855 DOI: 10.3390/biology12050678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/26/2023] [Accepted: 05/02/2023] [Indexed: 05/28/2023]
Abstract
The genes of the type VI secretion system (T6SS) from Rhizobium etli Mim1 (ReMim1) that contain possible effectors can be divided into three modules. The mutants in them indicated that they are not required for effective nodulation with beans. To analyze T6SS expression, a putative promoter region between the tssA and tssH genes was fused in both orientations to a reporter gene. Both fusions are expressed more in free living than in symbiosis. When the module-specific genes were studied using RT-qPCR, a low expression was observed in free living and in symbiosis, which was clearly lower than the structural genes. The secretion of Re78 protein from the T6SS gene cluster was dependent on the presence of an active T6SS. Furthermore, the expression of Re78 and Re79 proteins in E. coli without the ReMim1 nanosyringe revealed that these proteins behave as a toxic effector/immunity protein pair (E/I). The harmful action of Re78, whose mechanism is still unknown, would take place in the periplasmic space of the target cell. The deletion of this ReMim1 E/I pair resulted in reduced competitiveness for bean nodule occupancy and in lower survival in the presence of the wild-type strain.
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Affiliation(s)
- Bruna Fernanda Silva De Sousa
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - Lucía Domingo-Serrano
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - Alvaro Salinero-Lanzarote
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
| | - José Manuel Palacios
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
| | - Luis Rey
- Centro de Biotecnología y Genómica de Plantas, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA/CSIC), Campus de Montegancedo UPM, Universidad Politécnica de Madrid (UPM), 28223 Pozuelo de Alarcón, Spain; (B.F.S.D.S.)
- Departamento de Biotecnología y Biología Vegetal, ETSI Agronómica Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, 28040 Madrid, Spain
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30
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Wu L, Wang XW, Tao Z, Wang T, Zuo W, Zeng Y, Liu YY, Dai L. Data-driven prediction of colonization outcomes for complex microbial communities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.19.537502. [PMID: 37131715 PMCID: PMC10153232 DOI: 10.1101/2023.04.19.537502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Complex microbial interactions can lead to different colonization outcomes of exogenous species, be they pathogenic or beneficial in nature. Predicting the colonization of exogenous species in complex communities remains a fundamental challenge in microbial ecology, mainly due to our limited knowledge of the diverse physical, biochemical, and ecological processes governing microbial dynamics. Here, we proposed a data-driven approach independent of any dynamics model to predict colonization outcomes of exogenous species from the baseline compositions of microbial communities. We systematically validated this approach using synthetic data, finding that machine learning models (including Random Forest and neural ODE) can predict not only the binary colonization outcome but also the post-invasion steady-state abundance of the invading species. Then we conducted colonization experiments for two commensal gut bacteria species Enterococcus faecium and Akkermansia muciniphila in hundreds of human stool-derived in vitro microbial communities, confirming that the data-driven approach can successfully predict the colonization outcomes. Furthermore, we found that while most resident species were predicted to have a weak negative impact on the colonization of exogenous species, strongly interacting species could significantly alter the colonization outcomes, e.g., the presence of Enterococcus faecalis inhibits the invasion of E. faecium . The presented results suggest that the data-driven approach is a powerful tool to inform the ecology and management of complex microbial communities.
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31
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Pacheco AR, Vorholt JA. Resolving metabolic interaction mechanisms in plant microbiomes. Curr Opin Microbiol 2023; 74:102317. [PMID: 37062173 DOI: 10.1016/j.mib.2023.102317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 03/10/2023] [Accepted: 03/16/2023] [Indexed: 04/18/2023]
Abstract
Metabolic interactions are fundamental to the assembly and functioning of microbiomes, including those of plants. However, disentangling the molecular basis of these interactions and their specific roles remains a major challenge. Here, we review recent applications of experimental and computational methods toward the elucidation of metabolic interactions in plant-associated microbiomes. We highlight studies that span various scales of taxonomic and environmental complexity, including those that test interaction outcomes in vitro and in planta by deconstructing microbial communities. We also discuss how the continued integration of multiple methods can further reveal the general ecological characteristics of plant microbiomes, as well as provide strategies for applications in areas such as improved plant protection, bioremediation, and sustainable agriculture.
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Affiliation(s)
- Alan R Pacheco
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland.
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32
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Edwards JA, Saran UB, Bonnette J, MacQueen A, Yin J, Nguyen TU, Schmutz J, Grimwood J, Pennacchio LA, Daum C, Glavina Del Rio T, Fritschi FB, Lowry DB, Juenger TE. Genetic determinants of switchgrass-root-associated microbiota in field sites spanning its natural range. Curr Biol 2023; 33:1926-1938.e6. [PMID: 37080198 DOI: 10.1016/j.cub.2023.03.078] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 02/03/2023] [Accepted: 03/27/2023] [Indexed: 04/22/2023]
Abstract
A fundamental goal in plant microbiome research is to determine the relative impacts of host and environmental effects on root microbiota composition, particularly how host genotype impacts bacterial community composition. Most studies characterizing the effect of plant genotype on root microbiota undersample host genetic diversity and grow plants outside of their native ranges, making the associations between host and microbes difficult to interpret. Here, we characterized the root microbiota of a large diversity panel of switchgrass, a North American native C4 bioenergy crop, in three field locations spanning its native range. Our data, composed of 1,961 samples, suggest that field location is the primary determinant of microbiome composition; however, substantial heritable variation is widespread across bacterial taxa, especially those in the Sphingomonadaceae family. Despite diverse compositions, relatively few highly prevalent taxa make up the majority of the switchgrass root microbiota, a large fraction of which is shared across sites. Local genotypes preferentially recruit/filter for local microbes, supporting the idea of affinity between local plants and their microbiota. Using genome-wide association, we identified loci impacting the abundance of >400 microbial strains and found an enrichment of genes involved in immune responses, signaling pathways, and secondary metabolism. We found loci associated with over half of the core microbiota (i.e., microbes in >80% of samples), regardless of field location. Finally, we show a genetic relationship between a basal plant immunity pathway and relative abundances of root microbiota. This study brings us closer to harnessing and manipulating beneficial microbial associations via host genetics.
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Affiliation(s)
- Joseph A Edwards
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
| | - Usha Bishnoi Saran
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jason Bonnette
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Alice MacQueen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jun Yin
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Tu Uyen Nguyen
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Jeremy Schmutz
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA; Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Jane Grimwood
- Genome Sequencing Center, HudsonAlpha Institute for Biotechnology, 601 Genome Way Northwest, Huntsville, AL 35806, USA
| | - Len A Pennacchio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Chris Daum
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Tijana Glavina Del Rio
- Joint Genome Institute, Lawrence Berkeley National Laboratory, 91R183 1 Cyclotron Road, Berkeley, CA 94720, USA
| | - Felix B Fritschi
- Department of Plant Science and Technology, University of Missouri, Agriculture Bldg, 52, Columbia, MO 65201, USA
| | - David B Lowry
- Department of Plant Biology, Michigan State University, 612 Wilson Road, Rm 166, East Lansing, MI 48824, USA
| | - Thomas E Juenger
- Department of Integrative Biology, University of Texas, Austin, 2415 Speedway, Austin, TX 78712, USA.
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Zhang M, Wang Y, Hu Y, Wang H, Liu Y, Zhao B, Zhang J, Fang R, Yan Y. Heterosis in root microbiota inhibits growth of soil-borne fungal pathogens in hybrid rice. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023; 65:1059-1076. [PMID: 36426878 DOI: 10.1111/jipb.13416] [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: 10/09/2022] [Accepted: 11/24/2022] [Indexed: 06/16/2023]
Abstract
In nature, plants are colonized by various microbes that play essential roles in their growth and health. Heterosis is a natural genetic phenomenon whereby first-generation hybrids exhibit superior phenotypic performance relative to their parents. It remains unclear whether this concept can be extended to the "hybridization" of microbiota from two parents in their descendants and what benefits the hybrid microbiota might convey. Here, we investigated the structure and function of the root microbiota from three hybrid rice varieties and their parents through amplicon sequencing analysis of bacterial 16S ribosomal DNA (rDNA) and fungal internal transcribed spacer (ITS) regions. We show that the bacterial and fungal root microbiota of the varieties are distinct from those of their parental lines and exhibit potential heterosis features in diversity and composition. Moreover, the root bacterial microbiota of hybrid variety LYP9 protects rice against soil-borne fungal pathogens. Systematic analysis of the protective capabilities of individual strains from a 30-member bacterial synthetic community derived from LYP9 roots indicated that community members have additive protective roles. Global transcription profiling analyses suggested that LYP9 root bacterial microbiota activate rice reactive oxygen species production and cell wall biogenesis, contributing to heterosis for protection. In addition, we demonstrate that the protection conferred by the LYP9 root microbiota is transferable to neighboring plants, potentially explaining the observed hybrid-mediated superior effects of mixed planting. Our findings suggest that some hybrids exhibit heterosis in their microbiota composition that promotes plant health, highlighting the potential for microbiota heterosis in breeding hybrid crops.
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Affiliation(s)
- Mengting Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yinyue Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuanyi Hu
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Huacai Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yawen Liu
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Bingran Zhao
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Changsha, 410125, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Rongxiang Fang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
| | - Yongsheng Yan
- State Key Laboratory of Plant Genomics, Institute of Microbiology, the Chinese Academy of Sciences, Beijing, 100101, China
- Innovation Academy for Seed Design, the Chinese Academy of Sciences, Beijing, 100101, China
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34
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Pereira LB, Thomazella DPT, Teixeira PJPL. Plant-microbiome crosstalk and disease development. CURRENT OPINION IN PLANT BIOLOGY 2023; 72:102351. [PMID: 36848753 DOI: 10.1016/j.pbi.2023.102351] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 01/27/2023] [Accepted: 02/03/2023] [Indexed: 06/18/2023]
Abstract
Plants harbor a complex immune system to fight off invaders and prevent diseases. For decades, the interactions between plants and pathogens have been investigated primarily through the lens of binary interactions, largely neglecting the diversity of microbes that naturally inhabit plant tissues. Recent research, however, demonstrates that resident microbes are more than mere spectators. Instead, the plant microbiome extends host immune function and influences the outcome of a pathogen infection. Both plants and the interacting microbes produce a large diversity of metabolites that form an intricate chemical network of nutrients, signals, and antimicrobial molecules. In this review, we discuss the involvement of the plant microbiome in disease development, focusing on the biochemical conversation that occurs between plants and their associated microbiota before, during and after infection. We also highlight outstanding questions and possible directions for future research.
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Affiliation(s)
- Letícia B Pereira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Daniela P T Thomazella
- Department of Genetics, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil
| | - Paulo J P L Teixeira
- Department of Biological Sciences, "Luiz de Queiroz" College of Agriculture (ESALQ), University of São Paulo (USP), Piracicaba, SP, Brazil.
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35
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Geller AM, Levy A. "What I cannot create, I do not understand": elucidating microbe-microbe interactions to facilitate plant microbiome engineering. Curr Opin Microbiol 2023; 72:102283. [PMID: 36868050 DOI: 10.1016/j.mib.2023.102283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2022] [Revised: 01/22/2023] [Accepted: 01/24/2023] [Indexed: 03/05/2023]
Abstract
Plant-microbe interactions are important for both physiological and pathological processes. Despite the significance of plant-microbe interactions, microbe-microbe interactions themselves represent an important, complex, dynamic network that warrants deeper investigation. To understand how microbe-microbe interactions affect plant microbiomes, one approach is to systematically understand all the factors involved in successful engineering of a microbial community. This follows the physicist Richard Feynman's declaration: "what I cannot create, I do not understand". This review highlights recent studies that focus on aspects that we believe are important for building (ergo understanding) microbe-microbe interactions in the plant environment, including pairwise screening, intelligent application of cross-feeding models, spatial distributions of microbes, and understudied interactions between bacteria and fungi, phages, and protists. We offer a framework for systematic collection and centralized integration of data of plant microbiomes that could organize all the factors that can help ecologists understand microbiomes and help synthetic ecologists engineer beneficial microbiomes.
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Affiliation(s)
- Alexander M Geller
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, Robert H. Smith Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
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36
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Bhandari R, Sanz-Saez A, Leisner CP, Potnis N. Xanthomonas infection and ozone stress distinctly influence the microbial community structure and interactions in the pepper phyllosphere. ISME COMMUNICATIONS 2023; 3:24. [PMID: 36973329 PMCID: PMC10043289 DOI: 10.1038/s43705-023-00232-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023]
Abstract
While the physiological and transcriptional response of the host to biotic and abiotic stresses have been intensely studied, little is known about the resilience of associated microbiomes and their contribution towards tolerance or response to these stresses. We evaluated the impact of elevated tropospheric ozone (O3), individually and in combination with Xanthomonas perforans infection, under open-top chamber field conditions on overall disease outcome on resistant and susceptible pepper cultivars, and their associated microbiome structure, function, and interaction network across the growing season. Pathogen infection resulted in a distinct microbial community structure and functions on the susceptible cultivar, while concurrent O3 stress did not further alter the community structure, and function. However, O3 stress exacerbated the disease severity on resistant cultivar. This altered diseased severity was accompanied by enhanced heterogeneity in associated Xanthomonas population counts, although no significant shift in overall microbiota density, microbial community structure, and function was evident. Microbial co-occurrence networks under simultaneous O3 stress and pathogen challenge indicated a shift in the most influential taxa and a less connected network, which may reflect the altered stability of interactions among community members. Increased disease severity on resistant cultivar may be explained by such altered microbial co-occurrence network, indicating the altered microbiome-associated prophylactic shield against pathogens under elevated O3. Our findings demonstrate that microbial communities respond distinctly to individual and simultaneous stressors, in this case, O3 stress and pathogen infection, and can play a significant role in predicting how plant-pathogen interactions would change in the face of climate change.
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Affiliation(s)
- Rishi Bhandari
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA
| | - Alvaro Sanz-Saez
- Department of Crop, Soil and Environmental Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Courtney P Leisner
- Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, AL, 36849, USA.
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37
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Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome. mBio 2023; 14:e0017723. [PMID: 36877054 PMCID: PMC10128044 DOI: 10.1128/mbio.00177-23] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
The type VI secretion system (T6SS) is deployed by many proteobacteria to secrete effector proteins into bacterial competitors for competition or eukaryotic cells for pathogenesis. Agrobacteria, a group of soilborne phytopathogens causing crown gall disease on various plant species, deploy the T6SS to attack closely and distantly related bacterial species in vitro and in planta. Current evidence suggests that the T6SS is not essential for pathogenesis under direct inoculation, but it remains unknown whether the T6SS influences natural disease incidence or the microbial community within crown galls (i.e., the gallobiome). To address these two key questions, we established a soil inoculation method on wounded tomato seedlings that mimics natural infections and developed a bacterial 16S rRNA gene amplicon enrichment sequencing platform. By comparing the Agrobacterium wild-type strain C58 with two T6SS mutants, we demonstrate that the T6SS influences both disease occurrence and gallobiome composition. Based on multiple inoculation trials across seasons, all three strains induced tumors, but the mutants had significantly lower disease incidences. The season of inoculation played a more important role than the T6SS in shaping the gallobiome. The influence of the T6SS was evident in summer, during which two Sphingomonadaceae species and the family Burkholderiaceae were enriched in the gallobiome induced by the mutants. Further in vitro competition and colonization assays demonstrated the T6SS-mediated antagonism to a Sphingomonas sp. R1 strain isolated from tomato rhizosphere in this study. In conclusion, this work demonstrates that the Agrobacterium T6SS promotes tumorigenesis in infection processes and provides competitive advantages in gall-associated microbiota. IMPORTANCE The T6SS is widespread among proteobacteria and used for interbacterial competition by agrobacteria, which are soil inhabitants and opportunistic bacterial pathogens causing crown gall disease in a wide range of plants. Current evidence indicates that the T6SS is not required for gall formation when agrobacteria are inoculated directly on plant wounding sites. However, in natural settings, agrobacteria may need to compete with other bacteria in bulk soil to gain access to plant wounds and influence the microbial community inside crown galls. The role of the T6SS in these critical aspects of disease ecology have remained largely unknown. In this study, we successfully developed a soil inoculation method coupled with blocker-mediated enrichment of bacterial 16S rRNA gene amplicon sequencing, named SI-BBacSeq, to address these two important questions. We provided evidence that the T6SS promotes disease occurrence and influences crown gall microbiota composition by interbacterial competition.
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38
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Ahmed A, He P, He P, Wu Y, He Y, Munir S. Environmental effect of agriculture-related manufactured nano-objects on soil microbial communities. ENVIRONMENT INTERNATIONAL 2023; 173:107819. [PMID: 36842382 DOI: 10.1016/j.envint.2023.107819] [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: 10/21/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
Agriculture-related manufactured nano-objects (MNOs) can revolutionize the crop production and help to achieve sustainable development goals. MNOs with diverse physico-chemical properties and ability to encapsulate and deliver active ingredients in controlled, targeted and stimuli responsive manner can enhance the efficiency while minimizing collateral damage to non-target organisms and environment. Application of MNOs in the form of nanopesticides and nanofertilizers is known to affect soil microbial communities both positively and negatively, but detailed studies with varying dose, type and environmental conditions are scarce. Therefore, it is imperative to understand the complex mechanisms and factors which shape the MNOs-microbial interactions through integrating state of the art technologies including omics (transcriptomics, metabolomics, and proteomics), artificial intelligence, and statistical frameworks. Lastly, we propose the idea of MNOs-mediated manipulation of soil microbiome to modify the soil microbial communities for improved microbial services. These microbial services, if harnessed appropriately, can revolutionize modern agriculture and help in achieving sustainable development goals.
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Affiliation(s)
- Ayesha Ahmed
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengfei He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Pengbo He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yixin Wu
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Yueqiu He
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
| | - Shahzad Munir
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China.
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Poupin MJ, Ledger T, Roselló-Móra R, González B. The Arabidopsis holobiont: a (re)source of insights to understand the amazing world of plant-microbe interactions. ENVIRONMENTAL MICROBIOME 2023; 18:9. [PMID: 36803555 PMCID: PMC9938593 DOI: 10.1186/s40793-023-00466-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/19/2023] [Indexed: 06/18/2023]
Abstract
As holobiont, a plant is intrinsically connected to its microbiomes. However, some characteristics of these microbiomes, such as their taxonomic composition, biological and evolutionary role, and especially the drivers that shape them, are not entirely elucidated. Reports on the microbiota of Arabidopsis thaliana first appeared more than ten years ago. However, there is still a lack of a comprehensive understanding of the vast amount of information that has been generated using this holobiont. The main goal of this review was to perform an in-depth, exhaustive, and systematic analysis of the literature regarding the Arabidopsis-microbiome interaction. A core microbiota was identified as composed of a few bacterial and non-bacterial taxa. The soil (and, to a lesser degree, air) were detected as primary microorganism sources. From the plant perspective, the species, ecotype, circadian cycle, developmental stage, environmental responses, and the exudation of metabolites were crucial factors shaping the plant-microbe interaction. From the microbial perspective, the microbe-microbe interactions, the type of microorganisms belonging to the microbiota (i.e., beneficial or detrimental), and the microbial metabolic responses were also key drivers. The underlying mechanisms are just beginning to be unveiled, but relevant future research needs were identified. Thus, this review provides valuable information and novel analyses that will shed light to deepen our understanding of this plant holobiont and its interaction with the environment.
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Affiliation(s)
- M J Poupin
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - T Ledger
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile
| | - R Roselló-Móra
- Marine Microbiology Group, Department of Animal and Microbial Biodiversity, Mediterranean Institute for Advanced Studies (IMEDEA UIB-CSIC), Illes Balears, Majorca, Spain
| | - B González
- Laboratorio de Bioingeniería, Facultad de Ingeniería y Ciencias, Universidad Adolfo Ibáñez, 7941169, Santiago, Chile.
- Center of Applied Ecology and Sustainability (CAPES), Santiago, Chile.
- Millennium Nucleus for the Development of Super Adaptable Plants (MN-SAP), Santiago, Chile.
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Morales Moreira ZP, Chen MY, Yanez Ortuno DL, Haney CH. Engineering plant microbiomes by integrating eco-evolutionary principles into current strategies. CURRENT OPINION IN PLANT BIOLOGY 2023; 71:102316. [PMID: 36442442 DOI: 10.1016/j.pbi.2022.102316] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 09/30/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Engineering plant microbiomes has the potential to improve plant health in a rapid and sustainable way. Rapidly changing climates and relatively long timelines for plant breeding make microbiome engineering an appealing approach to improving food security. However, approaches that have shown promise in the lab have not resulted in wide-scale implementation in the field. Here, we suggest the use of an integrated approach, combining mechanistic molecular and genetic knowledge, with ecological and evolutionary theory, to target knowledge gaps in plant microbiome engineering that may facilitate translatability of approaches into the field. We highlight examples where understanding microbial community ecology is essential for a holistic understanding of the efficacy and consequences of microbiome engineering. We also review examples where understanding plant-microbe evolution could facilitate the design of plants able to recruit specific microbial communities. Finally, we discuss possible trade-offs in plant-microbiome interactions that should be considered during microbiome engineering efforts so as not to introduce off-target negative effects. We include classic and emergent approaches, ranging from microbial inoculants to plant breeding to host-driven microbiome engineering, and address areas that would benefit from multidisciplinary approaches.
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Affiliation(s)
- Zayda P Morales Moreira
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Melissa Y Chen
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Daniela L Yanez Ortuno
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
| | - Cara H Haney
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada.
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Berg G, Schweitzer M, Abdelfattah A, Cernava T, Wassermann B. Missing symbionts – emerging pathogens? Microbiome management for sustainable agriculture. Symbiosis 2023. [DOI: 10.1007/s13199-023-00903-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
AbstractPlant diversification and co-evolution shaped the plant microbiome and vice versa. This resulted in a specific composition of the plant microbiome and a strong connection with the host in terms of functional interplay. Symbionts are part of the microbiota, and important for the plant’s germination and growth, nutrition, as well as stress protection. However, human activities in the Anthropocene are linked to a significant shift of diversity, evenness and specificity of the plant microbiota. In addition, and very importantly, many plant symbionts are missing or no longer functional. It will require targeted microbiome management to support and reintroduce them. In future agriculture, we should aim at replacing harmful chemicals in the field, as well as post-harvest, by using precision microbiome engineering. This is because the plant microbiome is connected across systems and crucial for human and planetary health. This commentary aims to inspire holistic studies for the development of solutions for sustainable agriculture in framework of the One Health and the Planetary Health concepts.
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Hong S, Sun Y, Chen H, Wang C. Suppression of the insect cuticular microbiomes by a fungal defensin to facilitate parasite infection. THE ISME JOURNAL 2023; 17:1-11. [PMID: 36127432 PMCID: PMC9751272 DOI: 10.1038/s41396-022-01323-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 12/24/2022]
Abstract
Insects can assemble defensive microbiomes on their body surfaces to defend against fungal parasitic infections. The strategies employed by fungal pathogens to combat host cuticular microbiotas remains unclear. Here, we report the identification and functional characterization of the defensin-like antimicrobial gene BbAMP1 encoded by the entomopathogenic fungus Beauveria bassiana. The mature peptide of BbAMP1 can coat fungal spores and can be secreted by the fungus to target and damage Gram-positive bacterial cells. Significant differences in insect survival were observed between the wild-type and BbAMP1 mutant strains during topical infection but not during injection assays that bypassed insect cuticles. Thus, BbAMP1 deletion considerably reduced fungal virulence while gene overexpression accelerated the fungal colonization of insects compared with the wild-type strain in natural infections. Topical infection of axenic Drosophila adults evidenced no difference in fly survivals between strains. However, the gnotobiotic infections with the addition of Gram-positive but not Gram-negative bacterial cells in fungal spore suspensions substantially increased the survival of the flies treated with ∆BbAMP1 compared to those infected by the wild-type and gene-overexpression strains. Bacterial colony counts and microbiome analysis confirmed that BbAMP1 could assist the fungus to manipulate insect surface bacterial loads. This study reveals that fungal defensin can suppress the host surface defensive microbiomes, which underscores the importance to extend the research scope of fungus-host interactions.
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Affiliation(s)
- Song Hong
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanlei Sun
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haimin Chen
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Chengshu Wang
- Key Laboratory of Insect Developmental and Evolutionary Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, 200032, China.
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
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Saati-Santamaría Z, Baroncelli R, Rivas R, García-Fraile P. Comparative Genomics of the Genus Pseudomonas Reveals Host- and Environment-Specific Evolution. Microbiol Spectr 2022; 10:e0237022. [PMID: 36354324 PMCID: PMC9769992 DOI: 10.1128/spectrum.02370-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Accepted: 10/24/2022] [Indexed: 11/12/2022] Open
Abstract
Each Earth ecosystem has unique microbial communities. Pseudomonas bacteria have evolved to occupy a plethora of different ecological niches, including living hosts, such as animals and plants. Many genes necessary for the Pseudomonas-niche interaction and their encoded functions remain unknown. Here, we describe a comparative genomic study of 3,274 genomes with 19,056,667 protein-coding sequences from Pseudomonas strains isolated from diverse environments. We detected functional divergence of Pseudomonas that depends on the niche. Each group of strains from a certain environment harbored a distinctive set of metabolic pathways or functions. The horizontal transfer of genes, which mainly proceeded between closely related taxa, was dependent on the isolation source. Finally, we detected thousands of undescribed proteins and functions associated with each Pseudomonas lifestyle. This research represents an effort to reveal the mechanisms underlying the ecology, pathogenicity, and evolution of Pseudomonas, and it will enable clinical, ecological, and biotechnological advances. IMPORTANCE Microbes play important roles in the health of living beings and in the environment. The knowledge of these functions may be useful for the development of new clinical and biotechnological applications and the restoration and preservation of natural ecosystems. However, most mechanisms implicated in the interaction of microbes with the environment remain poorly understood; thus, this field of research is very important. Here, we try to understand the mechanisms that facilitate the differential adaptation of Pseudomonas-a large and ubiquitous bacterial genus-to the environment. We analyzed more than 3,000 Pseudomonas genomes and searched for genetic patterns that can be related with their coevolution with different hosts (animals, plants, or fungi) and environments. Our results revealed that thousands of genes and genetic features are associated with each niche. Our data may be useful to develop new technical and theoretical advances in the fields of ecology, health, and industry.
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Affiliation(s)
- Zaki Saati-Santamaría
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Institute of Microbiology of the Czech Academy of Sciences, Vídeňská, Prague, Czech Republic
| | - Riccardo Baroncelli
- Department of Agricultural and Food Sciences (DISTAL), University of Bologna, Bologna, Italy
| | - Raúl Rivas
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
| | - Paula García-Fraile
- Departamento de Microbiología y Genética, Universidad de Salamanca, Salamanca, Spain
- Institute for Agribiotechnology Research (CIALE), Villamayor, Salamanca, Spain
- Associated Research Unit of Plant-Microorganism Interaction, USAL-CSIC (IRNASA), Salamanca, Spain
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Ulhassan Z, Khan I, Hussain M, Khan AR, Hamid Y, Hussain S, Allakhverdiev SI, Zhou W. Efficacy of metallic nanoparticles in attenuating the accumulation and toxicity of chromium in plants: Current knowledge and future perspectives. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2022; 315:120390. [PMID: 36244495 DOI: 10.1016/j.envpol.2022.120390] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 08/22/2022] [Accepted: 10/05/2022] [Indexed: 06/16/2023]
Abstract
Nanoparticles have emerged as cutting-edge technology for the improvement of crops yield and safe cultivation of agricultural plants, especially in peripheral areas impaired with toxic heavy metals including chromium (Cr). The uncontrolled release of Cr mainly from anthropogenic factors is substantially polluting the surrounding environment, thereby extensively accumulated in soil-plant system. The excessive Cr-accretion in plant tissues disturbed the morph-physiological, biochemical, cellular, metabolic and molecular processes, and impaired the plants functionality. Therefore, it is obligatory to restrict the accumulation and toxic effects of Cr in plant organs. Recent studies on metallic nanoparticles (MNPs) such as iron oxide, silicon dioxide, copper oxide and zinc oxide have approved their efficacy as potent pool to curb the Cr-induced phytotoxicities and improved the plant tolerance. MNPs attenuated the bioaccumulation and phytotoxicity of Cr by utilizing key mechanisms such as improved photosynthetic machinery, regulation of cellular metabolites, greater chelation capacity to bind with Cr, release of corresponding metallic ions, upsurge in the uptake of essential nutrients, activation of antioxidants (enzymatic and non-enzymatic), reduction in oxidative stress, and cellular injuries, thus improvement in plant growth performances. We have briefly discussed the current knowledge and research gaps in existing literature along with possible recommendations for future research. Overall, Cr-detoxification by MNPs may depends upon the target plant species, Cr speciation, plant growth stages (seedling, vegetative and ripening etc.), treatment methods (foliar spray, seed priming and nutrient solution etc.), type, size, dose and coating of applied MNPs, and conditions (hydroponic and soil environment etc.). This review would help plant scientists to develop MNPs based strategies such as nano-fertilizers to alleviate the Cr-accumulation and its toxic impacts. This may leads to safe and healthy food production. The review outcomes can provide new horizons for research in the applications of MNPs for the sustainable agriculture.
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Affiliation(s)
- Zaid Ulhassan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Key Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, China
| | - Imran Khan
- State Key Laboratory of Grassland Agro-Ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, China
| | - Muzammil Hussain
- College of Life Science and Oceanography, Shenzhen University, Shenzhen, 518071, China
| | - Ali Raza Khan
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Key Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, China
| | - Yasir Hamid
- Ministry of Education Key Laboratory of Environmental Remediation and Ecosystem Health, College of Environmental and Resources Science, Zhejiang University, Hangzhou, 310058, China
| | - Sajad Hussain
- National Research Center of Intercropping, The Islamia University of Bahawalpur, Punjab, Pakistan
| | - Suleyman I Allakhverdiev
- Controlled Photobiosynthesis Laboratory, K.A. Timiryazev Institute of Plant Physiology, Russian Academy of Sciences, Botanicheskaya Street 35, 127276, Moscow, Russia
| | - Weijun Zhou
- Institute of Crop Science, Ministry of Agriculture and Rural Affairs Key Laboratory of Spectroscopy Sensing, Zhejiang University, Hangzhou, 310058, China.
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Ji C, Chen Z, Kong X, Xin Z, Sun F, Xing J, Li C, Li K, Liang Z, Cao H. Biocontrol and plant growth promotion by combined Bacillus spp. inoculation affecting pathogen and AMF communities in the wheat rhizosphere at low salt stress conditions. FRONTIERS IN PLANT SCIENCE 2022; 13:1043171. [PMID: 36570885 PMCID: PMC9773258 DOI: 10.3389/fpls.2022.1043171] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 10/28/2022] [Indexed: 06/17/2023]
Abstract
Applying plant growth-promoting rhizobacteria (PGPR) improves the efficiency of soil-borne disease control and is considered a sustainable practice. However, the effect of PGPR on the fungal community, especially pathogenic fungi and arbuscular mycorrhizal fungi (AMF), remains unclear. In this study, we examined the effects of a compound microbial agent (consisting of Bacillus subtilis HG-15 and Bacillus velezensis JC-K3) on the incidence and yield of wheat under low salt stress, as well as compared the diversity and community composition of the rhizosphere fungal and AMF communities of wheat in the CK (not inoculated bacterial agent) and BIO (inoculated with a bacterial agent) groups. Chlorophyll relative content (SPAD), net photosynthesis rate (Pn), transpiration rate (Tr), leaf water use efficiency (WUE L), grains per spike and wheat yield in the BIO group increased more than in the CK group. The number of diseased plants and disease incidence was observed to be reduced. The relative efficacy reached 79.80%. We classified 1007 fungal operational taxonomic units (OTU) based on Miseq sequencing data: 11 phyla, 173 families, 319 genera, and 521 species. Fifty-four OTUs were classified from the AMF effective sequences, including 1 phylum, 3 families, 3 genera, and 17 species. The inoculation of bacterial agents reduced the relative abundance of pathogen genera such as Gibberella, Fusarium, Cladosporium, and Alternaria in wheat rhizosphere. It increased the relative abundance of AMF species such as Glomus-group-B-Glomus-lamellosu-VTX00193, Glomus-viscosum-VTX00063, and Glomus-Glo2-VTX00280. In addition, pH, EC, exchangeable K, available N, total N, organic matter, and olsen P were the main driving forces for shaping wheat rhizosphere fungi. The pH value was positively correlated with the relative abundance of fungal communities in soil, especially Gibberella, Cladosporium, Fusarium, and Alternaria. In summary, inoculation with Bacillus subtilis HG-15 and Bacillus velezensis JC-K3 affected wheat yield, incidence, rhizosphere soil chemical properties, rhizosphere fungi, and AMF fungal diversity and community. The findings may provide a theoretical foundation and strain support for constructing efficient PGPR-community and clarifying its mechanism of pathogenic bacteria inhibition.
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Affiliation(s)
- Chao Ji
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
- Shandong Yongsheng Agricultural Development Co., Ltd. Yongsheng (Shouguang) Vegetable Technology Research Institute Co., Ltd, Shandong Engineering Research Center, Weifang, Shandong, China
- Runxin Fruit and Vegetable Cultivation Cooperative of Weifang Economic Development Zone, Weifang Agricultural Bureau, Weifang, Shandong, China
| | - Zhizhang Chen
- College of Foreign Languages, Weifang University, Weifang, Shandong, China
| | - Xuehua Kong
- Weifang Hanting Vestibule School, Weifang Education Bureau, Weifang, Shandong, China
| | - Zhiwen Xin
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Fujin Sun
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Runxin Fruit and Vegetable Cultivation Cooperative of Weifang Economic Development Zone, Weifang Agricultural Bureau, Weifang, Shandong, China
| | - Jiahao Xing
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Chunyu Li
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
| | - Kun Li
- College of Forestry, Shandong Agriculture University, Taian, Shandong, China
- Taishan Forest Ecosystem Research Station, Key Laboratory of State Forestry Administration for Silviculture of the Lower Yellow River, Shandong Agricultural University, Taian, Shandong, China
| | - Zengwen Liang
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
- Shandong Yongsheng Agricultural Development Co., Ltd. Yongsheng (Shouguang) Vegetable Technology Research Institute Co., Ltd, Shandong Engineering Research Center, Weifang, Shandong, China
| | - Hui Cao
- College of Seed and Facility Agricultural Engineering, Weifang University, Weifang, Shandong, China
- Key Laboratory of Biochemistry and Molecular Biology in University of Shandong Province, Weifang University, Weifang, Shandong, China
- Shandong Yongsheng Agricultural Development Co., Ltd. Yongsheng (Shouguang) Vegetable Technology Research Institute Co., Ltd, Shandong Engineering Research Center, Weifang, Shandong, China
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Zhan C, Matsumoto H, Liu Y, Wang M. Pathways to engineering the phyllosphere microbiome for sustainable crop production. NATURE FOOD 2022; 3:997-1004. [PMID: 37118297 DOI: 10.1038/s43016-022-00636-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 10/12/2022] [Indexed: 04/30/2023]
Abstract
Current disease resistance breeding, which is largely dependent on the exploitation of resistance genes in host plants, faces the serious challenges of rapidly evolving phytopathogens. The phyllosphere is the largest biological surface on Earth and an untapped reservoir of functional microbiomes. The phyllosphere microbiome has the potential to defend against plant diseases. However, the mechanisms of how the microbiota assemble and function in the phyllosphere remain largely elusive, and this restricts the exploitation of the targeted beneficial microbes in the field. Here we review the endogenous and exogenous cues impacting microbiota assembly in the phyllosphere and how the phyllosphere microbiota in turn facilitate the disease resistance of host plants. We further construct a holistic framework by integrating of holo-omics, genetic manipulation, culture-dependent characterization and emerging artificial intelligence techniques, such as deep learning, to engineer the phyllosphere microbiome for sustainable crop production.
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Affiliation(s)
- Chengfang Zhan
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Haruna Matsumoto
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - Yufei Liu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Mengcen Wang
- State Key Laboratory of Rice Biology & Ministry of Agricultural and Rural Affairs Laboratory of Molecular Biology of Crop Pathogens and Insects, Zhejiang University, Hangzhou, China.
- Key Laboratory of Biology of Crop Pathogens and Insects of Zhejiang Province, Institute of Pesticide and Environmental Toxicology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China.
- Global Education Program for AgriScience Frontiers, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan.
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The Arabidopsis thaliana–Streptomyces Interaction Is Controlled by the Metabolic Status of the Holobiont. Int J Mol Sci 2022; 23:ijms232112952. [PMID: 36361736 PMCID: PMC9655247 DOI: 10.3390/ijms232112952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/20/2022] [Accepted: 10/21/2022] [Indexed: 11/26/2022] Open
Abstract
How specific interactions between plant and pathogenic, commensal, or mutualistic microorganisms are mediated and how bacteria are selected by a plant are important questions to address. Here, an Arabidopsis thaliana mutant called chs5 partially deficient in the biogenesis of isoprenoid precursors was shown to extend its metabolic remodeling to phenylpropanoids and lipids in addition to carotenoids, chlorophylls, and terpenoids. Such a metabolic profile was concomitant to increased colonization of the phyllosphere by the pathogenic strain Pseudomonas syringae pv. tomato DC3000. A thorough microbiome analysis by 16S sequencing revealed that Streptomyces had a reduced colonization potential in chs5. This study revealed that the bacteria–Arabidopsis interaction implies molecular processes impaired in the chs5 mutant. Interestingly, our results revealed that the metabolic status of A. thaliana was crucial for the specific recruitment of Streptomyces into the microbiota. More generally, this study highlights specific as well as complex molecular interactions that shape the plant microbiota.
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Pradhan S, Tyagi R, Sharma S. Combating biotic stresses in plants by synthetic microbial communities: Principles, applications, and challenges. J Appl Microbiol 2022; 133:2742-2759. [PMID: 36039728 DOI: 10.1111/jam.15799] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 08/24/2022] [Indexed: 11/29/2022]
Abstract
Presently, agriculture worldwide is facing the major challenge of feeding the increasing population sustainably. The conventional practices have not only failed to meet the projected needs, but also led to tremendous environmental consequences. Hence, to ensure a food-secure and environmentally sound future, the major thrust is on sustainable alternatives. Due to challenges associated with conventional means of application of biocontrol agents in the management of biotic stresses in agro-ecosystems, significant transformations in this context is needed. The crucial role played by soil microbiomes in efficiently and sustainably managing the agricultural production has unfolded a newer approach of rhizospheric engineering that shows immense promise in mitigating biotic stresses in an eco-friendly manner. The strategy of generating synthetic microbial communities (SynCom), by integrating omics approaches with traditional techniques of enumeration and in-depth analysis of plant-microbe interactions, is encouraging. The review discusses the significance of the rhizospheric microbiome in plant's fitness, and its manipulation for enhancing plant attributes. The focus of the review is to critically analyze the potential tools for the design and utilization of SynCom as a sustainable approach for rhizospheric engineering to ameliorate biotic stresses in plants. Further, based on the synthesis of reports in the area, we have put forth possible solutions to some of the critical issues that impair the large-scale application of SynComs in agriculture.
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Affiliation(s)
- Salila Pradhan
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Rashi Tyagi
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
| | - Shilpi Sharma
- Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, New Delhi
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Schäfer M, Vogel CM, Bortfeld-Miller M, Mittelviefhaus M, Vorholt JA. Mapping phyllosphere microbiota interactions in planta to establish genotype–phenotype relationships. Nat Microbiol 2022; 7:856-867. [DOI: 10.1038/s41564-022-01132-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022]
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50
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Snelders NC, Rovenich H, Thomma BPHJ. Microbiota manipulation through the secretion of effector proteins is fundamental to the wealth of lifestyles in the fungal kingdom. FEMS Microbiol Rev 2022; 46:6590816. [PMID: 35604874 PMCID: PMC9438471 DOI: 10.1093/femsre/fuac022] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/19/2022] [Indexed: 11/13/2022] Open
Abstract
Fungi are well-known decomposers of organic matter that thrive in virtually any environment on earth where they encounter wealths of other microbes. Some fungi evolved symbiotic lifestyles, including pathogens and mutualists, that have mostly been studied in binary interactions with their hosts. However, we now appreciate that such interactions are greatly influenced by the ecological context in which they take place. While establishing their symbioses, fungi not only interact with their hosts, but also with the host-associated microbiota. Thus, they target the host and its associated microbiota as a single holobiont. Recent studies have shown that fungal pathogens manipulate the host microbiota by means of secreted effector proteins with selective antimicrobial activity to stimulate disease development. In this review we discuss the ecological contexts in which such effector-mediated microbiota manipulation is relevant for the fungal lifestyle and argue that this is not only relevant for pathogens of plants and animals, but beneficial in virtually any niche where fungi occur. Moreover, we reason that effector-mediated microbiota manipulation likely evolved already in fungal ancestors that encountered microbial competition long before symbiosis with land plants and mammalian animals evolved. Thus, we claim that effector-mediated microbiota manipulation is fundamental to fungal biology.
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Affiliation(s)
- Nick C Snelders
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Theoretical Biology & Bioinformatics Group, Department of Biology, Utrecht University, Utrecht, The Netherlands
| | - Hanna Rovenich
- Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Bart P H J Thomma
- Institute for Plant Sciences, University of Cologne, Cologne, Germany.,Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, CologneGermany
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