Prokaryotic Community Structure and Activity of Sulfate Reducers in Production Water from High-Temperature Oil Reservoirs with and Without Nitrate Treatment

Total Page:16

File Type:pdf, Size:1020Kb

Prokaryotic Community Structure and Activity of Sulfate Reducers in Production Water from High-Temperature Oil Reservoirs with and Without Nitrate Treatment Prokaryotic community structure and activity of sulfate reducers in production water from high-temperature oil reservoirs with and without nitrate treatment Dr. Antje Gittel Dept. of Biological Sciences, Aarhus University ISMOS 2 Aarhus 2009 Introduction Hypothesis Results Conclusions Offshore oil production systems Separation Oil Gas Water Production Injection ~80 degC 50-60 degC Reservoir ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Characteristics of the study sites Norway Halfdan • Injection of sulfate-rich seawater Denmark • High loads of organic carbon compounds in the reservoir Dan Enrichment of sulfate -reducing prokaryotes Danish Underground Consortium, Maersk Oil (SRP ) that produce H 2S Souring, plugging, biocorrosion, toxicity, ..... • Strategy to control SRP activity at Halfdan: Addition of nitrate to the injection water ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Principles of SRP inhibition by nitrate addition (i) Stimulation of heterothrophic nitrate- reducing bacteria (hNRB ) that hNRB outcompete SRP for electron donors (ii) Activity of nitrate -reducing, sulfide - oxidizing bacteria (NR-SOB ) resulting in SRP NR-SOB a decreasing net production of H2S (iii) Increase in redox potential by the production of nitrite and nitrous oxides and thereby and inhibition of SRP ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Compared to an untreated oil field (Dan), nitrate addition to the injection water at Halfdan stimulates the growth of hNRB and/or NR-SOB , resulting in: 1) A general change in the prokaryotic community composition, i.e. • Presence of competitive hNRB and NR-SOB and/or • Presence of SRP that are able to reduce nitrate instead of sulfate 2) A decrease in SRP abundance and activity and 3) A reduced net sulfide production. ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Quality & Quantity Identity & Abundance 16S rRNA & dsrAB gene analyses ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Novelty MPN, FISH Quality & Quantity Quantitative PCR (Talk by Ketil Sørensen) Identity & Abundance 16S rRNA & dsrAB gene analyses ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Bacterial 16S rRNA genes Dominance of the Firmicutes Dan (- nitrate) Sulfate reducers represented by different genera Deltaproteobacteria Desulfotomaculum spp. Halfdan Nitrate reducers only present at (+ nitrate) Halfdan Epsilonproteobacteria Deferribacterales ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Archaeal 16S rRNA genes Dominance of the Thermococcales Dan (- nitrate) Sulfate reducers Archaeoglobus spp . Lower clone frequency at Halfdan Halfdan Nitrate reducers (+ nitrate) (e.g. Pyrobaculum sp., Aeropyrum sp.) were not detected ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Bacterial and archaeal dsrAB genes Dan (- nitrate) Deltaproteobacteria Desulfotomaculum spp. Archaeoglobus spp . Same phylotypes as detected via Halfdan (+ nitrate) 16S rRNA-based analyses, but more detailed picture Lower clone frequency of Archaeoglobus relatives at Halfdan ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Dan, - nitrate Halfdan, + nitrate Bacteria DIVERSITY Bacteria Archaea Archaea ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Total prokaryotes (Quantification of bacterial and archaeal 16S rRNA gene copies with qPCR) (%) Dan 58 (- nitrate) 4.7 x 10 4 gene copies /mL 42 Halfdan 25 (+ nitrate) 1.1 x 10 6 gene copies /mL 75 Archaeal origin Bacterial origin ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Total sulfate-reducing prokaryotes (Quantification of deltaproteobacterial and archaeal dsrAB gene copies with qPCR) (% dsrAB / 16S rRNA) Dan 14.1 (- nitrate) 0.7 x 10 4 gene copies /mL 0.4 Halfdan 2.9 (+ nitrate) 3.5 x 10 4 gene copies /mL 0.3 Archaeal origin Bacterial origin ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Prokaryotic community structure and diversity Higher absolute abundances of total prokaryotes and SRP, but less diverse communities at the nitrate-treated field Bacterial sulfate reducers were present in low numbers in both systems, but represented by different genera Archaeal sulfate reducers were highly abundant and dominated the sulfate-reducing community, but their relative abundance was lower in the nitrate-treated field Nitrate reducers (almost) exclusively present in the nitrate-treated system and affilated with bacterial hNRB and NR-SOB ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Activity and identity of SRP in enrichment cultures Bacterial sulfate reduction Archaeal sulfate reduction (60 degC, piping) (80 degC, reservoir) ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Activity and identity of SRP in enrichment cultures Bacterial sulfate reduction Archaeal sulfate reduction (60 degC, piping) (80 degC, reservoir) • No activity in any of the samples ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Activity and identity of SRP in enrichment cultures Bacterial sulfate reduction Archaeal sulfate reduction (60 degC, piping) (80 degC, reservoir) • No activity in any of the samples • Only detectable in samples from Dan (- nitrate) • Activity accompanied by an increase in bacterial 16S rRNA and dsrAB gene copy numbers • Enriched organisms were related to either sulfate- or sulfur-reducing organisms (based on 16S rRNA gene analysis) ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Activity and identity of SRP in enrichment cultures Desulfovibrio vulgaris (U16723) Desulfomicrobium norvegicum (AB061532) dsrAB gene Desulfonatronovibrio hydrogenovorans (AF418197) Desulfobacula toluolica (AJ457136) Production water Desulfobacula phenolica (AF551758) Desulfobacter postgatei (AF418198) Enrichments Desulfobacterium autotrophicum (AF418182) Desulfosarcina variabilis (AF191907) Desulfotomaculum geothermicum (AF273029) Desulfo- Hda_dsr92T (FN376502) [3/31] * tomaculum Desulfobacterium anilini (AF482455) geothermicum Desulfotalea arctica (AY626032) Desulfotalea psychrophila LSv54 (NC_006138) Desulfobulbus elongatus (AJ310430) Desulfobulbus propionicus (AF218452) Desulfobulbus rhabdoformis (AJ250473) Dan_dsr25T (FN376469) [2/29] Dan60S_dsr17E (FN376523) [30/30]* Dan60_dsr11E (FN376523) [30/30]* Syntropho- Hda_dsr20T (FN376491) [5/31] * Desulfacinum infernum (AF418194) bacteraceae Thermodesulforhabdus norvegica (AF334597) Desulfovirga adipica (AF334591) Desulfotomaculum halophilum (AY626024) Archaeoglobus fulgidus (M95624) Dan_dsr69 (FN376461) [27/29]* Archaeo- Hda_dsr24 (FN376483) [23/29] * Archaeoglobus profundus (AF071499) globales Thermodesulfovibrio islandicus (AF334599) Thermodesulfovibrio yellowstonii (U58122) 0.10 ISMOS 2, June 2009 Antje Gittel Introduction Hypothesis Results Conclusions Majority of the obtained sequences from both production systems affiliated with thermophilic prokaryotes indigenous communities responsible for sulfide production Potential effects of nitrate addition at Halfdan 1) General community shift including the appearance of putative nitrate reducers (especially hNRB of the Deferribacterales ) 2) Lower relative abundance of archaeal SRP (Archaeoglobus spp .) 3) Lack of detectable SRP activity 4) Stimulation of the total prokaryotic community indicated by higher gene copies of all genes detected Larger biomass studies needed to estimate the potential of plugging and resumption of sulfide ISMOS 2, June 2009 Antje Gittel Acknowledgements Co-authors of this talk Kjeld Ingvorsen Andreas Schramm Ketil Sørensen Torben Lund Skovhus Technicians at the Microbiology Department, Aarhus University Britta Poulsen Trine Søgaard Thomsen Tove Wiegers Jan Larsen (Maersk Oil, Copenhagen) Adam Wieczorek (University of Bayreuth) .... and you for your attention! ISMOS 2, June 2009 Antje Gittel.
Recommended publications
  • Microbial Diversity Under Extreme Euxinia: Mahoney Lake, Canada V
    Geobiology (2012), 10, 223–235 DOI: 10.1111/j.1472-4669.2012.00317.x Microbial diversity under extreme euxinia: Mahoney Lake, Canada V. KLEPAC-CERAJ,1,2 C. A. HAYES,3 W. P. GILHOOLY,4 T. W. LYONS,5 R. KOLTER2 AND A. PEARSON3 1Department of Molecular Genetics, Forsyth Institute, Cambridge, MA, USA 2Department of Microbiology and Molecular Genetics, Harvard Medical School, Boston, MA, USA 3Department of Earth and Planetary Sciences, Harvard University, Cambridge, MA, USA 4Department of Earth and Planetary Sciences, Washington University, Saint Louis, MO, USA 5Department of Earth Sciences, University of California, Riverside, CA, USA ABSTRACT Mahoney Lake, British Columbia, Canada, is a stratified, 15-m deep saline lake with a euxinic (anoxic, sulfidic) hypolimnion. A dense plate of phototrophic purple sulfur bacteria is found at the chemocline, but to date the rest of the Mahoney Lake microbial ecosystem has been underexamined. In particular, the microbial community that resides in the aphotic hypolimnion and ⁄ or in the lake sediments is unknown, and it is unclear whether the sulfate reducers that supply sulfide for phototrophy live only within, or also below, the plate. Here we profiled distribu- tions of 16S rRNA genes using gene clone libraries and PhyloChip microarrays. Both approaches suggest that microbial diversity is greatest in the hypolimnion (8 m) and sediments. Diversity is lowest in the photosynthetic plate (7 m). Shallower depths (5 m, 7 m) are rich in Actinobacteria, Alphaproteobacteria, and Gammaproteo- bacteria, while deeper depths (8 m, sediments) are rich in Crenarchaeota, Natronoanaerobium, and Verrucomi- crobia. The heterogeneous distribution of Deltaproteobacteria and Epsilonproteobacteria between 7 and 8 m is consistent with metabolisms involving sulfur intermediates in the chemocline, but complete sulfate reduction in the hypolimnion.
    [Show full text]
  • Tree Scale: 1 D Bacteria P Desulfobacterota C Jdfr-97 O Jdfr-97 F Jdfr-97 G Jdfr-97 S Jdfr-97 Sp002010915 WGS ID MTPG01
    d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermodesulfobacterium s Thermodesulfobacterium commune WGS ID JQLF01 d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g Thermosulfurimonas s Thermosulfurimonas dismutans WGS ID LWLG01 d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f DG-60 g DG-60 s DG-60 sp001304365 WGS ID LJNA01 ID WGS sp001304365 DG-60 s DG-60 g DG-60 f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Desulfofervidia o Desulfofervidales f Desulfofervidaceae g Desulfofervidus s Desulfofervidus auxilii RS GCF 001577525 1 001577525 GCF RS auxilii Desulfofervidus s Desulfofervidus g Desulfofervidaceae f Desulfofervidales o Desulfofervidia c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfatatoraceae g Thermodesulfatator s Thermodesulfatator atlanticus WGS ID ATXH01 d Bacteria p Desulfobacterota c Desulfobacteria o Desulfatiglandales f NaphS2 g 4484-190-2 s 4484-190-2 sp002050025 WGS ID MVDB01 ID WGS sp002050025 4484-190-2 s 4484-190-2 g NaphS2 f Desulfatiglandales o Desulfobacteria c Desulfobacterota p Bacteria d d Bacteria p Desulfobacterota c Thermodesulfobacteria o Thermodesulfobacteriales f Thermodesulfobacteriaceae g QOAM01 s QOAM01 sp003978075 WGS ID QOAM01 d Bacteria p Desulfobacterota c BSN033 o UBA8473 f UBA8473 g UBA8473 s UBA8473 sp002782605 WGS
    [Show full text]
  • Reclassification of Desulfobacterium Phenolicum As Desulfobacula Phenolica Comb. Nov. and Description of Strain Saxt As Desulfot
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 171–177 Printed in Great Britain Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov., sp. nov. Jan Kuever,1 Martin Ko$ nneke,1 Alexander Galushko2 and Oliver Drzyzga3 Author for correspondence: Jan Kuever. Tel: j49 421 2028 734. Fax: j49 421 2028 580. e-mail: jkuever!mpi-bremen.de 1 Max-Planck-Institute for A mesophilic, sulfate-reducing bacterium (strain SaxT) was isolated from Marine Microbiology, marine coastal sediment in the Baltic Sea and originally described as a Department of Microbiology, ‘Desulfoarculus’ sp. It used a large variety of substrates, ranging from simple Celsiusstrasse 1, D-28359 organic compounds and fatty acids to aromatic compounds as electron donors. Bremen, Germany Autotrophic growth was possible with H2,CO2 and formate in the presence of 2 Fakulta$ tfu$ r Biologie, sulfate. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur Universita$ t Konstanz, and nitrate were not reduced. Fermentative growth was obtained with Postfach 5560, D-78457 Konstanz, Germany pyruvate, but not with fumarate or malate. Substrate oxidation was usually complete leading to CO , but at high substrate concentrations acetate 3 University of Bremen, 2 Center for Environmental accumulated. CO dehydrogenase activity was observed, indicating the Research and Technology operation of the CO dehydrogenase pathway (reverse Wood pathway) for CO2 (UFT), Department of fixation and complete oxidation of acetyl-CoA. The rod-shaped cells were Marine Microbiology, Leobener Strasse, D-28359 08–10 µm wide and 15–25 µm long. Spores were not produced and cells Bremen, Germany stained Gram-negative.
    [Show full text]
  • Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens
    microorganisms Article Core Sulphate-Reducing Microorganisms in Metal-Removing Semi-Passive Biochemical Reactors and the Co-Occurrence of Methanogens Maryam Rezadehbashi and Susan A. Baldwin * Chemical and Biological Engineering, University of British Columbia, 2360 East Mall, Vancouver, BC V6T 1Z3, Canada; [email protected] * Correspondence: [email protected]; Tel.: +1-604-822-1973 Received: 2 January 2018; Accepted: 17 February 2018; Published: 23 February 2018 Abstract: Biochemical reactors (BCRs) based on the stimulation of sulphate-reducing microorganisms (SRM) are emerging semi-passive remediation technologies for treatment of mine-influenced water. Their successful removal of metals and sulphate has been proven at the pilot-scale, but little is known about the types of SRM that grow in these systems and whether they are diverse or restricted to particular phylogenetic or taxonomic groups. A phylogenetic study of four established pilot-scale BCRs on three different mine sites compared the diversity of SRM growing in them. The mine sites were geographically distant from each other, nevertheless the BCRs selected for similar SRM types. Clostridia SRM related to Desulfosporosinus spp. known to be tolerant to high concentrations of copper were members of the core microbial community. Members of the SRM family Desulfobacteraceae were dominant, particularly those related to Desulfatirhabdium butyrativorans. Methanogens were dominant archaea and possibly were present at higher relative abundances than SRM in some BCRs. Both hydrogenotrophic and acetoclastic types were present. There were no strong negative or positive co-occurrence correlations of methanogen and SRM taxa. Knowing which SRM inhabit successfully operating BCRs allows practitioners to target these phylogenetic groups when selecting inoculum for future operations.
    [Show full text]
  • Reclassification of Desulfobacterium Phenolicum As Desulfobacula
    International Journal of Systematic and Evolutionary Microbiology (2001), 51, 171–177 Printed in Great Britain Reclassification of Desulfobacterium phenolicum as Desulfobacula phenolica comb. nov. and description of strain SaxT as Desulfotignum balticum gen. nov., sp. nov. Jan Kuever,1 Martin Ko$ nneke,1 Alexander Galushko2 and Oliver Drzyzga3 Author for correspondence: Jan Kuever. Tel: j49 421 2028 734. Fax: j49 421 2028 580. e-mail: jkuever!mpi-bremen.de 1 Max-Planck-Institute for A mesophilic, sulfate-reducing bacterium (strain SaxT) was isolated from Marine Microbiology, marine coastal sediment in the Baltic Sea and originally described as a Department of Microbiology, ‘Desulfoarculus’ sp. It used a large variety of substrates, ranging from simple Celsiusstrasse 1, D-28359 organic compounds and fatty acids to aromatic compounds as electron donors. Bremen, Germany Autotrophic growth was possible with H2,CO2 and formate in the presence of 2 Fakulta$ tfu$ r Biologie, sulfate. Sulfate, thiosulfate and sulfite were used as electron acceptors. Sulfur Universita$ t Konstanz, and nitrate were not reduced. Fermentative growth was obtained with Postfach 5560, D-78457 Konstanz, Germany pyruvate, but not with fumarate or malate. Substrate oxidation was usually complete leading to CO , but at high substrate concentrations acetate 3 University of Bremen, 2 Center for Environmental accumulated. CO dehydrogenase activity was observed, indicating the Research and Technology operation of the CO dehydrogenase pathway (reverse Wood pathway) for CO2 (UFT), Department of fixation and complete oxidation of acetyl-CoA. The rod-shaped cells were Marine Microbiology, Leobener Strasse, D-28359 08–10 µm wide and 15–25 µm long. Spores were not produced and cells Bremen, Germany stained Gram-negative.
    [Show full text]
  • An Ecological Basis for Dual Genetic Code Expansion in Marine Deltaproteobacteria
    bioRxiv preprint doi: https://doi.org/10.1101/2021.03.15.435355; this version posted March 15, 2021. 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. An ecological basis for dual genetic code expansion in marine deltaproteobacteria 1 Veronika Kivenson1, Blair G. Paul2, David L. Valentine2* 2 1Interdepartmental Graduate Program in Marine Science, University of California, Santa Barbara, CA 3 93106, USA 4 2Department of Earth Science and Marine Science Institute, University of California, Santa Barbara, 5 CA 93106, USA 6 * Correspondence: 7 David L. Valentine 8 [email protected] 9 Present Address 10 VK: Oregon State University, Corvallis, OR 97331 11 BGP: Marine Biological Laboratory, Woods Hole, MA 02543 12 13 Keywords: microbiome, pyrrolysine, selenocysteine, metabolism, metagenomics 14 15 Abstract 16 Marine benthic environments may be shaped by anthropogenic and other localized events, leading to 17 changes in microbial community composition evident decades after a disturbance. Marine sediments 18 in particular harbor exceptional taxonomic diversity and can shed light on distinctive evolutionary 19 strategies. Genetic code expansion may increase the structural and functional diversity of proteins in 20 cells, by repurposing stop codons to encode noncanonical amino acids: pyrrolysine (Pyl) and 21 selenocysteine (Sec). Here, we show that the genomes of abundant Deltaproteobacteria from the 22 sediments of a deep-ocean chemical waste dump site, have undergone genetic code expansion. Pyl 23 and Sec in these organisms appear to augment trimethylamine (TMA) and one-carbon metabolism, 24 representing key drivers of their ecology.
    [Show full text]
  • A First Acetate-Oxidizing, Extremely Salt-Tolerant
    Extremophiles (2015) 19:899–907 DOI 10.1007/s00792-015-0765-y ORIGINAL PAPER Desulfonatronobacter acetoxydans sp. nov.,: a first acetate‑oxidizing, extremely salt‑tolerant alkaliphilic SRB from a hypersaline soda lake D. Y. Sorokin1,2 · N. A. Chernyh1 · M. N. Poroshina3 Received: 6 May 2015 / Accepted: 26 May 2015 / Published online: 18 June 2015 © The Author(s) 2015. This article is published with open access at Springerlink.com Abstract Recent intensive microbiological investigation alkaliphile, growing with butyrate at salinity up to 4 M total of sulfidogenesis in soda lakes did not result in isolation of Na+ with a pH optimum at 9.5. It can grow with sulfate as any pure cultures of sulfate-reducing bacteria (SRB) able to e-acceptor with C3–C9 VFA and also with some alcohols. The directly oxidize acetate. The sulfate-dependent acetate oxida- most interesting property of strain APT3 is its ability to grow tion at haloalkaline conditions has, so far, been only shown in with acetate as e-donor, although not with sulfate, but with two syntrophic associations of novel Syntrophobacteraceae sulfite or thiosulfate as e-acceptors. The new isolate is pro- members and haloalkaliphilic hydrogenotrophic SRB. In the posed as a new species Desulfonatronobacter acetoxydans. course of investigation of one of them, obtained from a hyper- saline soda lake in South-Western Siberia, a minor component Keywords Soda lakes · Haloalkaliphilic · Acetate was observed showing a close relation to Desulfonatrono- oxidation · Sulfate-reducing bacteria (SRB) · bacter acidivorans—a “complete oxidizing” SRB from soda Desulfobacteracea lakes. This organism became dominant in a secondary enrich- ment with propionate as e-donor and sulfate as e-acceptor.
    [Show full text]
  • Mercury Methylation by Metabolically Versatile and Cosmopolitan Marine Bacteria
    bioRxiv preprint doi: https://doi.org/10.1101/2020.06.03.132969; this version posted June 4, 2020. 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 Mercury methylation by metabolically versatile and cosmopolitan marine 2 bacteria 3 4 Heyu Lin1, David B. Ascher2,3, Yoochan Myung2,3, Carl H. Lamborg4, Steven J. 5 Hallam5,6, Caitlin M. Gionfriddo7, Kathryn E. Holt8, 9 and John W. Moreau1,10,* 6 7 1School of Earth Sciences, The University of Melbourne, Parkville, VIC 3010, AUS 8 2Structural Biology and Bioinformatics, Department of Biochemistry and Molecular 9 Biology, Bio21 Molecular Science and Biotechnology Institute, The University of 10 Melbourne, Parkville, VIC 3010, AUS 11 3Computational Biology and Clinical Informatics, Baker Heart and Diabetes Institute, 12 PO Box 6492, Melbourne, VIC 3004, AUS 13 4Department of Ocean Sciences, University of California, Santa Cruz, CA 95064, USA 14 5Department of Microbiology and Immunology, University of British Columbia, 15 Vancouver, BC V6T 1Z1, CA 16 6Genome Science and Technology Program, University of British Columbia, 17 Vancouver, BC V6T 1Z4, CA 18 7Biosciences Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 19 37831, USA 20 8Department of Infectious Diseases, Central Clinical School, Monash University, VIC 21 3800, AUS 22 9Department of Infection Biology, London School of Hygiene & Tropical Medicine, 23 London WC1E 7HT, UK 24 10Currently at School of Geographical & Earth Sciences, University of Glasgow, 25 Glasgow G12 8QQ, UK 26 27 *Corresponding author: [email protected] 28 The authors declare no competing interests.
    [Show full text]
  • Afam D Bacteria P Desulfobacterota C Desulfobacteria O
    CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f Trichloromonadaceae g Deferrimonas s Deferrimonas soudanensis RS GCF 001278055 1 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o DesulfuromonadalesTrichloromonadaceae f g UBA12091 s UBA12091 sp001799485 WGS ID MGTQ01 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f Geopsychrobacteraceae g SLDV01 s SLDV01 sp007125165 WGS ID SKQT01 1 CFam d Bacteria p Desulfobacterota c Desulfobulbia o Desulfobulbales f Desulfurivibrionaceae g Desulfurivibrio s Desulfurivibrio alkaliphilus RS GCF 000092205 1 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f Trichloromonadaceae g ATBO01 s ATBO01 sp000472285 WGS ID ATBO01 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f UBA2294 g BM707 s BM707 sp002869615 WGS ID PKUH01 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f BM103 g VAUL01 s VAUL01 sp005774545 WGS ID VAUL01 1 CFam d Bacteria p DesulfobacterotaCFam d Bacteria D c UBA1144 p Desulfobacterota o UBA2774 c GWC2-55-46 f UBA2774 o g GWC2-55-46 2-12-FULL-53-21 f GWC2-55-46 s 2-12-FULL-53-21 g GWB2-55-19 sp001775255 s GWB2-55-19 WGS sp001797465 ID MFCJ01 WGS 1 ID MGPQ01 1 CFam d Bacteria p Desulfobacterota c MBNT15 o MBNT15 f MBNT15 g CG2-30-66-27 s CG2-30-66-27 sp001873935 WGS ID MNYH01 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Desulfuromonadales f Geopsychrobacteraceae g Seleniibacterium s Seleniibacterium seleniigenes WGS ID JOMG01 1 CFam
    [Show full text]
  • Abatus Agassizii
    fmicb-11-00308 February 27, 2020 Time: 15:33 # 1 ORIGINAL RESEARCH published: 28 February 2020 doi: 10.3389/fmicb.2020.00308 Characterization of the Gut Microbiota of the Antarctic Heart Urchin (Spatangoida) Abatus agassizii Guillaume Schwob1,2*, Léa Cabrol1,3, Elie Poulin1 and Julieta Orlando2* 1 Laboratorio de Ecología Molecular, Instituto de Ecología y Biodiversidad, Facultad de Ciencias, Universidad de Chile, Santiago, Chile, 2 Laboratorio de Ecología Microbiana, Departamento de Ciencias Ecológicas, Facultad de Ciencias, Universidad de Chile, Santiago, Chile, 3 Aix Marseille University, Univ Toulon, CNRS, IRD, Mediterranean Institute of Oceanography (MIO) UM 110, Marseille, France Abatus agassizii is an irregular sea urchin species that inhabits shallow waters of South Georgia and South Shetlands Islands. As a deposit-feeder, A. agassizii nutrition relies on the ingestion of the surrounding sediment in which it lives barely burrowed. Despite the low complexity of its feeding habit, it harbors a long and twice-looped digestive tract suggesting that it may host a complex bacterial community. Here, we characterized the gut microbiota of specimens from two A. agassizii populations at the south of the King George Island in the West Antarctic Peninsula. Using a metabarcoding approach targeting the 16S rRNA gene, we characterized the Abatus microbiota composition Edited by: David William Waite, and putative functional capacity, evaluating its differentiation among the gut content Ministry for Primary Industries, and the gut tissue in comparison with the external sediment. Additionally, we aimed New Zealand to define a core gut microbiota between A. agassizii populations to identify potential Reviewed by: Cecilia Brothers, keystone bacterial taxa.
    [Show full text]
  • Structure and Function of the Tungsten-Containing Active Site of Class II Benzoyl-Coa Reductases
    Structure and function of the tungsten-containing active site of class II benzoyl-CoA reductases Inaugural-Dissertation zur Erlangung der Doktorwürde (Doctor rerum naturalium) Fakultät für Biologie der Albert-Ludwigs-Universität Freiburg im Breisgau (D) vorgelegt von Simona G. Huwiler Freiburg im Breisgau (D), Dezember 2015 This thesis was conducted from November 2010 to November 2011 at the Institute of Biochemistry at Universität Leipzig (D) and from December 2011 to December 2015 at the Institute of Biology II (microbiology) at Albert-Ludwigs-Universität Freiburg i. Br. (D) in the group of Prof. Matthias Boll. Dekan der Fakultät für Biologie: Prof. Dr. Wolfgang Driever Promotionsvorsitzender: Prof. Dr. Stefan Rotter Betreuer der Arbeit: Prof. Dr. Matthias Boll Referent: Prof. Dr. Matthias Boll Koreferent: PD Dr. Ivan Berg Drittprüferin: Prof. Dr. Carola Hunte Datum der mündlichen Prüfung: 31.03.2016 Est autem admiratio desiderium quoddam sciendi, quod in homine contingit ex hoc quod vident effectum et ignorat causam, vel ex hoc quod causa talis effectus excedit cognitionem aut facultatem ipsius. Et ideo admiratio est causa delectationis, inquantum habet adjunctam spem consequendi cognitionem ejus quod scire desiderat. Thomas of Aquin (1225-1274)1 Now ‘wondering’ means ‘wanting to know something’: it is aroused when a man sees an effect and does not know its cause, or when he does not know or cannot understand how this cause could have that effect. Wondering therefore can cause him pleasure when it carries with it a real prospect of finding out what he wants to know.2 1 Summa theologiæ 1a2æ, 32,8 2 of Aquin, T.
    [Show full text]
  • Desulfoconvexum Algidum Gen. Nov., Sp. Nov., a Psychrophilic Sulfate-Reducing Bacterium Isolated from a Permanently Cold Marine Sediment
    International Journal of Systematic and Evolutionary Microbiology (2013), 63, 959–964 DOI 10.1099/ijs.0.043703-0 Desulfoconvexum algidum gen. nov., sp. nov., a psychrophilic sulfate-reducing bacterium isolated from a permanently cold marine sediment Martin Ko¨nneke,13 Jan Kuever,2 Alexander Galushko14 and Bo Barker Jørgensen11 Correspondence 1Max-Planck Institute for Marine Microbiology, Bremen, Germany Martin Ko¨nneke 2Bremen Institute for Materials Testing, Bremen, Germany [email protected] A sulfate-reducing bacterium, designated JHA1T, was isolated from a permanently cold marine sediment sampled in an Artic fjord on the north-west coast of Svalbard. The isolate was originally enriched at 4 6C in a highly diluted liquid culture amended with hydrogen and sulfate. Strain JHA1T was a psychrophile, growing fastest between 14 and 16 6C and not growing above 20 6C. Fastest growth was found at neutral pH (pH 7.2–7.4) and at marine concentrations of NaCl (20– 30 g l”1). Phylogenetic analysis of 16S rRNA gene sequences revealed that strain JHA1T was a member of the family Desulfobacteraceae in the Deltaproteobacteria. The isolate shared 99 % 16S rRNA gene sequence similarity with an environmental sequence obtained from permanently cold Antarctic sediment. The closest recognized relatives were Desulfobacula phenolica DSM 3384T and Desulfobacula toluolica DSM 7467T (both ,95 % sequence similarity). In contrast to its closest phylogenetic relatives, strain JHA1T grew chemolithoautotrophically with hydrogen as an electron donor. CO dehydrogenase activity indicated the operation of the reductive acetyl-CoA pathway for inorganic carbon assimilation. Beside differences in physiology and morphology, strain JHA1T could be distinguished chemotaxonomically from the genus Desulfobacula by the absence of the cellular fatty acid C16 : 0 10-methyl.
    [Show full text]