Living on the Edge: Biofilms Developing in Oscillating Environmental Conditions
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Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris
RESEARCH ARTICLE Microbes on a Bottle: Substrate, Season and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris Sonja Oberbeckmann1,2,3☯, A. Mark Osborn1,2,4, Melissa B. Duhaime5☯* 1 Department of Biological Sciences, University of Hull, Cottingham Road, Hull HU6 7RX, United Kingdom, a11111 2 School of Life Sciences, University of Lincoln, Brayford Pool Lincoln LN6 7TS, United Kingdom, 3 Environmental Microbiology Working Group, Leibniz Institute for Baltic Sea Research, Warnemünde, Germany, 4 School of Applied Sciences, Royal Melbourne Institute of Technology University, PO Box 77, Bundoora, VIC3083, Australia, 5 Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan, United States of America ☯ These authors contributed equally to this work. * [email protected] OPEN ACCESS Citation: Oberbeckmann S, Osborn AM, Duhaime MB (2016) Microbes on a Bottle: Substrate, Season Abstract and Geography Influence Community Composition of Microbes Colonizing Marine Plastic Debris. PLoS Plastic debris pervades in our oceans and freshwater systems and the potential ecosystem- ONE 11(8): e0159289. doi:10.1371/journal. level impacts of this anthropogenic litter require urgent evaluation. Microbes readily colonize pone.0159289 aquatic plastic debris and members of these biofilm communities are speculated to include Editor: Dee A. Carter, University of Sydney, pathogenic, toxic, invasive or plastic degrading-species. The influence of plastic-colonizing AUSTRALIA microorganisms on the fate of plastic debris is largely unknown, as is the role of plastic in Received: May 11, 2015 selecting for unique microbial communities. This work aimed to characterize microbial bio- Accepted: April 26, 2016 film communities colonizing single-use poly(ethylene terephthalate) (PET) drinking bottles, determine their plastic-specificity in contrast with seawater and glass-colonizing communi- Published: August 3, 2016 ties, and identify seasonal and geographical influences on the communities. -
A Robust Metaproteomics Pipeline for a Holistic Taxonomic and Functional
bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Title: A robust metaproteomics pipeline for a holistic taxonomic and functional 3 characterization of microbial communities from marine particles 4 Authors: Doreen Schultz,1 Daniela Zühlke,1 Jörg Bernhardt,1 Thomas Ben Francis,2 Dirk 5 Albrecht,1 Claudia Hirschfeld,1 Stephanie Markert,3 and Katharina Riedel 1* 6 7 Addresses: 1 Institute of Microbiology, University of Greifswald, Greifswald, Germany. 8 2 Max-Planck Institute for Marine Microbiology, Bremen, Germany. 9 3 Institute of Pharmacy, University of Greifswald, Greifswald, Germany. 10 11 *Corresponding author mailing address: Institute of Microbiology, Center for Functional 12 Genomics of Microbes (C_FunGene), University of Greifswald, Felix-Hausdorff-Straße 8, DE- 13 17487 Greifswald, Germany. E-mail [email protected]; Tel (+49) 3834 420 5900 14 15 Running title: Metaproteomic pipeline to analyse marine particles 1 bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Originality-Significance Statement 17 Marine particles consist of organic particulate matter (e.g. phyto- or zooplankton) and 18 particle-associated (PA) microbial communities, which are often embedded in a sugary 19 matrix. A significant fraction of the decaying algal biomass in marine ecosystems is expected 20 to be mineralized by PA heterotrophic communities, which are thus greatly contributing to 21 large-scale carbon fluxes. -
A Taxonomic Framework for Emerging Groups of Ecologically
Spring S, Scheuner C, Göker M, Klenk H-P. A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data. Frontiers in Microbiology 2015, 6, 281. Copyright: Copyright © 2015 Spring, Scheuner, Göker and Klenk. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. DOI link to article: http://dx.doi.org/10.3389/fmicb.2015.00281 Date deposited: 07/03/2016 This work is licensed under a Creative Commons Attribution 4.0 International License Newcastle University ePrints - eprint.ncl.ac.uk ORIGINAL RESEARCH published: 09 April 2015 doi: 10.3389/fmicb.2015.00281 A taxonomic framework for emerging groups of ecologically important marine gammaproteobacteria based on the reconstruction of evolutionary relationships using genome-scale data Stefan Spring 1*, Carmen Scheuner 1, Markus Göker 1 and Hans-Peter Klenk 1, 2 1 Department Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany, 2 School of Biology, Newcastle University, Newcastle upon Tyne, UK Edited by: Marcelino T. Suzuki, Sorbonne Universities (UPMC) and In recent years a large number of isolates were obtained from saline environments that are Centre National de la Recherche phylogenetically related to distinct clades of oligotrophic marine gammaproteobacteria, Scientifique, France which were originally identified in seawater samples using cultivation independent Reviewed by: Fabiano Thompson, methods and are characterized by high seasonal abundances in coastal environments. -
A Study of Biofilm Formation in Marine Bacteria Isolated from Ballast Tank
Trends in Research Research Article ISSN: 2516-7138 A study of biofilm formation in marine bacteria isolated from ballast tank fluids Lahiru Malalasekara, Douglas P Henderson and Athenia L Oldham* University of Texas Permian Basin, Odessa, Texas, USA Abstract Seawater-compensated fuel ballast systems maintain ship stability as fuel is spent but can introduce microorganisms that form biofilms, biodegrade fuel components, or enhance corrosion; all of which increase operating and maintenance costs. The aim of this study was to isolate planktonic bacteria from ballast tank fluids and taxonomically classify those that formed biofilm in culture. Twenty-two isolates were identified as belonging to seven genera based on 16S rRNA gene sequencing. Of the seven genera represented Alteromonas, Pseudoalteromonas, and Brevundimonas strains produced quantifiable biofilm in crystal violet assays. To test the hypothesis that the level of bulk nutrients would influence the extent of biofilm formation, isolates were grown in a conventional marine medium and marine medium supplemented with tryptone and yeast extract to represent standard and nutrient-replete media, respectively. While 80% of the Pseudoalteromonas strains produced 7 to 11-fold more biofilm in conventional medium vs. the supplemented medium, 64% of Alteromonas strains produced up to 50-fold less in the same medium. These results suggest that bulk nutrients influence the extent of biofilm formation in a taxa-specific fashion in these marine organisms. The sole Dasania marina isolate failed to display considerable biofilm growth in either media but was the only isolate to produce quorum sensing molecule(s), N-acyl homoserine lactone(s), in assays using an Agrobacterium tumefaciens reporter strain. -
(ST). the Table
1 SUPPLEMENTAL MATERIALS Growth Media Modern Condition Seawater Freshwater Light T°C Atmosphere AMCONA medium BG11 medium – Synechococcus – – Synechocystis – [C] in PAL [C] in the [C] in the Gas Nutrients Modern Nutrients (ppm) Medium Medium Ocean NaNO3 CO2 ~407.8 Na2SO4 25.0mM 29mM Nitrogen 50 Standard (17.65mM) μmol (ST) NaNO NaNO 20°C O ~209’460 Nitrogen 3 3 MgSO 0.304mM photon 2 (549µM) (13.7µM) 4 /m2s FeCl3 6.56µM 2nM Ammonium 0.6g/L ZnSO 254nM 0.5nM ferric stock N ~780’790 4 2 citrate (10ml NaMoO 105nM 105nM 4 green stock/1L) 2 Table S 1 Description of the experimental condition defined as Standard Condition (ST). The table 3 shows the concentrations of fundamental elements, such as C, N, S, and Fe used for the AMCONA 4 seawater medium (Fanesi et al., 2014) and BG11 freshwater medium (Stanier et al., 1971) flushing air 5 with using air pump (KEDSUM-310 8W pump; Xiolan, China) Growth Media Possible Proterozoic T° Condition Modified Seawater Modified Freshwater Light Atmosphere AMCONA medium BG11 medium C – Synechococcus – – Synechocystis – [C] in [C] in PPr Nutrients PPr Nutrients Medium Gas ppm Medium NH Cl Na SO 3mM Nitrogen 4 3 2 4 (0.0035mM) CO 2 10’000ppm (20%) NH Cl Possible (~ 2’450% Nitrogen 4 3 MgSO 0.035mM 50 with 20ml/ (100µM) 4 Proterozoic PAL) μmol 20° min (PPr) photon C O2 20’000ppm /m2s (in Air) (~ 10% FeCl 200nM with 5ml/ 3 PAL) Ammonium 0.6g/L stock min ferric 10ml N ZnSO 0.0nM 2 4 citrate green stock/1L (100%) Base gas with NaMoO4 10.5nM 200ml/min 6 Table S 2 Description of the experimental condition defined as Possible Proterozoic Condition (PPr). -
Metabolic Roles of Uncultivated Bacterioplankton Lineages in the Northern Gulf of Mexico 2 “Dead Zone” 3 4 J
bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Metabolic roles of uncultivated bacterioplankton lineages in the northern Gulf of Mexico 2 “Dead Zone” 3 4 J. Cameron Thrash1*, Kiley W. Seitz2, Brett J. Baker2*, Ben Temperton3, Lauren E. Gillies4, 5 Nancy N. Rabalais5,6, Bernard Henrissat7,8,9, and Olivia U. Mason4 6 7 8 1. Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, USA 9 2. Department of Marine Science, Marine Science Institute, University of Texas at Austin, Port 10 Aransas, TX, USA 11 3. School of Biosciences, University of Exeter, Exeter, UK 12 4. Department of Earth, Ocean, and Atmospheric Science, Florida State University, Tallahassee, 13 FL, USA 14 5. Department of Oceanography and Coastal Sciences, Louisiana State University, Baton Rouge, 15 LA, USA 16 6. Louisiana Universities Marine Consortium, Chauvin, LA USA 17 7. Architecture et Fonction des Macromolécules Biologiques, CNRS, Aix-Marseille Université, 18 13288 Marseille, France 19 8. INRA, USC 1408 AFMB, F-13288 Marseille, France 20 9. Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia 21 22 *Correspondence: 23 JCT [email protected] 24 BJB [email protected] 25 26 27 28 Running title: Decoding microbes of the Dead Zone 29 30 31 Abstract word count: 250 32 Text word count: XXXX 33 34 Page 1 of 31 bioRxiv preprint doi: https://doi.org/10.1101/095471; this version posted June 12, 2017. -
Phylogenetic Studies on Marine Bacteria Within the Phylum Proteobacteria and Bacteroidetes
Phylogenetic studies on marine bacteria within the phylum Proteobacteria and Bacteroidetes (Proteobacteria 門および Bacteroidetes 門に属する海洋細菌の 系統分類に関する研究) Sanghwa Park 朴 相和 Phylogenetic studies on marine bacteria within the phylum Proteobacteria and Bacteroidetes (Proteobacteria 門および Bacteroidetes 門に属する海洋細菌の 系統分類に関する研究) 東京大学農学生命科学研究科 応用生命工学 専攻 平成20年度博士課程入学 氏 名 朴 相和 指導教員名 横田 明 Phylogenetic studies on marine bacteria within the phylum Proteobacteria and Bacteroidetes by Sanghwa Park A dissertation submitted in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Department of Biotechnology Graduate School of Agricultural and Life Sciences The University of Tokyo January 2011 CONTENTS CHAPTER І. GENERAL INTRODUCTION...........................................................................1 1. Polyphasic taxonomy and phylogenetics of bacteria.............................................................2 2. Marine bacteria….................................................................................................................. 4 3. Marine sponge bacteria ..........................................................................................…….......5 4. Aims of this study ...................................................................................................7 CHAPTER ІІ. PHYLOGENETIC STUDIES ON THE NOVEL MARINE SPONGE BACTERIA IN THE CLASS ALPHAPROTEOBACTERIA……………………………...………..…8 1. Introduction……………………………………………………………...……………….....9 2. Materials and methods…......................…………………………………………………...10 -
Emergent €Œcore Communities― of Microbes, Meiofauna And
www.nature.com/ismecomms ARTICLE OPEN Emergent “core communities” of microbes, meiofauna and macrofauna at hydrothermal vents ✉ S. A. Murdock 1 , V. Tunnicliffe1,2, R. E. Boschen-Rose 2,3 and S. K. Juniper1,4 © The Author(s) 2021 Assessment of ecosystem health entails consideration of species interactions within and between size classes to determine their contributions to ecosystem function. Elucidating microbial involvement in these interactions requires tools to distil diverse microbial information down to relevant, manageable elements. We used covariance ratios (proportionality) between pairs of species and patterns of enrichment to identify “core communities” of likely interacting microbial (<64 µm), meiofaunal (64 µm to 1 mm) and macrofaunal (>1 mm) taxa within assemblages hosted by a foundation species, the hydrothermal vent tubeworm Ridgeia piscesae. Compared with samples from co-located hydrothermal fluids, microbial communities within R. piscesae assemblages are hotspots of taxonomic richness and are high in novelty (unclassified OTUs) and in relative abundance of Bacteroidetes. We also observed a robust temperature-driven distinction in assemblage composition above and below ~25 °C that spanned micro to macro size classes. The core high-temperature community included eight macro- and meiofaunal taxa and members of the Bacteroidetes and Epsilonbacteraeota, particularly the genera Carboxylicivirga, Nitratifractor and Arcobacter. The core low- temperature community included more meiofaunal species in addition to Alpha- and Gammaproteobacteria, and Actinobacteria. Inferred associations among high-temperature core community taxa suggest increased reliance on species interactions under more severe hydrothermal conditions. We propose refinement of species diversity to “core communities” as a tool to simplify investigations of relationships between taxonomic and functional diversity across domains and scales by narrowing the taxonomic scope. -
Biodegradation of Poly(Ethylene Terephthalate) by Marine Bacteria, and Strategies for Its Enhancement
Biodegradation of poly(ethylene terephthalate) by marine bacteria, and strategies for its enhancement Submitted in total fulfillment of the requirements for the degree of Doctor of Philosophy by Hayden Webb Environmental and Biotechnology Centre Faculty of Life and Social Sciences Swinburne University of Technology May 2012 ___________________________________________________________________ Abstract Plastic accumulation, particularly in the world’s oceans is of increasing environmental concern. One of the major components of plastic waste is poly(ethylene terephthalate) (PET), a polymer frequently used in many applications, including textiles and food packaging. The current methods of disposal of PET waste, landfill, incineration and recycling, each have inherent drawbacks and limitations, and as such there is a need for efficient and cost-effective alternative. Biodegradation is an attractive option for environmentally friendly and efficient disposal of plastic waste. To date, no protocol has yet been developed to feasibly dispose of PET by biodegradation con a commercial scale. The current works aims to investigate the potential of PET biodegradation as a plastic disposal procedure by providing fundamental knowledge of biodegradation processes, and to develop strategies for improving biodegradation efficiency. PET samples were incubated in marine bacterial community enrichment cultures, and the dynamics of the polymer – bacterial interactions traced. Modifications to polymer surfaces were monitored using a variety of surface characterisation techniques, including atomic force microscopy (AFM), x-ray photoelectron spectroscopy (XPS) and infrared microspectroscopy using Synchrotron radiation. Taxonomic members of the bacterial enrichment cultures that developed in the presence of PET were recovered and identified via 16S rRNA gene sequencing. Marine bacteria were shown to possess the ability to degrade PET surfaces. -
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Title Exploiting the diverse microbial ecology of marine sponges Author(s) Jackson, Stephen A. Publication date 2013 Original citation Jackson, S. A. 2013. Exploiting the diverse microbial ecology of marine sponges. PhD Thesis, University College Cork. Type of publication Doctoral thesis Rights © 2013, Stephen A. Jackson http://creativecommons.org/licenses/by-nc-nd/3.0/ Embargo information Restricted to everyone for three years Item downloaded http://hdl.handle.net/10468/1037 from Downloaded on 2017-02-12T13:45:47Z Exploiting the Diverse Microbial Ecology of Marine Sponges A Thesis presented to the National University of Ireland for the Degree of Doctor of Philosophy Stephen Anthony Jackson, BSc. Department of Microbiology National University of Ireland Cork Head of Department: Dr Gerald Fitzgerald Research Supervisors: Prof. Alan Dobson & Dr John Morrissey 2013 1 For Daniel, My inspiration 2 Index 1 Abstract 7 Chapter 1: Literature Review 10 1.1 Marine sponges 11 1.1.1 Sponge anatomy and physiology 12 1.1.1.1 Sponge skeletons 12 1.1.1.2 Sponge cell types 13 1.1.1.3 Sponge physiology 14 1.2 Sponge associated microorganisms 15 1.2.1 Sponge associated bacteria 15 1.2.1.1 Culture dependent analyses 15 1.2.1.2 Culture independent analyses 16 1.2.1.2.1 Microscopy 16 1.2.1.2.2 16S rRNA clone libraries 18 1.2.1.2.3 Pyrosequencing 20 1.2.2 Sponge associated archaea 22 1.2.3 Sponge associated eukaryota 22 1.2.3.1 Sponge associated fungi 22 1.2.3.2 Sponge associated diatoms 23 1.2.3.3 Sponge associated dinoflagellates 23 1.2.3.4 Other sponge associated -
Biostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’S Subarctic: a Microcosm-Simulated Oil Spill Study
University of Calgary PRISM: University of Calgary's Digital Repository Graduate Studies The Vault: Electronic Theses and Dissertations 2020-01-23 Biostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’s Subarctic: A Microcosm-Simulated Oil Spill Study Murphy, Sean Michael Colin Murphy, S. M. C. (2020). Biostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’s Subarctic: A Microcosm-Simulated Oil Spill Study (Unpublished master's thesis). University of Calgary, Calgary, AB. http://hdl.handle.net/1880/111552 doctoral thesis University of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission. Downloaded from PRISM: https://prism.ucalgary.ca UNIVERSITY OF CALGARY Biostimulation for Enhanced Bioremediation of Crude Oil and Diesel Fuel by Marine Sediment Communities of Canada’s Subarctic: A Microcosm-Simulated Oil Spill Study by Sean Michael Colin Murphy A THESIS SUBMITTED TO THE FACULTY OF GRADUATE STUDIES IN PARTIAL FULFILMENT OF THE REQUIREMENTS FOR THE DEGREE OF MASTER OF SCIENCE GRADUATE PROGRAM IN BIOLOGICAL SCIENCES CALGARY, ALBERTA JANUARY, 2020 © Sean Michael Colin Murphy 2020 Abstract Increases in shipping traffic, future mining, and oil and gas developments represent significant oil spill risks in Canada’s subarctic marine environment. The impact of oil on marine ecosystems and the traditional activities of local indigenous peoples are of major concern. -
A Robust Metaproteomics Pipeline for a Holistic Taxonomic and Functional
bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 2 Title: A robust metaproteomics pipeline for a holistic taxonomic and functional 3 characterization of microbial communities from marine particles 4 Authors: Doreen Schultz,1 Daniela Zühlke,1 Jörg Bernhardt,1 Thomas Ben Francis,2 Dirk 5 Albrecht,1 Claudia Hirschfeld,1 Stephanie Markert,3 and Katharina Riedel 1* 6 7 Addresses: 1 Institute of Microbiology, University of Greifswald, Greifswald, Germany. 8 2 Max-Planck Institute for Marine Microbiology, Bremen, Germany. 9 3 Institute of Pharmacy, University of Greifswald, Greifswald, Germany. 10 11 *Corresponding author mailing address: Institute of Microbiology, Center for Functional 12 Genomics of Microbes (C_FunGene), University of Greifswald, Felix-Hausdorff-Straße 8, DE- 13 17487 Greifswald, Germany. E-mail [email protected]; Tel (+49) 3834 420 5900 14 15 Running title: Metaproteomic pipeline to analyse marine particles 1 bioRxiv preprint doi: https://doi.org/10.1101/667428; this version posted June 11, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 16 Originality-Significance Statement 17 Marine particles consist of organic particulate matter (e.g. phyto- or zooplankton) and 18 particle-associated (PA) microbial communities, which are often embedded in a sugary 19 matrix. A significant fraction of the decaying algal biomass in marine ecosystems is expected 20 to be mineralized by PA heterotrophic communities, which are thus greatly contributing to 21 large-scale carbon fluxes.