DOCSLIB.ORG

Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Metagenomes of Native and Electrode-Enriched Microbial Communities from the Soudan Iron Mine Jonathan P Metagenomes of native and electrode-enriched microbial communities from the Soudan Iron Mine Jonathan P. Badalamenti and Daniel R. Bond Department of Microbiology and BioTechnology Institute, University of Minnesota - Twin Cities, Saint Paul, Minnesota, USA Twitter: @JonBadalamenti @wanderingbond Summary Approach - compare metagenomes from native and electrode-enriched deep subsurface microbial communities 30 Despite apparent carbon limitation, anoxic deep subsurface brines at the Soudan ) enriched 2 Underground Iron Mine harbor active microbial communities . To characterize these 20 A/cm µ assemblages, we performed shotgun metagenomics of native and enriched samples. enrich ( harvest cells collect inoculate +0.24 V extract 10 Follwing enrichment on poised electrodes and long read sequencing, we recovered Soudan brine electrode 20° C from DNA biodreactors current electrodes from the metagenome the closed, circular genome of a novel Desulfuromonas sp. 0 0 10 20 30 40 filtrate PacBio RS II Illumina HiSeq with remarkable genomic features that were not fully resolved by short read assem- extract time (d) long reads short reads TFF DNA unenriched bly alone. This organism was essentially absent in unenriched Soudan communities, 0.1 µm retentate assembled metagenomes reconstruct long read return de novo complete genome(s) assembly indicating that electrodes are highly selective for putative metal reducers. Native HGAP assembly community metagenomes suggest that carbon cycling is driven by methyl-C me- IDBA_UD 1 hybrid tabolism, in particular methylotrophic methanogenesis. Our results highlight the 3 µm prefilter assembly N4 binning promising potential for long reads in metagenomic surveys of low-diversity environ- borehole N4 binning read trimming and filtering brine de novo ments. collection bottle assembly IDBA_UD Introduction Results - long reads recover a closed genome from mine enrichements on electrodes ĖŤ'#Ť.4"-Ť 1.-Ť (-#Ť(-Ť-.13'#1-Ť (--#2.3Ť/1.5("#2ŤŤ1#"(+8Ť!!#22( +#Ť/.13+Ť datasets ‘Ca. Desulfuromonas biwabikus DDH964’ into carbon cycling the deep terrestrial biosphere unenriched enriched on electrodes complete genome short read assembled contigs c-type cytochromes mapped reads > 6.5 kbp phage DNA/transposons Ť ĖŤĄĉ ŤĄ7ă㹍 /Ť ++4,(-Ť1#"2 Ť ĖŤĄć ŤĄ7ăĉĂŤ /Ť ++4,(-Ť1#"2 3,924,648 bp circular mapped long read coverage rRNA ĖŤ'#Ť"##/Ť24 241$!#Ť'1 .12Ťlow-complexity microbial communities which drive 3.9 3.8 repeat sequences >500 bp ĖŤĄćĊŤ /Ť!(.Ť+.-%Ť1#"2ŤijĄŤ Ť!#++2ďŤ 0.1 62.23% G+C 3.7 repeat sequences >2,000 bp fundamental biogeochemical cycles, including redox transformations of metals 0.2 3.6 Ť ŤŤŤ5%ĎŤ1#"Ť+#-%3'ŤċďĉăćŤ /Ĵ 3,633 CDS 0.3 genes on + strand ĖŤ1#5(.42ŤăĊŤ1Ť%#-#Ť2415#82Ť.$Ť-.7(!Ť 1(-#2Ť3Ť.4"-Ť2'.6Ť+.6Ť1#+3(5#Ť 4-- 3.5 0.4 genes on − strand imcH Gamma- 54 tRNA cbcL dance of putative metal reducers proteobacteria Delta- 3.4 0.5 proteobacteria ĖŤ+#!31."#2Ť./#13#"Ť3Ťǫ7#"Ť/.3#-3(+Ť#+(,(-3#Ť"(2"5-3%#2Ť.$Ť#-1(!'(-%Ť,#3+Ť Firmicutes 3.3 0.6 Alpha- reducers on insoluble metal oxides as electron acceptors, such as variability in DBIWA_3010 0.7 proteobacteria DBIWA_3009 crystallinity, redox potential, and adsorption of other compounds Unclassified DBIWA_3008 Bacteria Alphaproteobacteria 0.8 ĖŤ'.13Ť1#"Ť22#, +8Ĭ 2#"Ť2'.3%4-Ť,#3%#-.,(!2Ť!!#22#2Ť#5#-Ť+.6Ť 4-"-!#Ť Euryarchaeota Gammaproteobacteria DBIWA_3000 microbes in natural communities, but at the expense of assembly contiguity other other 0.9 3.2 ĖŤThere is tremendous potential for long reads in improving metagenomic assem- 1 Mb blies and downstream phylogenetic, bioinformatic, and biochemical predic- assembly comparison - electrode enrichment 2500 250 3.1 18 IDBA_UD PacBio subread filtering hgcAB 1.1 tions SPAdes hybrid 15 2000 200 SPAdes with 3 Mb 1.2 (Mbp) Illumina only 12 1500 150 Soudan Underground Iron Mine 2.9 9 1.3 1000 100 rRNA 2 rRNA 1 6 PBcR # of subreads ĖŤ4--#+2Ť!15#"Ť3Ťċ㹍,Ť"#/3'Ť(-Ť (--#2.3ġ2Ť.+"#23Ť-"Ť"##/#23Ť4-"#1%1.4-"Ť 2.8 1.4 500 50 lengthMbp > read CRISPR1 CRISPR2 mine transect massive veins of hematite embedded in an Archaean (2.7 Gya) lengthcumulative 3 2.7 1.5 banded iron formation 0 800 1600 2400 3200 4000 10 20 30 1.6 2.6 ĖŤ-.7(!Ť!+!(4,Ť!'+.1("#Ť 1(-#2Ť2##/Ť$1.,Ť#7/+.13.18Ť"1(++Ť'.+#2Ť(-Ť-Ť.3'#16(2#Ť contigs read length (kbp) 1.7 2.5 dry mine 1.8 2.4 Int’l Falls 1.9 ONT A R I O adding PacBio long reads improves metagenomic assembly CANADA M 2.3 I 2.2 2 Mb ĖŤ#2/(3#Ť!1 .-Ť+(,(33(.-ďŤ 1(-#2Ť1#Ť1(!'Ť(-Ť N long reads 2.1 N genome features E +8 short reads only short and long reads S O only reduced metals, suggesting active microbial T glyoxlyate shunt Bemidji A I O R E R U P S K E UNITED STATES L A IDBA_UD SPAdes SPAdes hybrid PBcR hybrid HGAP nitrate respiration malate synthase aceB isoctrate lyase icl metabolism 40 km Duluth contigs 2820 3816 3338 581 132 degradation of aromatics DBIWA_3278 DBIWA_3279 ĖŤSoudan is actively maintained as a Minne- total length 16,849,449 15,149,004 15,417,681 5,660,852 4,451,391 phosphonate transport 3536800 3538400 3540000 sota state park, allowing year-round N50 38,339 16,604 25,567 58,773 3,932,815 evidence for conjugative mobule element transfer (tra genes) and chromosomal integration L 107 187 80 27 1 access to the deep terrestrial biosphere 50 heavy metal resistance; mercury resistance and methylation Results - native Soudan metagenomes datasets inner rings novel lineages natural, unenriched Soudan Mine communities Firmicutes Alphaproteobacteria Class level Ť ĖŤĄć ŤĄ7ă㹍 /Ť ++4,(-Ť1#"2Ť/#1Ť .1#'.+# Bacteroidetes Gammaproteobacteria Order level Genome Comparison of Metal-Reducing Deltaproteobacteria Ť ĖŤ22#, +#"Ť6(3'Ť į Euryarchaeota Deltaproteobacteria Family level Ť ĖŤ Ť1#!.-2314!3(.-Ť.$Ť$4++Ĭ+#-%3'ŤăĊŤ1Ť%#-#2 38 unclassified Geopsychrobacter electrodophilus 24 Ť ĖŤ Ť3#31-4!+#.3("#Ť (--(-% Desulfuromusa kysingii outgroup-rooted tree based on Proteobacteria alignment of concatenated set Methanolobus unclassified of 40 conserved single-copy unclassified Clostridiales Rhodobacterales Methanolobus unclassified Dehalobacter Dehalobacter 22 6 genes generated using Phylosift Rhodobacteraceae Methanolobus Desulfuromonas thiophila Desulfosporosinus 31 (v. 1.0.1) unclassified Halocella 49 Rhodobacteraceae unclassified Roseovarius Sphaerochaeta Halocella Desulfuromonas acetoxidans Geobacter Clostridiales unclassified Pelobacter seleniigenes Rhodovulum Clostridiales 28 Rhodovulum 51 Geoalkalibacter subterraneus Red1 Pelobacter carbinolicus Desulfuromonas subbituminosa DDH DDH DDH Marinobacter 41 Geoalkalibacter ferrihydriticus Z-0531 ‘Ca. #24+$41.,.-2Ť (6 (*42ŤčĊćġ 932 944 951 unclassified ‘Ca.Ť#24+$41.,.-2Ť2.4"-#-2(2Ť ġ34 Halothiobacillus Desulfuromonas sp. TF Halothiobacillus Peptococcaceae Desulfuvibrio vulgaris Hildenborough unclassified unclassified Desulfopila 0.08 Desulfitibacter Demequina 61 Geobacter daltonii FRC-32 Alteromonadales Proteobacteria 2 multiheme* c-type Dehalobacter Pelobacter propionicus 86 Demequina unclassified Geobacter lovleyi cytochrome count Marinobacter Halanaerobium Bacteroidales 42 unclassified unclassified unclassified 86 Geobacter uraniireducens Rf4 Geobacter argillaceus Marinobacter *3 or more heme- Halanaerobiaceae Bacteroidales Peptococcaceae Geobacter sp. OR-1 Halocella 55 binding motifs GeobacterGeobacter sp. GSS01 sulfurreducens PCA unclassified Geobacter bemidjiensis 65 Geobacter metallireducens shallower/ deeper/ Peptococcaceae samples collected along redox gradient more oxidized more reduced Geobacter bremensis 58 58 pan- and core genome analysis of avail- Geobacter sp. M21 70 Geobacter sp. M18 able Geobacter/Desulfuromonas clade 76 genomes, with cytochrome plots re- 68 71 ported using default clustering param- Conclusions Acknowledgments Geobacter pickeringii G13 eters in get_homologues (3-6-2015 re- 58 59 lease) ĖŤ'.3%4-Ť,#3%#-.,(!2Ť.$Ť.4"-Ť!.,,4-(3(#2Ť1#5#+#"Ť-.5#+Ť1"#1ĬŤ-"Ť We thank the Minnesota Supercomputing Institute (MSI) for developing, implementing, and main- ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● taining the PacBio SMRT Analysis suite, and the Marine Biological Laboratory (MBL) for Illumina se- ● ● ● ● ● ● ● ● ● 4000 Family-level lineages, particularly among Firmicutes pangenome ● core genome ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● quencing under a seed grant from the Deep Carbon Observatory Census of Deep Life. Long read data all genes ● ● ● ● all genes ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 60 ● ● ● ● ● ● ● ĖŤ +(%3#+8Ť,#3'8+.31./'(!ŤMethanolobus was the only Archaeon observed in ● ● ● ● 12000 ● ● ● ● ● ● ● ● ● ● ● ● ● ● was generously provided by Pacific Biosciences and we thank Karl Oles (Mayo Clinic Bioinformatics ● ● ● ● ● ● ● ● ● ● ● 3000 ● ● ● ● ● ● multiheme* ● ● ● ● ● unenriched metagenomes, suggesting active methyl-C metabolism in situ ● ● ● ● 1 ● ● ● ● ● ● ● ● Core) for sample preparation. We also thank Chris O’Brien (Pall Life Sciences) for guidance with TFF ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● c-type ● ● ● ● ● ● ● 30 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 100 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● cytochromes ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● -"Ť.4"-Ť1*Ť -%#1Ť (,Ť22(%Ť$.1Ť!..1"(-3(-%Ťǫ#+"Ť2,/+(-%ĎŤ'(2Ť6.1*Ť62Ť24//.13#"Ť 8Ť3'#Ť ● ● ● ĖŤ.(2#"Ť#+#!31."#2Ť#Ǫ#!3(5#+8Ť#-1(!'Ť-.5#+Ť,#3+Ĭ1#"4!(-%Ť !3#1(Ť$1.,Ť#-5(- ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 8000 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● 2000 ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● clusters gene ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ● ●
Load more

Recommended publications
  • The 2014 Golden Gate National Parks Bioblitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event
    National Park Service U.S. Department of the Interior Natural Resource Stewardship and Science The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 ON THIS PAGE Photograph of BioBlitz participants conducting data entry into iNaturalist. Photograph courtesy of the National Park Service. ON THE COVER Photograph of BioBlitz participants collecting aquatic species data in the Presidio of San Francisco. Photograph courtesy of National Park Service. The 2014 Golden Gate National Parks BioBlitz - Data Management and the Event Species List Achieving a Quality Dataset from a Large Scale Event Natural Resource Report NPS/GOGA/NRR—2016/1147 Elizabeth Edson1, Michelle O’Herron1, Alison Forrestel2, Daniel George3 1Golden Gate Parks Conservancy Building 201 Fort Mason San Francisco, CA 94129 2National Park Service. Golden Gate National Recreation Area Fort Cronkhite, Bldg. 1061 Sausalito, CA 94965 3National Park Service. San Francisco Bay Area Network Inventory & Monitoring Program Manager Fort Cronkhite, Bldg. 1063 Sausalito, CA 94965 March 2016 U.S. Department of the Interior National Park Service Natural Resource Stewardship and Science Fort Collins, Colorado The National Park Service, Natural Resource Stewardship and Science office in Fort Collins, Colorado, publishes a range of reports that address natural resource topics. These reports are of interest and applicability to a broad audience in the National Park Service and others in natural resource management, including scientists, conservation and environmental constituencies, and the public. The Natural Resource Report Series is used to disseminate comprehensive information and analysis about natural resources and related topics concerning lands managed by the National Park Service.
    [Show full text]
  • Regeneration of Unconventional Natural Gas by Methanogens Co
    www.nature.com/scientificreports OPEN Regeneration of unconventional natural gas by methanogens co‑existing with sulfate‑reducing prokaryotes in deep shale wells in China Yimeng Zhang1,2,3, Zhisheng Yu1*, Yiming Zhang4 & Hongxun Zhang1 Biogenic methane in shallow shale reservoirs has been proven to contribute to economic recovery of unconventional natural gas. However, whether the microbes inhabiting the deeper shale reservoirs at an average depth of 4.1 km and even co-occurring with sulfate-reducing prokaryote (SRP) have the potential to produce biomethane is still unclear. Stable isotopic technique with culture‑dependent and independent approaches were employed to investigate the microbial and functional diversity related to methanogenic pathways and explore the relationship between SRP and methanogens in the shales in the Sichuan Basin, China. Although stable isotopic ratios of the gas implied a thermogenic origin for methane, the decreased trend of stable carbon and hydrogen isotope value provided clues for increasing microbial activities along with sustained gas production in these wells. These deep shale-gas wells harbored high abundance of methanogens (17.2%) with ability of utilizing various substrates for methanogenesis, which co-existed with SRP (6.7%). All genes required for performing methylotrophic, hydrogenotrophic and acetoclastic methanogenesis were present. Methane production experiments of produced water, with and without additional available substrates for methanogens, further confrmed biomethane production via all three methanogenic pathways. Statistical analysis and incubation tests revealed the partnership between SRP and methanogens under in situ sulfate concentration (~ 9 mg/L). These results suggest that biomethane could be produced with more fexible stimulation strategies for unconventional natural gas recovery even at the higher depths and at the presence of SRP.
    [Show full text]
  • Actes Congrès MICROBIOD 1
    Actes du congrès international "Biotechnologie microbienne au service du développement" (MICROBIOD) Marrakech, MAROC 02-05 Novembre 2009 "Ce travail est publié avec le soutien du Ministère de l'Education Nationale, de l'Enseignement Supérieur, de la Formation des Cadres et de la Recherche Scientifique et du CNRST". MICROBIONA Edition www.ucam.ac.ma/microbiona 1 1 Mot du Comité d'organisation Cher (e) membre de MICROBIONA Cher(e) Participant(e), Sous le Haut Patronage de sa Majesté le Roi Mohammed VI, l'Association MICROBIONA et la Faculté des Sciences Semlalia, Université Cadi Ayyad, organisent du 02 au 05 Novembre 2009, en collaboration avec la Société Française de Microbiologie, le Pôle de Compétences Eau et Environnement et l'Incubateur Universitaire de Marrakech, le congrès international "Biotechnologie microbienne au service du développement" (MICROBIOD). Cette manifestation scientifique spécialisée permettra la rencontre de chercheurs de renommée internationale dans le domaine de la biotechnologie microbienne. Le congrès MICROBIOD est une opportunité pour les participants de mettre en relief l’importance socio-économique et environnementale de la valorisation et l’application de nouvelles techniques de biotechnologie microbienne dans divers domaines appliquées au développement et la gestion durable des ressources, à savoir l’agriculture, l'alimentation, l'environnement, la santé, l’industrie agro-alimentaire et le traitement et recyclage des eaux et des déchets par voie microbienne. Ce congrès sera également l’occasion pour les enseignants-chercheurs et les étudiants-chercheurs marocains d’actualiser leurs connaissances dans le domaine des biotechnologies microbiennes, qui serviront à l’amélioration de leurs recherches et enseignements. Le congrès MICROBIOD sera également l’occasion pour certains de nos collaborateurs étrangers de contribuer de près à la formation de nos étudiants en biotechnologie microbienne et ceci par la discussion des protocoles de travail, des méthodes d’analyse et des résultats obtenus.
    [Show full text]
  • Constraint-Based Modeling Analysis of the Metabolism of Two Pelobacter Species Jun Sun1*, Shelley a Haveman2,3, Olivia Bui1, Tom R Fahland1,4, Derek R Lovley2
    Sun et al. BMC Systems Biology 2010, 4:174 http://www.biomedcentral.com/1752-0509/4/174 RESEARCH ARTICLE Open Access Constraint-based modeling analysis of the metabolism of two Pelobacter species Jun Sun1*, Shelley A Haveman2,3, Olivia Bui1, Tom R Fahland1,4, Derek R Lovley2 Abstract Background: Pelobacter species are commonly found in a number of subsurface environments, and are unique members of the Geobacteraceae family. They are phylogenetically intertwined with both Geobacter and Desulfuromonas species. Pelobacter species likely play important roles in the fermentative degradation of unusual organic matters and syntrophic metabolism in the natural environments, and are of interest for applications in bioremediation and microbial fuel cells. Results: In order to better understand the physiology of Pelobacter species, genome-scale metabolic models for Pelobacter carbinolicus and Pelobacter propionicus were developed. Model development was greatly aided by the availability of models of the closely related Geobacter sulfurreducens and G. metallireducens. The reconstructed P. carbinolicus model contains 741 genes and 708 reactions, whereas the reconstructed P. propionicus model contains 661 genes and 650 reactions. A total of 470 reactions are shared among the two Pelobacter models and the two Geobacter models. The different reactions between the Pelobacter and Geobacter models reflect some unique metabolic capabilities such as fermentative growth for both Pelobacter species. The reconstructed Pelobacter models were validated by simulating published growth conditions including fermentations, hydrogen production in syntrophic co-culture conditions, hydrogen utilization, and Fe(III) reduction. Simulation results matched well with experimental data and indicated the accuracy of the models. Conclusions: We have developed genome-scale metabolic models of P.
    [Show full text]
  • The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment
    life Article The Eastern Nebraska Salt Marsh Microbiome Is Well Adapted to an Alkaline and Extreme Saline Environment Sierra R. Athen, Shivangi Dubey and John A. Kyndt * College of Science and Technology, Bellevue University, Bellevue, NE 68005, USA; [email protected] (S.R.A.); [email protected] (S.D.) * Correspondence: [email protected] Abstract: The Eastern Nebraska Salt Marshes contain a unique, alkaline, and saline wetland area that is a remnant of prehistoric oceans that once covered this area. The microbial composition of these salt marshes, identified by metagenomic sequencing, appears to be different from well-studied coastal salt marshes as it contains bacterial genera that have only been found in cold-adapted, alkaline, saline environments. For example, Rubribacterium was only isolated before from an Eastern Siberian soda lake, but appears to be one of the most abundant bacteria present at the time of sampling of the Eastern Nebraska Salt Marshes. Further enrichment, followed by genome sequencing and metagenomic binning, revealed the presence of several halophilic, alkalophilic bacteria that play important roles in sulfur and carbon cycling, as well as in nitrogen fixation within this ecosystem. Photosynthetic sulfur bacteria, belonging to Prosthecochloris and Marichromatium, and chemotrophic sulfur bacteria of the genera Sulfurimonas, Arcobacter, and Thiomicrospira produce valuable oxidized sulfur compounds for algal and plant growth, while alkaliphilic, sulfur-reducing bacteria belonging to Sulfurospirillum help balance the sulfur cycle. This metagenome-based study provides a baseline to understand the complex, but balanced, syntrophic microbial interactions that occur in this unique Citation: Athen, S.R.; Dubey, S.; inland salt marsh environment.
    [Show full text]
  • Uneven Distribution of Cobamide Biosynthesis and Dependence in Bacteria Predicted by Comparative Genomics
    The ISME Journal (2018) 13:789–804 https://doi.org/10.1038/s41396-018-0304-9 ARTICLE Uneven distribution of cobamide biosynthesis and dependence in bacteria predicted by comparative genomics 1 1 1 1,2 3,4 3 Amanda N. Shelton ● Erica C. Seth ● Kenny C. Mok ● Andrew W. Han ● Samantha N. Jackson ● David R. Haft ● Michiko E. Taga1 Received: 7 June 2018 / Revised: 14 September 2018 / Accepted: 4 October 2018 / Published online: 14 November 2018 © The Author(s) 2018. This article is published with open access Abstract The vitamin B12 family of cofactors known as cobamides are essential for a variety of microbial metabolisms. We used comparative genomics of 11,000 bacterial species to analyze the extent and distribution of cobamide production and use across bacteria. We find that 86% of bacteria in this data set have at least one of 15 cobamide-dependent enzyme families, but only 37% are predicted to synthesize cobamides de novo. The distribution of cobamide biosynthesis and use vary at the phylum level. While 57% of Actinobacteria are predicted to biosynthesize cobamides, only 0.6% of Bacteroidetes have the complete pathway, yet 96% of species in this phylum have cobamide-dependent enzymes. The form of cobamide produced 1234567890();,: 1234567890();,: by the bacteria could be predicted for 58% of cobamide-producing species, based on the presence of signature lower ligand biosynthesis and attachment genes. Our predictions also revealed that 17% of bacteria have partial biosynthetic pathways, yet have the potential to salvage cobamide precursors. Bacteria with a partial cobamide biosynthesis pathway include those in a newly defined, experimentally verified category of bacteria lacking the first step in the biosynthesis pathway.
    [Show full text]
  • Synchronized Dynamics of Bacterial Nichespecific Functions During
    Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool Item Type Article Authors Zhang, Weipeng; Wang, Yong; Bougouffa, Salim; Tian, Renmao; Cao, Huiluo; Li, Yongxin; Cai, Lin; Wong, Yue Him; Zhang, Gen; Zhou, Guowei; Zhang, Xixiang; Bajic, Vladimir B.; Al-Suwailem, Abdulaziz M.; Qian, Pei-Yuan Citation Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool 2015:n/a Environmental Microbiology Eprint version Post-print DOI 10.1111/1462-2920.12978 Publisher Wiley Journal Environmental Microbiology Rights This is the peer reviewed version of the following article: Zhang, Weipeng, Yong Wang, Salim Bougouffa, Renmao Tian, Huiluo Cao, Yongxin Li, Lin Cai et al. "Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool." Environmental microbiology (2015)., which has been published in final form at http:// doi.wiley.com/10.1111/1462-2920.12978. This article may be used for non-commercial purposes in accordance With Wiley Terms and Conditions for self-archiving. Download date 25/09/2021 02:54:27 Link to Item http://hdl.handle.net/10754/561085 Synchronized dynamics of bacterial niche-specific functions during biofilm development in a cold seep brine pool1 Weipeng Zhang1, Yong Wang2, Salim Bougouffa3, Renmao Tian1, Huiluo Cao1, Yongxin Li1 Lin Cai1, Yue Him Wong1, Gen Zhang1, Guowei Zhou1, Xixiang Zhang3, Vladimir B Bajic3, Abdulaziz Al-Suwailem3, Pei-Yuan Qian1,2# 1KAUST Global
    [Show full text]
  • 1 Characterization of Sulfur Metabolizing Microbes in a Cold Saline Microbial Mat of the Canadian High Arctic Raven Comery Mast
    Characterization of sulfur metabolizing microbes in a cold saline microbial mat of the Canadian High Arctic Raven Comery Master of Science Department of Natural Resource Sciences Unit: Microbiology McGill University, Montreal July 2015 A thesis submitted to McGill University in partial fulfillment of the requirements of the degree of Master in Science © Raven Comery 2015 1 Abstract/Résumé The Gypsum Hill (GH) spring system is located on Axel Heiberg Island of the High Arctic, perennially discharging cold hypersaline water rich in sulfur compounds. Microbial mats are found adjacent to channels of the GH springs. This thesis is the first detailed analysis of the Gypsum Hill spring microbial mats and their microbial diversity. Physicochemical analyses of the water saturating the GH spring microbial mat show that in summer it is cold (9°C), hypersaline (5.6%), and contains sulfide (0-10 ppm) and thiosulfate (>50 ppm). Pyrosequencing analyses were carried out on both 16S rRNA transcripts (i.e. cDNA) and genes (i.e. DNA) to investigate the mat’s community composition, diversity, and putatively active members. In order to investigate the sulfate reducing community in detail, the sulfite reductase gene and its transcript were also sequenced. Finally, enrichment cultures for sulfate/sulfur reducing bacteria were set up and monitored for sulfide production at cold temperatures. Overall, sulfur metabolism was found to be an important component of the GH microbial mat system, particularly the active fraction, as 49% of DNA and 77% of cDNA from bacterial 16S rRNA gene libraries were classified as taxa capable of the reduction or oxidation of sulfur compounds.
    [Show full text]
  • Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol
    Journal of Water and Environment Technology, Vol.13, No.2, 2015 Development of UASB-DHS System for Treating Industrial Wastewater Containing Ethylene Glycol Takahiro WATARI 1), Daisuke TANIKAWA2), Kyohei KURODA1), Akinobu NAKAMURA1), Nanako FUJII3), Fuminori YONEYAMA3), Osamu WAKISAKA3), Masashi HATAMOTO1), Takashi YAMAGUCHI 1) 1) Department of Environmental Systems Engineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan 2) Department of Civil and Environmental Engineering, National Institute of Technology, Kure College, 2-1-11 Agaminami, Kure, Hiroshima 737-8506, Japan 3) Fundamental Material Laboratory Office, Material Technology Research and Development Laboratory, Research and Development Headquarters, Sumitomo Riko Company Limited, 3-1 Higashi, Komaki, Aichi 485-8550, Japan ABSTRACT This study evaluated the performance of a novel treatment system consisting of an upflow anaerobic sludge blanket (UASB) and a downflow hanging sponge (DHS) for the treatment of industrial wastewater containing 8% ethylene glycol and 2% propylene glycol discharged from a rubber production unit. The system achieved high COD removal (91 ± 4.3%) and methane recovery (82 ± 20%) at an organic loading rate of 8.5 kg-COD/(m3·day). The UASB allowed an organic loading rate of 14 kg-COD/(m3·day) with a constant hydraulic retention time of 24 h. The COD of DHS effluent was 370 ± 250 mg-COD/L during the entire experimental period. Thus, the proposed system could be applicable for treating industrial wastewater containing ethylene glycol. Massively parallel 16S rRNA gene sequencing elucidated the microbial community structure of the UASB. The dominant family Pelobacteriaceae could mainly degrade the organic compounds of ethylene glycol and decomposed products of ethanol.
    [Show full text]
  • Electron Transfer Through the Outer Membrane of Geobacter Sulfurreducens a DISSERTATION SUBMITTED to the FACULTY of the UNIVE
    Electron transfer through the outer membrane of Geobacter sulfurreducens A DISSERTATION SUBMITTED TO THE FACULTY OF THE UNIVERSITY OF MINNESOTA BY Fernanda Jiménez Otero IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR IN PHILOSOPHY Dr. Daniel R. Bond May, 2018 Fernanda Jiménez Otero, 2018, © Acknowledgements This dissertation and the degree I have gained with it, would not have been possible without the help and support from an invaluable group of people. The training I received from Chi Ho Chan and Caleb Levar continues to be essential in the way I approach scientific endeavors. The quality of genetic studies and rigor in microbiology techniques they taught me is a standard I hope to meet throughout my career. Daniel Bond has been much more than I ever expected from an advisor. I have not only gained scientific knowledge from him, but I will take with me the example of what a great mentor represents. His enthusiasm for science is only rivaled by his commitment to past and present members of his laboratory. I am extremely honored to be able to count myself in that group, and I will do my best to represent him proudly in future endeavors. Throughout these five years, Jeff Gralnick has given me numerous opportunities to explore all aspects of a scientific career. Not only is Chapter 2 a result of his vision, but I feel less intimidated by a career in science as a result of his mentoring and support. The faculty members in my committee- Carrie Wilmot, Brandy Toner, and Larry Wackett, have made sure I am well prepared for i every step through graduate school.
    [Show full text]
  • The Genus Pelobacter
    s Genu Pelobacter The Genus Pelobacter BERNHARD SCHINK The genus Pelobacter was proposed as a taxonomic entity Viable counts using the characteristic substrates consisting of strictly anaerobic, Gram-negative, nonspore- gallic acid, acetoin, polyethylene glycol, and forming, rod-shaped bacteria that use only a very limited acetylene showed that there were approximately number of substrates. The members of the genus are all 100 cells/ml of each of the Pelobacter species in unable to ferment sugars and therefore cannot be grouped sediment and up to 2,500 cells/ml in sewage with any other genus in the family Bacteroidaceae (Krieg and Holt, 1984). The genus comprises five different species, P. sludge. Since their substrate ranges are compa- acidigallici (Schink and Pfennig, 1982), P. venetianus (Schink rably small, their ecological niche in such sedi- and Sti eb, 1983), P. carbinolicus (Schink, 1984), P. propioni- ments can be understood rather well in most cus (Schink, 1984), and P. acetylenicus (Schink, 1985), which cases. P. acidigallici is restricted to the utilization all are based on 3–5 described strains. of trihydroxybenzenoids, which are probably its Comparisons of the various Pelobacter species by DNA- only energy source in its natural habitat. P. vene- DNA hybridization experiments revealed that the genus is tianus, P. carbinolicus, P. propionicus, and P. rather inhomogenous; therefore, a reorganization may per- acetylenicus were enriched and isolated with haps be necessary in the future (J. P. Touzel and B. Schink, polyethylene glycol, 2,3-butanediol, and acety- unpublished observations). Whereas the species P. vene- lene, respectively, but the ecological importance tianus, P.
    [Show full text]
  • Fermentation of Acetylene by an Obligate Anaerobe, Pelobacter Acetylenicus Sp
    Archives of Arch Microbiol (1985) 142: 295- 301 Microbiology Springer-Verlag 1985 Fermentation of acetylene by an obligate anaerobe, Pelobacter acetylenicus sp. nov. * Bernhard Schink Fakult/it ffir Biologie, Universit/it Konstanz, Postfach 5560, D-7750 Konstanz, Federal Republic of Germany Abstract. Four strains of strictly anaerobic Gram-negative tion reactions (Schink 1985a). No significant anaerobic rod-shaped non-sporeforming bacteria were enriched and degradation could be observed with ethylene (ethene), the isolated from marine and freshwater sediments with acety- most simple unsaturated hydrocarbon (Schink 1985 a, b). lene (ethine) as sole source of carbon and energy. Acetylene, It was reported recently that also acetylene can be metab- acetoin, ethanolamine, choline, 1,2-propanediol, and glyc- olized in the absence of molecular oxygen (Watanabe and erol were the only substrates utilized for growth, the latter de Guzman 1980). Enrichment cultures with acetylene as two only in the presence of small amounts of acetate. Sub- sole carbon source were obtained in mineral media with strates were fermented by disproportionation to acetate and sulfate as electron acceptor, and acetate could be identified ethanol or the respective higher acids and alcohols. No as an intermediary metabolite (Culbertson et al. 1981). How- cytochromes were detectable; the guanine plus cytosine ever, these enrichment cultures were difficult to maintain, content of the DNA was 57.1 _+ 0.2 tool%. Alcohol dehy- and the acetylene-degrading bacteria could not be identified drogenase, aldehyde dehydrogenase, phosphate acetyl- (C. W. Culbertson and R. S. Oremland, Abstr. 3rd Int. transferase, and acetate kinase were found in high activities Syrup.
    [Show full text]