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Lin L, Tao M, He WM, Wu QH, Huang HK, Murero AK, Shao XL, Wang LM, Qian GL. Identification of non-canonical antagonistic bacteria via interspecies contact-dependent killing. PEST MANAGEMENT SCIENCE 2024; 80:3997-4005. [PMID: 38527976 DOI: 10.1002/ps.8103] [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: 10/31/2023] [Revised: 01/18/2024] [Accepted: 03/26/2024] [Indexed: 03/27/2024]
Abstract
BACKGROUND Canonical biocontrol bacteria were considered to inhibit pathogenic bacteria mainly by secreting antibiotic metabolites or enzymes. Recent studies revealed that some biocontrol bacteria can inhibit pathogenic bacteria through contact-dependent killing (CDK) mediated by contact-dependent secretion systems. The CDK was independent of antibiotic metabolites and often ignored in normal biocontrol activity assay. RESULTS In this study, we aimed to use a pathogen enrichment strategy to isolate non-canonical bacteria with CDK ability. Rhizosphere soil samples from Chinese cabbage showing soft rot symptom were collected and Pectobacterium carotovorum subsp. carotovorum (Pcc), the pathogen of cabbage soft rot, were added into these samples to enrich bacteria which attached on Pcc cells. By co-culture with Pcc, four bacteria strains (named as PcE1, PcE8, PcE12 and PcE13) showing antibacterial activity were isolated from Chinese cabbage rhizosphere. These four bacteria strains showed CDK abilities to different pathogenic bacteria of horticultural plants. Among them, PcE1 was identified as Chryseobacterium cucumeris. Genome sequencing showed that PcE1 genome encoded a type VI secretion system (T6SS) gene cluster. By heterologous expression, four predicted T6SS effectors of PcE1 showed antibacterial activity to Escherichia coli. CONCLUSION Overall, this study isolated four bacteria strains with CDK activity to various horticultural plant pathogens, and revealed possible involvement of T6SS of Chryseobacterium cucumeris in antibacterial activity. These results provide valuable insight for potential application of CDK activity in biocontrol bacteria. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Long Lin
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Min Tao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Wei-Mei He
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Qian-Hua Wu
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Hao-Kai Huang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Aprodisia Kavutu Murero
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Xiao-Long Shao
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Li-Min Wang
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
| | - Guo-Liang Qian
- College of Plant Protection (State Key Laboratory of Biological Interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, P. R. China
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Janse van Rensburg H, Stengele K, Schlaeppi K. Understanding plant responsiveness to microbiome feedbacks. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102603. [PMID: 39024858 DOI: 10.1016/j.pbi.2024.102603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2024] [Revised: 06/28/2024] [Accepted: 06/30/2024] [Indexed: 07/20/2024]
Abstract
Plant microbiome interactions are bidirectional with processes leading to microbiome assembly and processes leading to effects on plants, so called microbiome feedbacks. With belowground focus we systematically decomposed both of these directions into plant and (root and rhizosphere) microbiome components to identify methodological challenges and research priorities. We found that the bidirectionality of plant microbiome interactions presents a challenge for genetic studies. Establishing causality is particularly difficult when a plant mutant has both, an altered phenotype and an altered microbiome. Is the mutation directly affecting the microbiome (e.g., through root exudates), which then causes an altered phenotype of the plant and/or is the altered microbiome the consequence of the mutation altering the plant's phenotype (e.g., root architecture)? Here, we put forward that feedback experiments allow to separate cause and effect and furthermore, they are useful for investigating plant interactions with complex microbiomes in natural soils. They especially allow to investigate the plant genetic basis how plants respond to soil microbiomes and we stress that such microbiome feedbacks are understudied compared to the mechanisms contributing to microbiome assembly. Thinking towards application, this may allow to develop crops with both abilities to assemble a beneficial microbiome and to actively exploit its feedbacks.
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Affiliation(s)
| | - Katja Stengele
- Department of Environmental Sciences, University of Basel, Basel, Switzerland
| | - Klaus Schlaeppi
- Department of Environmental Sciences, University of Basel, Basel, Switzerland.
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3
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Poli N, Keel CJ, Garrido-Sanz D. Expanding the Pseudomonas diversity of the wheat rhizosphere: four novel species antagonizing fungal phytopathogens and with plant-beneficial properties. Front Microbiol 2024; 15:1440341. [PMID: 39077740 PMCID: PMC11284033 DOI: 10.3389/fmicb.2024.1440341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 07/01/2024] [Indexed: 07/31/2024] Open
Abstract
Plant-beneficial Pseudomonas bacteria hold the potential to be used as inoculants in agriculture to promote plant growth and health through various mechanisms. The discovery of new strains tailored to specific agricultural needs remains an open area of research. In this study, we report the isolation and characterization of four novel Pseudomonas species associated with the wheat rhizosphere. Comparative genomic analysis with all available Pseudomonas type strains revealed species-level differences, substantiated by both digital DNA-DNA hybridization and average nucleotide identity, underscoring their status as novel species. This was further validated by the phenotypic differences observed when compared to their closest relatives. Three of the novel species belong to the P. fluorescens species complex, with two representing a novel lineage in the Pseudomonas phylogeny. Functional genome annotation revealed the presence of specific features contributing to rhizosphere colonization, including flagella and components for biofilm formation. The novel species have the genetic potential to solubilize nutrients by acidifying the environment, releasing alkaline phosphatases and their metabolism of nitrogen species, indicating potential as biofertilizers. Additionally, the novel species possess traits that may facilitate direct promotion of plant growth through the modulation of the plant hormone balance, including the ACC deaminase enzyme and auxin metabolism. The presence of biosynthetic clusters for toxins such as hydrogen cyanide and non-ribosomal peptides suggests their ability to compete with other microorganisms, including plant pathogens. Direct inoculation of wheat roots significantly enhanced plant growth, with two strains doubling shoot biomass. Three of the strains effectively antagonized fungal phytopathogens (Thielaviopsis basicola, Fusarium oxysporum, and Botrytis cinerea), demonstrating their potential as biocontrol agents. Based on the observed genetic and phenotypic differences from closely related species, we propose the following names for the four novel species: Pseudomonas grandcourensis sp. nov., type strain DGS24T ( = DSM 117501T = CECT 31011T), Pseudomonas purpurea sp. nov., type strain DGS26T ( = DSM 117502T = CECT 31012T), Pseudomonas helvetica sp. nov., type strain DGS28T ( = DSM 117503T = CECT 31013T) and Pseudomonas aestiva sp. nov., type strain DGS32T ( = DSM 117504T = CECT 31014T).
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Affiliation(s)
| | - Christoph Joseph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Daniel Garrido-Sanz
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
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4
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A phage tail-like bacteriocin suppresses competitors in metapopulations of pathogenic bacteria. Science 2024; 384:eado0713. [PMID: 38870284 DOI: 10.1126/science.ado0713] [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: 01/16/2024] [Accepted: 04/24/2024] [Indexed: 06/15/2024]
Abstract
Bacteria can repurpose their own bacteriophage viruses (phage) to kill competing bacteria. Phage-derived elements are frequently strain specific in their killing activity, although there is limited evidence that this specificity drives bacterial population dynamics. Here, we identified intact phage and their derived elements in a metapopulation of wild plant-associated Pseudomonas genomes. We discovered that the most abundant viral cluster encodes a phage remnant resembling a phage tail called a tailocin, which bacteria have co-opted to kill bacterial competitors. Each pathogenic Pseudomonas strain carries one of a few distinct tailocin variants that target the variable polysaccharides in the outer membrane of co-occurring pathogenic Pseudomonas strains. Analysis of herbarium samples from the past 170 years revealed that the same tailocin and bacterial receptor variants have persisted in Pseudomonas populations. These results suggest that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control.
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Affiliation(s)
- Talia Backman
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Sergio M Latorre
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Efthymia Symeonidi
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Artur Muszyński
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Ella Bleak
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Lauren Eads
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | | | - Sarita Som
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Aubrey Hawks
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
| | - Andrew D Gloss
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - David M Belnap
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
- Department of Biochemistry, University of Utah, Salt Lake City, UT 84112, USA
| | - Allison M Manuel
- Mass Spectrometry and Proteomics Core, The University of Utah, Salt Lake City, UT 84112, USA
| | - Adam M Deutschbauer
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Joy Bergelson
- Center for Genomics and Systems Biology, New York University, New York, NY 10003, USA
| | - Parastoo Azadi
- Complex Carbohydrate Research Center, University of Georgia, Athens, GA 30602, USA
| | - Hernán A Burbano
- Centre for Life's Origins and Evolution, Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Biology, 72076 Tübingen, Germany
| | - Talia L Karasov
- School of Biological Sciences, University of Utah, Salt Lake City, UT 84112, USA
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5
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Barone GD, Zhou Y, Wang H, Xu S, Ma Z, Cernava T, Chen Y. Implications of bacteria‒bacteria interactions within the plant microbiota for plant health and productivity. J Zhejiang Univ Sci B 2024:1-16. [PMID: 38773879 DOI: 10.1631/jzus.b2300914] [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: 12/14/2023] [Accepted: 02/26/2024] [Indexed: 05/24/2024]
Abstract
Crop production currently relies on the widespread use of agrochemicals to ensure food security. This practice is considered unsustainable, yet has no viable alternative at present. The plant microbiota can fulfil various functions for its host, some of which could be the basis for developing sustainable protection and fertilization strategies for plants without relying on chemicals. To harness such functions, a detailed understanding of plant‒microbe and microbe‒microbe interactions is necessary. Among interactions within the plant microbiota, those between bacteria are the most common ones; they are not only of ecological importance but also essential for maintaining the health and productivity of the host plants. This review focuses on recent literature in this field and highlights various consequences of bacteria‒bacteria interactions under different agricultural settings. In addition, the molecular and genetic backgrounds of bacteria that facilitate such interactions are emphasized. Representative examples of commonly found bacterial metabolites with bioactive properties, as well as their modes of action, are given. Integrating our understanding of various binary interactions into complex models that encompass the entire microbiota will benefit future developments in agriculture and beyond, which could be further facilitated by artificial intelligence-based technologies.
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Affiliation(s)
| | - Yaqi Zhou
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Hongkai Wang
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Sunde Xu
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zhonghua Ma
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Tomislav Cernava
- School of Biological Sciences, Faculty of Environmental and Life Sciences, University of Southampton, SO17 1BJ Southampton, UK.
| | - Yun Chen
- State Key Laboratory of Rice Biology and Breeding; Ministry of Agriculture Key Lab of Molecular Biology of Crop Pathogens and Insects; Zhejiang Provincial Key Laboratory of Biology of Crop Pathogens and Insects; Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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6
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Han S, Cheng X, Wang T, Li X, Cai Z, Zheng H, Xiao B, Zhou J. AI-2 quorum sensing signal disrupts coral symbiotic homeostasis and induces host bleaching. ENVIRONMENT INTERNATIONAL 2024; 188:108768. [PMID: 38788416 DOI: 10.1016/j.envint.2024.108768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/19/2024] [Accepted: 05/20/2024] [Indexed: 05/26/2024]
Abstract
Symbiotic microorganisms play critical ecophysiological roles that facilitate the maintenance of coral health. Currently, information on the gene and protein pathways contributing to bleaching responses is lacking, including the role of autoinducers. Although the autoinducer AI-1 is well understood, information on AI-2 is insufficient. Here, we observed a 3.7-4.0 times higher abundance of the AI-2 synthesis gene luxS in bleached individuals relative to their healthy counterparts among reef-building coral samples from the natural environment. Laboratory tests further revealed that AI-2 contributed significantly to an increase in coral bleaching, altered the ratio of potential probiotic and pathogenic bacteria, and suppressed the antiviral activity of specific pathogenic bacteria while enhancing their functional potential, such as energy metabolism, chemotaxis, biofilm formation and virulence release. Structural equation modeling indicated that AI-2 influences the microbial composition, network structure, and pathogenic features, which collectively contribute to the coral bleaching status. Collectively, our results offer novel potential strategies for coral conservation based on a signal manipulation approach.
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Affiliation(s)
- Shuo Han
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Xueyu Cheng
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Tao Wang
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Xinyang Li
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Zhonghua Cai
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China
| | - Huina Zheng
- Guangdong Ocean University Shenzhen Research Institute, Shenzhen 518055, PR China
| | - Baohua Xiao
- Guangdong Ocean University Shenzhen Research Institute, Shenzhen 518055, PR China
| | - Jin Zhou
- Marine Ecology and Human Factors Assessment Technical Innovation Center of Natural Resources Ministry, Tsinghua Shenzhen International Graduate School, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Public Platform for Screening and Application of Marine Microbial Resources, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China; Shenzhen Key Laboratory of Advanced Technology for Marine Ecology, Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, Guangdong Province, PR China.
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7
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Fecht S, Paracuellos P, Subramoni S, Tan CAZ, Ilangovan A, Costa TRD, Filloux A. Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains. Nat Commun 2024; 15:4283. [PMID: 38769318 PMCID: PMC11106082 DOI: 10.1038/s41467-024-48487-8] [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: 03/19/2023] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.
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Affiliation(s)
- Selina Fecht
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Patricia Paracuellos
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Casandra Ai Zhu Tan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Aravindan Ilangovan
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, E1 4NS, UK
| | - Tiago R D Costa
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alain Filloux
- CBRB Centre for Bacterial Resistance Biology, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
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8
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Bernal P. How are microbes helping end hunger? Microb Biotechnol 2024; 17:e14432. [PMID: 38465536 PMCID: PMC10926054 DOI: 10.1111/1751-7915.14432] [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: 01/23/2024] [Revised: 02/12/2024] [Accepted: 02/14/2024] [Indexed: 03/12/2024] Open
Abstract
This article explores the potential of microbiology to positively impact all aspects of the food supply chain, improving the quantity, quality, safety, and nutritional value of food products by providing innovative ways of growing, processing, and preserving food and thus contributing to Zero Hunger, one of the Sustainable Development Goals (SDGs) of the United Nations.
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Affiliation(s)
- Patricia Bernal
- Departamento de Microbiología, Facultad de BiologíaUniversidad de SevillaSevilleSpain
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Zhao X, Gao L, Ali Q, Yu C, Yuan B, Huang H, Long J, Gu Q, Wu H, Gao X. A type VI secretion system effector TseG of Pantoea ananatis is involved in virulence and antibacterial activity. MOLECULAR PLANT PATHOLOGY 2024; 25:e13442. [PMID: 38476100 DOI: 10.1111/mpp.13442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 01/14/2024] [Accepted: 02/16/2024] [Indexed: 03/14/2024]
Abstract
The type VI secretion system (T6SS) of many gram-negative bacteria injects toxic effectors into adjacent cells to manipulate host cells during pathogenesis or to kill competing bacteria. However, the identification and function of the T6SS effectors remains only partly known. Pantoea ananatis, a gram-negative bacterium, is commonly found in various plants and natural environments, including water and soil. In the current study, genomic analysis of P. ananatis DZ-12 causing brown stalk rot on maize demonstrated that it carries three T6SS gene clusters, namely, T6SS-1, T6SS-2, and T6SS-3. Interestingly, only T6SS-1 secretion systems are involved in pathogenicity and bacterial competition. The study also investigated the T6SS-1 system in detail and identified an unknown T6SS-1-secreted effector TseG by using the upstream T6SS effector chaperone TecG containing a conserved domain of DUF2169. TseG can directly interact with the chaperone TecG for delivery and with a downstream immunity protein TsiG for protection from its toxicity. TseG, highly conserved in the Pantoea genus, is involved in virulence in maize, potato, and onion. Additionally, P. ananatis uses TseG to target Escherichia coli, gaining a competitive advantage. This study provides the first report on the T6SS-1-secreted effector from P. ananatis, thereby enriching our understanding of the various types and functions of type VI effector proteins.
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Affiliation(s)
- Xiaozhen Zhao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Lu Gao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Qurban Ali
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Chenjie Yu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Bingqin Yuan
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Hai Huang
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Juying Long
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Qin Gu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Huijun Wu
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
| | - Xuewen Gao
- Key Laboratory of Monitoring and Management of Crop Disease and Pest Insects, College of Plant Protection, Nanjing Agricultural University, Ministry of Education, Nanjing, China
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10
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Boo A, Toth T, Yu Q, Pfotenhauer A, Fields BD, Lenaghan SC, Stewart CN, Voigt CA. Synthetic microbe-to-plant communication channels. Nat Commun 2024; 15:1817. [PMID: 38418817 PMCID: PMC10901793 DOI: 10.1038/s41467-024-45897-6] [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: 02/10/2023] [Accepted: 02/07/2024] [Indexed: 03/02/2024] Open
Abstract
Plants and microbes communicate to collaborate to stop pests, scavenge nutrients, and react to environmental change. Microbiota consisting of thousands of species interact with each other and plants using a large chemical language that is interpreted by complex regulatory networks. In this work, we develop modular interkingdom communication channels, enabling bacteria to convey environmental stimuli to plants. We introduce a "sender device" in Pseudomonas putida and Klebsiella pneumoniae, that produces the small molecule p-coumaroyl-homoserine lactone (pC-HSL) when the output of a sensor or circuit turns on. This molecule triggers a "receiver device" in the plant to activate gene expression. We validate this system in Arabidopsis thaliana and Solanum tuberosum (potato) grown hydroponically and in soil, demonstrating its modularity by swapping bacteria that process different stimuli, including IPTG, aTc and arsenic. Programmable communication channels between bacteria and plants will enable microbial sentinels to transmit information to crops and provide the building blocks for designing artificial consortia.
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Affiliation(s)
- Alice Boo
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Tyler Toth
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Qiguo Yu
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Alexander Pfotenhauer
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Brandon D Fields
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Scott C Lenaghan
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - C Neal Stewart
- Center for Agricultural Synthetic Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Christopher A Voigt
- Department of Biological Engineering, Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA.
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11
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Yin R, Cheng J, Lin J. The role of the type VI secretion system in the stress resistance of plant-associated bacteria. STRESS BIOLOGY 2024; 4:16. [PMID: 38376647 PMCID: PMC10879055 DOI: 10.1007/s44154-024-00151-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 01/26/2024] [Indexed: 02/21/2024]
Abstract
The type VI secretion system (T6SS) is a powerful bacterial molecular weapon that can inject effector proteins into prokaryotic or eukaryotic cells, thereby participating in the competition between bacteria and improving bacterial environmental adaptability. Although most current studies of the T6SS have focused on animal bacteria, this system is also significant for the adaptation of plant-associated bacteria. This paper briefly introduces the structure and biological functions of the T6SS. We summarize the role of plant-associated bacterial T6SS in adaptability to host plants and the external environment, including resistance to biotic stresses such as host defenses and competition from other bacteria. We review the role of the T6SS in response to abiotic factors such as acid stress, oxidation stress, and osmotic stress. This review provides an important reference for exploring the functions of the T6SS in plant-associated bacteria. In addition, characterizing these anti-stress functions of the T6SS may provide new pathways toward eliminating plant pathogens and controlling agricultural losses.
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Affiliation(s)
- Rui Yin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Juanli Cheng
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China
| | - Jinshui Lin
- Shaanxi Key Laboratory of Chinese Jujube, College of Life Sciences, Yan'an University, Yan'an, 716000, Shaanxi, China.
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12
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Santos MNM, Pintor KL, Hsieh PY, Cheung YW, Sung LK, Shih YL, Lai EM. Agrobacteria deploy two classes of His-Me finger superfamily nuclease effectors exerting different antibacterial capacities against specific bacterial competitors. Front Microbiol 2024; 15:1351590. [PMID: 38426053 PMCID: PMC10902643 DOI: 10.3389/fmicb.2024.1351590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 01/22/2024] [Indexed: 03/02/2024] Open
Abstract
The type VI secretion system (T6SS) assembles into a contractile nanomachine to inject effectors across bacterial membranes for secretion. The Agrobacterium tumefaciens species complex is a group of soil inhabitants and phytopathogens that deploys T6SS as an antibacterial weapon against bacterial competitors at both inter-species and intra-species levels. The A. tumefaciens strain 1D1609 genome encodes one main T6SS gene cluster and four vrgG genes (i.e., vgrGa-d), each encoding a spike protein as an effector carrier. A previous study reported that vgrGa-associated gene 2, named v2a, encodes a His-Me finger nuclease toxin (also named HNH/ENDO VII nuclease), contributing to DNase-mediated antibacterial activity. However, the functions and roles of other putative effectors remain unknown. In this study, we identified vgrGc-associated gene 2 (v2c) that encodes another His-Me finger nuclease but with a distinct Serine Histidine Histidine (SHH) motif that differs from the AHH motif of V2a. We demonstrated that the ectopic expression of V2c caused growth inhibition, plasmid DNA degradation, and cell elongation in Escherichia coli using DNAse activity assay and fluorescence microscopy. The cognate immunity protein, V3c, neutralizes the DNase activity and rescues the phenotypes of growth inhibition and cell elongation. Ectopic expression of V2c DNase-inactive variants retains the cell elongation phenotype, while V2a induces cell elongation in a DNase-mediated manner. We also showed that the amino acids of conserved SHH and HNH motifs are responsible for the V2c DNase activity in vivo and in vitro. Notably, V2c also mediated the DNA degradation and cell elongation of the target cell in the context of interbacterial competition. Importantly, V2a and V2c exhibit different capacities against different bacterial species and function synergistically to exert stronger antibacterial activity against the soft rot phytopathogen, Dickeya dadantii.
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Affiliation(s)
- Mary Nia M. Santos
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
- Aquaculture Research and Development Division, Department of Agriculture-National Fisheries Research and Development Institute (DA-NFRDI), Manila, Philippines
| | | | - Pei-Yu Hsieh
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yee-Wai Cheung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
| | - Li-Kang Sung
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung-Hsing University, Taichung, Taiwan
| | - Yu-Ling Shih
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Erh-Min Lai
- Institute of Plant and Microbial Biology, Academia Sinica, Taipei, Taiwan
- Molecular and Biological Agricultural Sciences Program, Taiwan International Graduate Program, National Chung-Hsing University and Academia Sinica, Taipei, Taiwan
- Biotechnology Center, National Chung-Hsing University, Taichung, Taiwan
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13
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Backman T, Latorre SM, Symeonidi E, Muszyński A, Bleak E, Eads L, Martinez-Koury PI, Som S, Hawks A, Gloss AD, Belnap DM, Manuel AM, Deutschbauer AM, Bergelson J, Azadi P, Burbano HA, Karasov TL. A weaponized phage suppresses competitors in historical and modern metapopulations of pathogenic bacteria. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.04.17.536465. [PMID: 38352526 PMCID: PMC10862724 DOI: 10.1101/2023.04.17.536465] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Bacteriophages, the viruses of bacteria, are proposed to drive bacterial population dynamics, yet direct evidence of their impact on natural populations is limited. Here we identified viral sequences in a metapopulation of wild plant-associated Pseudomonas spp. genomes. We discovered that the most abundant viral cluster does not encode an intact phage but instead encodes a tailocin - a phage-derived element that bacteria use to kill competitors for interbacterial warfare. Each pathogenic Pseudomonas sp. strain carries one of a few distinct tailocin variants, which target variable polysaccharides in the outer membrane of co-occurring pathogenic strains. Analysis of historic herbarium samples from the last 170 years revealed that the same tailocin and receptor variants have persisted in the Pseudomonas populations for at least two centuries, suggesting the continued use of a defined set of tailocin haplotypes and receptors. These results indicate that tailocin genetic diversity can be mined to develop targeted "tailocin cocktails" for microbial control. One-Sentence Summary Bacterial pathogens in a host-associated metapopulation use a repurposed prophage to kill their competitors.
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14
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Xiong X, Wan W, Ding B, Cai M, Lu M, Liu W. Type VI secretion system drives bacterial diversity and functions in multispecies biofilms. Microbiol Res 2024; 279:127570. [PMID: 38096690 DOI: 10.1016/j.micres.2023.127570] [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: 10/06/2023] [Revised: 12/01/2023] [Accepted: 12/06/2023] [Indexed: 12/23/2023]
Abstract
Type VI secretion system (T6SS) plays an essential role in interspecies interactions and provides an advantage for a strain with T6SS in multispecies biofilms. However, how T6SS drives the bacterial community structure and functions in multispecies biofilms still needs to be determined. Using gene deletion and Illumina sequencing technique, we estimated bacterial community responses in multispecies biofilms to T6SS by introducing T6SS-containing Pseudomonas putida KT2440. Results showed that the niche structure shifts of multispecies biofilms were remarkably higher in the presence of T6SS than in the absence of T6SS. The presence of T6SS significantly drove the variation in microbial composition, reduced the alpha-diversity of bacterial communities in multispecies biofilms, and separately decreased and increased the relative abundance of Proteobacteria and Bacteroidota. Co-occurrence network analysis with inferred putative bacterial interactions indicated that P. putida KT2440 mainly displayed strong negative associations with the genera of Psychrobacter, Cellvibrio, Stenotrophomonas, and Brevundimonas. Moreover, the function redundancy index of the bacterial community was strikingly higher in the presence of T6SS than in the absence of T6SS, regardless of whether relative abundances of bacterial taxa were inhibited or promoted. Remarkably, the increased metabolic network similarity with T6SS-containing P. putida KT2440 could enhance the antibacterial activity of P. putida KT2440 on other bacterial taxa. Our findings extend knowledge of microbial adaptation strategies to potential bacterial weapons and could contribute to predicting biodiversity loss and change in ecological functions caused by T6SS.
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Affiliation(s)
- Xiang Xiong
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenjie Wan
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Bangjing Ding
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Miaomiao Cai
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Mingzhu Lu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China
| | - Wenzhi Liu
- Key Laboratory of Aquatic Botany and Watershed Ecology, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan 430070, PR China; Danjiangkou Wetland Ecosystem Field Scientific Observation and Research Station, Chinese Academy of Sciences & Hubei Province, Wuhan 430070, PR China.
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15
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Peng M, Lin W, Zhou A, Jiang Z, Zhou F, Wang Z. High genetic diversity and different type VI secretion systems in Enterobacter species revealed by comparative genomics analysis. BMC Microbiol 2024; 24:26. [PMID: 38238664 PMCID: PMC10797944 DOI: 10.1186/s12866-023-03164-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/18/2023] [Indexed: 01/22/2024] Open
Abstract
The human-pathogenic Enterobacter species are widely distributed in diverse environmental conditions, however, the understanding of the virulence factors and genetic variations within the genus is very limited. In this study, we performed comparative genomics analysis of 49 strains originated from diverse niches and belonged to eight Enterobacter species, in order to further understand the mechanism of adaption to the environment in Enterobacter. The results showed that they had an open pan-genome and high genomic diversity which allowed adaptation to distinctive ecological niches. We found the number of secretion systems was the highest among various virulence factors in these Enterobacter strains. Three types of T6SS gene clusters including T6SS-A, T6SS-B and T6SS-C were detected in most Enterobacter strains. T6SS-A and T6SS-B shared 13 specific core genes, but they had different gene structures, suggesting they probably have different biological functions. Notably, T6SS-C was restricted to E. cancerogenus. We detected a T6SS gene cluster, highly similar to T6SS-C (91.2%), in the remote related Citrobacter rodenitum, suggesting that this unique gene cluster was probably acquired by horizontal gene transfer. The genomes of Enterobacter strains possess high genetic diversity, limited number of conserved core genes, and multiple copies of T6SS gene clusters with differentiated structures, suggesting that the origins of T6SS were not by duplication instead by independent acquisition. These findings provide valuable information for better understanding of the functional features of Enterobacter species and their evolutionary relationships.
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Affiliation(s)
- Mu Peng
- Hubei Key Laboratory of Biological Resources Protection and Utilization, Hubei Minzu University, Enshi, China.
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
| | - Weiyuan Lin
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Aifen Zhou
- Institute for Environmental Genomics, Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK, USA
| | - Zhihui Jiang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Fangzhen Zhou
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China
| | - Zhiyong Wang
- College of Biological and Food Engineering, College of Biological and Food Engineering, Hubei Minzu University, Hubei Minzu University, No. 39 Xueyuan Street, Enshi, 445000, China.
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16
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Danov A, Segev O, Bograd A, Ben Eliyahu Y, Dotan N, Kaplan T, Levy A. Toxinome-the bacterial protein toxin database. mBio 2024; 15:e0191123. [PMID: 38117054 PMCID: PMC10790787 DOI: 10.1128/mbio.01911-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Accepted: 11/14/2023] [Indexed: 12/21/2023] Open
Abstract
IMPORTANCE Microbes use protein toxins as important tools to attack neighboring cells, microbial or eukaryotic, and for self-killing when attacked by viruses. These toxins work through different mechanisms to inhibit cell growth or kill cells. Microbes also use antitoxin proteins to neutralize the toxin activities. Here, we developed a comprehensive database called Toxinome of nearly two million toxins and antitoxins that are encoded in 59,475 bacterial genomes. We described the distribution of bacterial toxins and identified that they are depleted by bacteria that live in hot and cold temperatures. We found 5,161 cases in which toxins and antitoxins are densely clustered in bacterial genomes and termed these areas "Toxin Islands." The Toxinome database is a useful resource for anyone interested in toxin biology and evolution, and it can guide the discovery of new toxins.
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Affiliation(s)
- Aleks Danov
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ofir Segev
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Avi Bograd
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Yedidya Ben Eliyahu
- Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Noam Dotan
- Department of Brain Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Tommy Kaplan
- School of Computer Science and Engineering, The Hebrew University of Jerusalem, Jerusalem, Israel
- Department of Developmental Biology and Cancer Research, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Asaf Levy
- Department of Plant Pathology and Microbiology, Institute of Environmental Science, The Faculty of Agriculture, Food, and Environment, The Hebrew University of Jerusalem, Rehovot, Israel
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17
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Ramamoorthy S, Pena M, Ghosh P, Liao YY, Paret M, Jones JB, Potnis N. Transcriptome profiling of type VI secretion system core gene tssM mutant of Xanthomonas perforans highlights regulators controlling diverse functions ranging from virulence to metabolism. Microbiol Spectr 2024; 12:e0285223. [PMID: 38018859 PMCID: PMC10782981 DOI: 10.1128/spectrum.02852-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Accepted: 10/20/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE T6SS has received attention due to its significance in mediating interorganismal competition through contact-dependent release of effector molecules into prokaryotic and eukaryotic cells. Reverse-genetic studies have indicated the role of T6SS in virulence in a variety of plant pathogenic bacteria, including the one studied here, Xanthomonas. However, it is not clear whether such effect on virulence is merely due to a shift in the microbiome-mediated protection or if T6SS is involved in a complex virulence regulatory network. In this study, we conducted in vitro transcriptome profiling in minimal medium to decipher the signaling pathways regulated by tssM-i3* in X. perforans AL65. We show that TssM-i3* regulates the expression of a suite of genes associated with virulence and metabolism either directly or indirectly by altering the transcription of several regulators. These findings further expand our knowledge on the intricate molecular circuits regulated by T6SS in phytopathogenic bacteria.
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Affiliation(s)
- Sivakumar Ramamoorthy
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Michelle Pena
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Palash Ghosh
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
| | - Ying-Yu Liao
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Mathews Paret
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Jeffrey B. Jones
- Department of Plant Pathology, University of Florida, Gainesville, Florida, USA
| | - Neha Potnis
- Department of Entomology and Plant Pathology, Auburn University, Auburn, Alabama, USA
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18
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Garin T, Brin C, Préveaux A, Brault A, Briand M, Simonin M, Barret M, Journet L, Sarniguet A. The type VI secretion system of Stenotrophomonas rhizophila CFBP13503 limits the transmission of Xanthomonas campestris pv. campestris 8004 from radish seeds to seedlings. MOLECULAR PLANT PATHOLOGY 2024; 25:e13412. [PMID: 38279854 PMCID: PMC10777753 DOI: 10.1111/mpp.13412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/20/2023] [Accepted: 11/27/2023] [Indexed: 01/29/2024]
Abstract
Stenotrophomonas rhizophila CFBP13503 is a seedborne commensal bacterial strain, which is efficiently transmitted to seedlings and can outcompete the phytopathogenic bacterium Xanthomonas campestris pv. campestris (Xcc8004). The type VI secretion system (T6SS), an interference contact-dependent mechanism, is a critical component of interbacterial competition. The involvement of the T6SS of S. rhizophila CFBP13503 in the inhibition of Xcc8004 growth and seed-to-seedling transmission was assessed. The T6SS cluster of S. rhizophila CFBP13503 and nine putative effectors were identified. Deletion of two T6SS structural genes, hcp and tssB, abolished the competitive advantage of S. rhizophila against Xcc8004 in vitro. The population sizes of these two bacterial species were monitored in seedlings after inoculation of radish seeds with mixtures of Xcc8004 and either S. rhizophila wild-type (wt) strain or isogenic hcp mutant. A significant decrease in the population size of Xcc8004 was observed during confrontation with the S. rhizophila wt in comparison with T6SS-deletion mutants in germinated seeds and seedlings. We found that the T6SS distribution among 835 genomes of the Stenotrophomonas genus is scarce. In contrast, in all available S. rhizophila genomes, T6SS clusters are widespread and mainly belong to the T6SS group i4. In conclusion, the T6SS of S. rhizophila CFBP13503 is involved in the antibiosis against Xcc8004 and reduces seedling transmission of Xcc8004 in radish. The distribution of this T6SS cluster in the S. rhizophila complex could make it possible to exploit these strains as biocontrol agents against X. campestris pv. campestris.
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Affiliation(s)
- Tiffany Garin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Chrystelle Brin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Anne Préveaux
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Agathe Brault
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Martial Briand
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Marie Simonin
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Matthieu Barret
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
| | - Laure Journet
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, Institut de Microbiologie de la MéditerranéeAix‐Marseille Université‐CNRS, UMR 7255MarseilleFrance
| | - Alain Sarniguet
- Univ Angers, Institut Agro, INRAE, IRHS, SFR QUASAVAngersFrance
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19
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Civantos C, Ruiz A, Bernal P. A Robust Method to Perform In Vitro and In Planta Interbacterial Competition Assays: Killing Plant Pathogens by a Potent Biocontrol Agent. Methods Mol Biol 2024; 2751:115-129. [PMID: 38265713 DOI: 10.1007/978-1-0716-3617-6_8] [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] [Indexed: 01/25/2024]
Abstract
Interbacterial competition assays have become an essential tool for understanding the interactions between bacteria and their ability to outcompete one another in natural environments. This is especially relevant when studying the type VI secretion system (T6SS), a contact-dependent bacterial weapon that can be used to kill or inhibit the growth of other competing bacteria. Some beneficial environmental microorganisms such as Pseudomonas putida rely on the T6SS as their primary biocontrol mechanism to eliminate resilient plant pathogens. Competition assays are an essential methodology in this field that allows us to understand the efficacy of this bacterial nanoweapon. This chapter outlines the methodology for conducting in vitro and in planta competition assays between P. putida, a well-known biocontrol agent, and phytopathogenic bacterial species of economic and scientific interest.
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Affiliation(s)
- Cristina Civantos
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Adrián Ruiz
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain.
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20
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Shao X, Wu Q, Li L, He W, He X, Cheng D, Murero A, Lin L, Wang L, Zhong C, Huang L, Qian G. Adapting the inoculation methods of kiwifruit canker disease to identify efficient biocontrol bacteria from branch microbiome. MOLECULAR PLANT PATHOLOGY 2024; 25:e13399. [PMID: 37921929 PMCID: PMC10788592 DOI: 10.1111/mpp.13399] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 10/05/2023] [Accepted: 10/05/2023] [Indexed: 11/05/2023]
Abstract
Pseudomonas syringae pv. actinidiae (Psa), the bacterium that causes kiwifruit bacterial canker, is a common field occurrence that is difficult to control globally. Currently, exploring the resources for efficient biocontrol bacteria is a hot spot in the field. The common strategy for isolating biocontrol bacteria is to directly isolate biocontrol bacteria that can secrete diffusible antibacterial substances, most of which are members of Bacillus, Pseudomonas and Streptomycetaceae, from disease samples or soil. Here, we report a new approach by adapting the typical isolation methods of kiwifruit canker disease to identify efficient biocontrol bacteria from the branch microbiome. Using this unique approach, we isolated a group of kiwifruit biocontrol agents (KBAs) from the branch microbiome of Psa-resistant varieties. Thirteen of these showed no antagonistic activity in vitro, which depends on the secretion of antibacterial compounds. However, they exhibited antibacterial activity via cell-to-cell contacts mimicked by co-culture on agar plates. Through biocontrol tests on plants, two isolates, KBA13 and KBA19, demonstrated their effectiveness by protecting kiwifruit branches from Psa infection. Using KBA19, identified as Pantoea endophytica, as a representative, we found that this bacterium uses the type VI secretion system (T6SS) as the main contact-dependent antibacterial weapon that acts via translocating toxic effector proteins into Psa cells to induce cell death, and that this capacity expressed by KBA19 is common to various Psa strains from different countries. Our findings highlight a new strategy to identify efficient biocontrol agents that use the T6SS to function in an antibacterial metabolite-independent manner to control wood diseases.
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Affiliation(s)
- Xiaolong Shao
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Qianhua Wu
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Li Li
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhanHubei ProvinceChina
| | - Weimei He
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Xueting He
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Dongjin Cheng
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Aprodisia Murero
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Long Lin
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Limin Wang
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
| | - Caihong Zhong
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty AgricultureWuhan Botanical Garden, Chinese Academy of SciencesWuhanHubei ProvinceChina
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid AreasCollege of Plant Protection, Northwest A&F UniversityYanglingShanxiChina
| | - Guoliang Qian
- Key Laboratory of Integrated Management of Crop Diseases and PestsCollege of Plant Protection, State Key Laboratory of Biological Interactions and Crop Health, Nanjing Agricultural UniversityNanjingChina
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21
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Crisan CV, Van Tyne D, Goldberg JB. The type VI secretion system of the emerging pathogen Stenotrophomonas maltophilia complex has antibacterial properties. mSphere 2023; 8:e0058423. [PMID: 37975665 PMCID: PMC10732056 DOI: 10.1128/msphere.00584-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 11/19/2023] Open
Abstract
IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia complex can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the type VI secretion system (T6SS) allows S. maltophilia complex to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia complex. The T6SS may confer survival advantages to S. maltophilia complex isolates in polymicrobial communities in both environmental settings and during infections.
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Affiliation(s)
- Cristian V. Crisan
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
| | - Daria Van Tyne
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Joanna B. Goldberg
- Division of Pulmonary, Asthma, Cystic Fibrosis, and Sleep, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia, USA
- Emory+Children’s Center for Cystic Fibrosis and Airway Disease Research, Emory University School of Medicine, Atlanta, Georgia, USA
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22
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Stein NV, Eder M, Burr F, Stoss S, Holzner L, Kunz HH, Jung H. The RND efflux system ParXY affects siderophore secretion in Pseudomonas putida KT2440. Microbiol Spectr 2023; 11:e0230023. [PMID: 37800935 PMCID: PMC10715066 DOI: 10.1128/spectrum.02300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 08/28/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Gram-negative bacteria from the Pseudomonas group are survivors in various environmental niches. For example, the bacteria secrete siderophores to capture ferric ions under deficiency conditions. Tripartite efflux systems are involved in the secretion of siderophores, which are also important for antibiotic resistance. For one of these efflux systems, the resistance-nodulation-cell division transporter ParXY from the model organism Pseudomonas putida KT2440, we show that it influences the secretion of the siderophore pyoverdine in addition to its already known involvement in antibiotic resistance. Phenotypically, its role in pyoverdine secretion is only apparent when other pyoverdine secretion systems are inactive. The results confirm that the different tripartite efflux systems have overlapping substrate specificities and can at least partially functionally substitute for each other, especially in important physiological activities such as supplying the cell with iron ions. This fact must be taken into account when developing specific inhibitors for tripartite efflux systems.
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Affiliation(s)
- Nicola Victoria Stein
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Michelle Eder
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Fabienne Burr
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Sarah Stoss
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Lorenz Holzner
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Hans-Henning Kunz
- Plant Biochemistry and Physiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
| | - Heinrich Jung
- Microbiology, Faculty of Biology, Ludwig Maximilian University Munich, Martinsried, Germany
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23
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Ashajyothi M, Velmurugan S, Kundu A, Balamurugan A, Chouhan V, Kumar A. Hydroxamate siderophores secreted by plant endophytic Pseudomonas putida elicit defense against blast disease in rice incited by Magnaporthe oryzae. Lett Appl Microbiol 2023; 76:ovad139. [PMID: 38086617 DOI: 10.1093/lambio/ovad139] [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: 06/13/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 12/27/2023]
Abstract
Our study focuses on hydroxamate-type siderophores from Pseudomonas putida BP25, known for chelating ferric iron and aiding microbial growth in iron-deficient environments. Confirmed through CAS-agar and tetrazolium tests, a purified siderophore extract was obtained via ion-exchange chromatography. Applying varying concentrations of this siderophore to rice seedlings demonstrated concentration-dependent effects on shoot and root phenotypes. Prophylactic application on rice leaves significantly reduced blast severity (68.7%-97.0%), surpassing curative application (47.5%-86.87%). Additionally, the siderophore treatment elevated peroxidase, polyphenol oxidase, and total phenols in rice plants. Defense-related genes linked to salicylic acid (OsPR1.1, OsNPR1, and OsPDF2.2), and other pathways (Oshox24, OsCLE, and OsGLP3-3, OsEIN2.4, and OsCSE) promoting blast suppression showed upregulation. However, the OsACS6 gene associated with ethylene-induced internodal elongation was significantly downregulated. Overall, our findings propose that the siderophore from P. putida BP25 induces defense gene transcription, offering potential for sustainable rice production via bio-formulation.
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Affiliation(s)
- Mushineni Ashajyothi
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Shanmugam Velmurugan
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Aditi Kundu
- Division of Agricultural Chemicals, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Alexander Balamurugan
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Vinod Chouhan
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
| | - Aundy Kumar
- Division of Plant Pathology, ICAR - Indian Agricultural Research Institute, New Delhi 110012, India
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24
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Wang B, Zhang Z, Xu F, Yang Z, Li Z, Shen D, Wang L, Wu H, Li T, Yan Q, Wei Q, Shao X, Qian G. Soil bacterium manipulates antifungal weapons by sensing intracellular type IVA secretion system effectors of a competitor. THE ISME JOURNAL 2023; 17:2232-2246. [PMID: 37838821 PMCID: PMC10689834 DOI: 10.1038/s41396-023-01533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 09/22/2023] [Accepted: 10/05/2023] [Indexed: 10/16/2023]
Abstract
Soil beneficial bacteria can effectively inhibit bacterial pathogens by assembling contact-dependent killing weapons, such as the type IVA secretion system (T4ASS). It's not clear whether these antibacterial weapons are involved in biotrophic microbial interactions in soil. Here we showed that an antifungal antibiotic 2,4-DAPG production of the soil bacterium, Pseudomonas protegens can be triggered by another soil bacterium, Lysobacter enzymogenes, via T4ASS by co-culturing on agar plates to mimic cell-to-cell contact. We demonstrated that the induced 2,4-DAPG production of P. protegens is achieved by intracellular detection of the T4ASS effector protein Le1519 translocated from L. enzymogenes. We defined Le1519 as LtaE (Lysobacter T4E triggering antifungal effects), which specifically stimulates the expression of 2,4-DAPG biosynthesis genes in P. protegens, thereby protecting soybean seedlings from infection by the fungus Rhizoctonia solani. We further found that LtaE directly bound to PhlF, a pathway-specific transcriptional repressor of the 2,4-DAPG biosynthesis, then activated the 2,4-DAPG production. Our results highlight a novel pattern of microbial interspecies and interkingdom interactions, providing a unique case for expanding the diversity of soil microbial interactions.
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Affiliation(s)
- Bingxin Wang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zeyu Zhang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Fugui Xu
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zixiang Yang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Zihan Li
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Danyu Shen
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Limin Wang
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Huijun Wu
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Tao Li
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, 200241, PR China
| | - Qing Yan
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Qi Wei
- Industrial Crops Institute, Heilongjiang Academy of Agricultural Sciences, Harbin, 150086, China
| | - Xiaolong Shao
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China
| | - Guoliang Qian
- College of Plant Protection (State Key Laboratory of Biological interactions and Crop Health; Key Laboratory of Integrated Management of Crop Diseases and Pests), Nanjing Agricultural University, Nanjing, 210095, P.R. China.
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25
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Navarro-Monserrat ED, Taylor CG. T6SS: A Key to Pseudomonas's Success in Biocontrol? Microorganisms 2023; 11:2718. [PMID: 38004732 PMCID: PMC10673566 DOI: 10.3390/microorganisms11112718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/29/2023] [Accepted: 10/30/2023] [Indexed: 11/26/2023] Open
Abstract
Bacteria from the genus Pseudomonas have been extensively studied for their capacity to act as biological control agents of disease and pests and for their ability to enhance and promote crop production in agricultural systems. While initial research primarily focused on the human pathogenic bacteria Pseudomonas aeruginosa, recent studies indicate the significance of type VI secretion (T6SS) in other Pseudomonas strains for biocontrol purposes. This system possibly plays a pivotal role in restricting the biological activity of target microorganisms and may also contribute to the bolstering of the survival capabilities of the bacteria within their applied environment. The type VI secretion system is a phage-like structure used to translocate effectors into both prokaryotic and eukaryotic target cells. T6SSs are involved in a myriad of interactions, some of which have direct implications in the success of Pseudomonas as biocontrol agents. The prevalence of T6SSs in the genomes of Pseudomonas species is notably greater than the estimated 25% occurrence rate found in Gram-negative bacteria. This observation implies that T6SS likely plays a pivotal role in the survival and fitness of Pseudomonas. This review provides a brief overview of T6SS, its role in Pseudomonas with biocontrol applications, and future avenues of research within this subject matter.
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Affiliation(s)
| | - Christopher G. Taylor
- Department of Plant Pathology, Ohio Agricultural Research and Development Center, Wooster, OH 44691, USA;
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26
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Cummins EA, Moran RA, Snaith AE, Hall RJ, Connor CH, Dunn SJ, McNally A. Parallel loss of type VI secretion systems in two multi-drug-resistant Escherichia coli lineages. Microb Genom 2023; 9. [PMID: 37970873 DOI: 10.1099/mgen.0.001133] [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] [Indexed: 11/19/2023] Open
Abstract
The repeated emergence of multi-drug-resistant (MDR) Escherichia coli clones is a threat to public health globally. In recent work, drug-resistant E. coli were shown to be capable of displacing commensal E. coli in the human gut. Given the rapid colonization observed in travel studies, it is possible that the presence of a type VI secretion system (T6SS) may be responsible for the rapid competitive advantage of drug-resistant E. coli clones. We employed large-scale genomic approaches to investigate this hypothesis. First, we searched for T6SS genes across a curated dataset of over 20 000 genomes representing the full phylogenetic diversity of E. coli. This revealed large, non-phylogenetic variation in the presence of T6SS genes. No association was found between T6SS gene carriage and MDR lineages. However, multiple clades containing MDR clones have lost essential structural T6SS genes. We characterized the T6SS loci of ST410 and ST131 and identified specific recombination and insertion events responsible for the parallel loss of essential T6SS genes in two MDR clones.
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Affiliation(s)
- Elizabeth A Cummins
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Robert A Moran
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Ann E Snaith
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Rebecca J Hall
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Christopher H Connor
- Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne 3000, Australia
| | - Steven J Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
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27
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Lee S, Kang M, Jung CD, Bae JH, Lee JY, Park YK, Joo JC, Kim H, Sohn JH, Sung BH. Development of novel recombinant peroxidase secretion system from Pseudomonas putida for lignin valorisation. BIORESOURCE TECHNOLOGY 2023; 388:129779. [PMID: 37739186 DOI: 10.1016/j.biortech.2023.129779] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 08/25/2023] [Accepted: 09/11/2023] [Indexed: 09/24/2023]
Abstract
Pseudomonas putida is a promising strain for lignin valorisation. However, there is a dearth of stable and efficient systems for secreting enzymes to enhance the process. Therefore, a novel secretion system for recombinant lignin-depolymerising peroxidase was developed. By adopting a flagellar type III secretion system, P. putida KT-M2, a secretory host strain, was constructed and an optimal secretion signal fusion partner was identified. Application of the dye-decolourising peroxidase of P. putida to this system resulted in efficient oxidation activity of the cell-free supernatant against various chemicals, including lignin model compounds. This peroxidase-secreting strain was examined to confirm its lignin utilisation capability, resulting in the efficient assimilation of various lignin substrates with 2.6-fold higher growth than that of the wild-type strain after 72 h of cultivation. Finally, this novel system will lead efficient bacterial lignin breakdown and utilization through enzyme secretion, paving the way for sustainable lignin-consolidated bioprocessing.
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Affiliation(s)
- Siseon Lee
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Minsik Kang
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Chan-Duck Jung
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Jung-Hoon Bae
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea
| | - Ju Young Lee
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Young-Kwon Park
- School of Environmental Engineering, University of Seoul, Seoul 02504, Republic of Korea
| | - Jeong Chan Joo
- Department of Biotechnology, The Catholic University of Korea, Bucheon-si, Gyeonggi-do 14662, Republic of Korea
| | - Hoyong Kim
- Center for Bio-based Chemistry, Korea Research Institute of Chemical Technology (KRICT), Ulsan 44429, Republic of Korea
| | - Jung-Hoon Sohn
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea
| | - Bong Hyun Sung
- Synthetic Biology Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Biosystems and Bioengineering Program, Korea University of Science and Technology (UST), Daejeon 34113, Republic of Korea; Graduate School of Engineering Biology, Korea Advanced Institute of Science and Technology (KAIST), Daejeon 34141, Republic of Korea.
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28
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Bourigault Y, Dupont CA, Desjardins JB, Doan T, Bouteiller M, Le Guenno H, Chevalier S, Barbey C, Latour X, Cascales E, Merieau A. Pseudomonas fluorescens MFE01 delivers a putative type VI secretion amidase that confers biocontrol against the soft-rot pathogen Pectobacterium atrosepticum. Environ Microbiol 2023; 25:2564-2579. [PMID: 37622480 DOI: 10.1111/1462-2920.16492] [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: 12/14/2022] [Accepted: 08/15/2023] [Indexed: 08/26/2023]
Abstract
The type VI secretion system (T6SS) is a contractile nanomachine widespread in Gram-negative bacteria. The T6SS injects effectors into target cells including eukaryotic hosts and competitor microbial cells and thus participates in pathogenesis and intermicrobial competition. Pseudomonas fluorescens MFE01 possesses a single T6SS gene cluster that confers biocontrol properties by protecting potato tubers against the phytopathogen Pectobacterium atrosepticum (Pca). Here, we demonstrate that a functional T6SS is essential to protect potato tuber by reducing the pectobacteria population. Fluorescence microscopy experiments showed that MFE01 displays an aggressive behaviour with an offensive T6SS characterized by continuous and intense T6SS firing activity. Interestingly, we observed that T6SS firing is correlated with rounding of Pectobacterium cells, suggesting delivery of a potent cell wall targeting effector. Mutagenesis coupled with functional assays then revealed that a putative T6SS secreted amidase, Tae3Pf , is mainly responsible for MFE01 toxicity towards Pca. Further studies finally demonstrated that Tae3Pf is toxic when produced in the periplasm, and that its toxicity is counteracted by the Tai3Pf inner membrane immunity protein.
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Affiliation(s)
- Yvann Bourigault
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Charly A Dupont
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Jonas B Desjardins
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Thierry Doan
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Mathilde Bouteiller
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Hugo Le Guenno
- Plateforme de Microscopie, Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Sylvie Chevalier
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
| | - Corinne Barbey
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Xavier Latour
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
| | - Eric Cascales
- Laboratoire d'Ingénierie des Systèmes Macromoléculaires (LISM, UMR 7255), Institut de Microbiologie de la Méditerranée (IMM, FR3479), CNRS-Aix-Marseille Univ, Marseille, France
| | - Annabelle Merieau
- Laboratoire de Communication Bactérienne et Stratégies Anti-infectieuses (CBSA, UR 4312), Univ Rouen Normandie, Université Caen Normandie, Normandie Univ, Rouen, France
- Structure Fédérative de Recherche Normandie Végétale, NORVEGE Fed4277, Mont-Saint-Aignan, France
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29
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Durán D, Vazquez-Arias D, Blanco-Romero E, Garrido-Sanz D, Redondo-Nieto M, Rivilla R, Martín M. An Orphan VrgG Auxiliary Module Related to the Type VI Secretion Systems from Pseudomonas ogarae F113 Mediates Bacterial Killing. Genes (Basel) 2023; 14:1979. [PMID: 38002922 PMCID: PMC10671463 DOI: 10.3390/genes14111979] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 10/17/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The model rhizobacterium Pseudomonas ogarae F113, a relevant plant growth-promoting bacterium, encodes three different Type VI secretion systems (T6SS) in its genome. In silico analysis of its genome revealed the presence of a genetic auxiliary module containing a gene encoding an orphan VgrG protein (VgrG5a) that is not genetically linked to any T6SS structural cluster, but is associated with genes encoding putative T6SS-related proteins: a possible adaptor Tap protein, followed by a putative effector, Tfe8, and its putative cognate immunity protein, Tfi8. The bioinformatic analysis of the VgrG5a auxiliary module has revealed that this cluster is only present in several subgroups of the P. fluorescens complex of species. An analysis of the mutants affecting the vgrG5a and tfe8 genes has shown that the module is involved in bacterial killing. To test whether Tfe8/Tfi8 constitute an effector-immunity pair, the genes encoding Tfe8 and Tfi8 were cloned and expressed in E. coli, showing that the ectopic expression of tfe8 affected growth. The growth defect was suppressed by tfi8 ectopic expression. These results indicate that Tfe8 is a bacterial killing effector, while Tfi8 is its cognate immunity protein. The Tfe8 protein sequence presents homology to the proteins of the MATE family involved in drug extrusion. The Tfe8 effector is a membrane protein with 10 to 12 transmembrane domains that could destabilize the membranes of target cells by the formation of pores, revealing the importance of these effectors for bacterial interaction. Tfe8 represents a novel type of a T6SS effector present in pseudomonads.
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Affiliation(s)
- David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - David Vazquez-Arias
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Darwin, 2, 28049 Madrid, Spain; (D.D.); (D.V.-A.); (E.B.-R.); (D.G.-S.); (M.R.-N.); (R.R.)
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30
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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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Vitt JD, Hansen EG, Garg R, Bowden SD. Bacteria intrinsic to Medicago sativa (alfalfa) reduce Salmonella enterica growth in planta. J Appl Microbiol 2023; 134:lxad204. [PMID: 37669894 DOI: 10.1093/jambio/lxad204] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/03/2023] [Accepted: 09/01/2023] [Indexed: 09/07/2023]
Abstract
AIMS The purpose of this study was to determine whether plant-associated bacteria (PAB) can reduce Salmonella enterica colonization and infection of alfalfa sprouts to reduce the risk of foodborne illness. METHODS We isolated PAB from alfalfa seeds and sprouts. Monoclonal isolates of the bacteria were obtained and tested for their ability to inhibit Salmonella Typhimurium growth in alfalfa sprouts over 6 days. Genome sequencing and annotation were used to construct draft genomes of the bacteria isolated in this study using Illumina sequencing platform. RESULTS We observed that a cocktail of five PAB could reduce Salmonella growth in alfalfa sprouts from ∼108 to ∼105 CFU g-1, demonstrating a protective role. Genome sequencing revealed that these bacteria were members of the Pseudomonas, Pantoea, and Priestia genus, and did not possess genes that were pathogenic to plants or animals. CONCLUSIONS This work demonstrates that PAB can be utilized to reduce pathogen levels in fresh produce, which may be synergistic with other technologies to improve the safety of sprouts and other fresh produce.
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Affiliation(s)
- Jacob D Vitt
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Eleanore G Hansen
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Raghav Garg
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
| | - Steven D Bowden
- Department of Food Science and Nutrition, University of Minnesota-Twin Cities, Saint Paul, MN 55108, United States
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Kan Y, Zhang Y, Lin W, Dong T. Differential plant cell responses to Acidovorax citrulli T3SS and T6SS reveal an effective strategy for controlling plant-associated pathogens. mBio 2023; 14:e0045923. [PMID: 37288971 PMCID: PMC10470598 DOI: 10.1128/mbio.00459-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023] Open
Abstract
Acidovorax citrulli is a gram-negative plant pathogen that employs the type Ⅲ secretion system (T3SS) to infect cucurbit crops and cause bacterial fruit blotch. This bacterium also possesses an active type Ⅵ secretion system (T6SS) with strong antibacterial and antifungal activities. However, how plant cells respond to these two secretion systems and whether there is any cross talk between T3SS and T6SS during infection remain unknown. Here, we employ transcriptomic analysis to compare cellular responses to the T3SS and the T6SS during in planta infection and report distinctive effects on multiple pathways. The T3SS-mediated differentially expressed genes were enriched in the pathways of phenylpropanoid biosynthesis, plant-pathogen interaction, MAPK signaling pathway, and glutathione metabolism, while the T6SS uniquely affected genes were related to photosynthesis. The T6SS does not contribute to the in planta virulence of A. citrulli but is critical for the survival of the bacterium when mixed with watermelon phyllosphere bacteria. In addition, T3SS-mediated virulence is independent of the T6SS, and the inactivation of the T3SS does not affect the T6SS-mediated competition against a diverse set of bacterial pathogens that commonly contaminate edible plants or directly infect plants. A T6SS-active T3SS-null mutant (Acav) could inhibit the growth of Xanthomonas oryzae pv. oryzae significantly both in vitro and in vivo and also reduce symptoms of rice bacterial blight. In conclusion, our data demonstrate the T6SS in A. citrulli is nonpathogenic to the plant host and can be harnessed as a pathogen killer against plant-associated bacteria. IMPORTANCE Chemical pesticides are widely used to protect crops from various pathogens. Still, their extensive use has led to severe consequences, including drug resistance and environmental contamination. Here, we show that an engineered T6SS-active, but avirulent mutant of Acidovorax citrulli has strong inhibition capabilities against several pathogenic bacteria, demonstrating an effective strategy that is an alternative to chemical pesticides for sustainable agricultural practices.
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Affiliation(s)
- Yumin Kan
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Yanjie Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Wenhui Lin
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Tao Dong
- Department of Immunology and Microbiology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, China
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Hug S, Heiniger B, Bolli K, Paszti S, Eberl L, Ahrens CH, Pessi G. Paraburkholderia sabiae Uses One Type VI Secretion System (T6SS-1) as a Powerful Weapon against Notorious Plant Pathogens. Microbiol Spectr 2023; 11:e0162223. [PMID: 37439699 PMCID: PMC10434147 DOI: 10.1128/spectrum.01622-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 06/21/2023] [Indexed: 07/14/2023] Open
Abstract
Paraburkholderia sabiae LMG24235 is a nitrogen-fixing betaproteobacterium originally isolated from a root nodule of Mimosa caesalpiniifolia in Brazil. We show here that this strain effectively kills strains from several bacterial families (Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae) which include important plant pathogens in a contact-dependent manner. De novo assembly of the first complete genome of P. sabiae using long sequencing reads and subsequent annotation revealed two gene clusters predicted to encode type VI secretion systems (T6SS), which we named T6SS-1 and T6SS-3 according to previous classification methods (G. Shalom, J. G. Shaw, and M. S. Thomas, Microbiology, 153:2689-2699, 2007, https://doi.org/10.1099/mic.0.2007/006585-0). We created P. sabiae with mutations in each of the two T6SS gene clusters that abrogated their function, and the T6SS-1 mutant was no longer able to outcompete other strains in a contact-dependent manner. Notably, our analysis revealed that T6SS-1 is essential for competition against several important plant pathogens in vitro, including Burkholderia plantarii, Ralstonia solanacearum, Pseudomonas syringae, and Pectobacterium carotovorum. The 9-log reduction in P. syringae cells in the presence of P. sabiae was particularly remarkable. Importantly, in an in vivo assay, P. sabiae was able to protect potato tubers from bacterial soft rot disease caused by P. carotovorum, and this protection was partly dependent on T6SS-1. IMPORTANCE Rhizobia often display additional beneficial traits such as the production of plant hormones and the acquisition of limited essential nutrients that improve plant growth and enhance plant yields. Here, we show that the rhizobial strain P. sabiae antagonizes important phytopathogens such as P. carotovorum, P. syringae, and R. solanacearum and that this effect is due to contact-dependent killing mediated by one of two T6SS systems identified in the complete, de novo assembled genome sequence of P. sabiae. Importantly, co-inoculation of Solanum tuberosum tubers with P. sabiae also resulted in a drastic reduction of soft rot caused by P. carotovorum in an in vivo model system. This result highlights the protective potential of P. sabiae against important bacterial plant diseases, which makes it a valuable candidate for application as a biocontrol agent. It also emphasizes the particular potential of rhizobial inoculants that combine several beneficial effects such as plant growth promotion and biocontrol for sustainable agriculture.
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Affiliation(s)
- Sebastian Hug
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Benjamin Heiniger
- Agroscope – Molecular Ecology, Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Kim Bolli
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Sarah Paszti
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
| | - Christian H. Ahrens
- Agroscope – Molecular Ecology, Swiss Institute of Bioinformatics, Zurich, Switzerland
| | - Gabriella Pessi
- Department of Plant and Microbial Biology, University of Zürich, Zurich, Switzerland
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Naranjo HD, Rat A, De Zutter N, De Ridder E, Lebbe L, Audenaert K, Willems A. Uncovering Genomic Features and Biosynthetic Gene Clusters in Endophytic Bacteria from Roots of the Medicinal Plant Alkanna tinctoria Tausch as a Strategy To Identify Novel Biocontrol Bacteria. Microbiol Spectr 2023; 11:e0074723. [PMID: 37436171 PMCID: PMC10434035 DOI: 10.1128/spectrum.00747-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 06/25/2023] [Indexed: 07/13/2023] Open
Abstract
The world's population is increasing at a rate not seen in the past. Agriculture, providing food for this increasing population, is reaching its boundaries of space and natural resources. In addition, changing legislation and increased ecological awareness are forcing agriculture to reduce its environmental impact. This entails the replacement of agrochemicals with nature-based solutions. In this regard, the search for effective biocontrol agents that protect crops from pathogens is in the spotlight. In this study, we have investigated the biocontrol activity of endophytic bacteria isolated from the medicinal plant Alkanna tinctoria Tausch. To do so, an extensive collection of bacterial strains was initially genome sequenced and in silico screened for features related to plant stimulation and biocontrol. Based on this information, a selection of bacteria was tested in vitro for antifungal activity using direct antagonism in a plate assay and in planta with a detached-leaf assay. Bacterial strains were tested individually and in combinations to assess the best-performing treatments. The results revealed that many bacteria could produce metabolites that efficiently inhibit the proliferation of several fungi, especially Fusarium graminearum. Among these, Pseudomonas sp. strain R-71838 showed a strong antifungal effect, in both dual-culture and in planta assays, making it the most promising candidate for biocontrol application. Using microbes from medicinal plants, this study highlights the opportunities of using genomic information to speed up the screening of a taxonomically diverse set of bacteria with biocontrol properties. IMPORTANCE Phytopathogenic fungi are a major threat to global food production. The most common management practice to prevent plant infections involves the intensive use of fungicides. However, with the growing awareness of the ecological and human impacts of chemicals, there is a need for alternative strategies, such as the use of bacterial biocontrol agents. Limitations in the design of bacterial biocontrol included the need for labor-intensive and time-consuming experiments to test a wide diversity of strains and the lack of reproducibility of their activity against pathogens. Here, we show that genomic information is an effective tool to select bacteria of interest quickly. Also, we highlight that the strain Pseudomonas sp. R-71838 produced a reproducible antifungal effect both in vitro and in planta. These findings build a foundation for designing a biocontrol strategy based on Pseudomonas sp. R-71838.
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Affiliation(s)
- Henry D. Naranjo
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Angélique Rat
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Noémie De Zutter
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Emmelie De Ridder
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Liesbeth Lebbe
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
| | - Kris Audenaert
- Laboratory of Applied Mycology and Phenomics, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Anne Willems
- Laboratory of Microbiology, Department of Biochemistry and Microbiology, Faculty of Sciences, Ghent University, Ghent, Belgium
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35
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Sánchez-Gil JJ, Poppeliers SWM, Vacheron J, Zhang H, Odijk B, Keel C, de Jonge R. The conserved iol gene cluster in Pseudomonas is involved in rhizosphere competence. Curr Biol 2023; 33:3097-3110.e6. [PMID: 37419116 DOI: 10.1016/j.cub.2023.05.057] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 04/25/2023] [Accepted: 05/24/2023] [Indexed: 07/09/2023]
Abstract
The Pseudomonas genus has shown great potential as a sustainable solution to support agriculture through its plant-growth-promoting and biocontrol activities. However, their efficacy as bioinoculants is limited by unpredictable colonization in natural conditions. Our study identifies the iol locus, a gene cluster in Pseudomonas involved in inositol catabolism, as a feature enriched among superior root colonizers in natural soil. Further characterization revealed that the iol locus increases competitiveness, potentially caused by an observed induction of swimming motility and the production of fluorescent siderophore in response to inositol, a plant-derived compound. Public data analyses indicate that the iol locus is broadly conserved in the Pseudomonas genus and linked to diverse host-microbe interactions. Together, our findings suggest the iol locus as a potential target for developing more effective bioinoculants for sustainable agriculture.
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Affiliation(s)
- Juan J Sánchez-Gil
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Sanne W M Poppeliers
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Jordan Vacheron
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Hao Zhang
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Bart Odijk
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands
| | - Christoph Keel
- Department of Fundamental Microbiology, University of Lausanne, Lausanne CH-1015, Switzerland
| | - Ronnie de Jonge
- Plant-Microbe Interactions, Department of Biology, Science for Life, Utrecht University, Utrecht 3584 CH, The Netherlands.
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Lin L, Li L, Tao M, Wu Q, Zhou L, Wang B, Wang L, Shao X, Zhong C, Qian G. Assembly of an active microbial consortium by engineering compatible combinations containing foreign and native biocontrol bacteria of kiwifruit. Comput Struct Biotechnol J 2023; 21:3672-3679. [PMID: 37576746 PMCID: PMC10412838 DOI: 10.1016/j.csbj.2023.07.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 07/12/2023] [Accepted: 07/19/2023] [Indexed: 08/15/2023] Open
Abstract
Assembling functional bacterial biocontrol consortia is expected to expand the scope and efficiency of biocontrol agents. Generally, bacterial interspecies interactions lead to incompatibility events, as bacteria can produce antibacterial compounds and/or assemble contact-dependent killing (CDK) devices. Here, we aimed to assemble a bacterial consortium comprising Lysobacter enzymogenes OH11 and Bacillus safensis ZK-1 for the synergistic control of bacterial and fungal diseases of kiwifruit. ZK-1, a native kiwifruit biocontrol bacterium, is effective against Pseudomonas syringae pv. actinidiae (Psa) that causes bacterial kiwifruit canker, but has weak antifungal activity. OH11 is a foreign kiwifruit biocontrol agent with strong antifungal activity. While OH11 was unable to produce anti-Gram-negative metabolites, this strain could utilize type IV secretion system as an antibacterial CDK weapon. We first observed that OH11 could inhibit growth of ZK-1 by generating diffusible anti-Gram-positive antibiotic WAP-8294A2, whereas ZK-1 failed to generate diffusible antibacterial compound to inhibit growth of OH11. To disrupt this interspecies incompatibility, we generated a transgenic OH11-derived strain, OH11W, by deleting the WAP-8294A2 biosynthetic gene and found that OH11W did not kill ZK-1. We further observed that when OH11W and ZK-1 were co-inoculated on agar plates, no CDK effect was observed between them, whereas co-culture of OH11W or ZK-1 with Psa on agar plates resulted in Psa killing, suggesting L. enzymogenes and B. safensis assemble antibacterial CDK weapons against bacterial pathogens, and these CDK weapons did not affect the compatibility between OH11W and ZK-1. Based on these findings, we assembled an OH11W/ZK-1 dependent consortium that was shown to be functional in controlling bacterial canker and several representative fungal diseases of kiwifruit.
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Affiliation(s)
- Long Lin
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Li Li
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Min Tao
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Qianhua Wu
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Longteng Zhou
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Bozhen Wang
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Limin Wang
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Xiaolong Shao
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
| | - Caihong Zhong
- CAS Engineering Laboratory for Kiwifruit Industrial Technology, CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, Hubei Province 430074, China
| | - Guoliang Qian
- Key Laboratory of Biological interactions and Crop Health, Key Laboratory of Integrated Management of Crop Diseases and Pests, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, PR China
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Allsopp LP, Bernal P. Killing in the name of: T6SS structure and effector diversity. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001367. [PMID: 37490402 PMCID: PMC10433429 DOI: 10.1099/mic.0.001367] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/27/2023]
Abstract
The life of bacteria is challenging, to endure bacteria employ a range of mechanisms to optimize their environment, including deploying the type VI secretion system (T6SS). Acting as a bacterial crossbow, this system delivers effectors responsible for subverting host cells, killing competitors and facilitating general secretion to access common goods. Due to its importance, this lethal machine has been evolutionarily maintained, disseminated and specialized to fulfil these vital functions. In fact, T6SS structural clusters are present in over 25 % of Gram-negative bacteria, varying in number from one to six different genetic clusters per organism. Since its discovery in 2006, research on the T6SS has rapidly progressed, yielding remarkable breakthroughs. The identification and characterization of novel components of the T6SS, combined with biochemical and structural studies, have revealed fascinating mechanisms governing its assembly, loading, firing and disassembly processes. Recent findings have also demonstrated the efficacy of this system against fungal and Gram-positive cells, expanding its scope. Ongoing research continues to uncover an extensive and expanding repertoire of T6SS effectors, the genuine mediators of T6SS function. These studies are shedding light on new aspects of the biology of prokaryotic and eukaryotic organisms. This review provides a comprehensive overview of the T6SS, highlighting recent discoveries of its structure and the diversity of its effectors. Additionally, it injects a personal perspective on avenues for future research, aiming to deepen our understanding of this combative system.
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Affiliation(s)
- Luke P. Allsopp
- National Heart and Lung Institute, Imperial College London, London, UK
| | - Patricia Bernal
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Sevilla 41012, Spain
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Crisan CV, Van Tyne D, Goldberg JB. The Type VI Secretion System of the Emerging Pathogen Stenotrophomonas maltophilia has Antibacterial Properties. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.30.542968. [PMID: 37398041 PMCID: PMC10312562 DOI: 10.1101/2023.05.30.542968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Antagonistic behaviors between bacterial cells can have profound effects on microbial populations and disease outcomes. Polymicrobial interactions may be mediated by contact-dependent proteins with antibacterial properties. The Type VI Secretion System (T6SS) is a macromolecular weapon used by Gram-negative bacteria to translocate proteins into adjacent cells. The T6SS is used by pathogens to escape immune cells, eliminate commensal bacteria, and facilitate infection. Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that causes a wide range of infections in immunocompromised patients and infects the lungs of patients with cystic fibrosis. Infections with the bacterium can be deadly and are challenging to treat because many isolates are multidrug-resistant. We found that globally dispersed S. maltophilia clinical and environmental strains possess T6SS genes. We demonstrate that the T6SS of an S. maltophilia patient isolate is active and can eliminate other bacteria. Furthermore, we provide evidence that the T6SS contributes to the competitive fitness of S. maltophilia against a co-infecting Pseudomonas aeruginosa isolate, and that the T6SS alters the cellular organization of S. maltophilia and P. aeruginosa co-cultures. This study expands our knowledge of the mechanisms employed by S. maltophilia to secrete antibacterial proteins and compete against other bacteria. IMPORTANCE Infections with the opportunistic pathogen Stenotrophomonas maltophilia can be fatal for immunocompromised patients. The mechanisms used by the bacterium to compete against other prokaryotes are not well understood. We found that the T6SS allows S. maltophilia to eliminate other bacteria and contributes to the competitive fitness against a co-infecting isolate. The presence of T6SS genes in isolates across the globe highlights the importance of this apparatus as a weapon in the antibacterial arsenal of S. maltophilia . The T6SS may confer survival advantages to S. maltophilia isolates in polymicrobial communities in both environmental settings and during infections.
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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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40
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Rudzite M, Subramoni S, Endres RG, Filloux A. Effectiveness of Pseudomonas aeruginosa type VI secretion system relies on toxin potency and type IV pili-dependent interaction. PLoS Pathog 2023; 19:e1011428. [PMID: 37253075 PMCID: PMC10281587 DOI: 10.1371/journal.ppat.1011428] [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: 11/30/2022] [Revised: 06/20/2023] [Accepted: 05/17/2023] [Indexed: 06/01/2023] Open
Abstract
The type VI secretion system (T6SS) is an antibacterial weapon that is used by numerous Gram-negative bacteria to gain competitive advantage by injecting toxins into adjacent prey cells. Predicting the outcome of a T6SS-dependent competition is not only reliant on presence-absence of the system but instead involves a multiplicity of factors. Pseudomonas aeruginosa possesses 3 distinct T6SSs and a set of more than 20 toxic effectors with diverse functions including disruption of cell wall integrity, degradation of nucleic acids or metabolic impairment. We generated a comprehensive collection of mutants with various degrees of T6SS activity and/or sensitivity to each individual T6SS toxin. By imaging whole mixed bacterial macrocolonies, we then investigated how these P. aeruginosa strains gain a competitive edge in multiple attacker/prey combinations. We observed that the potency of single T6SS toxin varies significantly from one another as measured by monitoring the community structure, with some toxins acting better in synergy or requiring a higher payload. Remarkably the degree of intermixing between preys and attackers is also key to the competition outcome and is driven by the frequency of contact as well as the ability of the prey to move away from the attacker using type IV pili-dependent twitching motility. Finally, we implemented a computational model to better understand how changes in T6SS firing behaviours or cell-cell contacts lead to population level competitive advantages, thus providing conceptual insight applicable to all types of contact-based competition.
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Affiliation(s)
- Marta Rudzite
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Robert G. Endres
- Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London, United Kingdom
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, United Kingdom
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
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41
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Granato ET, Smith WPJ, Foster KR. Collective protection against the type VI secretion system in bacteria. THE ISME JOURNAL 2023:10.1038/s41396-023-01401-4. [PMID: 37095301 DOI: 10.1038/s41396-023-01401-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 03/11/2023] [Accepted: 03/20/2023] [Indexed: 04/26/2023]
Abstract
Bacteria commonly face attacks from other strains using the type VI secretion system (T6SS), which acts like a molecular speargun to stab and intoxicate competitors. Here we show how bacteria can work together to collectively defend themselves against these attacks. This project began with an outreach activity: while developing an online computer game of bacterial warfare, we noticed that one strategist ("Slimy") that made extracellular polymeric substances (EPS) was able to resist attacks from another strategist that employed the T6SS ("Stabby"). This observation motivated us to model this scenario more formally, using dedicated agent-based simulations. The model predicts that EPS production can serve as a collective defence mechanism, which protects both producing cells and neighbouring cells that do not make EPS. We then tested our model with a synthetic community that contains a T6SS-wielding attacker (Acinetobacter baylyi), and two T6SS-sensitive target strains (Escherichia coli) that either secrete EPS, or not. As predicted by our modelling, we find that the production of EPS leads to collective protection against T6SS attacks, where EPS producers protect each other and nearby non-producers. We identify two processes that explain this protection: EPS sharing between cells and a second general mechanism whereby groups of resistant cells shield susceptible cells, which we call "flank protection". Our work shows how EPS-producing bacteria can work together to defend themselves from the type VI secretion system.
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Affiliation(s)
- Elisa T Granato
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
| | - William P J Smith
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Division of Genomics, Infection and Evolution, University of Manchester, Manchester, UK.
| | - Kevin R Foster
- Department of Biology, University of Oxford, Oxford, UK.
- Department of Biochemistry, University of Oxford, Oxford, UK.
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Rubio A, Sprang M, Garzón A, Moreno-Rodriguez A, Pachón-Ibáñez ME, Pachón J, Andrade-Navarro MA, Pérez-Pulido AJ. Analysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems. SCIENCE ADVANCES 2023; 9:eadd8911. [PMID: 36961900 PMCID: PMC10038342 DOI: 10.1126/sciadv.add8911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 02/17/2023] [Indexed: 06/18/2023]
Abstract
CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.
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Affiliation(s)
- Alejandro Rubio
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013 Seville, Spain
| | - Maximilian Sprang
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Andrés Garzón
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013 Seville, Spain
| | - Antonio Moreno-Rodriguez
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013 Seville, Spain
| | - Maria Eugenia Pachón-Ibáñez
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío Hospital/CSIC/University of Seville, Seville, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Jerónimo Pachón
- Institute of Biomedicine of Seville (IBiS), Virgen del Rocío Hospital/CSIC/University of Seville, Seville, Spain
- Department of Medicine, School of Medicine, University of Seville, Seville, Spain
| | - Miguel A. Andrade-Navarro
- Faculty of Biology, Johannes Gutenberg-Universität Mainz, Biozentrum I, Hans-Dieter-Hüsch-Weg 15, 55128 Mainz, Germany
| | - Antonio J. Pérez-Pulido
- Andalusian Centre for Developmental Biology (CABD, UPO-CSIC-JA), Faculty of Experimental Sciences (Genetics Department), University Pablo de Olavide, 41013 Seville, Spain
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Pérez-Lorente AI, Molina-Santiago C, de Vicente A, Romero D. Sporulation Activated via σ W Protects Bacillus from a Tse1 Peptidoglycan Hydrolase Type VI Secretion System Effector. Microbiol Spectr 2023; 11:e0504522. [PMID: 36916921 PMCID: PMC10100999 DOI: 10.1128/spectrum.05045-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 02/21/2023] [Indexed: 03/16/2023] Open
Abstract
Within bacterial communities, community members engage in interactions employing diverse offensive and defensive tools to reach coexistence. Extracellular-matrix production and sporulation are defensive mechanisms used by Bacillus subtilis cells when they interact with Pseudomonas chlororaphis strains expressing a type VI secretion system (T6SS). Here, we define Tse1 as the main toxin mobilized by the Pseudomonas chlororaphis T6SS that triggers sporulation in Bacillus subtilis. We characterize Tse1 as a peptidoglycan hydrolase that indirectly alters the dynamics and functionality of the Bacillus cell membrane. We also delineate the response of Bacillus cells to Tse1, which through the coordinated actions of the extracellular sigma factor σW and the cytoplasmic histidine kinases KinA and KinB, culminates in activation of the sporulation cascade. We propose that this cellular developmental response permits bacilli to defend against the toxicity of T6SS-mobilized Tse1 effector. IMPORTANCE The study of bacterial interactions is helping to define species-specific strategies used to modulate the competition dynamics underlying the development of community compositions. In this study, we deciphered the role of Pseudomonas T6SS when competing with Bacillus and the mechanism by which a T6SS-toxin modifies Bacillus physiology. We found that Pseudomonas triggers Bacillus sporulation by injecting through T6SS a toxin that we called Tse1. We found that Tse1 is a hydrolase that degrades Bacillus peptidoglycan and indirectly damages Bacillus membrane functionality. In addition, we demonstrated the mechanism by which Bacillus cells increase the sporulation rate upon recognition of the presence of Tse1. Interestingly, asporogenic Bacillus cells are more sensitive to T6SS activity, which led us to propose sporulation as a last resort of bacilli to overcome this family of toxins.
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Affiliation(s)
- Alicia I. Pérez-Lorente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea La Mayora, Universidad de Málaga-Consejo Superior de Investigaciones Científicas, Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
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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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45
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Singh RP, Kumari K. Bacterial type VI secretion system (T6SS): an evolved molecular weapon with diverse functionality. Biotechnol Lett 2023; 45:309-331. [PMID: 36683130 DOI: 10.1007/s10529-023-03354-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 12/14/2022] [Accepted: 01/05/2023] [Indexed: 01/24/2023]
Abstract
Bacterial secretion systems are nanomolecular complexes that release a diverse set of virulence factors/or proteins into its surrounding or translocate to their target host cells. Among these systems, type VI secretion system 'T6SS' is a recently discovered molecular secretion system which is widely distributed in Gram-negative (-ve) bacteria, and shares structural similarity with the puncturing device of bacteriophages. The presence of T6SS is an advantage to many bacteria as it delivers toxins to its neighbour pathogens for competitive survival, and also translocates protein effectors to the host cells, leading to disruption of lipid membranes, cell walls, and cytoskeletons etc. Recent studies have characterized both anti-prokaryotic and anti-eukaryotic effectors, where T6SS is involved in diverse cellular functions including favouring colonization, enhancing the survival, adhesive modifications, internalization, and evasion of the immune system. With the evolution of advanced genomics and proteomics tools, there has been an increase in the number of characterized T6SS effector arsenals and also more clear information about the adaptive significance of this complex system. The functions of T6SS are generally regulated at the transcription, post-transcription and post-translational levels through diverse mechanisms. In the present review, we aimed to provide information about the distribution of T6SS in diverse bacteria, any structural similarity/or dissimilarity, effectors proteins, functional significance, and regulatory mechanisms. We also tried to provide information about the diverse roles played by T6SS in its natural environments and hosts, and further any changes in the microbiome.
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Affiliation(s)
- Rajnish Prakash Singh
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India.
| | - Kiran Kumari
- Department of Bioengineering and Biotechnology, Birla Institute of Technology, Mesra, Ranchi, Jharkhand, 835215, India
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46
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Price-Christenson G, Yannarell A. Use of Ecological Theory to Understand the Efficacy and Mechanisms of Multistrain Biological Control. PHYTOPATHOLOGY 2023; 113:381-389. [PMID: 36656290 DOI: 10.1094/phyto-04-22-0115-rvw] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Since the 1970s, over 6,500 articles have been published about microbial biocontrols and over 200 microbial isolates have been registered for commercial use. However, many of these solutions have seen limited use due to limitations with their in-field efficacy. Even when multiple biocontrol agents are combined to create multistrain biocontrols, the resulting combinations can be less effective than the individual agents. One likely contributor is due to how multistrain microbial biocontrols are created. Multistrain microbial biocontrols are generally produced under controlled settings that are divorced from the ecological conditions they will need to function under. Traditionally, researchers culture, identify, and screen isolates for pathogen suppression traits. Then these researchers will combine the most promising isolates in an attempt to create more effective solutions. This approach, while effective for identifying suppressive isolates and determining the mechanisms of pathogen suppression, does not take into consideration the variability of natural environments, nor the complex ecological interactions that occur between plant hosts, pathogens, and component biocontrol agents, thus limiting the range of circumstances that these multistrain solutions can reliably succeed. To address these limitations, we suggest the application of relevant ecological theory to determine which isolates should be combined to create more reliable multistrain biocontrols. In this synthesis, we build on prior work focused on addressing plant pathogens through the use of multistrain microbial biocontrols, but we argue that viewing this work through the lens of ecology reveals key "design principles" from natural communities that are stable, functioning, and comprise multiple species.
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Affiliation(s)
- Gabriel Price-Christenson
- Department of Agricultural Microbiology, Earnest Agriculture, Rantoul, IL 61866
- Program in Ecology, Evolution, and Conservation Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801
| | - Anthony Yannarell
- Department of Natural Resources and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, IL 61801
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47
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Hespanhol JT, Karman L, Sanchez-Limache DE, Bayer-Santos E. Intercepting biological messages: Antibacterial molecules targeting nucleic acids during interbacterial conflicts. Genet Mol Biol 2023; 46:e20220266. [PMID: 36880694 PMCID: PMC9990079 DOI: 10.1590/1678-4685-gmb-2022-0266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 12/25/2022] [Indexed: 03/08/2023] Open
Abstract
Bacteria live in polymicrobial communities and constantly compete for resources. These organisms have evolved an array of antibacterial weapons to inhibit the growth or kill competitors. The arsenal comprises antibiotics, bacteriocins, and contact-dependent effectors that are either secreted in the medium or directly translocated into target cells. During bacterial antagonistic encounters, several cellular components important for life become a weak spot prone to an attack. Nucleic acids and the machinery responsible for their synthesis are well conserved across the tree of life. These molecules are part of the information flow in the central dogma of molecular biology and mediate long- and short-term storage for genetic information. The aim of this review is to summarize the diversity of antibacterial molecules that target nucleic acids during antagonistic interbacterial encounters and discuss their potential to promote the emergence antibiotic resistance.
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Affiliation(s)
- Julia Takuno Hespanhol
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | - Lior Karman
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
| | | | - Ethel Bayer-Santos
- Universidade de São Paulo, Instituto de Ciências Biomédicas, Departamento de Microbiologia, São Paulo, SP, Brazil
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48
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Thai TD, Lim W, Na D. Synthetic bacteria for the detection and bioremediation of heavy metals. Front Bioeng Biotechnol 2023; 11:1178680. [PMID: 37122866 PMCID: PMC10133563 DOI: 10.3389/fbioe.2023.1178680] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 04/04/2023] [Indexed: 05/02/2023] Open
Abstract
Toxic heavy metal accumulation is one of anthropogenic environmental pollutions, which poses risks to human health and ecological systems. Conventional heavy metal remediation approaches rely on expensive chemical and physical processes leading to the formation and release of other toxic waste products. Instead, microbial bioremediation has gained interest as a promising and cost-effective alternative to conventional methods, but the genetic complexity of microorganisms and the lack of appropriate genetic engineering technologies have impeded the development of bioremediating microorganisms. Recently, the emerging synthetic biology opened a new avenue for microbial bioremediation research and development by addressing the challenges and providing novel tools for constructing bacteria with enhanced capabilities: rapid detection and degradation of heavy metals while enhanced tolerance to toxic heavy metals. Moreover, synthetic biology also offers new technologies to meet biosafety regulations since genetically modified microorganisms may disrupt natural ecosystems. In this review, we introduce the use of microorganisms developed based on synthetic biology technologies for the detection and detoxification of heavy metals. Additionally, this review explores the technical strategies developed to overcome the biosafety requirements associated with the use of genetically modified microorganisms.
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49
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Bernal P, Civantos C, Pacheco-Sánchez D, Quesada JM, Filloux A, Llamas MA. Transcriptional organization and regulation of the Pseudomonas putida K1 type VI secretion system gene cluster. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001295. [PMID: 36748579 PMCID: PMC9993120 DOI: 10.1099/mic.0.001295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The type VI secretion system (T6SS) is an antimicrobial molecular weapon that is widespread in Proteobacteria and offers competitive advantages to T6SS-positive micro-organisms. Three T6SSs have recently been described in Pseudomonas putida KT2440 and it has been shown that one, K1-T6SS, is used to outcompete a wide range of phytopathogens, protecting plants from pathogen infections. Given the relevance of this system as a powerful and innovative mechanism of biological control, it is critical to understand the processes that govern its expression. Here, we experimentally defined two transcriptional units in the K1-T6SS cluster. One encodes the structural components of the system and is transcribed from two adjacent promoters. The other encodes two hypothetical proteins, the tip of the system and the associated adapters, and effectors and cognate immunity proteins, and it is also transcribed from two adjacent promoters. The four identified promoters contain the typical features of σ70-dependent promoters. We have studied the expression of the system under different conditions and in a number of mutants lacking global regulators. P. putida K1-T6SS expression is induced in the stationary phase, but its transcription does not depend on the stationary σ factor RpoS. In fact, the expression of the system is indirectly repressed by RpoS. Furthermore, it is also repressed by RpoN and the transcriptional regulator FleQ, an enhancer-binding protein typically acting in conjunction with RpoN. Importantly, expression of the K1-T6SS gene cluster is positively regulated by the GacS-GacA two-component regulatory system (TCS) and repressed by the RetS sensor kinase, which inhibits this TCS. Our findings identified a complex regulatory network that governs T6SS expression in general and P. putida K1-T6SS in particular, with implications for controlling and manipulating a bacterial agent that is highly relevant in biological control.
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Affiliation(s)
- Patricia Bernal
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain.,MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, 41012 Seville, Spain
| | - Cristina Civantos
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Daniel Pacheco-Sánchez
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - José M Quesada
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
| | - Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, UK.,Singapore Centre for Environmental Life Sciences Engineering. Nanyang Technological University, Singapore
| | - María A Llamas
- Department of Environmental Protection, Estación Experimental del Zaidín (CSIC), Granada, Spain
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50
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Zboralski A, Biessy A, Ciotola M, Cadieux M, Albert D, Blom J, Filion M. Harnessing the genomic diversity of Pseudomonas strains against lettuce bacterial pathogens. Front Microbiol 2022; 13:1038888. [PMID: 36620043 PMCID: PMC9814014 DOI: 10.3389/fmicb.2022.1038888] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Lettuce is a major vegetable crop worldwide that is affected by numerous bacterial pathogens, including Xanthomonas hortorum pv. vitians, Pseudomonas cichorii, and Pectobacterium carotovorum. Control methods are scarce and not always effective. To develop new and sustainable approaches to contain these pathogens, we screened more than 1,200 plant-associated Pseudomonas strains retrieved from agricultural soils for their in vitro antagonistic capabilities against the three bacterial pathogens under study. Thirty-five Pseudomonas strains significantly inhibited some or all three pathogens. Their genomes were fully sequenced and annotated. These strains belong to the P. fluorescens and P. putida phylogenomic groups and are distributed in at least 27 species, including 15 validly described species. They harbor numerous genes and clusters of genes known to be involved in plant-bacteria interactions, microbial competition, and biocontrol. Strains in the P. putida group displayed on average better inhibition abilities than strains in the P. fluorescens group. They carry genes and biosynthetic clusters mostly absent in the latter strains that are involved in the production of secondary metabolites such as 7-hydroxytropolone, putisolvins, pyochelin, and xantholysin-like and pseudomonine-like compounds. The presence of genes involved in the biosynthesis of type VI secretion systems, tailocins, and hydrogen cyanide also positively correlated with the strains' overall inhibition abilities observed against the three pathogens. These results show promise for the development of biocontrol products against lettuce bacterial pathogens, provide insights on some of the potential biocontrol mechanisms involved, and contribute to public Pseudomonas genome databases, including quality genome sequences on some poorly represented species.
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Affiliation(s)
- Antoine Zboralski
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Adrien Biessy
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Marie Ciotola
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Mélanie Cadieux
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Daphné Albert
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada
| | - Jochen Blom
- Bioinformatics and Systems Biology, Justus Liebig University Giessen, Giessen, Germany
| | - Martin Filion
- Centre de Recherche et de Développement de Saint-Jean-sur-Richelieu, Agriculture et Agroalimentaire Canada, Saint-Jean-sur-Richelieu, QC, Canada,*Correspondence: Martin Filion,
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