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Mahadevaswamy UR, Mugunthan S, Seviour T, Kjelleberg S, Lim S. Evaluating a polymicrobial biofilm model for structural components by co-culturing Komagataeibacter hansenii produced bacterial cellulose with Pseudomonas aeruginosa PAO1. Biofilm 2024; 7:100176. [PMID: 38322579 PMCID: PMC10845243 DOI: 10.1016/j.bioflm.2024.100176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 12/21/2023] [Accepted: 01/04/2024] [Indexed: 02/08/2024] Open
Abstract
A polymicrobial biofilm model of Komagataeibacter hansenii and Pseudomonas aeruginosa was developed to understand whether a pre-existing matrix affects the ability of another species to build a biofilm. P. aeruginosa was inoculated onto the preformed K. hansenii biofilm consisting of a cellulose matrix. P. aeruginosa PAO1 colonized and infiltrated the K. hansenii bacterial cellulose biofilm (BC), as indicated by the presence of cells at 19 μm depth in the translucent hydrogel matrix. Bacterial cell density increased along the imaged depth of the biofilm (17-19 μm). On day 5, the average bacterial count across sections was 67 ± 4 % P. aeruginosa PAO1 and 33 ± 6 % K. hansenii. Biophysical characterization of the biofilm indicated that colonization by P. aeruginosa modified the biophysical properties of the BC matrix, which inlcuded increased density, heterogeneity, degradation temperature and thermal stability, and reduced crystallinity, swelling ability and moisture content. This further indicates colonization of the biofilm by P. aeruginosa. While eDNA fibres - a key viscoelastic component of P. aeruginosa biofilm - were present on the surface of the co-cultured biofilm on day 1, their abundance decreased over time, and by day 5, no eDNA was observed, either on the surface or within the matrix. P. aeruginosa-colonized biofilm devoid of eDNA retained its mechanical properties. The observations demonstrate that a pre-existing biofilm scaffold of K. hansenii inhibits P. aeruginosa PAO1 eDNA production and suggest that eDNA production is a response by P. aeruginosa to the viscoelastic properties of its environment.
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Affiliation(s)
- Usha Rani Mahadevaswamy
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, Australia
| | - Sierin Lim
- School of Chemistry, Chemical Engineering and Biotechnology, Nanyang Technological University, Singapore
- Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore
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Mugunthan S, Wong LL, Winnerdy FR, Summers S, Bin Ismail MH, Foo YH, Jaggi TK, Meldrum OW, Tiew PY, Chotirmall SH, Rice SA, Phan AT, Kjelleberg S, Seviour T. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nat Commun 2023; 14:7772. [PMID: 38012164 PMCID: PMC10682433 DOI: 10.1038/s41467-023-43533-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 11/13/2023] [Indexed: 11/29/2023] Open
Abstract
The extracellular matrix of bacterial biofilms consists of diverse components including polysaccharides, proteins and DNA. Extracellular RNA (eRNA) can also be present, contributing to the structural integrity of biofilms. However, technical difficulties related to the low stability of RNA make it difficult to understand the precise roles of eRNA in biofilms. Here, we show that eRNA associates with extracellular DNA (eDNA) to form matrix fibres in Pseudomonas aeruginosa biofilms, and the eRNA is enriched in certain bacterial RNA transcripts. Degradation of eRNA associated with eDNA led to a loss of eDNA fibres and biofilm viscoelasticity. Compared with planktonic and biofilm cells, the biofilm matrix was enriched in specific mRNA transcripts, including lasB (encoding elastase). The mRNA transcripts colocalised with eDNA fibres in the biofilm matrix, as shown by single molecule inexpensive FISH microscopy (smiFISH). The lasB mRNA was also observed in eDNA fibres in a clinical sputum sample positive for P. aeruginosa. Thus, our results indicate that the interaction of specific mRNAs with eDNA facilitates the formation of viscoelastic networks in the matrix of Pseudomonas aeruginosa biofilms.
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Affiliation(s)
- Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
| | | | - Stephen Summers
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- St John's Island National Marine Laboratory c/o Tropical Marine Science Institute, National University of Singapore, 119227, Singapore
| | | | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- Institute for Digital Molecular Analytics and Science (IDMxS), Nanyang Technological University, Singapore, 636921, Singapore
| | - Tavleen Kaur Jaggi
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Oliver W Meldrum
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
| | - Pei Yee Tiew
- Department of Respiratory and Critical Care Medicine, Singapore General Hospital, Singapore, Singapore
| | - Sanjay H Chotirmall
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, 636921, Singapore
- Department of Respiratory and Critical Care Medicine, Tan Tock Seng Hospital, Singapore, Singapore
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore
- The iThree Institute, University of Technology Sydney, Sydney, 2007, Australia
- CSIRO, Agriculture and Food, Westmead and Microbiomes for One Systems Health, Canberra, Australia
| | - Anh Tuân Phan
- School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore, 637371, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological Sciences, Nanyang Technological University, Singapore, 637551, Singapore.
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, 2052, Australia.
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
- Centre for Water Technology (WATEC), Department of Biological and Chemical Engineering, Aarhus University, Aarhus, 8000, Denmark.
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Wong LL, Mugunthan S, Kundukad B, Ho JCS, Rice SA, Hinks J, Seviour T, Parikh AN, Kjelleberg S. Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix. Environ Microbiol 2023; 25:199-208. [PMID: 36502515 DOI: 10.1111/1462-2920.16306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - James Chin Shing Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- CSIRO, Agriculture and Food, Microbiomes for One Systems Health, Canberra, Australia
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,WATEC Aarhus University Centre for Water Technology, Aarhus, Denmark
| | - Atul N Parikh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore.,Department of Biomedical Engineering, University of California, Davis, California, USA
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Seviour T, Winnerdy FR, Wong LL, Shi X, Mugunthan S, Foo YH, Castaing R, Adav SS, Subramoni S, Kohli GS, Shewan HM, Stokes JR, Rice SA, Phan AT, Kjelleberg S. The biofilm matrix scaffold of Pseudomonas aeruginosa contains G-quadruplex extracellular DNA structures. NPJ Biofilms Microbiomes 2021; 7:27. [PMID: 33741996 PMCID: PMC7979868 DOI: 10.1038/s41522-021-00197-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/12/2021] [Indexed: 12/31/2022] Open
Abstract
Extracellular DNA, or eDNA, is recognised as a critical biofilm component; however, it is not understood how it forms networked matrix structures. Here, we isolate eDNA from static-culture Pseudomonas aeruginosa biofilms using ionic liquids to preserve its biophysical signatures of fluid viscoelasticity and the temperature dependency of DNA transitions. We describe a loss of eDNA network structure as resulting from a change in nucleic acid conformation, and propose that its ability to form viscoelastic structures is key to its role in building biofilm matrices. Solid-state analysis of isolated eDNA, as a proxy for eDNA structure in biofilms, reveals non-canonical Hoogsteen base pairs, triads or tetrads involving thymine or uracil, and guanine, suggesting that the eDNA forms G-quadruplex structures. These are less abundant in chromosomal DNA and disappear when eDNA undergoes conformation transition. We verify the occurrence of G-quadruplex structures in the extracellular matrix of intact static and flow-cell biofilms of P. aeruginosa, as displayed by the matrix to G-quadruplex-specific antibody binding, and validate the loss of G-quadruplex structures in vivo to occur coincident with the disappearance of eDNA fibres. Given their stability, understanding how extracellular G-quadruplex structures form will elucidate how P. aeruginosa eDNA builds viscoelastic networks, which are a foundational biofilm property.
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Affiliation(s)
- Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore. .,WATEC Aarhus University Centre for Water Technology, Aarhus, Denmark.
| | - Fernaldo Richtia Winnerdy
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Xiangyan Shi
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Yong Hwee Foo
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Remi Castaing
- Materials and Chemical Characterisation Facility (MC2), University of Bath, Bath, UK
| | - Sunil S Adav
- Singapore Phenome Centre, Nanyang Technological University, Singapore, Singapore
| | - Sujatha Subramoni
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Gurjeet Singh Kohli
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Heather M Shewan
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, Australia
| | - Jason R Stokes
- School of Chemical Engineering, University of Queensland, Brisbane, QLD, Australia
| | - Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,The iThree Institute, University of Technology Sydney, Sydney, NSW, Australia.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore, Singapore
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore. .,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore. .,School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia.
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5
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Mai-Prochnow A, Zhou R, Zhang T, Ostrikov K(K, Mugunthan S, Rice SA, Cullen PJ. Interactions of plasma-activated water with biofilms: inactivation, dispersal effects and mechanisms of action. NPJ Biofilms Microbiomes 2021; 7:11. [PMID: 33504802 PMCID: PMC7841176 DOI: 10.1038/s41522-020-00180-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 12/11/2020] [Indexed: 01/30/2023] Open
Abstract
Biofilms have several characteristics that ensure their survival in a range of adverse environmental conditions, including high cell numbers, close cell proximity to allow easy genetic exchange (e.g., for resistance genes), cell communication and protection through the production of an exopolysaccharide matrix. Together, these characteristics make it difficult to kill undesirable biofilms, despite the many studies aimed at improving the removal of biofilms. An elimination method that is safe, easy to deliver in physically complex environments and not prone to microbial resistance is highly desired. Cold atmospheric plasma, a lightning-like state generated from air or other gases with a high voltage can be used to make plasma-activated water (PAW) that contains many active species and radicals that have antimicrobial activity. Recent studies have shown the potential for PAW to be used for biofilm elimination without causing the bacteria to develop significant resistance. However, the precise mode of action is still the subject of debate. This review discusses the formation of PAW generated species and their impacts on biofilms. A focus is placed on the diffusion of reactive species into biofilms, the formation of gradients and the resulting interaction with the biofilm matrix and specific biofilm components. Such an understanding will provide significant benefits for tackling the ubiquitous problem of biofilm contamination in food, water and medical areas.
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Affiliation(s)
- Anne Mai-Prochnow
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2006 Australia
| | - Renwu Zhou
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2006 Australia
| | - Tianqi Zhang
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2006 Australia
| | - Kostya (Ken) Ostrikov
- grid.1024.70000000089150953School of Chemistry and Physics, Queensland University of Technology, Brisbane, QLD 4000 Australia
| | - Sudarsan Mugunthan
- grid.59025.3b0000 0001 2224 0361The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 639798 Singapore
| | - Scott A. Rice
- grid.59025.3b0000 0001 2224 0361The Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 639798 Singapore ,grid.59025.3b0000 0001 2224 0361The School of Biological Sciences, Nanyang Technological University, Singapore, 639798 Singapore ,grid.117476.20000 0004 1936 7611The ithree Institute, The University of Technology Sydney, Sydney, NSW 2007 Australia
| | - Patrick J. Cullen
- grid.1013.30000 0004 1936 834XSchool of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2006 Australia
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