1
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Qi PY, Zhang TH, Yang YK, Liang H, Feng YM, Wang N, Ding ZH, Xiang HM, Zhou X, Liu LW, Jin LH, Li XY, Yang S. Beyond the β-amino alcohols framework: identification of novel β-hydroxy pyridinium salt-decorated pterostilbene derivatives as bacterial virulence factor inhibitors. PEST MANAGEMENT SCIENCE 2024; 80:4098-4109. [PMID: 38578108 DOI: 10.1002/ps.8116] [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: 11/03/2023] [Revised: 02/16/2024] [Accepted: 04/02/2024] [Indexed: 04/06/2024]
Abstract
BACKGROUND Bacterial virulence factors are involved in various biological processes and mediate persistent bacterial infections. Focusing on virulence factors of phytopathogenic bacteria is an attractive strategy and crucial direction in pesticide discovery to prevent invasive and persistent bacterial infection. Hence, discovery and development of novel agrochemicals with high activity, low-risk, and potent anti-virulence is urgently needed to control plant bacterial diseases. RESULTS A series of novel β-hydroxy pyridinium cation decorated pterostilbene derivatives were prepared and their antibacterial activities against Xanthomonas oryzae pv. oryzae (Xoo) were systematacially assessed. Among these pterostilbene derivatives, compound 4S exhibited the best antibacterial activity against Xoo in vitro, with an half maximal effective concentration (EC50) value of 0.28 μg mL-1. A series of biochemical assays including scanning electron microscopy, crystal violet staining, and analysis of biofilm formation, swimming motility, and related virulence factor gene expression levels demonstrated that compound 4S could function as a new anti-virulence factor inhibitor by interfering with the bacterial infection process. Furthermore, the pot experiments provided convinced evidence that compound 4S had the high control efficacy (curative activity: 71.4%, protective activity: 72.6%), and could be used to effectively manage rice bacterial leaf blight in vivo. CONCLUSION Compounds 4S is an attractive virulence factor inhibitor with potential for application in treating plant bacterial diseases by suppressing production of several virulence factors. © 2024 Society of Chemical Industry.
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Affiliation(s)
- Pu-Ying Qi
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Tai-Hong Zhang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yi-Ke Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Hong Liang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Yu-Mei Feng
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Na Wang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Zheng-Hao Ding
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Hong-Mei Xiang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Xiang Zhou
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Li-Wei Liu
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Lin-Hong Jin
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Xiang-Yang Li
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
| | - Song Yang
- National Key Laboratory of Green Pesticide, Key Laboratory of Green Pesticide and Agricultural Bioengineering, Ministry of Education, Center for R&D of Fine Chemicals of Guizhou University, Guiyang, China
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Dorfan Y, Nahami A, Morris Y, Shohat B, Kolodkin-Gal I. The Utilization of Bacillus subtilis to Design Environmentally Friendly Living Paints with Anti-Mold Properties. Microorganisms 2024; 12:1226. [PMID: 38930607 PMCID: PMC11205451 DOI: 10.3390/microorganisms12061226] [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: 04/23/2024] [Revised: 05/31/2024] [Accepted: 06/07/2024] [Indexed: 06/28/2024] Open
Abstract
The anti-fungal properties of the probiotic bacterium Bacillus subtilis have been studied extensively in agriculture and ecology, but their applications in the built environment remain to be determined. Our work aims to utilize this biological component to introduce new diverse anti-mold properties into paint. "Mold" refers to the ubiquitous fungal species that generate visible multicellular filaments commonly found in household dust. The development of mold leads to severe health problems for occupants, including allergic response, hypersensitivity pneumonitis, and asthma, which have significant economic and clinical outcomes. We here demonstrate the robust effect of a commercial paint enhanced with Bacillus subtilis cells against the common mold agent, Aspergillus niger, and identify three biosynthetic clusters essential for this effect. Our results lay the foundation for bio-convergence and synthetic biology approaches to introduce renewable and environmentally friendly bio-anti-fungal agents into the built environment.
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Affiliation(s)
- Yuval Dorfan
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Avichay Nahami
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
| | - Yael Morris
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Benny Shohat
- Faculty of Electrical Engineering, Holon Institute of Technology, Holon 5810201, Israel; (A.N.); (B.S.)
| | - Ilana Kolodkin-Gal
- The Scojen Institute for Synthetic Biology, Reichman University, Herzliya 4610101, Israel
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3
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Ye J, Salti T, Zanditenas E, Trebicz-Geffen M, Benhar M, Ankri S. Impact of Reactive Sulfur Species on Entamoeba histolytica: Modulating Viability, Motility, and Biofilm Degradation Capacity. Antioxidants (Basel) 2024; 13:245. [PMID: 38397843 PMCID: PMC10886169 DOI: 10.3390/antiox13020245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 02/15/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Reactive sulfur species (RSS) like hydrogen sulfide (H2S) and cysteine persulfide (Cys-SSH) emerged as key signaling molecules with diverse physiological roles in the body, depending on their concentration and the cellular environment. While it is known that H2S and Cys-SSH are produced by both colonocytes and by the gut microbiota through sulfur metabolism, it remains unknown how these RSS affect amebiasis caused by Entamoeba histolytica, a parasitic protozoan that can be present in the human gastrointestinal tract. This study investigates H2S and Cys-SSH's impact on E. histolytica physiology and explores potential therapeutic implications. Exposing trophozoites to the H2S donor, sodium sulfide (Na2S), or to Cys-SSH led to rapid cytotoxicity. A proteomic analysis of Cys-SSH-challenged trophozoites resulted in the identification of >500 S-sulfurated proteins, which are involved in diverse cellular processes. Functional assessments revealed inhibited protein synthesis, altered cytoskeletal dynamics, and reduced motility in trophozoites treated with Cys-SSH. Notably, cysteine proteases (CPs) were significantly inhibited by S-sulfuration, affecting their bacterial biofilm degradation capacity. Immunofluorescence microscopy confirmed alterations in actin dynamics, corroborating the proteomic findings. Thus, our study reveals how RSS perturbs critical cellular functions in E. histolytica, potentially influencing its pathogenicity and interactions within the gut microbiota. Understanding these molecular mechanisms offers novel insights into amebiasis pathogenesis and unveils potential therapeutic avenues targeting RSS-mediated modifications in parasitic infections.
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Affiliation(s)
- Jun Ye
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel (M.T.-G.)
| | - Talal Salti
- Department of Biochemistry, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel (M.T.-G.)
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel (M.T.-G.)
| | - Moran Benhar
- Department of Biochemistry, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel (M.T.-G.)
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4
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Lyng M, Jørgensen JPB, Schostag MD, Jarmusch SA, Aguilar DKC, Lozano-Andrade CN, Kovács ÁT. Competition for iron shapes metabolic antagonism between Bacillus subtilis and Pseudomonas marginalis. THE ISME JOURNAL 2024; 18:wrad001. [PMID: 38365234 PMCID: PMC10811728 DOI: 10.1093/ismejo/wrad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 11/03/2023] [Indexed: 02/18/2024]
Abstract
Siderophores have long been implicated in sociomicrobiology as determinants of bacterial interrelations. For plant-associated genera, like Bacillus and Pseudomonas, siderophores are well known for their biocontrol functions. Here, we explored the functional role of the Bacillus subtilis siderophore bacillibactin (BB) in an antagonistic interaction with Pseudomonas marginalis. The presence of BB strongly influenced the outcome of the interaction in an iron-dependent manner. The BB producer B. subtilis restricts colony spreading of P. marginalis by repressing the transcription of histidine kinase-encoding gene gacS, thereby abolishing production of secondary metabolites such as pyoverdine and viscosin. By contrast, lack of BB restricted B. subtilis colony growth. To explore the specificity of the antagonism, we cocultured B. subtilis with a collection of fluorescent Pseudomonas spp. and found that the Bacillus-Pseudomonas interaction is conserved, expanding our understanding of the interplay between two of the most well-studied genera of soil bacteria.
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Affiliation(s)
- Mark Lyng
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Johan P B Jørgensen
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Morten D Schostag
- Bacterial Ecophysiology & Biotechnology, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Scott A Jarmusch
- Natural Product Discovery, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Diana K C Aguilar
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Carlos N Lozano-Andrade
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kgs Lyngby 2800, Denmark
- Institute of Biology Leiden, Leiden University, Leiden 2333 BE, The Netherlands
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5
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Zanditenas E, Trebicz-Geffen M, Kolli D, Domínguez-García L, Farhi E, Linde L, Romero D, Chapman M, Kolodkin-Gal I, Ankri S. Digestive exophagy of biofilms by intestinal amoeba and its impact on stress tolerance and cytotoxicity. NPJ Biofilms Microbiomes 2023; 9:77. [PMID: 37813896 PMCID: PMC10562373 DOI: 10.1038/s41522-023-00444-x] [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: 04/05/2023] [Accepted: 09/26/2023] [Indexed: 10/11/2023] Open
Abstract
The human protozoan parasite Entamoeba histolytica is responsible for amebiasis, a disease endemic to developing countries. E. histolytica trophozoites colonize the large intestine, primarily feeding on bacteria. However, in the gastrointestinal tract, bacterial cells form aggregates or structured communities called biofilms too large for phagocytosis. Remarkably, trophozoites are still able to invade and degrade established biofilms, utilizing a mechanism that mimics digestive exophagy. Digestive exophagy refers to the secretion of digestive enzymes that promote the digestion of objects too large for direct phagocytosis by phagocytes. E. histolytica cysteine proteinases (CPs) play a crucial role in the degradation process of Bacillus subtilis biofilm. These proteinases target TasA, a major component of the B. subtilis biofilm matrix, also contributing to the adhesion of the parasite to the biofilm. In addition, they are also involved in the degradation of biofilms formed by Gram-negative and Gram-positive enteric pathogens. Furthermore, biofilms also play an important role in protecting trophozoites against oxidative stress. This specific mechanism suggests that the amoeba has adapted to prey on biofilms, potentially serving as an untapped reservoir for novel therapeutic approaches to treat biofilms. Consistently, products derived from the amoeba have been shown to restore antibiotic sensitivity to biofilm cells. In addition, our findings reveal that probiotic biofilms can act as a protective shield for mammalian cells, hindering the progression of the parasite towards them.
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Affiliation(s)
- Eva Zanditenas
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Meirav Trebicz-Geffen
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Divya Kolli
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Einan Farhi
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Liat Linde
- Technion Genomics Center, Technion - Israel Institute of Technology, Haifa, Israel
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea 'La Mayora', Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Universidad de Málaga, Málaga, Spain
| | - Matthew Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, USA
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, the Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
- Scojen Institute for Synthetic Biology, Reichman University, Herzliya, Israel.
| | - Serge Ankri
- Department of Molecular Microbiology, Ruth and Bruce Rappaport Faculty of Medicine, Technion, Haifa, Israel.
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6
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Yannarell SM, Beaudoin ES, Talley HS, Schoenborn AA, Orr G, Anderton CR, Chrisler WB, Shank EA. Extensive cellular multi-tasking within Bacillus subtilis biofilms. mSystems 2023; 8:e0089122. [PMID: 37527273 PMCID: PMC10469600 DOI: 10.1128/msystems.00891-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 03/08/2023] [Indexed: 08/03/2023] Open
Abstract
Bacillus subtilis is a soil-dwelling bacterium that can form biofilms, or communities of cells surrounded by a self-produced extracellular matrix. In biofilms, genetically identical cells often exhibit heterogeneous transcriptional phenotypes, so that subpopulations of cells carry out essential yet costly cellular processes that allow the entire population to thrive. Surprisingly, the extent of phenotypic heterogeneity and the relationships between subpopulations of cells within biofilms of even in well-studied bacterial systems like B. subtilis remains largely unknown. To determine relationships between these subpopulations of cells, we created 182 strains containing pairwise combinations of fluorescent transcriptional reporters for the expression state of 14 different genes associated with potential cellular subpopulations. We determined the spatial organization of the expression of these genes within biofilms using confocal microscopy, which revealed that many reporters localized to distinct areas of the biofilm, some of which were co-localized. We used flow cytometry to quantify reporter co-expression, which revealed that many cells "multi-task," simultaneously expressing two reporters. These data indicate that prior models describing B. subtilis cells as differentiating into specific cell types, each with a specific task or function, were oversimplified. Only a few subpopulations of cells, including surfactin and plipastatin producers, as well as sporulating and competent cells, appear to have distinct roles based on the set of genes examined here. These data will provide us with a framework with which to further study and make predictions about the roles of diverse cellular phenotypes in B. subtilis biofilms. IMPORTANCE Many microbes differentiate, expressing diverse phenotypes to ensure their survival in various environments. However, studies on phenotypic differentiation have typically examined only a few phenotypes at one time, thus limiting our knowledge about the extent of differentiation and phenotypic overlap in the population. We investigated the spatial organization and gene expression relationships for genes important in B. subtilis biofilms. In doing so, we mapped spatial gene expression patterns and expanded the number of cell populations described in the B. subtilis literature. It is likely that other bacteria also display complex differentiation patterns within their biofilms. Studying the extent of cellular differentiation in other microbes may be important when designing therapies for disease-causing bacteria, where studying only a single phenotype may be masking underlying phenotypic differentiation relevant to infection outcomes.
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Affiliation(s)
- Sarah M. Yannarell
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Eric S. Beaudoin
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
| | - Hunter S. Talley
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Alexi A. Schoenborn
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina, USA
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Galya Orr
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Christopher R. Anderton
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - William B. Chrisler
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington, USA
| | - Elizabeth A. Shank
- Department of Systems Biology, University of Massachusetts Chan Medical School, Worcester, Massachusetts, USA
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Chen P, Yu K, He Y. The dynamics and transmission of antibiotic resistance associated with plant microbiomes. ENVIRONMENT INTERNATIONAL 2023; 176:107986. [PMID: 37257204 DOI: 10.1016/j.envint.2023.107986] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/02/2023]
Abstract
Antibiotic resistance genes (ARGs) have been widely found and studied in soil and water environments. However, the propagation of ARGs in plant microbiomes has attracted insufficient attention. Plant microbiomes, especially the rhizosphere microorganisms, are closely connected with water, soil, and air, which allows ARGs to spread widely in ecosystems and pose a threat to human health after entering the human body with bacteria. Therefore, it is necessary to deeply understand and explore the dynamics and the transmission of ARGs in rhizosphere microorganisms and endophytes of plants. In this review, the transmission and influencing factors of ARGs in the microorganisms associated with plants, especially the influence of root exudates on plant microbiomes, are analyzed. Notably, the role of intrinsic genes of plants in determining root exudates and their potential effects on ARGs are proposed and analyzed. The important role of phyllosphere microorganisms and endophytes in the transmission of ARGs and co-resistance of antibiotics and other substances are also emphasized. The proliferation and transmission of ARGs associated with plant microbiomes addressed in this review is conducive to revealing the fate of ARGs in plant microorganisms and alleviating ARG pollution.
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Affiliation(s)
- Ping Chen
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Kaifeng Yu
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China
| | - Yiliang He
- School of Environmental Science & Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai 200240, China.
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Andrić S, Rigolet A, Argüelles Arias A, Steels S, Hoff G, Balleux G, Ongena L, Höfte M, Meyer T, Ongena M. Plant-associated Bacillus mobilizes its secondary metabolites upon perception of the siderophore pyochelin produced by a Pseudomonas competitor. THE ISME JOURNAL 2023; 17:263-275. [PMID: 36357782 PMCID: PMC9860033 DOI: 10.1038/s41396-022-01337-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 10/12/2022] [Accepted: 10/13/2022] [Indexed: 11/12/2022]
Abstract
Bacillus velezensis is considered as model species for plant-associated bacilli providing benefits to its host such as protection against phytopathogens. This is mainly due to the potential to secrete a wide range of secondary metabolites with specific and complementary bioactivities. This metabolite arsenal has been quite well defined genetically and chemically but much remains to be explored regarding how it is expressed under natural conditions and notably how it can be modulated upon interspecies interactions in the competitive rhizosphere niche. Here, we show that B. velezensis can mobilize a substantial part of its metabolome upon the perception of Pseudomonas, as a soil-dwelling competitor. This metabolite response reflects a multimodal defensive strategy as it includes polyketides and the bacteriocin amylocyclicin, with broad antibiotic activity, as well as surfactin lipopeptides, contributing to biofilm formation and enhanced motility. Furthermore, we identified the secondary Pseudomonas siderophore pyochelin as an info-chemical, which triggers this response via a mechanism independent of iron stress. We hypothesize that B. velezensis relies on such chelator sensing to accurately identify competitors, illustrating a new facet of siderophore-mediated interactions beyond the concept of competition for iron and siderophore piracy. This phenomenon may thus represent a new component of the microbial conversations driving the behavior of members of the rhizosphere community.
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Affiliation(s)
- Sofija Andrić
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Augustin Rigolet
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Anthony Argüelles Arias
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Sébastien Steels
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Grégory Hoff
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.5477.10000000120346234Present Address: Ecology and Biodiversity, Department of Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Guillaume Balleux
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
| | - Loïc Ongena
- grid.4861.b0000 0001 0805 7253Laboratory of Gene Expression and Cancer, GIGA-MBD, University of Liège, Liège, Belgium
| | - Monica Höfte
- grid.5342.00000 0001 2069 7798Laboratory of Phytopathology, Department of Plants and Crops, Faculty of Bioscience Engineering, Ghent University, Ghent, Belgium
| | - Thibault Meyer
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium ,grid.7849.20000 0001 2150 7757Present Address: UMR Ecologie Microbienne, F-69622, University of Lyon, Université Claude Bernard Lyon 1, CNRS, INRAE, VetAgro Sup, Villeurbanne, France
| | - Marc Ongena
- grid.410510.10000 0001 2297 9043Microbial Processes and Interactions Laboratory, Terra Teaching and Research Center, Gembloux Agro-Bio Tech, University of Liège, Gembloux, Belgium
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Mixed-species bacterial swarms show an interplay of mixing and segregation across scales. Sci Rep 2022; 12:16500. [PMID: 36192570 PMCID: PMC9529924 DOI: 10.1038/s41598-022-20644-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 09/16/2022] [Indexed: 11/28/2022] Open
Abstract
Bacterial swarms are a highly-researched example of natural active matter. In particular, the interplay between biological interactions and the physics underlying the swarming dynamics is of both biological and physical interest. In this paper, we study mixed swarms of Bacillus subtilis and Pseudomonas aeruginosa. We find intricate interactions between the species, showing both cooperation and segregation across different spatial and temporal scales. On one hand, even though axenic colonies grow on disparate time scale, an order of magnitude apart, the two-species swarm together, forming a single, combined colony. However, the rapidly moving populations are locally segregated, with different characteristic speeds and lengths (or cluster sizes) that depend on the ratio between the species. Comparison with controlled mutant strains suggest that both the physical and known biological differences in species characteristics may not be enough to explain the segregation between the species in the mixed swarm. We hypothesize that the heterogeneous spatial distribution is due to some mechanism that enables bacteria to recognize their own kind, whose precise origin we could not identify.
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An open-source computational tool for measuring bacterial biofilm morphology and growth kinetics upon one-sided exposure to an antimicrobial source. Sci Rep 2022; 12:16125. [PMID: 36167741 PMCID: PMC9515175 DOI: 10.1038/s41598-022-20275-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 09/12/2022] [Indexed: 11/28/2022] Open
Abstract
Bacillus subtilis biofilms are well known for their complex and highly adaptive morphology. Indeed, their phenotypical diversity and intra-biofilm heterogeneity make this gram-positive bacterium the subject of many scientific papers on the structure of biofilms. The “robustness” of biofilms is a term often used to describe their level of susceptibility to antimicrobial agents and various mechanical and molecular inhibition/eradication methods. In this paper, we use computational analytics to quantify Bacillus subtilis morphological response to proximity to an antimicrobial source, in the form of the antiseptic chlorhexidine. Chlorhexidine droplets, placed in proximity to Bacillus subtilis macrocolonies at different distances result in morphological changes, quantified using Python-based code, which we have made publicly available. Our results quantify peripheral and inner core deformation as well as differences in cellular viability of the two regions. The results reveal that the inner core, which is often characterized by the presence of wrinkled formations in the macrocolony, is more preserved than the periphery. Furthermore, the paper describes a crescent-shaped colony morphology which occurs when the distance from the chlorhexidine source is 0.5 cm, as well as changes observed in the growth substrate of macrocolonies exposed to chlorhexidine.
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11
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Park AM, Khadka S, Sato F, Omura S, Fujita M, Hashiwaki K, Tsunoda I. Bacterial and fungal isolation from face masks under the COVID-19 pandemic. Sci Rep 2022; 12:11361. [PMID: 35851044 PMCID: PMC9293923 DOI: 10.1038/s41598-022-15409-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 06/23/2022] [Indexed: 02/08/2023] Open
Abstract
The COVID-19 pandemic has led people to wear face masks daily in public. Although the effectiveness of face masks against viral transmission has been extensively studied, there have been few reports on potential hygiene issues due to bacteria and fungi attached to the face masks. We aimed to (1) quantify and identify the bacteria and fungi attaching to the masks, and (2) investigate whether the mask-attached microbes could be associated with the types and usage of the masks and individual lifestyles. We surveyed 109 volunteers on their mask usage and lifestyles, and cultured bacteria and fungi from either the face-side or outer-side of their masks. The bacterial colony numbers were greater on the face-side than the outer-side; the fungal colony numbers were fewer on the face-side than the outer-side. A longer mask usage significantly increased the fungal colony numbers but not the bacterial colony numbers. Although most identified microbes were non-pathogenic in humans; Staphylococcus epidermidis, Staphylococcus aureus, and Cladosporium, we found several pathogenic microbes; Bacillus cereus, Staphylococcus saprophyticus, Aspergillus, and Microsporum. We also found no associations of mask-attached microbes with the transportation methods or gargling. We propose that immunocompromised people should avoid repeated use of masks to prevent microbial infection.
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Affiliation(s)
- Ah-Mee Park
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan.
| | - Sundar Khadka
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Fumitaka Sato
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Seiichi Omura
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Mitsugu Fujita
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Kazuki Hashiwaki
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
| | - Ikuo Tsunoda
- Department of Microbiology, Kindai University Faculty of Medicine, 377-2 Ohnohigashi, Osakasayama, Osaka, 589-8511, Japan
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12
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Bueno CB, dos Santos RM, de Souza Buzo F, de Andrade da Silva MSR, Rigobelo EC. Effects of Chemical Fertilization and Microbial Inoculum on Bacillus subtilis Colonization in Soybean and Maize Plants. Front Microbiol 2022; 13:901157. [PMID: 35875531 PMCID: PMC9298503 DOI: 10.3389/fmicb.2022.901157] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 06/09/2022] [Indexed: 11/13/2022] Open
Abstract
Plant growth-promoting endophytic microorganisms in agriculture have been expanding in Brazil and are an excellent strategy to face the challenges of current agriculture, such as reducing production costs with fewer environmental impacts, without detriment to productivity. However, little is known about the factors that can affect the colonization of endophytic such as inoculant concentration and mineral fertilization. The present study aimed to evaluate the influence of these factors on soybean and maize crops and found that for soybean crops, the highest Bacillus subtilis concentration of 1 × 104 and 1 × 1010 CFU ml−1 promoted the highest number of recovered bacteria, when there was no mineral fertilization. However, mineral fertilization limited the number of recovered bacteria, suggesting that mineral fertilization interferes with endophytic colonization. For maize crops, the highest number of recovered bacteria occurred from the concentration of 1 × 106 CFU ml−1, not differing from the highest concentrations. A mineral fertilization dose of 25% promoted the greatest B. subtilis recovery compared to the other treatments. Regarding plant development, the highest microbial inoculum concentrations did not necessarily promote greater positive growth promotion effects compared to the concentration of 1 × 104 CFU ml−1 for both crops. The results also suggest that the higher number of endophytic bacteria recovered in the plant does not necessarily affect plant growth in the same proportion. For soybean plants, there is a strong tendency that with the increase in the B. subtilis inoculant concentration, the need for mineral fertilization doses to achieve the same plant development is consequently increased, and inoculations with 1 × 105 and 1 × 106 CFU ml−1 with fertilization doses between 44% and 62% are the ideal combinations for greater plant development. In maize plants, the best growth promotion response (height) was obtained using inoculation concentration of 1 × 102 and 1 × 1010 CFU ml−1, increasing according to the increase in fertilization doses. The findings suggest, for soybean crop, that these high inoculum concentrations required more photosynthetic metabolites from the plants and more nutrients from the soil. Thus, the need for mineral fertilization for plant growth must be increased.
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Affiliation(s)
- Clara Barros Bueno
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, Brazil
| | - Roberta Mendes dos Santos
- Agricultural and Livestock Microbiology Graduation Program, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Fernando de Souza Buzo
- Department of Plant Science, Food Technology and Socioeconomics, Faculty of Engineering of Ilha Solteira/UNESP, Ilha Solteira, Brazil
| | - Maura Santos Reis de Andrade da Silva
- Agricultural and Livestock Microbiology Graduation Program, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
| | - Everlon Cid Rigobelo
- Agricultural and Livestock Microbiology Graduation Program, São Paulo State University (UNESP), School of Agricultural and Veterinarian Sciences, Jaboticabal, São Paulo, Brazil
- *Correspondence: Everlon Cid Rigobelo,
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13
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Jose A, Ariel G, Be'er A. Physical characteristics of mixed-species swarming colonies. Phys Rev E 2022; 105:064404. [PMID: 35854624 DOI: 10.1103/physreve.105.064404] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 04/28/2022] [Indexed: 06/15/2023]
Abstract
In nature, bacterial collectives typically consist of multiple species, which are interacting both biochemically and physically. Nonetheless, past studies on the physical properties of swarming bacteria were focused on axenic (single-species) populations. In bacterial swarming, intricate interactions between the individuals lead to clusters, rapid jets, and vortices that depend on cell characteristics such as speed and length. In this work, we show the first results of rapidly swarming mixed-species populations of Bacillus subtilis and Serratia marcescens, two model swarm species that are known to swarm well in axenic situations. In mixed liquid cultures, both species have higher reproduction rates. We show that the mixed population swarms together well and that the fraction between the species determines all dynamical scales-from the microscopic (e.g., speed distribution), mesoscopic (vortex size), and macroscopic (colony structure and size). Understanding mixed-species swarms is essential for a comprehensive understanding of the bacterial swarming phenomenon and its biological and evolutionary implications.
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Affiliation(s)
- Ajesh Jose
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel
| | - Gil Ariel
- Department of Mathematics, Bar-Ilan University, 52000 Ramat Gan, Israel
| | - Avraham Be'er
- Zuckerberg Institute for Water Research, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede Boqer Campus 84990, Midreshet Ben-Gurion, Israel and Department of Physics, Ben-Gurion University of the Negev 84105, Beer-Sheva, Israel
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14
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Comerci CJ, Gillman AL, Galera-Laporta L, Gutierrez E, Groisman A, Larkin JW, Garcia-Ojalvo J, Süel GM. Localized electrical stimulation triggers cell-type-specific proliferation in biofilms. Cell Syst 2022; 13:488-498.e4. [PMID: 35512710 PMCID: PMC9233089 DOI: 10.1016/j.cels.2022.04.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 12/20/2021] [Accepted: 04/11/2022] [Indexed: 01/18/2023]
Abstract
Biological systems ranging from bacteria to mammals utilize electrochemical signaling. Although artificial electrochemical signals have been utilized to characterize neural tissue responses, the effects of such stimuli on non-neural systems remain unclear. To pursue this question, we developed an experimental platform that combines a microfluidic chip with a multielectrode array (MiCMA) to enable localized electrochemical stimulation of bacterial biofilms. The device also allows for the simultaneous measurement of the physiological response within the biofilm with single-cell resolution. We find that the stimulation of an electrode locally changes the ratio of the two major cell types comprising Bacillus subtilis biofilms, namely motile and extracellular-matrix-producing cells. Specifically, stimulation promotes the proliferation of motile cells but not matrix cells, even though these two cell types are genetically identical and reside in the same microenvironment. Our work thus reveals that an electronic interface can selectively target bacterial cell types, enabling the control of biofilm composition and development.
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Affiliation(s)
- Colin J Comerci
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Alan L Gillman
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Leticia Galera-Laporta
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Edgar Gutierrez
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Alex Groisman
- Department of Physics, University of California San Diego, La Jolla, CA 92093, USA
| | - Joseph W Larkin
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Jordi Garcia-Ojalvo
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Gürol M Süel
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA; San Diego Center for Systems Biology, University of California San Diego, La Jolla, CA 92093, USA.
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15
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Maan H, Itkin M, Malitsky S, Friedman J, Kolodkin-Gal I. Resolving the conflict between antibiotic production and rapid growth by recognition of peptidoglycan of susceptible competitors. Nat Commun 2022; 13:431. [PMID: 35058430 PMCID: PMC8776889 DOI: 10.1038/s41467-021-27904-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 12/16/2021] [Indexed: 11/09/2022] Open
Abstract
Microbial communities employ a variety of complex strategies to compete successfully against competitors sharing their niche, with antibiotic production being a common strategy of aggression. Here, by systematic evaluation of four non-ribosomal peptides/polyketide (NRPs/PKS) antibiotics produced by Bacillus subtilis clade, we revealed that they acted synergistically to effectively eliminate phylogenetically distinct competitors. The production of these antibiotics came with a fitness cost manifested in growth inhibition, rendering their synthesis uneconomical when growing in proximity to a phylogenetically close species, carrying resistance against the same antibiotics. To resolve this conflict and ease the fitness cost, antibiotic production was only induced by the presence of a peptidoglycan cue from a sensitive competitor, a response mediated by the global regulator of cellular competence, ComA. These results experimentally demonstrate a general ecological concept - closely related communities are favoured during competition, due to compatibility in attack and defence mechanisms.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Maxim Itkin
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Jonathan Friedman
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Plant Pathology and Microbiology, The Robert H. Smith Faculty of Agriculture, Food & Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
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16
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Abstract
Some Bacillus species, such as B. velezensis, are important members of the plant-associated microbiome, conferring protection against phytopathogens. However, our knowledge about multitrophic interactions determining the ecological fitness of these biocontrol bacteria in the competitive rhizosphere niche is still limited. Here, we investigated molecular mechanisms underlying interactions between B. velezensis and Pseudomonas as a soil-dwelling competitor. Upon their contact-independent in vitro confrontation, a multifaceted macroscopic outcome was observed and characterized by Bacillus growth inhibition, white line formation in the interaction zone, and enhanced motility. We correlated these phenotypes with the production of bioactive secondary metabolites and identified specific lipopeptides as key compounds involved in the interference interaction and motile response. Bacillus mobilizes its lipopeptide surfactin not only to enhance motility but also to act as a chemical trap to reduce the toxicity of lipopeptides formed by Pseudomonas. We demonstrated the relevance of these unsuspected roles of lipopeptides in the context of competitive tomato root colonization by the two bacterial genera. IMPORTANCE Plant-associated Bacillus velezensis and Pseudomonas spp. represent excellent model species as strong producers of bioactive metabolites involved in phytopathogen inhibition and the elicitation of plant immunity. However, the ecological role of these metabolites during microbial interspecies interactions and the way their expression may be modulated under naturally competitive soil conditions has been poorly investigated. Through this work, we report various phenotypic outcomes from the interactions between B. velezensis and 10 Pseudomonas strains used as competitors and correlate them with the production of specific metabolites called lipopeptides from both species. More precisely, Bacillus overproduces surfactin to enhance motility, which also, by acting as a chemical trap, reduces the toxicity of other lipopeptides formed by Pseudomonas. Based on data from interspecies competition on plant roots, we assume this would allow Bacillus to gain fitness and persistence in its natural rhizosphere niche. The discovery of new ecological functions for Bacillus and Pseudomonas secondary metabolites is crucial to rationally design compatible consortia, more efficient than single-species inoculants, to promote plant health and growth by fighting economically important pathogens in sustainable agriculture.
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17
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Maan H, Povolotsky TL, Porat Z, Itkin M, Malitsky S, Kolodkin-Gal I. Imaging flow cytometry reveals a dual role for exopolysaccharides in biofilms: To promote self-adhesion while repelling non-self-community members. Comput Struct Biotechnol J 2021; 20:15-25. [PMID: 34976308 PMCID: PMC8666610 DOI: 10.1016/j.csbj.2021.11.043] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 11/29/2021] [Accepted: 11/30/2021] [Indexed: 11/16/2022] Open
Abstract
In nature, bacteria frequently reside in differentiated communities or biofilms. These multicellular communities are held together by self-produced polymers that allow the community members to adhere to the surface as well as to neighbor bacteria. Here, we report that exopolysaccharides prevent Bacillus subtilis from co-aggregating with a distantly related bacterium Bacillus mycoides, while maintaining their role in promoting self-adhesion and co-adhesion with phylogenetically related bacterium, Bacillus atrophaeus. The defensive role of the exopolysaccharides is due to the specific regulation of bacillaene. Single cell analysis of biofilm and free-living bacterial cells using imaging flow cytometry confirmed a specific role for the exopolysaccharides in microbial competition repelling B. mycoides. Unlike exopolysaccharides, the matrix protein TasA induced bacillaene but inhibited the expression of the biosynthetic clusters for surfactin, and therefore its overall effect on microbial competition during floating biofilm formation was neutral. Thus, the exopolysaccharides provide a dual fitness advantage for biofilm-forming cells, as it acts to promote co-aggregation of related species, as well as, a secreted cue for chemical interference with non-compatible partners. These results experimentally demonstrate a general assembly principle of complex communities and provides an appealing explanation for how closely related species are favored during community assembly. Furthermore, the differential regulation of surfactin and bacillaene by the extracellular matrix may explain the spatio-temporal gradients of antibiotic production within biofilms.
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Affiliation(s)
- Harsh Maan
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Ziv Porat
- Flow Cytometry Unit, Life Sciences Core Facilities, Weizmann Institute of Science, Rehovot, Israel
| | - Maxim Itkin
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Sergey Malitsky
- Life Science Core Facilities Weizmann Institute of Science, 234 Herzl Street, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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18
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Li Q, Liu L, Guo A, Zhang X, Liu W, Ruan Y. Formation of Multispecies Biofilms and Their Resistance to Disinfectants in Food Processing Environments: A Review. J Food Prot 2021; 84:2071-2083. [PMID: 34324690 DOI: 10.4315/jfp-21-071] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/16/2021] [Indexed: 11/11/2022]
Abstract
ABSTRACT In food processing environments, various microorganisms can adhere and aggregate on the surface of equipment, resulting in the formation of multispecies biofilms. Complex interactions among microorganisms may affect the formation of multispecies biofilms and resistance to disinfectants, which are food safety and quality concerns. This article reviews the various interactions among microorganisms in multispecies biofilms, including competitive, cooperative, and neutral interactions. Then, the preliminary mechanisms underlying the formation of multispecies biofilms are discussed in relation to factors, such as quorum-sensing signal molecules, extracellular polymeric substances, and biofilm-regulated genes. Finally, the resistance mechanisms of common contaminating microorganisms to disinfectants in food processing environments are also summarized. This review is expected to facilitate a better understanding of interspecies interactions and provide some implications for the control of multispecies biofilms in food processing. HIGHLIGHTS
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Affiliation(s)
- Qun Li
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Ling Liu
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Ailing Guo
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China.,National Research and Development Center for Egg Processing, Wuhan, Hubei 430070, People's Republic of China
| | - Xinshuai Zhang
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Wukang Liu
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
| | - Yao Ruan
- College of Food Science and Technology, Huazhong Agriculture University, Wuhan, Hubei 430070, People's Republic of China
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19
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Multiunit In Vitro Colon Model for the Evaluation of Prebiotic Potential of a Fiber Plus D-Limonene Food Supplement. Foods 2021; 10:foods10102371. [PMID: 34681420 PMCID: PMC8535099 DOI: 10.3390/foods10102371] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Revised: 10/01/2021] [Accepted: 10/03/2021] [Indexed: 12/12/2022] Open
Abstract
The search for new fiber supplements that can claim to be "prebiotic" is expanding fast, as the role of prebiotics and intestinal microbiota in well-being has been well established. This work explored the prebiotic potential of a novel fiber plus D-Limonene supplement (FLS) in comparison to fructooligosaccharides (FOS) over distal colonic fermentation with the in vitro model MICODE (multi-unit in vitro colon gut model). During fermentation, volatilome characterization and core microbiota quantifications were performed, then correlations among volatiles and microbes were interpreted. The results indicated that FLS generated positive effects on the host gut model, determining: (i) eubiosis; (ii) increased abundance of beneficial bacteria, as Bifidobacteriaceae; (iii) production of beneficial compounds, as n-Decanoic acid; (iv) reduction in detrimental bacteria, as Enterobaceteriaceae; (v) reduction in detrimental compounds, as skatole. The approach that we followed permitted us to describe the prebiotic potential of FLS and its ability to steadily maintain the metabolism of colon microbiota over time. This aspect is two-faced and should be investigated further because if a fast microbial turnover and production of beneficial compounds is a hallmark of a prebiotic, the ability to reduce microbiota changes and to reduce imbalances in the productions of microbial metabolites could be an added value to FLS. In fact, it has been recently demonstrated that these aspects could serve as an adjuvant in metabolic disorders and cognitive decline.
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20
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Arnaouteli S, Bamford NC, Stanley-Wall NR, Kovács ÁT. Bacillus subtilis biofilm formation and social interactions. Nat Rev Microbiol 2021; 19:600-614. [PMID: 33824496 DOI: 10.1038/s41579-021-00540-9] [Citation(s) in RCA: 161] [Impact Index Per Article: 53.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
Biofilm formation is a process in which microbial cells aggregate to form collectives that are embedded in a self-produced extracellular matrix. Bacillus subtilis is a Gram-positive bacterium that is used to dissect the mechanisms controlling matrix production and the subsequent transition from a motile planktonic cell state to a sessile biofilm state. The collective nature of life in a biofilm allows emergent properties to manifest, and B. subtilis biofilms are linked with novel industrial uses as well as probiotic and biocontrol processes. In this Review, we outline the molecular details of the biofilm matrix and the regulatory pathways and external factors that control its production. We explore the beneficial outcomes associated with biofilms. Finally, we highlight major advances in our understanding of concepts of microbial evolution and community behaviour that have resulted from studies of the innate heterogeneity of biofilms.
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Affiliation(s)
- Sofia Arnaouteli
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Natalie C Bamford
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, UK.
| | - Ákos T Kovács
- Bacterial Interactions and Evolution Group, DTU Bioengineering, Technical University of Denmark, Kongens Lyngby, Denmark.
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21
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Spore-Associated Proteins Involved in c-di-GMP Synthesis and Degradation of Bacillus anthracis. J Bacteriol 2021; 203:e0013521. [PMID: 34096779 DOI: 10.1128/jb.00135-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Bis-(3'-5')-cyclic-dimeric GMP (c-di-GMP) is an important bacterial regulatory signaling molecule affecting biofilm formation, toxin production, motility, and virulence. The genome of Bacillus anthracis, the causative agent of anthrax, is predicted to encode ten putative GGDEF/EAL/HD-GYP-domain containing proteins. Heterologous expression in Bacillus subtilis hosts indicated that there are five active GGDEF domain-containing proteins and four active EAL or HD-GYP domain-containing proteins. Using an mCherry gene fusion-Western blotting approach, the expression of the c-di-GMP-associated proteins was observed throughout the in vitro life cycle. Of the six c-di-GMP-associated proteins found to be present in sporulating cells, four (CdgA, CdgB, CdgD, and CdgG) contain active GGDEF domains. The six proteins expressed in sporulating cells are retained in spores in a CotE-independent manner and thus are not likely to be localized to the exosporium layer of the spores. Individual deletion mutations involving the nine GGDEF/EAL protein-encoding genes and one HD-GYP protein-encoding gene did not affect sporulation efficiency, the attachment of the exosporium glycoprotein BclA, or biofilm production. Notably, expression of anthrax toxin was not affected by deletion of any of the cdg determinants. Three determinants encoding proteins with active GGDEF domains were found to affect germination kinetics. This study reveals a spore association of cyclic-di-GMP regulatory proteins and a likely role for these proteins in the biology of the B. anthracis spore. IMPORTANCE The genus Bacillus is composed of Gram-positive, rod shaped, soil-dwelling bacteria. As a mechanism for survival in the harsh conditions in soil, the organisms undergo sporulation, and the resulting spores permit the organisms to survive harsh environmental conditions. Although most species are saprophytes, Bacillus cereus and Bacillus anthracis are human pathogens and Bacillus thuringiensis is an insect pathogen. The bacterial c-di-GMP regulatory system is an important control system affecting motility, biofilm formation, and toxin production. The role of c-di-GMP has been studied in the spore-forming bacilli Bacillus subtilis, Bacillus amyloliquefaciens, B. cereus, and B. thuringiensis. However, this regulatory system has not heretofore been examined in the high-consequence zoonotic pathogen of this genus, B. anthracis.
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22
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Wang X, Zhang D, Dong F, Liu S, Zhang J, Zhao H. Cell differentiation and motion determine the Bacillus subtilis biofilm morphological evolution under the competitive growth. J Basic Microbiol 2021; 61:396-405. [PMID: 33682160 DOI: 10.1002/jobm.202000635] [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: 10/24/2020] [Revised: 12/23/2020] [Accepted: 01/12/2021] [Indexed: 11/06/2022]
Abstract
The growth discrepancy of Bacillus subtilis biofilms along different directions under the competitive growth drive the formation of anisotropic biofilm morphology directly. Two biofilms growing from two inoculating positions with different distances exhibit promoting or inhibiting growth behavior. Here we develop an optical imaging technology to observe the cell differentiation and the growth dynamics when the biofilm grows. It shows that the spatiotemporal distribution of different phenotypes affects the biofilm morphological evolution. We develop a program to calculate the velocity of cell motion within the biofilm, which is based on the feature point matching approach. We find the cell differentiation ununiformity in the neighboring region and its opposite region leads to the cell velocity difference in the competitive environment, the different cell motion further influences the biofilm morphology evolution. When biofilms grow with a long inoculating distance, there is always a gap between the them; when biofilms grow with a short inoculating distance, two biofilms gradually merge into a whole. Our work establishes a relationship between microscopic cells and macroscopic biofilm morphological which enables us to study the competitive growth process of biofilms from multiple perspectives.
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Affiliation(s)
- Xiaoling Wang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China.,School of Engineering and Applied Sciences, Harvard University, Cambridge, MA, USA
| | - Duohuai Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Fulin Dong
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Song Liu
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Jinchang Zhang
- School of Mechanical Engineering, University of Science and Technology Beijing, Beijing, China
| | - Hui Zhao
- University of Chinese Academy of Sciences, State Key Laboratory of Computer Science, Institute of Software, China
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23
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Hou Q, Kolodkin-Gal I. Harvesting the complex pathways of antibiotic production and resistance of soil bacilli for optimizing plant microbiome. FEMS Microbiol Ecol 2021; 96:5872479. [PMID: 32672816 DOI: 10.1093/femsec/fiaa142] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/13/2020] [Indexed: 01/04/2023] Open
Abstract
A sustainable future increasing depends on our capacity to utilize beneficial plant microbiomes to meet our growing needs. Plant microbiome symbiosis is a hallmark of the beneficial interactions between bacteria and their host. Specifically, colonization of plant roots by biocontrol agents and plant growth-promoting bacteria can play an important role in maintaining the optimal rhizosphere environment, supporting plant growth and promoting its fitness. Rhizosphere communities confer immunity against a wide range of foliar diseases by secreting antibiotics and activating plant defences. At the same time, the rhizosphere is a highly competitive niche, with multiple microbial species competing for space and resources, engaged in an arms race involving the production of a vast array of antibiotics and utilization of a variety of antibiotic resistance mechanisms. Therefore, elucidating the mechanisms that govern antibiotic production and resistance in the rhizosphere is of great significance for designing beneficial communities with enhanced biocontrol properties. In this review, we used Bacillus subtilis and B. amyloliquefaciens as models to investigate the genetics of antibiosis and the potential for its translation of into improved plant microbiome performance.
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Affiliation(s)
- Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
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Joshi RV, Gunawan C, Mann R. We Are One: Multispecies Metabolism of a Biofilm Consortium and Their Treatment Strategies. Front Microbiol 2021; 12:635432. [PMID: 33584635 PMCID: PMC7876221 DOI: 10.3389/fmicb.2021.635432] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 01/11/2021] [Indexed: 12/12/2022] Open
Abstract
The ecological and medical significance of bacterial biofilms have been well recognized. Biofilms are harder to control than their planktonic free-living counterparts and quite recently, the focus of the study has shifted to the multispecies consortia, which represent the vast majority of real-case infection scenarios. Studies have begun to explore the complex interspecies interactions within these biofilms. However, only little attention is currently given to the role of cellular metabolites in the cell-to-cell communication. The concentration gradients of metabolic substrates and products affect the spatial growth of bacteria in multispecies biofilm. This, if looked into more deeply, can lead to identification of potential therapies targeting the specific metabolites and hence the coordinated protection in the bacterial community. Herein, we review the interspecies communications, including their metabolic cross-talking, in multispecies biofilm, to signify the importance of such interactions on the initial formation and subsequent growth of these biofilms. Multispecies biofilms with their species heterogeneity are more resilient to antimicrobial agents than their single species biofilm counterparts and this characteristic is of particular interest when dealing with pathogenic bacteria. In this Review, we also discuss the treatment options available, to include current and emerging avenues to combat pathogenic multispecies biofilms in the clinical, environmental, as well as industrial settings.
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Affiliation(s)
| | - Cindy Gunawan
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
- School of Chemical Engineering, University of New South Wales, Sydney, NSW, Australia
| | - Riti Mann
- iThree Institute, University of Technology Sydney, Sydney, NSW, Australia
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25
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Hou Q, Keren-Paz A, Korenblum E, Oved R, Malitsky S, Kolodkin-Gal I. Weaponizing volatiles to inhibit competitor biofilms from a distance. NPJ Biofilms Microbiomes 2021; 7:2. [PMID: 33402677 PMCID: PMC7785731 DOI: 10.1038/s41522-020-00174-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 11/19/2020] [Indexed: 01/29/2023] Open
Abstract
The soil bacterium Bacillus subtilis forms beneficial biofilms that induce plant defences and prevent the growth of pathogens. It is naturally found in the rhizosphere, where microorganisms coexist in an extremely competitive environment, and thus have evolved a diverse arsenal of defence mechanisms. In this work, we found that volatile compounds produced by B. subtilis biofilms inhibited the development of competing biofilm colonies, by reducing extracellular matrix gene expression, both within and across species. This effect was dose-dependent, with the structural defects becoming more pronounced as the number of volatile-producing colonies increased. This inhibition was mostly mediated by organic volatiles, and we identified the active molecules as 3-methyl-1-butanol and 1-butanol. Similar results were obtained with biofilms formed by phylogenetically distinct bacterium sharing the same niche, Escherichia coli, which produced the biofilm-inhibiting 3-methyl-1-butanol and 2-nonanon. The ability of established biofilms to inhibit the development and spreading of new biofilms from afar might be a general mechanism utilized by bacterial biofilms to protect an occupied niche from the invasion of competing bacteria.
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Affiliation(s)
- Qihui Hou
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Elisa Korenblum
- grid.13992.300000 0004 0604 7563Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel
| | - Rela Oved
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sergey Malitsky
- grid.13992.300000 0004 0604 7563Metabolic Profiling Unit, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- grid.13992.300000 0004 0604 7563Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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26
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Hernandez-Valdes JA, Zhou L, de Vries MP, Kuipers OP. Impact of spatial proximity on territoriality among human skin bacteria. NPJ Biofilms Microbiomes 2020; 6:30. [PMID: 32764612 PMCID: PMC7413532 DOI: 10.1038/s41522-020-00140-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/14/2020] [Indexed: 12/30/2022] Open
Abstract
Bacteria display social behavior and establish cooperative or competitive interactions in the niches they occupy. The human skin is a densely populated environment where many bacterial species live. Thus, bacterial inhabitants are expected to find a balance in these interactions, which eventually defines their spatial distribution and the composition of our skin microbiota. Unraveling the physiological basis of the interactions between bacterial species in organized environments requires reductionist analyses using functionally relevant species. Here, we study the interaction between two members of our skin microbiota, Bacillus subtilis and Staphylococcus epidermidis. We show that B. subtilis actively responds to the presence of S. epidermidis in its proximity by two strategies: antimicrobial production and development of a subpopulation with migratory response. The initial response of B. subtilis is production of chlorotetain, which degrades the S. epidermidis at the colony level. Next, a subpopulation of B. subtilis motile cells emerges. Remarkably this subpopulation slides towards the remaining S. epidermidis colony and engulfs it. A slow response back from S. epidermidis cells give origin to resistant cells that prevent both attacks from B. subtilis. We hypothesized that this niche conquering and back-down response from B. subtilis and S. epidermidis, respectively, which resembles other conflicts in nature as the ones observed in animals, may play a role in defining the presence of certain bacterial species in the specific microenvironments that these bacteria occupy on our skin.
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Affiliation(s)
- Jhonatan A Hernandez-Valdes
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Lu Zhou
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands
| | - Marcel P de Vries
- Department of Biomedical Engineering Antonius Deusinglaan 1, University Medical Center Groningen, Groningen University, 9713 AW, Groningen, Netherlands
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG, Groningen, The Netherlands.
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Miljaković D, Marinković J, Balešević-Tubić S. The Significance of Bacillus spp. in Disease Suppression and Growth Promotion of Field and Vegetable Crops. Microorganisms 2020; 8:microorganisms8071037. [PMID: 32668676 PMCID: PMC7409232 DOI: 10.3390/microorganisms8071037] [Citation(s) in RCA: 140] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/08/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022] Open
Abstract
Bacillus spp. produce a variety of compounds involved in the biocontrol of plant pathogens and promotion of plant growth, which makes them potential candidates for most agricultural and biotechnological applications. Bacilli exhibit antagonistic activity by excreting extracellular metabolites such as antibiotics, cell wall hydrolases, and siderophores. Additionally, Bacillus spp. improve plant response to pathogen attack by triggering induced systemic resistance (ISR). Besides being the most promising biocontrol agents, Bacillus spp. promote plant growth via nitrogen fixation, phosphate solubilization, and phytohormone production. Antagonistic and plant growth-promoting strains of Bacillus spp. might be useful in formulating new preparations. Numerous studies of a wide range of plant species revealed a steady increase in the number of Bacillus spp. identified as potential biocontrol agents and plant growth promoters. Among different mechanisms of action, it remains unclear which individual or combined traits could be used as predictors in the selection of the best strains for crop productivity improvement. Due to numerous factors that influence the successful application of Bacillus spp., it is necessary to understand how different strains function in biological control and plant growth promotion, and distinctly define the factors that contribute to their more efficient use in the field.
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Affiliation(s)
- Dragana Miljaković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
- Correspondence:
| | - Jelena Marinković
- Department of Microbiological Preparations, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
| | - Svetlana Balešević-Tubić
- Soybean Department, Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000 Novi Sad, Serbia;
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The contest of microbial pigeon neighbors: Interspecies competition between Serratia marcescens and the human pathogen Cryptococcus neoformans. Fungal Biol 2020; 124:629-638. [PMID: 32540186 DOI: 10.1016/j.funbio.2020.03.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Revised: 03/04/2020] [Accepted: 03/10/2020] [Indexed: 11/21/2022]
Abstract
In nature, microorganisms often exhibit competitive behavior for nutrients and limited space, allowing them to alter the virulence determinants of pathogens. The human pathogenic yeast Cryptococcus neoformans can be found organized in biofilms, a complex community composed of an extracellular matrix which confers protection against predation. The aim of this study was to evaluate and characterize antagonistic interactions between two cohabiting microorganisms: C. neoformans and the bacteria Serratia marcescens. The interaction of S. marcescens with C. neoformans expressed a negative effect on biofilm formation, polysaccharide capsule, production of urease, and melanization of the yeast. These findings evidence that competition in mixed communities can result in dominance by one species, with direct impact on the physiological modulation of virulence determinants. Such an approach is key for understating the response of communities to the presence of competitors and, ultimately, rationally designing communities to prevent and treat certain diseases.
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Steinberg N, Keren-Paz A, Hou Q, Doron S, Yanuka-Golub K, Olender T, Hadar R, Rosenberg G, Jain R, Cámara-Almirón J, Romero D, van Teeffelen S, Kolodkin-Gal I. The extracellular matrix protein TasA is a developmental cue that maintains a motile subpopulation within Bacillus subtilis biofilms. Sci Signal 2020; 13:13/632/eaaw8905. [PMID: 32430292 DOI: 10.1126/scisignal.aaw8905] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In nature, bacteria form biofilms-differentiated multicellular communities attached to surfaces. Within these generally sessile biofilms, a subset of cells continues to express motility genes. We found that this subpopulation enabled Bacillus subtilis biofilms to expand on high-friction surfaces. The extracellular matrix (ECM) protein TasA was required for the expression of flagellar genes. In addition to its structural role as an adhesive fiber for cell attachment, TasA acted as a developmental signal stimulating a subset of biofilm cells to revert to a motile phenotype. Transcriptomic analysis revealed that TasA stimulated the expression of a specific subset of genes whose products promote motility and repress ECM production. Spontaneous suppressor mutations that restored motility in the absence of TasA revealed that activation of the biofilm-motility switch by the two-component system CssR/CssS antagonized the TasA-mediated reversion to motility in biofilm cells. Our results suggest that although mostly sessile, biofilms retain a degree of motility by actively maintaining a motile subpopulation.
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Affiliation(s)
- Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.,Department of Microbiology, Institute Pasteur, Paris, France
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Qihui Hou
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Shany Doron
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Keren Yanuka-Golub
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tsviya Olender
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rotem Hadar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rakeshkumar Jain
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Jesus Cámara-Almirón
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Departamento de Microbiología, Universidad de Málaga, Málaga, Spain
| | | | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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30
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Arjes HA, Vo L, Dunn CM, Willis L, DeRosa CA, Fraser CL, Kearns DB, Huang KC. Biosurfactant-Mediated Membrane Depolarization Maintains Viability during Oxygen Depletion in Bacillus subtilis. Curr Biol 2020; 30:1011-1022.e6. [PMID: 32059765 PMCID: PMC7153240 DOI: 10.1016/j.cub.2020.01.073] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/09/2019] [Accepted: 01/23/2020] [Indexed: 12/26/2022]
Abstract
The presence or absence of oxygen in the environment is a strong effector of cellular metabolism and physiology. Like many eukaryotes and some bacteria, Bacillus subtilis primarily utilizes oxygen during respiration to generate ATP. Despite the importance of oxygen for B. subtilis survival, we know little about how populations adapt to shifts in oxygen availability. Here, we find that when oxygen was depleted from stationary phase B. subtilis cultures, ∼90% of cells died while the remaining cells maintained colony-forming ability. We discover that production of the antimicrobial surfactin confers two oxygen-related fitness benefits: it increases aerobic growth yield by increasing oxygen diffusion, and it maintains viability during oxygen depletion by depolarizing the membrane. Strains unable to produce surfactin exhibited an ∼50-fold reduction in viability after oxygen depletion. Surfactin treatment of these cells led to membrane depolarization and reduced ATP production. Chemical and genetic perturbations that alter oxygen consumption or redox state support a model in which surfactin-mediated membrane depolarization maintains viability through slower oxygen consumption and/or a shift to a more reduced metabolic profile. These findings highlight the importance of membrane potential in regulating cell physiology and growth, and demonstrate that antimicrobials that depolarize cell membranes can benefit cells when the terminal electron acceptor in respiration is limiting. This foundational knowledge has deep implications for environmental microbiology, clinical anti-bacterial therapy, and industrial biotechnology.
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Affiliation(s)
- Heidi A Arjes
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Lam Vo
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Caroline M Dunn
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA
| | - Lisa Willis
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA
| | - Christopher A DeRosa
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Cassandra L Fraser
- Department of Chemistry, McCormick Road, University of Virginia, Charlottesville, VA 22904, USA
| | - Daniel B Kearns
- Department of Biology, 1001 E 3rd Street, Indiana University, Bloomington, IN 47405, USA.
| | - Kerwyn Casey Huang
- Department of Bioengineering, Stanford University School of Medicine, 443 via Ortega, Stanford, CA 94305, USA; Department of Microbiology & Immunology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, 499 Illinois Street, San Francisco, CA 94158, USA.
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Harnessing the Potential of Killers and Altruists within the Microbial Community: A Possible Alternative to Antibiotic Therapy? Antibiotics (Basel) 2019; 8:antibiotics8040230. [PMID: 31766366 PMCID: PMC6963621 DOI: 10.3390/antibiotics8040230] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 11/17/2019] [Accepted: 11/19/2019] [Indexed: 12/29/2022] Open
Abstract
In the context of a post-antibiotic era, the phenomenon of microbial allolysis, which is defined as the partial killing of bacterial population induced by other cells of the same species, may take on greater significance. This phenomenon was revealed in some bacterial species such as Streptococcus pneumoniae and Bacillus subtilis, and has been suspected to occur in some other species or genera, such as enterococci. The mechanisms of this phenomenon, as well as its role in the life of microbial populations still form part of ongoing research. Herein, we describe recent developments in allolysis in the context of its practical benefits as a form of cell death that may give rise to developing new strategies for manipulating the life and death of bacterial communities. We highlight how such findings may be viewed with importance and potential within the fields of medicine, biotechnology, and pharmacology.
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32
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Velazquez S, Griffiths W, Dietz L, Horve P, Nunez S, Hu J, Shen J, Fretz M, Bi C, Xu Y, Van Den Wymelenberg KG, Hartmann EM, Ishaq SL. From one species to another: A review on the interaction between chemistry and microbiology in relation to cleaning in the built environment. INDOOR AIR 2019; 29:880-894. [PMID: 31429989 PMCID: PMC6852270 DOI: 10.1111/ina.12596] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 08/11/2019] [Accepted: 08/15/2019] [Indexed: 05/12/2023]
Abstract
Since the advent of soap, personal hygiene practices have revolved around removal, sterilization, and disinfection-both of visible soil and microscopic organisms-for a myriad of cultural, aesthetic, or health-related reasons. Cleaning methods and products vary widely in their recommended use, effectiveness, risk to users or building occupants, environmental sustainability, and ecological impact. Advancements in science and technology have facilitated in-depth analyses of the indoor microbiome, and studies in this field suggest that the traditional "scorched-earth cleaning" mentality-that surfaces must be completely sterilized and prevent microbial establishment-may contribute to long-term human health consequences. Moreover, the materials, products, activities, and microbial communities indoors all contribute to, or remove, chemical species to the indoor environment. This review examines the effects of cleaning with respect to the interaction of chemistry, indoor microbiology, and human health.
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Affiliation(s)
| | - Willem Griffiths
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Leslie Dietz
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Patrick Horve
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Susie Nunez
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
| | - Jinglin Hu
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Jiaxian Shen
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Mark Fretz
- Institute for Health and the Built EnvironmentUniversity of OregonPortlandOR
| | - Chenyang Bi
- Department of Civil Environmental EngineeringVirginia Polytechnic Institute and State UniversityBlacksburgVA
| | - Ying Xu
- Department of Building ScienceTsinghua UniversityBeijingChina
| | - Kevin G. Van Den Wymelenberg
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
- Institute for Health and the Built EnvironmentUniversity of OregonPortlandOR
| | - Erica M. Hartmann
- Department of Civil and Environmental EngineeringNorthwestern UniversityEvanstonIL
| | - Suzanne L. Ishaq
- Biology and the Built Environment CenterUniversity of OregonEugeneOR
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Ganin H, Kemper N, Meir S, Rogachev I, Ely S, Massalha H, Mandaby A, Shanzer A, Keren-Paz A, Meijler MM, Malitsky S, Aharoni A, Kolodkin-Gal I. Indole Derivatives Maintain the Status Quo Between Beneficial Biofilms and Their Plant Hosts. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2019; 32:1013-1025. [PMID: 30811315 DOI: 10.1094/mpmi-12-18-0327-r] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Biofilms formed by bacteria on plant roots play an important role in maintaining an optimal rhizosphere environment that supports plant growth and fitness. Bacillus subtilis is a potent plant growth promoter, forming biofilms that play a key role in protecting the host from fungal and bacterial infections. In this work, we demonstrate that the development of B. subtilis biofilms is antagonized by specific indole derivatives that accumulate during symbiotic interactions with plant hosts. Indole derivatives are more potent signals when the plant polysaccharide xylan serves as a carbon source, a mechanism to sustain beneficial biofilms at a biomass that can be supported by the plant. Moreover, B. subtilis biofilms formed by mutants resistant to indole derivatives become deleterious to the plants due to their capacity to consume and recycle plant polysaccharides. These results demonstrate how a dynamic metabolite-based dialogue can promote homeostasis between plant hosts and their beneficial biofilm communities.
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Affiliation(s)
- Hadas Ganin
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Natalie Kemper
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Sagit Meir
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Rogachev
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Shir Ely
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Hassan Massalha
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Aviad Mandaby
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Alona Keren-Paz
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Michael M Meijler
- 3Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | | | - Asaph Aharoni
- 2Department of Plant and Environmental Sciences, Weizmann Institute of Science
| | - Ilana Kolodkin-Gal
- 1Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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Ogran A, Yardeni EH, Keren-Paz A, Bucher T, Jain R, Gilhar O, Kolodkin-Gal I. The Plant Host Induces Antibiotic Production To Select the Most-Beneficial Colonizers. Appl Environ Microbiol 2019; 85:e00512-19. [PMID: 31003984 PMCID: PMC6581183 DOI: 10.1128/aem.00512-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2019] [Accepted: 04/11/2019] [Indexed: 12/17/2022] Open
Abstract
Microbial ecosystems tightly associated with a eukaryotic host are widespread in nature. The genetic and metabolic networks of the eukaryotic hosts and the associated microbes have coevolved to form a symbiotic relationship. Both the Gram-positive Bacillus subtilis and the Gram-negative Serratia plymuthica can form biofilms on plant roots and thus can serve as a model system for the study of interspecies interactions in a host-associated ecosystem. We found that B. subtilis biofilms expand collectively and asymmetrically toward S. plymuthica, while expressing a nonribosomal antibiotic bacillaene and an extracellular protease. As a result, B. subtilis biofilms outcompeted S. plymuthica for successful colonization of the host. Strikingly, the plant host was able to enhance the efficiency of this killing by inducing bacillaene synthesis. In turn, B. subtilis biofilms increased the resistance of the plant host to pathogens. These results provide an example of how plant-bacterium symbiosis promotes the immune response of the plant host and the fitness of the associated bacteria.IMPORTANCE Our study sheds mechanistic light on how multicellular biofilm units compete to successfully colonize a eukaryote host, using B. subtilis microbial communities as our lens. The microbiota and its interactions with its host play various roles in the development and prevention of diseases. Using competing beneficial biofilms that are essential microbiota members on the plant host, we found that B. subtilis biofilms activate collective migration to capture their prey, followed by nonribosomal antibiotic synthesis. Plant hosts increase the efficiency of antibiotic production by B. subtilis biofilms, as they activate the synthesis of polyketides; therefore, our study provides evidence of a mechanism by which the host can indirectly select for beneficial microbiota members.
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Affiliation(s)
- Ariel Ogran
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Eliane Hadas Yardeni
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Alona Keren-Paz
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Tabitha Bucher
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Rakeshkumar Jain
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Omri Gilhar
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
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35
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Popp PF, Mascher T. Coordinated Cell Death in Isogenic Bacterial Populations: Sacrificing Some for the Benefit of Many? J Mol Biol 2019; 431:4656-4669. [PMID: 31029705 DOI: 10.1016/j.jmb.2019.04.024] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Revised: 04/11/2019] [Accepted: 04/14/2019] [Indexed: 01/22/2023]
Abstract
Antibiotics are classically perceived as biological weapons that bacteria produce to hold their ground against competing species in their natural habitat. But in the context of multicellular differentiation processes, antimicrobial compounds sometimes also play a role in intraspecies competition, resulting in the death of a sub-population of genetically identical siblings for the benefit of the population. Such a strategy is based on the diversification and hence phenotypic heterogeneity of an isogenic bacterial population. This review article will address three such phenomena. In Bacillus subtilis, cannibalism is a differentiation strategy that enhances biofilm formation, prolongs or potentially even prevents full commitment to endospore formation under starvation conditions, and protects cells within the biofilm against competing species. The nutrients released by lysed cells can be used by the toxin producers, thereby delaying the full activation of the master regulator of sporulation. A related strategy is associated with the initiation of competence development under nutrient excess in Streptococcus pneumoniae. This process, termed fratricide, causes allolysis in a sub-population and is thought to enhance genetic diversity within the species. In Myxococcus xanthus, a large fraction of the population undergoes programmed cell death during the formation of fruiting bodies. This sacrifice ensures the survival of the sporulating sub-population by providing nutrients and hence energy to complete this differentiation process. The biological relevance and underlying regulatory mechanisms of these three processes will be discussed in order to extract common features of such strategies. Moreover, open questions and future challenges will be addressed.
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Affiliation(s)
- Philipp F Popp
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062 Dresden, Germany
| | - Thorsten Mascher
- Institute of Microbiology, Technische Universität (TU) Dresden, 01062 Dresden, Germany.
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36
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Molina-Santiago C, Pearson JR, Navarro Y, Berlanga-Clavero MV, Caraballo-Rodriguez AM, Petras D, García-Martín ML, Lamon G, Haberstein B, Cazorla FM, de Vicente A, Loquet A, Dorrestein PC, Romero D. The extracellular matrix protects Bacillus subtilis colonies from Pseudomonas invasion and modulates plant co-colonization. Nat Commun 2019; 10:1919. [PMID: 31015472 PMCID: PMC6478825 DOI: 10.1038/s41467-019-09944-x] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Accepted: 04/05/2019] [Indexed: 12/15/2022] Open
Abstract
Bacteria of the genera Pseudomonas and Bacillus can promote plant growth and protect plants from pathogens. However, the interactions between these plant-beneficial bacteria are understudied. Here, we explore the interaction between Bacillus subtilis 3610 and Pseudomonas chlororaphis PCL1606. We show that the extracellular matrix protects B. subtilis colonies from infiltration by P. chlororaphis. The absence of extracellular matrix results in increased fluidity and loss of structure of the B. subtilis colony. The P. chlororaphis type VI secretion system (T6SS) is activated upon contact with B. subtilis cells, and stimulates B. subtilis sporulation. Furthermore, we find that B. subtilis sporulation observed prior to direct contact with P. chlororaphis is mediated by histidine kinases KinA and KinB. Finally, we demonstrate the importance of the extracellular matrix and the T6SS in modulating the coexistence of the two species on melon plant leaves and seeds. Pseudomonas and Bacillus can promote plant growth but their mutual interactions are unclear. Here, the authors show that the extracellular matrix protects Bacillus colonies from infiltration by Pseudomonas cells, while the Pseudomonas type VI secretion system stimulates Bacillus sporulation.
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Affiliation(s)
- Carlos Molina-Santiago
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - John R Pearson
- Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, 29071, Málaga, Spain
| | - Yurena Navarro
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - María Victoria Berlanga-Clavero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | | | - Daniel Petras
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, 92093, USA
| | - María Luisa García-Martín
- Nano-imaging Unit, Andalusian Centre for Nanomedicine and Biotechnology, BIONAND, 29071, Málaga, Spain
| | - Gaelle Lamon
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Birgit Haberstein
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain
| | - Antoine Loquet
- Institute of Chemistry & Biology of Membranes & Nanoobjects (UMR5248 CBMN), CNRS, Université Bordeaux, Institut Européen de Chimie et Biologie, 33600, Pessac, France
| | - Pieter C Dorrestein
- University of California San Diego, Collaborative Mass Spectrometry Innovation Center, La Jolla, CA, 92093, USA
| | - Diego Romero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga-Consejo Superior de Investigaciones Científicas (IHSM-UMA-CSIC), Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur 31 (Campus Universitario de Teatinos), 29071, Málaga, Spain.
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37
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Luzzatto-Knaan T, Melnik AV, Dorrestein PC. Mass Spectrometry Uncovers the Role of Surfactin as an Interspecies Recruitment Factor. ACS Chem Biol 2019; 14:459-467. [PMID: 30763059 DOI: 10.1021/acschembio.8b01120] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Microbes use metabolic exchange to sense and respond to their changing environment. Surfactins, produced by Bacillus subtilis, have been extensively studied for their role in biofilm formation, biosurfactant properties, and antimicrobial activity, affecting the surrounding microbial consortia. Using mass spectrometry, we reveal that Paenibacillus dendritiformis, originally isolated with B. subtilis, is not antagonized by the presence of surfactins and is actually attracted to them. We demonstrate here for the first time that P. dendritiformis is also actively degrading surfactins produced by B. subtilis and accumulating the degradation products that serve as territorial markers. This new attribute as an attractant of selected microbes and the conversion into a deterrent highlight the diverse role natural products have in shaping the environment and establishing mixed communities.
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Affiliation(s)
- Tal Luzzatto-Knaan
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Alexey V. Melnik
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
| | - Pieter C. Dorrestein
- Collaborative Mass Spectrometry Innovation Center, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego, La Jolla, California 92093, United States
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38
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Libberton B, Binz M, van Zalinge H, Nicolau DV. Efficiency of the flagellar propulsion of Escherichia coli in confined microfluidic geometries. Phys Rev E 2019; 99:012408. [PMID: 30780339 DOI: 10.1103/physreve.99.012408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Indexed: 12/23/2022]
Abstract
Bacterial movement in confined spaces is routinely encountered either in a natural environment or in artificial structures. Consequently, the ability to understand and predict the behavior of motile bacterial cells in confined geometries is essential to many applications, spanning from the more classical, such as the management complex microbial networks involved in diseases, biomanufacturing, mining, and environment, to the more recent, such as single cell DNA sequencing and computation with biological agents. Fortunately, the development of this understanding can be helped by the decades-long advances in semiconductor microfabrication, which allow the design and the construction of complex confining structures used as test beds for the study of bacterial motility. To this end, here we use microfabricated channels with varying sizes to study the interaction of Escherichia coli with solid confining spaces. It is shown that an optimal channel size exists for which the hydrostatic potential allows the most efficient movement of the cells. The improved understanding of how bacteria move will result in the ability to design better microfluidic structures based on their interaction with bacterial movement.
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Affiliation(s)
- Ben Libberton
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Marie Binz
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Harm van Zalinge
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
| | - Dan V Nicolau
- Department of Electrical Engineering and Electronics, University of Liverpool, L69 3GJ Liverpool, United Kingdom
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39
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Alvarez-Ordóñez A, Coughlan LM, Briandet R, Cotter PD. Biofilms in Food Processing Environments: Challenges and Opportunities. Annu Rev Food Sci Technol 2019; 10:173-195. [PMID: 30653351 DOI: 10.1146/annurev-food-032818-121805] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This review examines the impact of microbial communities colonizing food processing environments in the form of biofilms on food safety and food quality. The focus is both on biofilms formed by pathogenic and spoilage microorganisms and on those formed by harmless or beneficial microbes, which are of particular relevance in the processing of fermented foods. Information is presented on intraspecies variability in biofilm formation, interspecies relationships of cooperativism or competition within biofilms, the factors influencing biofilm ecology and architecture, and how these factors may influence removal. The effect on the biofilm formation ability of particular food components and different environmental conditions that commonly prevail during food processing is discussed. Available tools for the in situ monitoring and characterization of wild microbial biofilms in food processing facilities are explored. Finally, research on novel agents or strategies for the control of biofilm formation or removal is summarized.
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Affiliation(s)
- Avelino Alvarez-Ordóñez
- Department of Food Hygiene and Technology and Institute of Food Science and Technology, Universidad de León, 24071 León, Spain;
| | - Laura M Coughlan
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland.,School of Microbiology, University College Cork, County Cork, Ireland
| | - Romain Briandet
- Micalis Institute, INRA, AgroParisTech, Université Paris-Saclay, Jouy-en-Josas, 78350 France
| | - Paul D Cotter
- Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland.,APC Microbiome Ireland, Cork, County Cork, Ireland
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40
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Parijs I, Steenackers HP. Competitive inter-species interactions underlie the increased antimicrobial tolerance in multispecies brewery biofilms. ISME JOURNAL 2018; 12:2061-2075. [PMID: 29858577 DOI: 10.1038/s41396-018-0146-5] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 03/17/2018] [Accepted: 03/20/2018] [Indexed: 11/09/2022]
Abstract
Genetic diversity often enhances the tolerance of microbial communities against antimicrobial treatment. However the sociobiology underlying this antimicrobial tolerance remains largely unexplored. Here we analyze how inter-species interactions can increase antimicrobial tolerance. We apply our approach to 17 industrially relevant multispecies biofilm models, based on species isolated from 58 contaminating biofilms in three breweries. Sulfathiazole was used as antimicrobial agent because it showed the highest activity out of 22 biofilm inhibitors tested. Our analysis reveals that competitive interactions dominate among species within brewery biofilms. We show that antimicrobial treatment can reduce the level of competition and therefore cause a subset of species to bloom. The result is a 1.2-42.7-fold lower percentage inhibition of these species and increased overall tolerance. In addition, we show that the presence of Raoultella can also directly enhance the inherent tolerance of Pseudomonas to antimicrobial treatment, either because the species protect each other or because they induce specific tolerance phenotypes as a response to competitors. Overall, our study emphasizes that the dominance of competitive interactions is central to the enhanced antimicrobial tolerance of the multispecies biofilms, and that the activity of antimicrobials against multispecies biofilms cannot be predicted based on their effect against monocultures.
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Affiliation(s)
- Ilse Parijs
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20 - box 2460, B-3001, Leuven, Belgium
| | - Hans P Steenackers
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics (CMPG), KU Leuven, Kasteelpark Arenberg 20 - box 2460, B-3001, Leuven, Belgium.
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41
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Corbett MK, Eksteen JJ, Niu XZ, Watkin ELJ. Syntrophic effect of indigenous and inoculated microorganisms in the leaching of rare earth elements from Western Australian monazite. Res Microbiol 2018; 169:558-568. [PMID: 29852218 DOI: 10.1016/j.resmic.2018.05.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 05/16/2018] [Accepted: 05/19/2018] [Indexed: 10/14/2022]
Abstract
The unique physiochemical properties exhibited by rare earth elements (REEs) and their increasing application in high-tech industries has created a demand for secure supply lines with established recovery procedures that create minimal environmental damage. Bioleaching experiments conducted on a non-sterile monazite concentrate with a known phosphate solubilising microorganism (PSM) resulted in greater mobilisation of REEs into solution in comparison to experiments conducted on sterile monazite. By combining the native consortia with an introduced PSM, a syntrophic effect between the populations effectively leached a greater amount of REEs than either a single PSM or the indigenous population alone. With sterile monazite, Penicillium sp.CF1 inoculated experiments released a total REE concentration of 12.32 mg L-1 after incubation for 8 days, whereas on non-sterile ore, double the soluble REE concentration was recorded (23.7 mg L-1). Comparable effects were recorded with Enterobacter aerogenes, Pantoea agglomerans and Pseudomonas putida. Alterations in the microbial populations during bioleaching of the monazite ore were determined by diversity profiling and demonstrated noticeable changes in community inhabitants over 14 days. The presence of native Firmicutes on the monazite appears to greatly contribute to the increased leaching recorded when using non-sterile monazite for REE recovery.
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Affiliation(s)
- Melissa K Corbett
- School of Pharmacy and Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Jacques J Eksteen
- Western Australian School of Mines, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Xi-Zhi Niu
- Curtin Water Quality Research Centre, Department of Chemistry, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
| | - Elizabeth L J Watkin
- School of Pharmacy and Biomedical Sciences, CHIRI Biosciences, Curtin University, GPO Box U1987, Perth, WA 6845, Australia.
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42
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Gafri HFS, Mohamed Zuki F, Aroua MK, Hashim NA. Mechanism of bacterial adhesion on ultrafiltration membrane modified by natural antimicrobial polymers (chitosan) and combination with activated carbon (PAC). REV CHEM ENG 2018. [DOI: 10.1515/revce-2017-0006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Abstract
Bacterial adhesion to surfaces is related to several factors, such as surface charge, surface energy, and substrate characteristics (leading to the formation of biofilms). Organisms are dominant in most environmental, industrial, and medical problems and processes that are of interest to microbiologists. Biofilm cells are at least 500 times more resistant to antibacterial agents compared to planktonic cells. The usage of ultrafiltration membranes is fast becoming popular for water treatment. Membrane lifetime and permeate flux are primarily affected by the phenomena of microbial accumulation and fouling at the membrane’s surface. This review intends to understand the mechanism of membrane fouling by bacterial attachment on polymeric ultrafiltration membrane modified by natural antimicrobial polymers (chitosan) combined with powder activated carbon. Also, to guide future research on membrane water treatment processes, adhesion prediction using the extended Derjaguin-Landau-Verwey-Overbeek theory is discussed.
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Affiliation(s)
- Hasan Fouzi S. Gafri
- Department of Chemical Engineering , University of Malaya , 50603 Kuala Lumpur , Malaysia
| | - Fathiah Mohamed Zuki
- Department of Chemical Engineering , University of Malaya , 50603 Kuala Lumpur , Malaysia
| | - Mohamed Kheireddine Aroua
- Centre for Carbon Dioxide Capture and Utilization (CCDCU), School of Science and Technology , Sunway University, Bandar Sunway , 47500 Petaling Jaya , Malaysia
- Department of Engineering , Lancaster University , Lancaster, LA1 4YW , UK
| | - Nur Awanis Hashim
- Department of Chemical Engineering , University of Malaya , 50603 Kuala Lumpur , Malaysia
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43
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Feng K, Zhang Z, Cai W, Liu W, Xu M, Yin H, Wang A, He Z, Deng Y. Biodiversity and species competition regulate the resilience of microbial biofilm community. Mol Ecol 2017; 26:6170-6182. [DOI: 10.1111/mec.14356] [Citation(s) in RCA: 195] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/30/2017] [Accepted: 09/05/2017] [Indexed: 01/30/2023]
Affiliation(s)
- Kai Feng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- Department of Chemical and Biochemical Engineering Technical University of Denmark Lyngby Denmark
- Sino‐Danish Center for Education and Research Beijing China
- University of Chinese Academy of Sciences Beijing China
| | - Zhaojing Zhang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Industrial Ecology and Environmental Engineering (Ministry of Education, China) School of Environmental Science and Technology Dalian University of Technology Dalian China
| | - Weiwei Cai
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- State Key Laboratory of Urban Water Resource and Environment Harbin Institute of Technology (SKLUWRE, HIT) Harbin China
| | - Wenzong Liu
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
| | - Meiying Xu
- Guangdong Provincial Key Laboratory of Microbial Culture Collection and Application Guangdong Institute of Microbiology Guangzhou China
| | - Huaqun Yin
- School of Minerals Processing and Bioengineering Central South University Changsha China
| | - Aijie Wang
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
| | - Zhili He
- School of Environmental Science and Engineering Sun Yat‐sen University Guangzhou China
- Department of Microbiology and Plant Biology Institute for Environmental Genomics University of Oklahoma Norman OK USA
| | - Ye Deng
- CAS Key Laboratory for Environmental Biotechnology Research Center for Eco‐Environmental Sciences Chinese Academy of Sciences Beijing China
- College of Resources and Environment University of Chinese Academy of Sciences Beijing China
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44
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An improved protocol for harvesting Bacillus subtilis colony biofilms. J Microbiol Methods 2017; 134:7-13. [PMID: 28069469 DOI: 10.1016/j.mimet.2017.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/03/2017] [Accepted: 01/03/2017] [Indexed: 12/11/2022]
Abstract
Bacterial biofilms cause severe problems in medicine and industry due to the high resistance to disinfectants and environmental stress of organisms within biofilms. Addressing challenges caused by biofilms requires full understanding of the underlying mechanisms for bacterial resistance and survival in biofilms. However, such work is hampered by a relative lack of systems for biofilm cultivation that are practical and reproducible. To address this problem, we developed a readily applicable method to culture Bacillus subtilis biofilms on a membrane filter. The method results in biofilms with highly reproducible characteristics, and which can be readily analyzed by a variety of methods with little further manipulation. This biofilm preparation method simplifies routine generation of B. subtilis biofilms for molecular and cellular analysis, and could be applicable to other microbial systems.
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45
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Adegoke AA, Faleye AC, Singh G, Stenström TA. Antibiotic Resistant Superbugs: Assessment of the Interrelationship of Occurrence in Clinical Settings and Environmental Niches. Molecules 2016; 22:E29. [PMID: 28035988 PMCID: PMC6155606 DOI: 10.3390/molecules22010029] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Revised: 12/11/2016] [Accepted: 12/22/2016] [Indexed: 02/06/2023] Open
Abstract
The increasing threat to global health posed by antibiotic resistance remains of serious concern. Human health remains at higher risk due to several reported therapeutic failures to many life threatening drug resistant microbial infections. The resultant effects have been prolonged hospital stay, higher cost of alternative therapy, increased mortality, etc. This opinionated review considers the two main concerns in integrated human health risk assessment (i.e., residual antibiotics and antibiotic resistant genes) in various compartments of human environment, as well as clinical dynamics associated with the development and transfer of antibiotic resistance (AR). Contributions of quorum sensing, biofilms, enzyme production, and small colony variants in bacteria, among other factors in soil, water, animal farm and clinical settings were also considered. Every potential factor in environmental and clinical settings that brings about AR needs to be identified for the summative effects in overall resistance. There is a need to embrace coordinated multi-locational approaches and interrelationships to track the emergence of resistance in different niches in soil and water versus the hospital environment. The further integration with advocacy, legislation, enforcement, technological innovations and further research input and recourse to WHO guidelines on antibiotic policy would be advantageous towards addressing the emergence of antibiotic resistant superbugs.
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Affiliation(s)
- Anthony Ayodeji Adegoke
- SARChI, Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
- Department of Microbiology, University of Uyo, 520211 Uyo, Akwa Ibom State, Nigeria.
- Department of Biochemistry and Microbiology, University of Fort Hare, Alice 5700, Eastern Cape, South Africa.
| | - Adekunle Christopher Faleye
- SARChI, Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
| | - Gulshan Singh
- SARChI, Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
| | - Thor Axel Stenström
- SARChI, Institute for Water and Wastewater Technology, Durban University of Technology, Durban 4000, South Africa.
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46
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Ma Y, Kong Q, Qin C, Chen Y, Chen Y, Lv R, Zhou G. Identification of lipopeptides in Bacillus megaterium by two-step ultrafiltration and LC-ESI-MS/MS. AMB Express 2016; 6:79. [PMID: 27639854 PMCID: PMC5026979 DOI: 10.1186/s13568-016-0252-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 09/08/2016] [Indexed: 11/10/2022] Open
Abstract
A two-step ultrafiltration and liquid chromatography-electronic spray ionization-tandem mass spectrometry (LC-ESI-MS/MS) were applied to investigate the nature of lipopeptides in the methanol extract harvested from marine Bacillus megaterium. The structure of lipopeptide homologs were characterized by using collision-induced dissociation mass spectrometry analysis. Collectively, two kinds of linear fengycin A and B with a double bond were characterized for the first time besides the popular cyclic fengycin A and B with the difference in the amino acid at position 6 of the peptide moiety. It is worth noting that two kinds of linear isoforms of surfactins and two kinds of cyclic isoforms of esperin with a smaller peptide ring formed by the fifth L-Asp and β-hydroxy fatty acid were also separated and identified in addition to the all seven kinds of cyclic isoforms of surfactins. Only one analogue (bacillomycin D) of iturin family was identified in this research. To our best knowledge, this is the first report that more than 40 variants of lipopeptides from one strain of Bacillus were identified using our potent purification and identification methods.
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47
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Ghoul M, Mitri S. The Ecology and Evolution of Microbial Competition. Trends Microbiol 2016; 24:833-845. [DOI: 10.1016/j.tim.2016.06.011] [Citation(s) in RCA: 378] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Revised: 06/15/2016] [Accepted: 06/28/2016] [Indexed: 01/23/2023]
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48
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Bloom-Ackermann Z, Steinberg N, Rosenberg G, Oppenheimer-Shaanan Y, Pollack D, Ely S, Storzi N, Levy A, Kolodkin-Gal I. Toxin-Antitoxin systems eliminate defective cells and preserve symmetry in Bacillus subtilis biofilms. Environ Microbiol 2016; 18:5032-5047. [PMID: 27450630 DOI: 10.1111/1462-2920.13471] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Revised: 07/07/2016] [Accepted: 07/20/2016] [Indexed: 01/02/2023]
Abstract
Toxin-antitoxin modules are gene pairs encoding a toxin and its antitoxin, and are found on the chromosomes of many bacteria, including pathogens. Here, we characterize the specific contribution of the TxpA and YqcG toxins in elimination of defective cells from developing Bacillus subtilis biofilms. On nutrient limitation, defective cells accumulated in the biofilm breaking its symmetry. Deletion of the toxins resulted in accumulation of morphologically abnormal cells, and interfered with the proper development of the multicellular community. Dual physiological responses are of significance for TxpA and YqcG activation: nitrogen deprivation enhances the transcription of both TxpA and YqcG toxins, and simultaneously sensitizes the biofilm cells to their activity. Furthermore, we demonstrate that while both toxins when overexpressed affect the morphology of the developing biofilm, the toxin TxpA can act to lyse and dissolve pre-established B. subtilis biofilms.
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Affiliation(s)
- Zohar Bloom-Ackermann
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nitai Steinberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Gili Rosenberg
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | | | - Dan Pollack
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Shir Ely
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Nimrod Storzi
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Asaf Levy
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Ilana Kolodkin-Gal
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
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