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Freddi S, Rajabal V, Tetu SG, Gillings MR, Penesyan A. Microbial biofilms on macroalgae harbour diverse integron gene cassettes. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001446. [PMID: 38488860 PMCID: PMC10963911 DOI: 10.1099/mic.0.001446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 02/27/2024] [Indexed: 03/19/2024]
Abstract
Integrons are genetic platforms that capture, rearrange and express mobile modules called gene cassettes. The best characterized gene cassettes encode antibiotic resistance, but the function of most integron gene cassettes remains unknown. Functional predictions suggest that many gene cassettes could encode proteins that facilitate interactions with other cells and with the extracellular environment. Because cell interactions are essential for biofilm stability, we sequenced gene cassettes from biofilms growing on the surface of the marine macroalgae Ulva australis and Sargassum linearifolium. Algal samples were obtained from coastal rock platforms around Sydney, Australia, using seawater as a control. We demonstrated that integrons in microbial biofilms did not sample genes randomly from the surrounding seawater, but harboured specific functions that potentially provided an adaptive advantage to both the bacterial cells in biofilm communities and their macroalgal host. Further, integron gene cassettes had a well-defined spatial distribution, suggesting that each bacterial biofilm acquired these genetic elements via sampling from a large but localized pool of gene cassettes. These findings suggest two forms of filtering: a selective acquisition of different integron-containing bacterial species into the distinct biofilms on Ulva and Sargassum surfaces, and a selective retention of unique populations of gene cassettes at each sampling location.
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Affiliation(s)
- Stefano Freddi
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Faculty of Science and Engineering, Macquarie University, NSW 2109, Australia
- Australian Research Council Centre of Excellence in Synthetic Biology, Macquarie University, NSW 2109, Australia
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2
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Song W, Zhang S, Majzoub ME, Egan S, Kjelleberg S, Thomas T. The impact of interspecific competition on the genomic evolution of Phaeobacter inhibens and Pseudoalteromonas tunicata during biofilm growth. Environ Microbiol 2024; 26:e16553. [PMID: 38062568 DOI: 10.1111/1462-2920.16553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Accepted: 11/24/2023] [Indexed: 01/30/2024]
Abstract
Interspecific interactions in biofilms have been shown to cause the emergence of community-level properties. To understand the impact of interspecific competition on evolution, we deep-sequenced the dispersal population of mono- and co-culture biofilms of two antagonistic marine bacteria (Phaeobacter inhibens 2.10 and Pseudoalteromononas tunicata D2). Enhanced phenotypic and genomic diversification was observed in the P. tunicata D2 populations under both mono- and co-culture biofilms in comparison to P. inhibens 2.10. The genetic variation was exclusively due to single nucleotide variants and small deletions, and showed high variability between replicates, indicating their random emergence. Interspecific competition exerted an apparent strong positive selection on a subset of P. inhibens 2.10 genes (e.g., luxR, cobC, argH, and sinR) that could facilitate competition, while the P. tunicata D2 population was genetically constrained under competition conditions. In the absence of interspecific competition, the P. tunicata D2 replicate populations displayed high levels of mutations affecting the same genes involved in cell motility and biofilm formation. Our results show that interspecific biofilm competition has a complex impact on genomic diversification, which likely depends on the nature of the competing strains and their ability to generate genetic variants due to their genomic constraints.
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Affiliation(s)
- Weizhi Song
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Shan Zhang
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Marwan E Majzoub
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
| | - Staffan Kjelleberg
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Torsten Thomas
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, New South Wales, Australia
- School of Biological, Earth and Environmental Sciences, University of New South Wales, Kensington, New South Wales, Australia
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3
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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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4
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Nowruzi B, Shishir MA, Porzani SJ, Ferdous UT. Exploring the Interactions between Algae and Bacteria. Mini Rev Med Chem 2022; 22:2596-2607. [PMID: 35507745 DOI: 10.2174/1389557522666220504141047] [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: 01/21/2022] [Revised: 03/01/2022] [Accepted: 03/17/2022] [Indexed: 11/22/2022]
Abstract
Humans have used algae for hundreds of years to make various products viz. agar, fertilizer, food, and pigments. Algae are also used in bioremediation to clean up polluted water and as essential laboratory tools in genomics, proteomics, and other research applications such as environmental warnings. Several special features of algae, including the oxygenic photosynthesis, higher yield in biomass, growth on the non-arable lands, their survival in a wide range of water supplies (contaminated or filtered waters), the production of necessary byproducts and biofuels, the enhancement of soil productivity, and the greenhouse gas emissions, etc. altogether rendered them as vital bio-resources in the sustainable development. Algae and bacteria have been assumed to coexist from the early stages of the development of the earth, and a wide variety of interactions were observed between them which have influenced the ecosystems ranging from the oceans to the lichens. Research has shown that bacteria and algae interact synergistically, especially roseobacter-algae interactions being the most common. These interactions are common to all ecosystems and characterize their primary efficiency. The commercialization of algae for industrial purposes, an important field, is also influenced by this interaction which frequently results in bacterial infections among the consumers. However, the recent findings have revealed that the bacteria improve algal growth and support flocculation which are very crucial in algal biotechnology. Some of the most exciting advancements in the area of algal biotic interactions and potential difficulties were reviewed in this article. Information gleaned in this study would provide a firm foundation for launching more contemporaneous research efforts in understanding and utilizing the algal species in biotechnology industries and medical sectors.
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Affiliation(s)
- Bahareh Nowruzi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | | | - Samaneh J Porzani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Umme Tamanna Ferdous
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor, Malaysia
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5
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Roseobacter group probiotics exhibit differential killing of fish pathogenic Tenacibaculum species. Appl Environ Microbiol 2022; 88:e0241821. [PMID: 35080904 DOI: 10.1128/aem.02418-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fish pathogenic bacteria of the Tenacibaculum genus are a serious emerging concern in modern aquaculture, causing tenacibaculosis in a broad selection of cultured finfish. Data describing their virulence mechanisms are scarce and few means, antibiotic treatment aside, are available to control their proliferation in aquaculture systems. We genome sequenced a collection of 19 putative Tenacibaculum isolates from outbreaks at two aquaculture facilities and tested their susceptibility to treatment with tropodithietic acid (TDA)-producing Roseobacter group probiotics. We found that local outbreaks of Tenacibaculum can involve heterogeneous assemblages of species and strains with the capacity to produce multiple different virulence factors related to host invasion and infection. The probiotic Phaeobacter piscinae S26 proved efficient in killing pathogenic Tenacibaculum species such as T. maritimum, T. soleae, and some T. discolor strains. However, the T. mesophilum and T. gallaicum species exhibit natural tolerance towards TDA and are hence not likely to be easily killed by TDA-producing probiotics. Tolerance towards TDA in Tenacibaculum is likely involving multiple inherent physiological features pertaining to electron and proton transport, iron sequestration, and potentially also drug efflux mechanisms, as genetic determinants encoding such features were significantly associated with TDA tolerance. Collectively, our results support the use of TDA-producers to prevent tenacibaculosis, however, their efficacy is likely limited to some Tenacibaculum species. Importance A productive and sustainable aquaculture sector is needed to meet the UN sustainable development goals (SDGs) and supply the growing world population with high-protein food sources. A sustainable way to prevent disease outbreaks in the industry is the application of probiotic bacteria that can antagonize fish pathogens in the aquaculture systems. TDA-producing Roseobacter group probiotics have proven efficient in killing important vibrio pathogens and protecting fish larvae against infection, yet their efficacy against different fish pathogenic species of the Tenacibaculum genus has not been explored. Therefore, we tested the efficacy of such potential probiotics against a collection of different Tenacibaculum isolates and found the probiotic to efficiently kill a subset of relevant strains and species, supporting their use as sustainable disease control measure in aquaculture.
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Menaa F, Wijesinghe PAUI, Thiripuranathar G, Uzair B, Iqbal H, Khan BA, Menaa B. Ecological and Industrial Implications of Dynamic Seaweed-Associated Microbiota Interactions. Mar Drugs 2020; 18:md18120641. [PMID: 33327517 PMCID: PMC7764995 DOI: 10.3390/md18120641] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/09/2020] [Accepted: 12/13/2020] [Indexed: 02/07/2023] Open
Abstract
Seaweeds are broadly distributed and represent an important source of secondary metabolites (e.g., halogenated compounds, polyphenols) eliciting various pharmacological activities and playing a relevant ecological role in the anti-epibiosis. Importantly, host (as known as basibiont such as algae)–microbe (as known as epibiont such as bacteria) interaction (as known as halobiont) is a driving force for coevolution in the marine environment. Nevertheless, halobionts may be fundamental (harmless) or detrimental (harmful) to the functioning of the host. In addition to biotic factors, abiotic factors (e.g., pH, salinity, temperature, nutrients) regulate halobionts. Spatiotemporal and functional exploration of such dynamic interactions appear crucial. Indeed, environmental stress in a constantly changing ocean may disturb complex mutualistic relations, through mechanisms involving host chemical defense strategies (e.g., secretion of secondary metabolites and antifouling chemicals by quorum sensing). It is worth mentioning that many of bioactive compounds, such as terpenoids, previously attributed to macroalgae are in fact produced or metabolized by their associated microorganisms (e.g., bacteria, fungi, viruses, parasites). Eventually, recent metagenomics analyses suggest that microbes may have acquired seaweed associated genes because of increased seaweed in diets. This article retrospectively reviews pertinent studies on the spatiotemporal and functional seaweed-associated microbiota interactions which can lead to the production of bioactive compounds with high antifouling, theranostic, and biotechnological potential.
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Affiliation(s)
- Farid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
- Correspondence: or
| | - P. A. U. I. Wijesinghe
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Gobika Thiripuranathar
- College of Chemical Sciences, Institute of Chemistry Ceylon, Rajagiriya 10107, Sri Lanka; (P.A.U.I.W.); (G.T.)
| | - Bushra Uzair
- Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan;
| | - Haroon Iqbal
- Department of Pharmaceutics, College of Pharmaceutical Sciences, Soochow University, Suzhou 215123, China;
| | - Barkat Ali Khan
- Department of Pharmacy, Gomal University, Dera Ismail Khan 29050, Pakistan;
| | - Bouzid Menaa
- Department of Nanomedicine, California Innovations Corporation, San Diego, CA 92037, USA;
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7
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Ali S, Jenkins B, Cheng J, Lobb B, Wei X, Egan S, Charles TC, McConkey BJ, Austin J, Doxey AC. Slr4, a newly identified S-layer protein from marine Gammaproteobacteria, is a major biofilm matrix component. Mol Microbiol 2020; 114:979-990. [PMID: 32804439 PMCID: PMC7821379 DOI: 10.1111/mmi.14588] [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] [Received: 03/17/2020] [Revised: 08/06/2020] [Indexed: 01/03/2023]
Abstract
S‐layers are paracrystalline proteinaceous lattices that surround prokaryotic cells, forming a critical interface between the cells and their extracellular environment. Here, we report the discovery of a novel S‐layer protein present in the Gram‐negative marine organism, Pseudoalteromonas tunicata D2. An uncharacterized protein (EAR28894) was identified as the most abundant protein in planktonic cultures and biofilms. Bioinformatic methods predicted a beta‐helical structure for EAR28894 similar to the Caulobacter S‐layer protein, RsaA, despite sharing less than 20% sequence identity. Transmission electron microscopy revealed that purified EAR28894 protein assembled into paracrystalline sheets with a unique square lattice symmetry and a unit cell spacing of ~9.1 nm. An S‐layer was found surrounding the outer membrane in wild‐type cells and completely removed from cells in an EAR28894 deletion mutant. S‐layer material also appeared to be “shed” from wild‐type cells and was highly abundant in the extracellular matrix where it is associated with outer membrane vesicles and other matrix components. EAR28894 and its homologs form a new family of S‐layer proteins that are widely distributed in Gammaproteobacteria including species of Pseudoalteromonas and Vibrio, and found exclusively in marine metagenomes. We propose the name Slr4 for this novel protein family.
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Affiliation(s)
- Sura Ali
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Benjamin Jenkins
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jiujun Cheng
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.,Metagenom Bio Life Science Inc., Waterloo, ON, Canada
| | - Briallen Lobb
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Xin Wei
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Suhelen Egan
- Centre for Marine Science and Innovation and School of Biological, Earth and Environmental Sciences, The University of New South Wales Sydney, Sydney, NSW, Australia
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada.,Metagenom Bio Life Science Inc., Waterloo, ON, Canada
| | | | - John Austin
- Bureau of Microbial Hazards, Health Products and Food Branch, Health Canada, Ottawa, ON, Canada
| | - Andrew C Doxey
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
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Majzoub ME, McElroy K, Maczka M, Thomas T, Egan S. Causes and Consequences of a Variant Strain of Phaeobacter inhibens With Reduced Competition. Front Microbiol 2018; 9:2601. [PMID: 30450086 PMCID: PMC6224355 DOI: 10.3389/fmicb.2018.02601] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 10/11/2018] [Indexed: 11/13/2022] Open
Abstract
Phaeobacter inhibens 2.10 is an effective biofilm former and colonizer of marine surfaces and has the ability to outcompete other microbiota. During biofilm dispersal P. inhibens 2.10 produces heritable phenotypic variants, including those that have a reduced ability to inhibit the co-occurring bacterium Pseudoalteromonas tunicata. However, the genetic changes that underpin the phenotypic variation and what the ecological consequences are for variants within the population are unclear. To answer these questions we sequenced the genomes of strain NCV12a1, a biofilm variant of P. inhibens 2.10 with reduced inhibitory activity and the P. inhibens 2.10 WT parental strain. Genome wide analysis revealed point mutations in genes involved in synthesis of the antibacterial compound tropodithietic acid (TDA) and indirectly in extracellular polymeric substances (EPS) production. However, confocal laser scanning microscopy analyses found little differences in biofilm growth between P. inhibens 2.10 WT (parental) and NCV12a1. P. inhibens NCV12a1 was also not outcompeted in co-cultured biofilms with P. tunicata, despite its reduced inhibitory activity, rather these biofilms were thicker than those produced when the WT strain was co-cultured with P. tunicata. Notably, dispersal populations from biofilms of P. inhibens NCV12a1 had a higher proportion of WT-like morphotypes when co-cultured with P. tunicata. These observations may explain why the otherwise non-inhibiting variant persists in the presence of a natural competitor, adding to our understanding of the relative importance of genetic diversification in microbial biofilms.
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Affiliation(s)
- Marwan E Majzoub
- Centre for Marine Bio-Innovation, School of Biotechnology and Biomolecular Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Kerensa McElroy
- Agriculture and Food, Commonwealth Scientific and Industrial Research Organisation, Canberra, ACT, Australia
| | - Michael Maczka
- Institute of Organic Chemistry, Technische Universität Braunschweig, Braunschweig, Germany
| | - Torsten Thomas
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Bio-Innovation, School of Biological, Earth and Environmental Sciences, The University of New South Wales, Sydney, NSW, Australia
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9
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Roth‐Schulze AJ, Pintado J, Zozaya‐Valdés E, Cremades J, Ruiz P, Kjelleberg S, Thomas T. Functional biogeography and host specificity of bacterial communities associated with the Marine Green Alga
Ulva
spp. Mol Ecol 2018; 27:1952-1965. [DOI: 10.1111/mec.14529] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 01/30/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Alexandra J. Roth‐Schulze
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - José Pintado
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
- Instituto de Investigacións Mariñas (IIM ‐ CSIC) Vigo Spain
| | - Enrique Zozaya‐Valdés
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - Javier Cremades
- BIOCOST Centro de Investigaciones Científicas Avanzadas (CICA) Universidade da Coruña A Coruña Spain
| | - Patricia Ruiz
- Instituto de Investigacións Mariñas (IIM ‐ CSIC) Vigo Spain
| | - Staffan Kjelleberg
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
| | - Torsten Thomas
- Centre for Marine Bio‐Innovation School of Biological, Earth and Environmental Sciences The University of New South Wales Sydney NSW Australia
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10
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Freese HM, Methner A, Overmann J. Adaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton. Front Microbiol 2017; 8:1659. [PMID: 28912769 PMCID: PMC5583230 DOI: 10.3389/fmicb.2017.01659] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Accepted: 08/16/2017] [Indexed: 02/03/2023] Open
Abstract
The marine Roseobacter group encompasses numerous species which occupy a large variety of ecological niches. However, members of the genus Phaeobacter are specifically adapted to a surface-associated lifestyle and have so far been found nearly exclusively in disjunct, man-made environments including shellfish and fish aquacultures, as well as harbors. Therefore, the possible natural habitats, dispersal and evolution of Phaeobacter spp. have largely remained obscure. Applying a high-throughput cultivation strategy along a longitudinal Pacific transect, the present study revealed for the first time a widespread natural occurrence of Phaeobacter in the marine pelagial. These bacteria were found to be specifically associated to mesoplankton where they constitute a small but detectable proportion of the bacterial community. The 16S rRNA gene sequences of 18 isolated strains were identical to that of Phaeobacter gallaeciensis DSM26640T but sequences of internal transcribed spacer and selected genomes revealed that the strains form a distinct clade within P. gallaeciensis. The genomes of the Pacific and the aquaculture strains were highly conserved and had a fraction of the core genome of 89.6%, 80 synteny breakpoints, and differed 2.2% in their nucleotide sequences. Diversification likely occurred through neutral mutations. However, the Pacific strains exclusively contained two active Type I restriction modification systems which is commensurate with a reduced acquisition of mobile elements in the Pacific clade. The Pacific clade of P. gallaeciensis also acquired a second, homolog phosphonate transport system compared to all other P. gallaeciensis. Our data indicate that a previously unknown, distinct clade of P. gallaeciensis acquired a limited number of clade-specific genes that were relevant for its association with mesozooplankton and for colonization of the marine pelagial. The divergence of the Pacific clade most likely was driven by the adaptation to this novel ecological niche rather than by geographic isolation.
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Affiliation(s)
- Heike M Freese
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und ZellkulturenBraunschweig, Germany
| | - Anika Methner
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und ZellkulturenBraunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und ZellkulturenBraunschweig, Germany
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11
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Abstract
The dense aggregation of cells on a surface, as seen in biofilms, inevitably results in both environmental and cellular heterogeneity. For example, nutrient gradients can trigger cells to differentiate into various phenotypic states. Not only do cells adapt physiologically to the local environmental conditions, but they also differentiate into cell types that interact with each other. This allows for task differentiation and, hence, the division of labor. In this article, we focus on cell differentiation and the division of labor in three bacterial species: Myxococcus xanthus, Bacillus subtilis, and Pseudomonas aeruginosa. During biofilm formation each of these species differentiates into distinct cell types, in some cases leading to cooperative interactions. The division of labor and the cooperative interactions between cell types are assumed to yield an emergent ecological benefit. Yet in most cases the ecological benefits have yet to be elucidated. A notable exception is M. xanthus, in which cell differentiation within fruiting bodies facilitates the dispersal of spores. We argue that the ecological benefits of the division of labor might best be understood when we consider the dynamic nature of both biofilm formation and degradation.
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12
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Zhao W, Dao C, Karim M, Gomez-Chiarri M, Rowley D, Nelson DR. Contributions of tropodithietic acid and biofilm formation to the probiotic activity of Phaeobacter inhibens. BMC Microbiol 2016; 16:1. [PMID: 26728027 PMCID: PMC4700733 DOI: 10.1186/s12866-015-0617-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Accepted: 12/22/2015] [Indexed: 11/30/2022] Open
Abstract
Background The probiotic bacterium Phaeobacter inhibens strain S4Sm, isolated from the inner shell surface of a healthy oyster, secretes the antibiotic tropodithietic acid (TDA), is an excellent biofilm former, and increases oyster larvae survival when challenged with bacterial pathogens. In this study, we investigated the specific roles of TDA secretion and biofilm formation in the probiotic activity of S4Sm. Results Mutations in clpX (ATP-dependent ATPase) and exoP (an exopolysaccharide biosynthesis gene) were created by insertional mutagenesis using homologous recombination. Mutation of clpX resulted in the loss of TDA production, no decline in biofilm formation, and loss of the ability to inhibit the growth of Vibrio tubiashii and Vibrio anguillarum in co-colonization experiments. Mutation of exoP resulted in a ~60 % decline in biofilm formation, no decline in TDA production, and delayed inhibitory activity towards Vibrio pathogens in co-colonization experiments. Both clpX and exoP mutants exhibited reduced ability to protect oyster larvae from death when challenged by Vibrio tubiashii. Complementation of the clpX and exoP mutations restored the wild type phenotype. We also found that pre-colonization of surfaces by S4Sm was critical for this bacterium to inhibit pathogen colonization and growth. Conclusions Our observations demonstrate that probiotic activity by P. inhibens S4Sm involves contributions from both biofilm formation and the production of the antibiotic TDA. Further, probiotic activity also requires colonization of surfaces by S4Sm prior to the introduction of the pathogen. Electronic supplementary material The online version of this article (doi:10.1186/s12866-015-0617-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Wenjing Zhao
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd., Kingston, RI, 02881, USA. .,Present Address: Department of Microbiology and Immunology, Harvard Medical School, Boston, MA 02115, USA.
| | - Christine Dao
- Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, 02881, USA. .,Present Address: Department of Chemistry and Biochemistry, University of Massachusetts Dartmouth, Darmouth, MA 02747, USA.
| | - Murni Karim
- Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, RI, 02881, USA. .,Present Address: Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - Marta Gomez-Chiarri
- Fisheries, Animal and Veterinary Sciences, University of Rhode Island, Kingston, RI, 02881, USA.
| | - David Rowley
- Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI, 02881, USA.
| | - David R Nelson
- Department of Cell and Molecular Biology, University of Rhode Island, 120 Flagg Rd., Kingston, RI, 02881, USA.
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Egan S, Harder T, Burke C, Steinberg P, Kjelleberg S, Thomas T. The seaweed holobiont: understanding seaweed-bacteria interactions. FEMS Microbiol Rev 2012; 37:462-76. [PMID: 23157386 DOI: 10.1111/1574-6976.12011] [Citation(s) in RCA: 310] [Impact Index Per Article: 25.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/29/2012] [Accepted: 11/07/2012] [Indexed: 11/28/2022] Open
Abstract
Seaweeds (macroalgae) form a diverse and ubiquitous group of photosynthetic organisms that play an essential role in aquatic ecosystems. These ecosystem engineers contribute significantly to global primary production and are the major habitat formers on rocky shores in temperate waters, providing food and shelter for aquatic life. Like other eukaryotic organisms, macroalgae harbor a rich diversity of associated microorganisms with functions related to host health and defense. In particular, epiphytic bacterial communities have been reported as essential for normal morphological development of the algal host, and bacteria with antifouling properties are thought to protect chemically undefended macroalgae from detrimental, secondary colonization by other microscopic and macroscopic epibiota. This tight relationship suggests that macroalgae and epiphytic bacteria interact as a unified functional entity or holobiont, analogous to the previously suggested relationship in corals. Moreover, given that the impact of diseases in marine ecosystems is apparently increasing, understanding the role of bacteria as saprophytes and pathogens in seaweed communities may have important implications for marine management strategies. This review reports on the recent advances in the understanding of macroalgal-bacterial interactions with reference to the diversity and functional role of epiphytic bacteria in maintaining algal health, highlighting the holobiont concept.
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Affiliation(s)
- Suhelen Egan
- School of Biotechnology and Biomolecular Sciences, Centre for Marine Bio-Innovation, The University of New South Wales, Sydney, NSW, Australia.
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