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Arbour CA, Nagar R, Bernstein HM, Ghosh S, Al-Sammarraie Y, Dorfmueller HC, Ferguson MAJ, Stanley-Wall NR, Imperiali B. Defining early steps in Bacillus subtilis biofilm biosynthesis. mBio 2023; 14:e0094823. [PMID: 37650625 PMCID: PMC10653937 DOI: 10.1128/mbio.00948-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 05/08/2023] [Indexed: 09/01/2023] Open
Abstract
IMPORTANCE Biofilms are the communal way of life that microbes adopt to increase survival. Key to our ability to systematically promote or ablate biofilm formation is a detailed understanding of the biofilm matrix macromolecules. Here, we identify the first two essential steps in the Bacillus subtilis biofilm matrix exopolysaccharide (EPS) synthesis pathway. Together, our studies and approaches provide the foundation for the sequential characterization of the steps in EPS biosynthesis, using prior steps to enable chemoenzymatic synthesis of the undecaprenyl diphosphate-linked glycan substrates.
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Affiliation(s)
- Christine A. Arbour
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Rupa Nagar
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Hannah M. Bernstein
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Soumi Ghosh
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Yusra Al-Sammarraie
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Helge C. Dorfmueller
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Michael A. J. Ferguson
- Wellcome Centre for Anti-Infectives Research, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Barbara Imperiali
- Department of Biology and Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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2
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Rosazza T, Eigentler L, Earl C, Davidson FA, Stanley‐Wall NR. Bacillus subtilis extracellular protease production incurs a context-dependent cost. Mol Microbiol 2023; 120:105-121. [PMID: 37380434 PMCID: PMC10952608 DOI: 10.1111/mmi.15110] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/30/2023]
Abstract
Microbes encounter a wide range of polymeric nutrient sources in various environmental settings, which require processing to facilitate growth. Bacillus subtilis, a bacterium found in the rhizosphere and broader soil environment, is highly adaptable and resilient due to its ability to utilise diverse sources of carbon and nitrogen. Here, we explore the role of extracellular proteases in supporting growth and assess the cost associated with their production. We provide evidence of the essentiality of extracellular proteases when B. subtilis is provided with an abundant, but polymeric nutrient source and demonstrate the extracellular proteases as a shared public good that can operate over a distance. We show that B. subtilis is subjected to a public good dilemma, specifically in the context of growth sustained by the digestion of a polymeric food source. Furthermore, using mathematical simulations, we uncover that this selectively enforced dilemma is driven by the relative cost of producing the public good. Collectively, our findings reveal how bacteria can survive in environments that vary in terms of immediate nutrient accessibility and the consequent impact on the population composition. These findings enhance our fundamental understanding of how bacteria respond to diverse environments, which has importance to contexts ranging from survival in the soil to infection and pathogenesis scenarios.
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Affiliation(s)
- Thibault Rosazza
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
| | - Lukas Eigentler
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
- Mathematics, School of Science and EngineeringUniversity of DundeeDundeeUK
- Present address:
Evolutionary Biology DepartmentUniversität BielefeldKonsequenz 45Bielefeld33615Germany
| | - Chris Earl
- Division of Molecular Microbiology, School of Life ScienceUniversity of DundeeDundeeUK
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3
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Kalamara M, Abbott J, Sukhodub T, MacPhee C, Stanley-Wall NR. The putative role of the epipeptide EpeX in Bacillus subtilis intra-species competition. MICROBIOLOGY (READING, ENGLAND) 2023; 169:001344. [PMID: 37289492 PMCID: PMC7614699 DOI: 10.1099/mic.0.001344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 05/19/2023] [Indexed: 06/09/2023]
Abstract
Bacteria engage in competitive interactions with neighbours that can either be of the same or different species. Multiple mechanisms are deployed to ensure the desired outcome and one tactic commonly implemented is the production of specialised metabolites. The Gram-positive bacterium Bacillus subtilis uses specialized metabolites as part of its intra-species competition determinants to differentiate between kin and non-kin isolates. It is, however, unknown if the collection of specialized metabolites defines competitive fitness when the two isolates start as a close, interwoven community that grows into a densely packed colony biofilm. Moreover, the identity of specialized metabolites that have an active role in defining the outcome of an intra-species interaction has not been revealed. Here, we determine the competition outcomes that manifest when 21 environmental isolates of B. subtilis are individually co-incubated with the model isolate NCIB 3610 in a colony biofilm. We correlated these data with the suite of specialized metabolite biosynthesis clusters encoded by each isolate. We found that the epeXEPAB gene cluster was primarily present in isolates with a strong competitive phenotype. This cluster is responsible for producing the epipeptide EpeX. We demonstrated that EpeX is a competition determinant of B. subtilis in an otherwise isogenic context for NCBI 3610. However, when we competed the NCIB 3610 EpeX-deficient strain against our suite of environmental isolates we found that the impact of EpeX in competition is isolate-specific, as only one of the 21 isolates showed increased survival when EpeX was lacking. Taken together, we have shown that EpeX is a competition determinant used by B. subtilis that impacts intra-species interactions but only in an isolate-specific manner.
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Affiliation(s)
- Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - James Abbott
- Data Analysis Group, Division of Computational Biology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Tetyana Sukhodub
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
| | - Cait MacPhee
- National Biofilms Innovation Centre, School of Physics & Astronomy, University of Edinburgh, EH9 3FD Edinburgh, UK
| | - Nicola R. Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD5 4EH, UK
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4
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Eigentler L, Kalamara M, Ball G, MacPhee CE, Stanley-Wall NR, Davidson FA. Founder cell configuration drives competitive outcome within colony biofilms. THE ISME JOURNAL 2022; 16:1512-1522. [PMID: 35121821 PMCID: PMC9122948 DOI: 10.1038/s41396-022-01198-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 01/03/2022] [Accepted: 01/17/2022] [Indexed: 11/19/2022]
Abstract
Bacteria can form dense communities called biofilms, where cells are embedded in a self-produced extracellular matrix. Exploiting competitive interactions between strains within the biofilm context can have potential applications in biological, medical, and industrial systems. By combining mathematical modelling with experimental assays, we reveal that spatial structure and competitive dynamics within biofilms are significantly affected by the location and density of the founder cells used to inoculate the biofilm. Using a species-independent theoretical framework describing colony biofilm formation, we show that the observed spatial structure and relative strain biomass in a mature biofilm comprising two isogenic strains can be mapped directly to the geographical distributions of founder cells. Moreover, we define a predictor of competitive outcome that accurately forecasts relative abundance of strains based solely on the founder cells’ potential for radial expansion. Consequently, we reveal that variability of competitive outcome in biofilms inoculated at low founder density is a natural consequence of the random positioning of founding cells in the inoculum. Extension of our study to non-isogenic strains that interact through local antagonisms, shows that even for strains with different competition strengths, a race for space remains the dominant mode of competition in low founder density biofilms. Our results, verified by experimental assays using Bacillus subtilis, highlight the importance of spatial dynamics on competitive interactions within biofilms and hence to related applications.
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Affiliation(s)
- Lukas Eigentler
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Mathematics, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK
| | - Margarita Kalamara
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Graeme Ball
- Dundee Imaging Facility, School of Life Sciences, University of Dundee, Dundee, DD1 5HN, UK
| | - Cait E MacPhee
- School of Physics and Astronomy, The University of Edinburgh, Edinburgh, EH9 3FD, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.
| | - Fordyce A Davidson
- Mathematics, School of Science and Engineering, University of Dundee, Dundee, DD1 4HN, UK.
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5
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Thomas GH. Microbial Musings - September 2021. MICROBIOLOGY (READING, ENGLAND) 2021; 167. [PMID: 34672917 PMCID: PMC8698185 DOI: 10.1099/mic.0.001115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Gavin H. Thomas
- Department of Biology, University of York, YO10 5YW, UK
- *Correspondence: Gavin H. Thomas,
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