DOCSLIB.ORG

The Response of Anaerobic Prokaryotic Processes And

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text

Load more

The Response of Anaerobic Prokaryotic Processes and Communities in Severn Estuary Sediments to Environmental Change Shaun Thomas A thesis submitted to Cardiff University in accordance with the regulations governing the award of Philosophiae Doctor October 2014 Cardiff University School of Earth and Ocean Sciences i DECLARATION This work has not been submitted in substance for any other degree or award at this or any other university or place of learning, nor is being submitted concurrently in candidature for any degree or other award. Signed………………………………………………………………(candidate) Date………………………….. STATEMENT 1 This thesis is being submitted in partial fulfilment of the requirements for the degree of ……………………. (insert MCh, MD, MPhil, PhD etc. as appropriate). Signed………………………………………………………………(candidate) Date………………………….. STATEMENT 2 This thesis is the result of my own independent work/investigation, except where otherwise stated. Other sources are acknowledged by explicit references. The views expressed are my own. Signed………………………………………………………………(candidate) Date………………………….. STATEMENT 3 I hereby give consent for my thesis, if accepted, to be available online in the University’s Open Access repository and for inter-library loan, and for the title and summary to be made available to outside organisations. Signed………………………………………………………………(candidate) Date………………………….. STATEMENT 4: PREVIOUSLY APPROVED BAR ON ACCESS I hereby give consent for my thesis, if accepted, to be available online in the University’s Open Access repository and for inter-library loans after expiry of a bar on access previously approved by the Academic Standards & Quality Committee. Signed………………………………………………………………(candidate) Date………………………….. ii Acknowlegements First off I’d like to thank my parents, thank you for always believing in me and giving me the confidence I needed to get through this. Special thanks to my supervisors, John, Henrik, and Andy for putting together this project and for their assistance and helpful comments throughout. Also to Sir Martin Evans for providing the funding for the President’s Scholarship program. I’d also like to thank everyone who assisted me with lab or fieldwork: Barry Cragg, Miriam Olivier, Gordon Webster, Xiaohong Tang, Erwan Roussel, Andrew Watkins Andrea Sass, Sarah Lee, Ian Fryett, Paul Evans, Chris Wooldridge, Nick Rodgers, Luke Croudace, Angharad Williams, Jen Pinnion and Paul Biggs (and to anyone else I’ve forgotten, sorry and thank you too). Additional thanks are also due to anyone who was willing to brave a mudflat or boat trip to the always sunny and mirror-calm Severn Estuary (doubly so for those mad enough to do so more than once). Finally thanks to Kate, Loz and Tom for always being there when I needed someone to talk to, for being the best friends a guy could ask for and for always making me laugh and keeping me sane (especially during the write up). iii “And heaved and heaved, still unrestingly heaved the black sea, as if its vast tides were a conscience; and the great mundane soul were in anguish and remorse for the long sin and suffering it had bred.” Herman Melville, Moby Dick “I cannot think of the deep sea without shuddering at the nameless things that may at this very moment be crawling and floundering on its slimy bed” H. P. Lovecraft, Dagon “There is no point trying to hide from your bacteria… This is their planet, and we are only on it because they allow us to be” Bill Bryson, A Short History Of Nearly Everything iv Summary The Severn Estuary in the south-western UK is one of the most tidally dynamic environments on the planet. However, despite this the sediments of the estuary remain relatively understudied with regards to their biogeochemical potential. The aim of this project was to investigate how the constantly changing sedimentary environment in the estuary, in which millions of tonnes of sediment are eroded and deposited over the tidal cycle, affects the prokaryotes within the sediments and the processes they control, and also to determine what effect environmental changes in the estuarine system might have on these processes. The study showed that the sediments of the Severn Estuary have high rates of sediment oxygen demand (SOD) indicating a high degree of organic matter (OM) degradation. However, the sediments have low rates of the anaerobic processes that are expected to dominate in shallow marine systems (e.g. sulphate reduction and methanogenesis), suggesting that most OM degradation must be linked to processes further up the redox cascade. The sediments also showed a lack of microbial guild depth zonation, with methanogenesis occurring above or alongside sulphate reduction. Both of these unusual factors can be linked to the regular re-suspension of the estuary’s sediments by tidal action, resulting in large-scale oxidation and mixing of the sediment column and the suppression of anaerobic processes while potentially stimulating aerobic and dysaerobic activity. This same mixing would also distribute guilds of organisms throughout the sediment, creating isolated pioneer populations with a general lack of competition. Re-suspension is also likely responsible for the high cell counts that persist to significant depth around the estuary, as the mixing of sediment and entrainment of OM would produce high and homogeneous cell profiles upon deposition, which in turn can be linked to the high SOD of the estuary’s sediments. Despite this dominance of aerobic and dysaerobic processes throughout most of the estuary some isolated sites do show increased rates of anaerobic processes, particularly at locations that have undergone significant environmental change. These include fluidised mud pools in the deeper areas of the estuary, salt marsh peat deposits at St Brides Wentlooge (especially within the “activated interface”) and Cardiff Bay, an anthropogenic lake and former mudflat environment which shows significant methanogenic potential. Overall this study has shown that the dynamic conditions in the Severn Estuary promote the activity of aerobic and dysaerobic prokaryotic groups over the anaerobic groups traditionally thought to dominate in shallow marine sediments. However, this promotion is not uniform across the estuary, instead varying with topography/bathymetry and the degree of sediment disturbance. v Contents Title p. i Declaration p. ii Acknowledgements p. iii Quotations p. iv Summary p. v Contents p. vi List of Figures p. xi List of Tables p. xvi List of Abbreviations p. xvi Chapter 1. – An Introduction to Estuarine Sediment Biogeochemistry and the Severn Estuary 1.1 The Redox Cascade p. 1 1.1.1 Aerobic Respiration p. 4 1.1.2 Nitrogen Cycling - Denitrification, DNRA and Nitrification/ Ammonium Oxidation p. 5 1.1.3 Dissimilatory Manganese Reduction and Oxidation p. 7 1.1.4 Dissimilatory Iron Reduction and Oxidation p. 8 1.1.5 Dissimilatory Sulphate Reduction and Sulphide Oxidation p. 9 1.1.6 Methanogenesis, Fermentation and AOM p. 14 1.2 Environmental Factors influencing Prokaryotic Growth p. 20 1.2.1 Salinity p. 20 1.2.2 Temperature p. 23 1.3 An Introduction to the Severn Estuary 1.3.1 Geographical Setting p. 26 1.3.2 Geological History and Formation p. 30 1.3.3 Tidal Range p. 30 1.3.4 Biogeochemistry of the Severn Estuary p. 34 1.3.5 Benthic Macrofauna of the Severn Estuary p. 37 1.3.6 Sediments of the Severn Estuary p. 39 vi 1.3.7 Hydrology and Water Chemistry of the Severn Estuary p. 47 1.3.8 Research Objectives and Site Selection p. 50 Chapter 2. – Methodology 2.1 Sediment Coring p. 53 2.2 Oxygen Uptake Measurements p. 55 2.3 Sectioning of Sediment Cores p. 58 2.4 Pore Water Analysis p. 58 2.5 Sediment Gas Content p. 60 2.6 Total Cell Counts p. 61 2.7 Rates of Anaerobic Processes p. 64 3.7.1 Active Sulphate Reduction Rate Measurements p. 64 3.7.2 Active Methanogenesis Rate Measurements p. 70 2.8 Sediment Porosity p. 73 Chapter 3. – The Severn Estuary Transect: Cores ST1, ST2 and ST3 3.1 Site Locations and Lithology p. 74 3.2 The Severn Estuary Transect – Results p. 76 3.2.1 Biogeochemistry of Core ST1 p. 76 3.2.2 Biogeochemistry of Core ST2 p. 81 3.2.3 Biogeochemistry of Core ST3 p. 85 3.3 The Severn Estuary Transect – Discussion p. 90 3.3.1 Sedimentology p. 90 3.3.2 Organic Acids – Acetate, Lactate and Formate p. 91 3.3.3 Nitrate and Ammonium p. 93 3.3.4 Chloride and the Alkali Metals p. 95 3.3.5 Sulphate p. 99 3.3.6 Methane p. 100 3.3.7 Total Cell Counts p. 102 3.4 The Severn Estuary Transect – Conclusions p. 104 vii Chapter 4. – Severn Estuary Tidal Flats, Part 1: Cores ST4 and ST5 4.1 Site Locations and Lithology p. 106 4.2 Severn Estuary Tidal Flats, Part 1 – Results p. 111 4.2.1 Biogeochemistry of Core ST4 p. 111 4.2.2 Biogeochemistry of Core ST5 p. 119 4.3 Severn Estuary Tidal Flats, Part 1 – Discussion p. 126 4.4 Severn Estuary Tidal Flats, Part 1 – Conclusions p. 130 Chapter 5. – Severn Estuary Tidal Flats, Part 2: Core ST6 5.1 Site Location and Lithology p. 131 5.2 Severn Estuary Tidal Flats, Part 2 – Results p. 133 5.2.1 Biogeochemistry of ST6 p. 133 5.3 Severn Estuary Tidal Flats, Part 2 – Discussion p. 142 5.3.1 Comparison with Core ST4 p. 142 5.3.2 Comparison with Core ST5 p. 145 5.4 Severn Estuary Tidal Flats, Part 2 – Conclusions p. 147 Chapter 6. – Bridgwater Bay: Cores ST7 and ST8 6.1 Site Locations and Lithology p. 148 6.2 Bridgwater Bay – Results p. 150 6.2.1 Biogeochemistry of Core ST7 p. 150 6.2.2 Biogeochemistry of Core ST8 p. 156 6.3 Bridgwater Bay – Discussion p.
Recommended publications
  • Impacts of Desulfobacterales and Chromatiales on Sulfate Reduction in The

    Impacts of Desulfobacterales and Chromatiales on Sulfate Reduction in The

    bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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-ND 4.0 International license. 1 Impacts of Desulfobacterales and Chromatiales on sulfate reduction in the 2 subtropical mangrove ecosystem as revealed by SMDB analysis 3 Shuming Mo 1, †, Jinhui Li 1, †, Bin Li 2, Ran Yu 1, Shiqing Nie 1, Zufan Zhang 1, Jianping 4 Liao 3, Qiong Jiang 1, Bing Yan 2, *, and Chengjian Jiang 1, 2 * 5 1 State Key Laboratory for Conservation and Utilization of Subtropical Agro- 6 bioresources, Guangxi Research Center for Microbial and Enzyme Engineering 7 Technology, College of Life Science and Technology, Guangxi University, Nanning 8 530004, China. 9 2 Guangxi Key Lab of Mangrove Conservation and Utilization, Guangxi Mangrove 10 Research Center, Guangxi Academy of Sciences, Beihai 536000, China. 11 3 School of Computer and Information Engineering, Nanning Normal University, 12 Nanning 530299, China. 13 † These authors contributed equally to this work. 14 *: Corresponding Author: 15 Tel: +86-771-3270736; Fax: +86-771-3237873 16 Email: [email protected] (CJ); [email protected] (BY) 17 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.08.16.252635; this version posted November 6, 2020. 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.
  • Exploring the Lipidomes of Shallow-Water and Deep-Sea Hydrothermal Systems

    Exploring the Lipidomes of Shallow-Water and Deep-Sea Hydrothermal Systems

    Exploring the lipidomes of shallow-water and deep-sea hydrothermal systems Dissertation zur Erlangung des Doktorgrades der Naturwissenschaften - Dr. rer. nat. - Am Fachbereich Geowissenschaften der Universität Bremen vorgelegt von Miriam Sollich Bremen Mai 2018 1. Gutachter: Dr. Solveig I. Bühring 2. Gutachter: Associate Prof. Dr. Eoghan P. Reeves Tag des Promotionskolloquiums:16. Februar 2018 Den Wissenschaftlern geht es wie den Chaoten. Es ist alles da, man muss es nur suchen. - Franz Kern - CONTENTS Abstract Zusammenfassung Acknowledgements List of Abbreviations Chapter I 1 Introduction and Methods Chapter II 37 Scope and Outline Chapter III 43 Heat stress dictates the microbial lipid composition along a thermal gradient in marine sediments Chapter IV 91 Shallow-water hydrothermal systems offer ideal conditions to study archaeal lipid membrane adaptations to environmental extremes Chapter V 113 Transfer of chemosynthetic fixed carbon and its ecological significance revealed by lipid analysis of fluids at diffuse flow deep-sea vents (East Pacific Rise 9°50’N) Chapter VI 143 Concluding Remarks and Future Perspectives ABSTRACT Shallow-water and deep-sea hydrothermal systems are environments where seawater percolates downward through fractures in the oceanic crust, and becomes progressively heated and chemically altered. Finally, the entrained water is expelled into the overlying water column as a hydrothermal fluid. Hydrothermal circulation occurs at all active plate boundaries like mid-ocean ridges, submarine volcanic arcs and backarc basins. They represent one of the most extreme and dynamic ecosystems on the planet with steep physico-chemical gradients. Nevertheless, these environments are characterized by exceptional high biomass representing hotspots of life in the mostly hostile and desolated deep sea.
  • High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-Methylalkyl)Succinate Synthase Genes

    High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-Methylalkyl)Succinate Synthase Genes

    ORIGINAL RESEARCH published: 07 January 2016 doi: 10.3389/fmicb.2015.01511 High Diversity of Anaerobic Alkane-Degrading Microbial Communities in Marine Seep Sediments Based on (1-methylalkyl)succinate Synthase Genes Marion H. Stagars1,S.EmilRuff1,2† , Rudolf Amann1 and Katrin Knittel1* 1 Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Bremen, Germany, 2 HGF MPG Joint Research Group for Deep-Sea Ecology and Technology, Max Planck Institute for Marine Microbiology, Bremen, Germany Edited by: Alkanes comprise a substantial fraction of crude oil and are prevalent at marine seeps. Hans H. Richnow, These environments are typically anoxic and host diverse microbial communities that Helmholtz Centre for Environmental Research, Germany grow on alkanes. The most widely distributed mechanism of anaerobic alkane activation Reviewed by: is the addition of alkanes to fumarate by (1-methylalkyl)succinate synthase (Mas). Here Beth Orcutt, we studied the diversity of MasD, the catalytic subunit of the enzyme, in 12 marine Bigelow Laboratory for Ocean sediments sampled at seven seeps. We aimed to identify cosmopolitan species as well Sciences, USA Zhidan Liu, as to identify factors structuring the alkane-degrading community. Using next generation China Agricultural University, China sequencing we obtained a total of 420 MasD species-level operational taxonomic units *Correspondence: (OTU0.96) at 96% amino acid identity. Diversity analysis shows a high richness and Katrin Knittel [email protected] evenness of alkane-degrading bacteria. Sites with similar hydrocarbon composition harbored similar alkane-degrading communities based on MasD genes; the MasD †Present address: community structure is clearly driven by the hydrocarbon source available at the various S.
  • Advance View Proofs

    Advance View Proofs

    M&E Papers in Press. Published online on March 23, 2012 doi:10.1264/jsme2.ME11357 1 2 Revised ME11357 3 4 Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of 5 Anaerobic Degradation of p-Xylene 6 * 7 YURIKO HIGASHIOKA, HISAYA KOJIMA , AND MANABU FUKUI 8 9 The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, 10 Kita-ku, Sapporo, Hokkaido 060-0819, Japan 11 Proofs 12 (Received December 21, 2011-Accepted February 2, 2012) 13 View 14 Running headline: p-Xylene-Degrading Sulfate Reducer 15 16 * Corresponding author. E-mail: [email protected]; Tel: 17 +81-11-706-5460;Advance Fax: +81-11-706-5460. 18 19 20 21 1 Copyright 2012 by the Japanese Society of Microbial Ecology / the Japanese Society of Soil Microbiology 22 A novel strain of p-xylene-degrading sulfate reducer was isolated in pure culture. 23 Strain PP31 was obtained from a p-xylene-degrading enrichment culture established 24 from polluted marine sediment. Analyses of the 16S rRNA gene and two functional 25 genes involved in sulfate respiration and anaerobic degradation of aromatic compounds 26 revealed that the isolate was closely related to members of the genus Desulfosarcina. 27 Strain PP31 was capable of growing on p-xylene under sulfate-reducing conditions, and 28 the ratio of generated sulfide and consumed p-xylene suggested complete oxidation by 29 the novel isolate. The strain could not grow on benzene, toluene, ethylbenzene, 30 m-xylene o-xylene, or n-hexane as an electron donor. Strain PP31 is the first isolated 31 bacterium that degrades p-xylene anaerobically, and will be useful to understanding the 32 mechanism of anaerobic degradation of p-xylene.
  • Full Text in Pdf Format

    Full Text in Pdf Format

    Vol. 86: 1–19, 2021 AQUATIC MICROBIAL ECOLOGY Published online January 28 https://doi.org/10.3354/ame01954 Aquat Microb Ecol OPEN ACCESS Nitrogen cycling in coastal sediment microbial communities with seasonally variable benthic nutrient fluxes Alexis J. Marshall1,2,5,*, Andrew Longmore3, Lori Phillips2,6, Caixian Tang1, Helen L. Hayden2, Karla B. Heidelberg4, Pauline Mele1,2 1La Trobe University, AgriBio Centre for AgriBiosciences, Melbourne, VIC 3086, Australia 2Agriculture Victoria, Department of Jobs, Precincts and Regions, AgriBio, Centre for AgriBiosciences, Melbourne, VIC 3086, Australia 3Centre for Aquatic Pollution Identification and Management, Melbourne University, Parkville, VIC 3010, Australia 4The University of Southern California, Department of Biology, Los Angeles, CA 90089, USA 5Present address: University of Waikato, Hillcrest, Hamilton 3216, New Zealand 6Present address: Agriculture and Agri-Food Canada, Harrow Research and Development Centre, Harrow, ON N0R1G0, Canada ABSTRACT: Benthic microbial communities contribute to nitrogen (N) cycling in coastal ecosystems through taxon-specific processes such as anammox, nitrification and N-fixation and community attributed pathways such as denitrification. By measuring the total (DNA-based) and active (RNA- based) surface sediment microbial community composition and the abundance and activity profiles of key N-cycling genes in a semi-enclosed embayment — Port Phillip Bay (PPB), Australia — we show that although the total relative abundance of N-cycling taxa is comparatively lower close to estuary inputs (Hobsons Bay [HB]), the capacity for this community to perform diverse N-cycling processes is comparatively higher than in sediments isolated from inputs (Central PPB [CPPB]). In HB, seasonal structuring of the sediment microbial community occurred between spring and sum- mer, co-occurring with decreases in the activity profiles of anammox bacteria and organic carbon content.
  • Microscopic Methods for Identification of Sulfate-Reducing Bacteria From

    Microscopic Methods for Identification of Sulfate-Reducing Bacteria From

    International Journal of Molecular Sciences Review Microscopic Methods for Identification of Sulfate-Reducing Bacteria from Various Habitats Ivan Kushkevych 1,* , Blanka Hýžová 1, Monika Vítˇezová 1 and Simon K.-M. R. Rittmann 2,* 1 Department of Experimental Biology, Faculty of Science, Masaryk University, 62500 Brno, Czech Republic; [email protected] (B.H.); [email protected] (M.V.) 2 Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, Universität Wien, 1090 Wien, Austria * Correspondence: [email protected] (I.K.); [email protected] (S.K.-M.R.R.); Tel.: +420-549-495-315 (I.K.); +431-427-776-513 (S.K.-M.R.R.) Abstract: This paper is devoted to microscopic methods for the identification of sulfate-reducing bacteria (SRB). In this context, it describes various habitats, morphology and techniques used for the detection and identification of this very heterogeneous group of anaerobic microorganisms. SRB are present in almost every habitat on Earth, including freshwater and marine water, soils, sediments or animals. In the oil, water and gas industries, they can cause considerable economic losses due to their hydrogen sulfide production; in periodontal lesions and the colon of humans, they can cause health complications. Although the role of these bacteria in inflammatory bowel diseases is not entirely known yet, their presence is increased in patients and produced hydrogen sulfide has a cytotoxic effect. For these reasons, methods for the detection of these microorganisms were described. Apart from selected molecular techniques, including metagenomics, fluorescence microscopy was one of the applied methods. Especially fluorescence in situ hybridization (FISH) in various modifications Citation: Kushkevych, I.; Hýžová, B.; was described.
  • Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017

    Ecophysiology of Sulfate-Reducing Bacteria and Syntrophic Communities in Marine Anoxic Sediments” Derya Özüölmez Wageningen, 12 September 2017

    Propositions 1. Prolonged incubation is a key strategy toward the enrichment of marine syntrophs. (this thesis) 2. Hydrogen-consuming methanogens can effectively compete with hydrogen- consuming sulfate reducers even at high sulfate concentration. (this thesis) 3. The plastic-eating wax worm, Galleria mellonella, can help cleaning up existing plastic mass (Bombelli et al. 2017, Current Biology 27(8): 292-293), but the real solution to environmental pollution still relies on shifting from disposable plastics to reusable and biodegradable materials. 4. With the discovery of abundant molecular hydrogen in Enceladus’ salty ocean (Waite et al. (2017) Science 356:6334, 155-159) extraterrestrial life in our solar system has become highly probable, and should shift our life-hunting focus from distant stars to our nearby neighbors. 5. With the "Help me to do it myself" motto, the Montessori education leads children to grow into mature, creative and self-confident adults. 6. Nothing is impossible as long as the dream is held close to the heart and patience and persistence are applied for the accomplishment. Propositions belonging to the PhD thesis entitled: “Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments” Derya Özüölmez Wageningen, 12 September 2017 Ecophysiology of sulfate-reducing bacteria and syntrophic communities in marine anoxic sediments Derya Özüölmez Thesis committee Promotor Prof. Dr Alfons J.M. Stams Personal chair at the Laboratory of Microbiology Wageningen University & Research Co-promotor Dr Caroline M. Plugge Associate professor, Laboratory of Microbiology Wageningen University & Research Other members Prof. Dr Tinka Murk, Wageningen University & Research Prof. Dr Gerard Muyzer, University of Amsterdam, The Netherlands Prof.
  • Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of Anaerobic Degradation of P-Xylene

    Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of Anaerobic Degradation of P-Xylene

    Microbes Environ. Vol. 27, No. 3, 273–277, 2012 http://wwwsoc.nii.ac.jp/jsme2/ doi:10.1264/jsme2.ME11357 Isolation and Characterization of Novel Sulfate-Reducing Bacterium Capable of Anaerobic Degradation of p-Xylene YURIKO HIGASHIOKA1, HISAYA KOJIMA1*, and MANABU FUKUI1 1The Institute of Low Temperature Science, Hokkaido University, Nishi 8, Kita 19, Kita-ku, Sapporo, Hokkaido 060–0819, Japan (Received December 21, 2011—Accepted February 2, 2012—Published online March 23, 2012) A novel strain of p-xylene-degrading sulfate reducer was isolated in pure culture. Strain PP31 was obtained from a p-xylene-degrading enrichment culture established from polluted marine sediment. Analyses of the 16S rRNA gene and two functional genes involved in sulfate respiration and anaerobic degradation of aromatic compounds revealed that the isolate was closely related to members of the genus Desulfosarcina. Strain PP31 was capable of growing on p-xylene under sulfate-reducing conditions, and the ratio of generated sulfide and consumed p-xylene suggested complete oxidation by the novel isolate. The strain could not grow on benzene, toluene, ethylbenzene, m-xylene o- xylene, or n-hexane as an electron donor. Strain PP31 is the first isolated bacterium that degrades p-xylene anaerobically, and will be useful to understanding the mechanism of anaerobic degradation of p-xylene. Key words: Sulfate-reducing bacteria, p-xylene, anaerobic biodegradation Due to its relatively high toxicity and water solubility, our laboratory by periodic transfer to fresh medium. The basal p-xylene is considered a noteworthy organic pollutant. medium used was identical to that used in the previous study.
  • Expanding the Repertoire of Electron Acceptors for the Anaerobic Oxidation of Methane in Carbonates in the Atlantic and Pacific

    Expanding the Repertoire of Electron Acceptors for the Anaerobic Oxidation of Methane in Carbonates in the Atlantic and Pacific

    The ISME Journal (2021) 15:2523–2536 https://doi.org/10.1038/s41396-021-00918-w ARTICLE Expanding the repertoire of electron acceptors for the anaerobic oxidation of methane in carbonates in the Atlantic and Pacific Ocean 1,3 1 1 1 2 Sabrina Beckmann ● Ibrahim F. Farag ● Rui Zhao ● Glenn D. Christman ● Nancy G. Prouty ● Jennifer F. Biddle 1 Received: 12 June 2020 / Revised: 21 January 2021 / Accepted: 29 January 2021 / Published online: 12 March 2021 © The Author(s), under exclusive licence to International Society for Microbial Ecology 2021 Abstract Authigenic carbonates represent a significant microbial sink for methane, yet little is known about the microbiome responsible for the methane removal. We identify carbonate microbiomes distributed over 21 locations hosted by seven different cold seeps in the Pacific and Atlantic Oceans by carrying out a gene-based survey using 16S rRNA- and mcrA gene sequencing coupled with metagenomic analyses. Based on 16S rRNA gene amplicon analyses, these sites were dominated by bacteria affiliated to the Firmicutes, Alpha- and Gammaproteobacteria. ANME-1 and -2 archaeal clades were abundant in the carbonates yet their typical syntrophic partners, sulfate-reducing bacteria, were not significantly present. Based on mcrA 1234567890();,: 1234567890();,: amplicon analyses, the Candidatus Methanoperedens clades were also highly abundant. Our metagenome analysis indicated that methane oxidizers affiliated to the ANME-1 and -2, may be capable of performing complete methane- and potentially short-chain alkane oxidation independently using oxidized sulfur and nitrogen compounds as terminal electron acceptors. Gammaproteobacteria are hypothetically capable of utilizing oxidized nitrogen compounds and may be involved in syntrophy with methane-oxidizing archaea.
  • Notes on the Characterization of Prokaryote Strains for Taxonomic

    Notes on the Characterization of Prokaryote Strains for Taxonomic

    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Digital.CSIC International Journal of Systematic and Evolutionary Microbiology (2010), 60, 249–266 DOI 10.1099/ijs.0.016949-0 Taxonomic Notes on the characterization of prokaryote strains Note for taxonomic purposes B. J. Tindall,1 R. Rossello´-Mo´ra,2 H.-J. Busse,3 W. Ludwig4 and P. Ka¨mpfer5 Correspondence 1DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Inhoffenstraße 7B, Brian J. Tindall D-38124 Braunschweig, Germany [email protected] 2Grup de Microbiologia Marina, Departament d’Ecologia I Recursos Marins, IMEDEA (CSIC-UIB), C/Miquel Marque´s 21, E-07190, Esporles, Spain 3Institut fu¨r Bakteriologie, Mykologie und Hygiene, University of Veterinary Medicine Vienna, Veterina¨rplatz 1, A-1210 Vienna, Austria 4Lehrstuhl fu¨r Mikrobiologie, Technische Universita¨t Mu¨nchen, Am Hochanger 4, D-85354 Freising-Weihenstephan, Germany 5Institut fu¨r Angewandte Mikrobiologie, Justus-Liebig-Universita¨t Giessen, Heinrich-Buff-Ring 26- 32 (IFZ), D-35392 Giessen, Germany Taxonomy relies on three key elements: characterization, classification and nomenclature. All three elements are dynamic fields, but each step depends on the one which precedes it. Thus, the nomenclature of a group of organisms depends on the way they are classified, and the classification (among other elements) depends on the information gathered as a result of characterization. While nomenclature is governed by the Bacteriological Code, the classification and characterization of prokaryotes is an area that is not formally regulated and one in which numerous changes have taken place in the last 50 years.
  • Activity and Interactions of Methane Seep Microorganisms Assessed by Parallel Transcription and FISH-Nanosims Analyses

    Activity and Interactions of Methane Seep Microorganisms Assessed by Parallel Transcription and FISH-Nanosims Analyses

    The ISME Journal (2016) 10, 678–692 © 2016 International Society for Microbial Ecology All rights reserved 1751-7362/16 OPEN www.nature.com/ismej ORIGINAL ARTICLE Activity and interactions of methane seep microorganisms assessed by parallel transcription and FISH-NanoSIMS analyses Anne E Dekas1, Stephanie A Connon, Grayson L Chadwick, Elizabeth Trembath-Reichert and Victoria J Orphan Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, CA, USA To characterize the activity and interactions of methanotrophic archaea (ANME) and Deltaproteo- bacteria at a methane-seeping mud volcano, we used two complimentary measures of microbial activity: a community-level analysis of the transcription of four genes (16S rRNA, methyl coenzyme M reductase A (mcrA), adenosine-5′-phosphosulfate reductase α-subunit (aprA), dinitrogenase reductase (nifH)), and a single-cell-level analysis of anabolic activity using fluorescence in situ hybridization coupled to nanoscale secondary ion mass spectrometry (FISH-NanoSIMS). Transcript analysis revealed that members of the deltaproteobacterial groups Desulfosarcina/Desulfococcus (DSS) and Desulfobulbaceae (DSB) exhibit increased rRNA expression in incubations with methane, suggestive of ANME-coupled activity. Direct analysis of anabolic activity in DSS cells in consortia with ANME by FISH-NanoSIMS confirmed their dependence on methanotrophy, with no 15 + NH4 assimilation detected without methane. In contrast, DSS and DSB cells found physically independent of ANME (i.e., single cells) were anabolically active in incubations both with and without methane. These single cells therefore comprise an active ‘free-living’ population, and are not dependent on methane or ANME activity. We investigated the possibility of N2 fixation by seep Deltaproteobacteria and detected nifH transcripts closely related to those of cultured diazotrophic 15 Deltaproteobacteria.

  • From Planctomycetes to Microbial Community

    MEA 2.º CICLO FCUP 2017 microbial community microbial to Planctomycetes from hydrocarbons: with Dealing Dealing with Hydrocarbons: from Planctomycetes to microbial community Teresa Filipa Botelho Carvalho Dissertação de Mestrado apresentada à Faculdade de Ciências da Universidade do Porto em Teresa Filipa Botelho Caralho Ecologia e Ambiente 2017 Dealing with Hydrocarbons: from Planctomycetes to microbial community Teresa Filipa Botelho Carvalho Mestrado em Ecologia e Ambiente Departamento de Biologia 2017 Orientador Olga Maria Oliveira da Silva Lage, Professor auxiliar, Faculdade de Ciências da Universidade do Porto Todas as correções determinadas pelo júri, e só essas, foram efetuadas. O Presidente do Júri, Porto, ______/______/_________ Dissertação para a candidatura ao grau de Mestre em Ecologia e Ambiente submetida à Faculdade de Ciências da Universidade do Porto. O presente trabalho foi desenvolvido sob a orientação científica da Professora Doutora Olga Maria Oliveira da Silva Lage e foi realizado na Faculdade de Ciências da Universidade do Porto. Dissertation to apply for the Master’s Degree in Ecology and Environmental, submitted to the Faculty of Sciences of the University of Porto. The present work was developed under the scientific supervision of Professor Dr. Olga Maria Oliveira da Silva Lage and was conducted at the Faculty of Sciences of the University of Porto. “It is not the strongest of the species that survives, not the most intelligent that survives. It is the one that is the most adaptable to change.” Charles Darwin FCUP I Dealing with Hydrocarbons: from Planctomycetes to microbial community Agradecimentos Gostava de dirigir as minhas primeiras palavras de agradecimento a todos aqueles que me ajudaram em todo o percurso durante a realização deste Tese de Mestrado.