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Nappi J, Goncalves P, Khan T, Majzoub ME, Grobler AS, Marzinelli EM, Thomas T, Egan S. Differential priority effects impact taxonomy and functionality of host-associated microbiomes. Mol Ecol 2023; 32:6278-6293. [PMID: 34995388 DOI: 10.1111/mec.16336] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/01/2021] [Accepted: 12/16/2021] [Indexed: 01/24/2023]
Abstract
Most multicellular eukaryotes host complex communities of microorganisms, but the factors that govern their assembly are poorly understood. The settlement of specific microorganisms may have a lasting impact on community composition, a phenomenon known as the priority effect. Priority effects of individual bacterial strains on a host's microbiome are, however, rarely studied and their impact on microbiome functionality remains unknown. We experimentally tested the effect of two bacterial strains (Pseudoalteromonas tunicata D2 and Pseudovibrio sp. D323) on the assembly and succession of the microbial communities associated with the green macroalga Ulva australis. Using 16S rRNA gene sequencing and qPCR, we found that both strains exert a priority effect, with strain D2 causing initially strong but temporary taxonomic changes and strain D323 causing weaker but consistent changes. Consistent changes were predominately facilitatory and included taxa that may benefit the algal host. Metagenome analyses revealed that the strains elicited both shared (e.g., depletion of type III secretion system genes) and unique (e.g., enrichment of antibiotic resistance genes) effects on the predicted microbiome functionality. These findings indicate strong idiosyncratic effects of colonizing bacteria on the structure and function of host-associated microbial communities. Understanding the idiosyncrasies in priority effects is key for the development of novel probiotics to improve host condition.
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Affiliation(s)
- Jadranka Nappi
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Priscila Goncalves
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Tahsin Khan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Marwan E Majzoub
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Anna Sophia Grobler
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Ezequiel M Marzinelli
- Faculty of Science, School of Life and Environmental Sciences, The University of Sydney, Sydney, NSW, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- Sydney Institute of Marine Science, Mosman, NSW, Australia
| | - Torsten Thomas
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre of Marine Science and Innovation, School of Biological and Environmental Science, University of New South Wales, Sydney, NSW, Australia
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2
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Knisz J, Eckert R, Gieg LM, Koerdt A, Lee JS, Silva ER, Skovhus TL, An Stepec BA, Wade SA. Microbiologically influenced corrosion-more than just microorganisms. FEMS Microbiol Rev 2023; 47:fuad041. [PMID: 37437902 PMCID: PMC10479746 DOI: 10.1093/femsre/fuad041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 06/29/2023] [Accepted: 07/11/2023] [Indexed: 07/14/2023] Open
Abstract
Microbiologically influenced corrosion (MIC) is a phenomenon of increasing concern that affects various materials and sectors of society. MIC describes the effects, often negative, that a material can experience due to the presence of microorganisms. Unfortunately, although several research groups and industrial actors worldwide have already addressed MIC, discussions are fragmented, while information sharing and willingness to reach out to other disciplines are limited. A truly interdisciplinary approach, which would be logical for this material/biology/chemistry-related challenge, is rarely taken. In this review, we highlight critical non-biological aspects of MIC that can sometimes be overlooked by microbiologists working on MIC but are highly relevant for an overall understanding of this phenomenon. Here, we identify gaps, methods, and approaches to help solve MIC-related challenges, with an emphasis on the MIC of metals. We also discuss the application of existing tools and approaches for managing MIC and propose ideas to promote an improved understanding of MIC. Furthermore, we highlight areas where the insights and expertise of microbiologists are needed to help progress this field.
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Affiliation(s)
- J Knisz
- Department of Water Supply and Sewerage, Faculty of Water Sciences, University of Public Service, 6500, Baja, Hungary
| | - R Eckert
- Microbial Corrosion Consulting, LLC, Commerce Township, 48382, MI, USA
| | - L M Gieg
- Petroleum Microbiology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - A Koerdt
- Federal Institute for Materials Research and Testing (BAM), 12205, Berlin, Germany
| | - J S Lee
- Naval Research Laboratory, Ocean Sciences Division, Stennis Space Center, 39529, MS, USA
| | - E R Silva
- BioISI—Biosystems and Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, Campo Grande, C8 bdg, 1749-016, Lisboa, Portugal
- CERENA - Centre for Natural Resources and the Environment, Instituto Superior Técnico, University of Lisbon, Av. Rovisco Pais, 1, 1049-001, Lisboa, Portugal
| | - T L Skovhus
- Research Center for Built Environment, Energy, Water and Climate, VIA, University College, 8700, Horsens, Denmark
| | - B A An Stepec
- Department of Energy and Technology, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | - S A Wade
- Bioengineering Research Group, Swinburne University of Technology, 3122, Melbourne, Australia
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3
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Dal Co A, Ackermann M, van Vliet S. Spatial self-organization of metabolism in microbial systems: A matter of enzymes and chemicals. Cell Syst 2023; 14:98-108. [PMID: 36796335 DOI: 10.1016/j.cels.2022.12.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 08/14/2022] [Accepted: 12/21/2022] [Indexed: 02/17/2023]
Abstract
Most bacteria live in dense, spatially structured communities such as biofilms. The high density allows cells to alter the local microenvironment, whereas the limited mobility can cause species to become spatially organized. Together, these factors can spatially organize metabolic processes within microbial communities so that cells in different locations perform different metabolic reactions. The overall metabolic activity of a community depends both on how metabolic reactions are arranged in space and on how they are coupled, i.e., how cells in different regions exchange metabolites. Here, we review mechanisms that lead to the spatial organization of metabolic processes in microbial systems. We discuss factors that determine the length scales over which metabolic activities are arranged in space and highlight how the spatial organization of metabolic processes affects the ecology and evolution of microbial communities. Finally, we define key open questions that we believe should be the main focus of future research.
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Affiliation(s)
- Alma Dal Co
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Martin Ackermann
- Department of Environmental Systems Science, ETH Zurich, 8092 Zurich, Switzerland; Department of Environmental Microbiology, Eawag, 8600 Duebendorf, Switzerland.
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4
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Zhang W, Mi X, Zhang C, Cheng Y, Wang S, Ji J, Yuan Y, Wang L, Liu W, Jiang Y. Meat-derived Escherichia coli and Pseudomonas fragi manage to co-exist in dual-species biofilms by adjusting gene-regulated competitive strength. Food Microbiol 2022; 109:104122. [DOI: 10.1016/j.fm.2022.104122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 08/19/2022] [Accepted: 08/20/2022] [Indexed: 10/15/2022]
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5
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Twardy BS, Yasmin M, Bej T, Wera GD, Marshall SH, Rojas LJ, Bonomo RA, Jump RLP. Orthopedic Implant-Associated and Central Venous Catheter-Associated Infections Caused by Microbacterium spp. in the Veterans Affairs Healthcare System from 2000 to 2020. Surg Infect (Larchmt) 2021; 23:84-88. [PMID: 34668786 DOI: 10.1089/sur.2021.133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Background: A 72-year-old male developed a late-onset infection of an internal fixation device caused by Microbacterium oxydans. Although often considered contaminants, bacteria from the genus Microbacterium may also be pathogens. We also summarize cases from the Veteran Health Administration (VHA) from which Microbacterium isolates were recovered and review the relevant literature. Patients and Methods: Using the national VHA database, we identified patients with cultures that grew Microbacterium spp. We also review published clinical reports describing Microbacterium spp. as a cause of infections. Results: Between January 2000 and September 2020, 18 cases had Microbacterium spp. Of those, Microbacterium isolates were regarded as pathogens for seven cases; all involved prosthetic material that was consequently removed. Two patients had internal fixation devices whereas the remaining five were patients with a central venous catheter. Conclusions: For patients with prosthetic material, recovery of Microbacterium spp. from device-related clinical cultures should prompt consideration of device removal when possible.
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Affiliation(s)
- Brandon S Twardy
- Division of Infectious Diseases, MetroHealth Medical Center, Cleveland, Ohio, USA.,Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Mohamad Yasmin
- Geriatric Research Education and Clinical Center (GRECC), VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA.,Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Taissa Bej
- Geriatric Research Education and Clinical Center (GRECC), VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Glenn D Wera
- Orthopedic Surgery, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Steven H Marshall
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Laura J Rojas
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA
| | - Robert A Bonomo
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Geriatric Research Education and Clinical Center (GRECC), VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA.,Research Service, VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA.,Departments of Pathology, Pharmacology, Biochemistry, Molecular Biology and Microbiology, and Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Robin L P Jump
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Geriatric Research Education and Clinical Center (GRECC), VA Northeast Ohio Healthcare System, Cleveland, Ohio, USA.,Population and Quantitative Health Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
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6
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Røder HL, Trivedi U, Russel J, Kragh KN, Herschend J, Thalsø-Madsen I, Tolker-Nielsen T, Bjarnsholt T, Burmølle M, Madsen JS. Biofilms can act as plasmid reserves in the absence of plasmid specific selection. NPJ Biofilms Microbiomes 2021; 7:78. [PMID: 34620879 PMCID: PMC8497521 DOI: 10.1038/s41522-021-00249-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 09/15/2021] [Indexed: 02/06/2023] Open
Abstract
Plasmids facilitate rapid bacterial adaptation by shuttling a wide variety of beneficial traits across microbial communities. However, under non-selective conditions, maintaining a plasmid can be costly to the host cell. Nonetheless, plasmids are ubiquitous in nature where bacteria adopt their dominant mode of life - biofilms. Here, we demonstrate that biofilms can act as spatiotemporal reserves for plasmids, allowing them to persist even under non-selective conditions. However, under these conditions, spatial stratification of plasmid-carrying cells may promote the dispersal of cells without plasmids, and biofilms may thus act as plasmid sinks.
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Affiliation(s)
- Henriette Lyng Røder
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Urvish Trivedi
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Russel
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Nørskov Kragh
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Jakob Herschend
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Ida Thalsø-Madsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Bjarnsholt
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Microbiology, University Hospital of Copenhagen, Rigshospitalet, Copenhagen, Denmark
| | - Mette Burmølle
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Jonas Stenløkke Madsen
- Section of Microbiology, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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7
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Gryndler M, Gryndlerová H, Hujslová M, Bystrianský L, Malinská H, Šimsa D, Hršelová H. In vitro Evaluation of Biofilm Biomass Dynamics. Microbiology (Reading) 2021. [DOI: 10.1134/s0026261721050064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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8
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Cheong JZA, Johnson CJ, Wan H, Liu A, Kernien JF, Gibson ALF, Nett JE, Kalan LR. Priority effects dictate community structure and alter virulence of fungal-bacterial biofilms. THE ISME JOURNAL 2021; 15:2012-2027. [PMID: 33558690 PMCID: PMC8245565 DOI: 10.1038/s41396-021-00901-5] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/21/2020] [Accepted: 01/18/2021] [Indexed: 02/06/2023]
Abstract
Polymicrobial biofilms are a hallmark of chronic wound infection. The forces governing assembly and maturation of these microbial ecosystems are largely unexplored but the consequences on host response and clinical outcome can be significant. In the context of wound healing, formation of a biofilm and a stable microbial community structure is associated with impaired tissue repair resulting in a non-healing chronic wound. These types of wounds can persist for years simmering below the threshold of classically defined clinical infection (which includes heat, pain, redness, and swelling) and cycling through phases of recurrent infection. In the most severe outcome, amputation of lower extremities may occur if spreading infection ensues. Here we take an ecological perspective to study priority effects and competitive exclusion on overall biofilm community structure in a three-membered community comprised of strains of Staphylococcus aureus, Citrobacter freundii, and Candida albicans derived from a chronic wound. We show that both priority effects and inter-bacterial competition for binding to C. albicans biofilms significantly shape community structure on both abiotic and biotic substrates, such as ex vivo human skin wounds. We further show attachment of C. freundii to C. albicans is mediated by mannose-binding lectins. Co-cultures of C. freundii and C. albicans trigger the yeast-to-hyphae transition, resulting in a significant increase in neutrophil death and inflammation compared to either species alone. Collectively, the results presented here facilitate our understanding of fungal-bacterial interactions and their effects on host-microbe interactions, pathogenesis, and ultimately, wound healing.
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Affiliation(s)
- J Z Alex Cheong
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Chad J Johnson
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Hanxiao Wan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Aiping Liu
- Department of Surgery, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - John F Kernien
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Angela L F Gibson
- Department of Surgery, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Jeniel E Nett
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA
| | - Lindsay R Kalan
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA.
- Department of Medicine, Division of Infectious Disease, University of Wisconsin-Madison, School of Medicine and Public Health, Madison, WI, USA.
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9
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Bengtsson-Palme J. Microbial model communities: To understand complexity, harness the power of simplicity. Comput Struct Biotechnol J 2020; 18:3987-4001. [PMID: 33363696 PMCID: PMC7744646 DOI: 10.1016/j.csbj.2020.11.043] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/23/2020] [Accepted: 11/23/2020] [Indexed: 12/14/2022] Open
Abstract
Natural microbial communities are complex ecosystems with myriads of interactions. To deal with this complexity, we can apply lessons learned from the study of model organisms and try to find simpler systems that can shed light on the same questions. Here, microbial model communities are essential, as they can allow us to learn about the metabolic interactions, genetic mechanisms and ecological principles governing and structuring communities. A variety of microbial model communities of varying complexity have already been developed, representing different purposes, environments and phenomena. However, choosing a suitable model community for one's research question is no easy task. This review aims to be a guide in the selection process, which can help the researcher to select a sufficiently well-studied model community that also fulfills other relevant criteria. For example, a good model community should consist of species that are easy to grow, have been evaluated for community behaviors, provide simple readouts and - in some cases - be of relevance for natural ecosystems. Finally, there is a need to standardize growth conditions for microbial model communities and agree on definitions of community-specific phenomena and frameworks for community interactions. Such developments would be the key to harnessing the power of simplicity to start disentangling complex community interactions.
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Affiliation(s)
- Johan Bengtsson-Palme
- Department of Infectious Diseases, Institute of Biomedicine, The Sahlgrenska Academy, University of Gothenburg, Guldhedsgatan 10, SE-413 46 Gothenburg, Sweden
- Centre for Antibiotic Resistance Research (CARe) at University of Gothenburg, Gothenburg, Sweden
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10
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Silva MOD, Pernthaler J. Biomass addition alters community assembly in ultrafiltration membrane biofilms. Sci Rep 2020; 10:11552. [PMID: 32665605 PMCID: PMC7360762 DOI: 10.1038/s41598-020-68460-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 06/15/2020] [Indexed: 11/25/2022] Open
Abstract
Freshwater biofilms assemble from a pool of rare water column genotypes. Random density fluctuations and temporal species turnover of functionally equivalent potential colonizers result in compositional variability of newly formed biofilm communities. We hypothesized that stronger environmental filtering as induced by enhanced substrate levels might reduce the impact of a locally variable pool of colonizers and instead select for more universal habitat specialists. Our model were heterotrophic biofilms that form on membranes during gravity-driven ultrafiltration of lake water. In four separate experiments, biomass of the cyanobacterium Microcystis was added to the feed water of one set of treatments (BM) and the resulting biofilm communities were compared to unamended controls (CTRL). Biomass addition led to a significant shift of community assembly processes: Replicate BM biofilms were more similar to each other than by chance in 3 of 4 experiments, whereas the opposite was the case for CTRL communities. Moreover, BM communities were more stochastically assembled across experiments from a common 'regional' pool of biofilm colonizers, whereas the composition of CTRL communities was mainly determined by experiment-specific 'local' genotypes. Interestingly, community assembly processes were also related to both, physiology (aerobic vs. anaerobic lifestyle) and the phylogenetic affiliation of biofilm bacteria.
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Affiliation(s)
- Marisa O D Silva
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland
| | - Jakob Pernthaler
- Limnological Station, Department of Plant and Microbial Biology, University of Zurich, Seestrasse 187, 8802, Kilchberg, Switzerland.
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11
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Røder HL, Olsen NMC, Whiteley M, Burmølle M. Unravelling interspecies interactions across heterogeneities in complex biofilm communities. Environ Microbiol 2019; 22:5-16. [DOI: 10.1111/1462-2920.14834] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 10/15/2019] [Accepted: 10/17/2019] [Indexed: 01/29/2023]
Affiliation(s)
- Henriette L. Røder
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Nanna M. C. Olsen
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
| | - Marvin Whiteley
- School of Biological SciencesGeorgia Institute of Technology, Atlanta Georgia USA
- Emory‐Children's Cystic Fibrosis Center, Atlanta Georgia USA
- Center for Microbial Dynamics and InfectionGeorgia Institute of Technology, Atlanta Georgia USA
| | - Mette Burmølle
- Section of Microbiology, Department of BiologyUniversity of Copenhagen Copenhagen Denmark
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