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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: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [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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2
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Feng C, Lotti T, Canziani R, Lin Y, Tagliabue C, Malpei F. Extracellular biopolymers recovered as raw biomaterials from waste granular sludge and potential applications: A critical review. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 753:142051. [PMID: 33207449 DOI: 10.1016/j.scitotenv.2020.142051] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/26/2020] [Accepted: 08/27/2020] [Indexed: 06/11/2023]
Abstract
Granular sludge (GS) is a special self-aggregation biofilm. Extracellular polymeric substances (EPS) are mainly associated with the architectural structure, rheological behaviour and functional stability of fine granules, given that their significance to the physicochemical features of the biomass catalysing the biological purification process. This review targets the EPS excretion from GS and introduces newly identified EPS components, EPS distribution in different granules, how to effectively extract and recover EPS from granules, key parameters affecting EPS production, and the potential applications of EPS-based biomaterials. GS-based EPS components are highly diverse and a series of new contents are highlighted. Due to high diversity, emerging extraction standards are proposed and recovery process is capturing particular attention. The major components of EPS are found to be polysaccharides and proteins, which manifest a larger diversity of relative abundance, structures, physical and chemical characteristics, leading to the possibility to sustainably recover raw materials. EPS-based biomaterials not only act as alternatives to synthetic polymers in several applications but also figure in innovative industrial/environmental applications, including gel-forming materials for paper industry, biosorbents, cement curing materials, and flame retardant materials. In the upcoming years, it is foreseen that productions of EPS-based biomaterials from renewable origins would make a significant contribution to the advancement of the circular economy.
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Affiliation(s)
- Cuijie Feng
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy.
| | - Tommaso Lotti
- Department of Civil and Environmental Engineering, University of Florence, Via di Santa Marta 3, 50139 Florence, Italy
| | - Roberto Canziani
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Yuemei Lin
- Department of Biotechnology, Faculty of Applied Sciences, Delft University of Technology, Van der Maasweg 9, 2629 HZ Delft, the Netherlands
| | - Camilla Tagliabue
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
| | - Francesca Malpei
- Department of Civil and Environmental Engineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milan, Italy
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3
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Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation. mBio 2020; 11:mBio.02052-20. [PMID: 32900808 PMCID: PMC7482068 DOI: 10.1128/mbio.02052-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development. This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.
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4
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Extracellular protein isolation from the matrix of anammox biofilm using ionic liquid extraction. Appl Microbiol Biotechnol 2020; 104:3643-3654. [PMID: 32095864 DOI: 10.1007/s00253-020-10465-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 02/04/2020] [Accepted: 02/12/2020] [Indexed: 10/24/2022]
Abstract
Anaerobic ammonium oxidation (anammox)-performing bacteria self-assemble into compact biofilms by expressing extracellular polymeric substances (EPS). Anammox EPS are poorly characterized, largely due to their low solubility in typical aqueous solvents. Pronase digestion achieved 19.5 ± 0.9 and 41.4 ± 1.4% (w/w) more solubilization of laboratory enriched Candidatus Brocadia sinica anammox granules than DNase and amylase, respectively. Nuclear magnetic resonance profiling of the granules confirmed proteins as dominant biopolymer within the EPS. Ionic liquid (IL) 1-ethyl-3-methylimidazolium acetate and N,N-dimethylacetamide (EMIM-Ac/DMAc) mixture was applied to extract the major structural proteins. Further treatment by anion exchange chromatography isolated homologous serine (S)- and threonine (T)-rich proteins BROSI_A1236 and UZ01_01563, which were major components of the extracted proteins, and sequentially highly similar to putative anammox extracellular proteins KUSTD1514 and WP_070066018.1 of Ca. Kuenenia stuttgartiensis and Ca. Brocadia sapporoensis, respectively. Six monosaccharides (i.e., arabinose, xylose, rhamnose, fucose, galactose, and mannose) were enriched for BROSI_A1236 against all other major proteins. The sugars, however, contributed < 0.5% (w/w) of total granular biomass and were likely co-enriched as glycoprotein appendages. This study demonstrates that BROSI_A1236 is a major extracellular component of Ca. B. sinica anammox biofilms that is likely a common anammox extracellular polymer, and can be isolated from the matrix following ionic liquid extraction.
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Boleij M, Seviour T, Wong LL, van Loosdrecht MCM, Lin Y. Solubilization and characterization of extracellular proteins from anammox granular sludge. WATER RESEARCH 2019; 164:114952. [PMID: 31408759 DOI: 10.1016/j.watres.2019.114952] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Revised: 07/18/2019] [Accepted: 08/03/2019] [Indexed: 06/10/2023]
Abstract
Elucidating the extracellular polymeric substances (EPS) of anammox granular sludge is important for stable nitrogen removal processes in wastewater treatment. However, due to a lack of standardized methods for extraction and characterization, the composition of anammox granule EPS remains mostly unknown. In this study, alkaline (NaOH) and ionic liquid (IL) extractions were compared in terms of the proteins they extracted from different "Candidatus Brocadia" cultures. We aimed to identify structural proteins and evaluated to which extend these extraction methods bias the outcome of EPS characterization. Extraction was focussed on solubilization of the EPS matrix, and the NaOH and IL extraction recovered on average 20% and 26% of the VSS, respectively. Using two extraction methods targeting different intermolecular interactions increased the possibility of identifying structural extracellular proteins. Of the extracted proteins, ∼40% were common between the extraction methods. The high number of common abundant proteins between the extraction methods, illustrated how extraction biases can be reduced when solubility of the granular sludge is enhanced. Physicochemical analyses of the granules indicated that extracellular structural matrix proteins likely have β-sheet dominated secondary structures. These β-sheet structures were measured in EPS extracted with both methods. The high number of uncharacterized proteins and possible moonlighting proteins confounded identifying structural (i.e. β-sheet dominant) proteins. Nonetheless, new candidates for structural matrix proteins are described. Further current bottlenecks in assigning specific proteins to key extracellular functions in anammox granular sludge are discussed.
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Affiliation(s)
- Marissa Boleij
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | - Mark C M van Loosdrecht
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands
| | - Yuemei Lin
- Department of Biotechnology, Delft University of Technology, van der Maasweg 9, 2629, HZ, Delft, the Netherlands.
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6
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Seviour T, Derlon N, Dueholm MS, Flemming HC, Girbal-Neuhauser E, Horn H, Kjelleberg S, van Loosdrecht MCM, Lotti T, Malpei MF, Nerenberg R, Neu TR, Paul E, Yu H, Lin Y. Extracellular polymeric substances of biofilms: Suffering from an identity crisis. WATER RESEARCH 2019; 151:1-7. [PMID: 30557778 DOI: 10.1016/j.watres.2018.11.020] [Citation(s) in RCA: 155] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 11/02/2018] [Accepted: 11/10/2018] [Indexed: 06/09/2023]
Abstract
Microbial biofilms can be both cause and cure to a range of emerging societal problems including antimicrobial tolerance, water sanitation, water scarcity and pollution. The identities of extracellular polymeric substances (EPS) responsible for the establishment and function of biofilms are poorly understood. The lack of information on the chemical and physical identities of EPS limits the potential to rationally engineer biofilm processes, and impedes progress within the water and wastewater sector towards a circular economy and resource recovery. Here, a multidisciplinary roadmap for addressing this EPS identity crisis is proposed. This involves improved EPS extraction and characterization methodologies, cross-referencing between model biofilms and full-scale biofilm systems, and functional description of isolated EPS with in situ techniques (e.g. microscopy) coupled with genomics, proteomics and glycomics. The current extraction and spectrophotometric characterization methods, often based on the principle not to compromise the integrity of the microbial cells, should be critically assessed, and more comprehensive methods for recovery and characterization of EPS need to be developed.
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Affiliation(s)
- Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore.
| | - Nicolas Derlon
- EAWAG, Swiss Federal Institute of Aquatic Science and Technology, Department of Process Engineering, CH-8600, Dübendorf, Switzerland
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore; University of Duisburg-Essen, Faculty of Chemistry, Biofilm Centre, Essen, Germany
| | - Elisabeth Girbal-Neuhauser
- Laboratoire de Biotechnologies Agroalimentaire et Environmentale (LBAE), Universite Paul Sabatier, Toulouse, France
| | - Harald Horn
- Karlsruhe Institute of Technology (KIT), Engler-Bunte-Institut, Water Chemistry and Water Technology and DVGW Research Laboratories, Karlsruhe, Germany
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, 637551, Singapore
| | | | - Tommaso Lotti
- Department of Civil and Environmental Engineering - DICEA, University of Florence, Florence, Italy
| | - M Francesca Malpei
- Dipartimento di Ingegneria Civile e Ambientale, Politecnico di Milano, Milan, Italy
| | - Robert Nerenberg
- Department of Civil and Environmental Engineering and Earth Sciences, University of Notre Dame, Notre Dame, USA
| | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Etienne Paul
- Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés, Université de Toulouse, Toulouse, France
| | - Hanqing Yu
- Department of Chemistry, University of Science and Technology of China, Hefei, China
| | - Yuemei Lin
- Department of Biotechcnology, Delft University of Technology, Delft, the Netherlands.
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7
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Tan CH, Lee KWK, Burmølle M, Kjelleberg S, Rice SA. All together now: experimental multispecies biofilm model systems. Environ Microbiol 2017; 19:42-53. [DOI: 10.1111/1462-2920.13594] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Chuan Hao Tan
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Kai Wei Kelvin Lee
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of CopenhagenCopenhagen Denmark
| | - Staffan Kjelleberg
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
| | - Scott A. Rice
- The Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological University Singapore
- The School of Biological SciencesNanyang Technological University Singapore
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8
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Rice SA, Wuertz S, Kjelleberg S. Next-generation studies of microbial biofilm communities. Microb Biotechnol 2016; 9:677-80. [PMID: 27471123 PMCID: PMC4993187 DOI: 10.1111/1751-7915.12390] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 07/09/2016] [Indexed: 11/30/2022] Open
Abstract
As we look into the future of microbial biofilm research, there is clearly an emerging focus on communities rather than populations. This represents an essential change in direction to more accurately understand how and why microorganisms assemble into communities, as well as the functional implications for such a life style. For example, current research studies shows that communities display emergent properties or functions that are not predicted from the individual single species populations, including elevated stress tolerance and resistance to antibiotics. Models for mixed species biofilms can be very simple, comprised only a handful of species or can be extremely species rich, with hundreds or thousands of species present. The future holds much promise for this area of research, where investigators will increasingly be able to resolve, at the molecular and biochemical levels, interspecies relationships and mechanisms of interaction. The outcome of these studies will greatly enhance our understanding of the ecological and evolutionary factors that drive community function in natural and engineered systems.
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Affiliation(s)
- Scott A Rice
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Civil and Environmental Engineering, 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
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