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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 d Bacteria p DesulfobacterotaCFam d Bacteria c Desulfuromonadia p Desulfobacterota oc GeobacteralesDesulfuromonadia f Geobacteraceae o Geobacterales gf GeobacteraceaeCitrifermentans sg CitrifermentansCitrifermentans ssp000023645 Citrifermentans RS pelophilum GCF 000023645 WGS ID 1BDQG01 2 2 CFam d Bacteria p Desulfobacterota c MBNT15 o J040 f J040 g J040 s J040 sp003696505 WGS ID RFHC01 1 CFam d Bacteria p Desulfobacterota D c UBA1144 o UBA2774 f CSP1-2 g HRBIN37 s HRBIN37 sp002898375 WGS ID BEIN01 1 CFam d Bacteria p Desulfobacterota c Desulfobacteria o Desulfobacterales f Desulfococcaceae g Desulfococcus s Desulfococcus multivorans WGS ID ATHJ01 1 CFam d Bacteria p Desulfobacterota c Desulfobacteria o Desulfobacterales f Desulfobacteraceae g Desulfobacterium B s Desulfobacterium B autotrophicum RS GCF 000020365 1 1 CFam d Bacteria p Desulfobacterota c Desulfuromonadia o Geobacterales f Geobacteraceae g Geotalea s Geotalea daltonii RS GCF 000022265 1 1 CFam d Bacteria p Desulfobacterota c Syntrophia o Syntrophales f UBA6807 g UBA6807 s UBA6807 sp002441265 WGS ID DKFB01 1 CFam d Bacteria p Desulfobacterota c Syntrophia o Syntrophales f UBA4778 g UBA4778 s UBA4778 sp002403175 WGS ID DHHG01 1 CFam d Bacteria p Desulfobacterota c Desulfobacteria o Desulfobacterales f UBA2174 g UBA2174 s UBA2174 sp002327445 WGS ID DCWA01 1 Bfam d Bacteria p Desulfobacterota B c Binatia o HRBIN30 f HRBIN30 g HRBIN30 s HRBIN30 sp002898795 WGS ID BEIG01 1 BEIG01 ID WGS sp002898795 HRBIN30 s HRBIN30 g HRBIN30 f HRBIN30 o Binatia c B Desulfobacterota p Bacteria d Bfam Bfam d Bacteria p Desulfobacterota D c UBA1144 o UBA2774 f CSP1-2 g HRBIN37 s HRBIN37 sp002898375 WGS ID BEIN01 1 BEIN01 ID WGS sp002898375 HRBIN37 s HRBIN37 g CSP1-2 f UBA2774 o UBA1144 c D Desulfobacterota p Bacteria d Bfam Bfam d Bacteria p Desulfobacterota B c Binatia o Binatales f Binataceae g Binatus s Binatus soli WGS ID DLMJ01 1 DLMJ01 ID WGS soli Binatus s Binatus g Binataceae f Binatales o Binatia c B Desulfobacterota p Bacteria d Bfam CFam d Bacteria p Desulfobacterota c Syntrophobacteria o Syntrophobacterales f Syntrophobacteraceae g SLCH01 s SLCH01 sp003566995 WGS ID PXBG01 1 CFam d Bacteria p Desulfobacterota c Syntrophobacteria o Syntrophobacterales f Syntrophobacteraceae g Desulforhabdus s Desulforhabdus sp007244385 WGS ID SCVX01 1 CFam Desulfurivibrio alkaliphilus AHT2 1 CFam d Bacteria p DesulfobacterotaCFam d Bacteria c pDesulfobacteria Desulfobacterota o Desulfobacteralesc Syntrophobacteria f UBA5852 o BM002 fg BM002 UBA5852 g BM002 s UBA5852 s BM002 sp002432195 sp002899795 WGS WGS ID ID DJGG01 PPDG01 1 1 CFam d Bacteria p Desulfobacterota c Desulfobacteria o Desulfatiglandales f HGW-15 g HGW-15 s HGW-15 sp002840535 WGS ID PHBH01 1 CFam d Bacteria p Desulfobacterota c Syntrophorhabdia o Syntrophorhabdales f WCHB1-27 g BOG-1155 s BOG-1155 sp002067405 WGS ID MVRP01 2 Tree scale: 1 CFam Desulfococcus multivorans DSM2059 1 AFam d Bacteria p Desulfobacterota c GWC2-55-46 o GWC2-55-46 f GWC2-55-46 g GWC2-55-46 s GWC2-55-46 sp001595385 WGS ID LVEI03 2 LVEI03 ID WGS sp001595385 GWC2-55-46 s GWC2-55-46 g GWC2-55-46 f GWC2-55-46 o GWC2-55-46 c Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota c GWC2-55-46 o GWC2-55-46 f GWC2-55-46 g UBA5799 s UBA5799 sp002418185 WGS ID DIDN01 1 DIDN01 ID WGS sp002418185 UBA5799 s UBA5799 g GWC2-55-46 f GWC2-55-46 o GWC2-55-46 c Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota c GWC2-55-46 o GWC2-55-46 f UBA9637 g UBA10170 s UBA10170 sp001798165 WGS ID MGRL01 1 MGRL01 ID WGS sp001798165 UBA10170 s UBA10170 g UBA9637 f GWC2-55-46 o GWC2-55-46 c Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota c GWC2-55-46 o GWC2-55-46 f SCQA01 g SCQA01 s SCQA01 sp004298725 WGS ID SCQA01 1 SCQA01 ID WGS sp004298725 SCQA01 s SCQA01 g SCQA01 f GWC2-55-46 o GWC2-55-46 c Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o UBA12015 f UBA12015 g UBA12015 s UBA12015 sp003447545 WGS ID DLYX01 2 DLYX01 ID WGS sp003447545 UBA12015 s UBA12015 g UBA12015 f UBA12015 o Binatia c B Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o UBA9968 f UBA9968 g 2-12-FULL-60-19 s 2-12-FULL-60-19 sp001798595 WGS ID MGSS01 2 MGSS01 ID WGS sp001798595 2-12-FULL-60-19 s 2-12-FULL-60-19 g UBA9968 f UBA9968 o Binatia c B Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o UBA1149 f UBA1149 g UBA1149 s UBA1149 sp002311335 WGS ID DBZX01 1 DBZX01 ID WGS sp002311335 UBA1149 s UBA1149 g UBA1149 f UBA1149 o Binatia c B Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o UBA12015 f UBA12015 g SXLG01 s SXLG01 sp005777805 WGS ID SXLG01 1 SXLG01 ID WGS sp005777805 SXLG01 s SXLG01 g UBA12015 f UBA12015 o Binatia c B Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o HRBIN30 f HRBIN30 g HRBIN30 s HRBIN30 sp002898795 WGS ID BEIG01 3 BEIG01 ID WGS sp002898795 HRBIN30 s HRBIN30 g HRBIN30 f HRBIN30 o Binatia c B Desulfobacterota p Bacteria d AFam AFam d Bacteria p Desulfobacterota B c Binatia o HRBIN30 f HRBIN30 g HRBIN30 s HRBIN30 sp002898795 WGS ID BEIG01 2 BEIG01 ID WGS sp002898795 HRBIN30 s HRBIN30 g HRBIN30 f HRBIN30 o Binatia c B Desulfobacterota p Bacteria d AFam 0.59 0.65 0.89 0.82 1.00 0.90 AFam d Bacteria p Desulfobacterota B c Binatia o Binatales f Binataceae g Binatus s Binatus soli WGS ID DLMJ01 3 DLMJ01 ID WGS soli Binatus s Binatus g Binataceae f Binatales o Binatia c B Desulfobacterota p Bacteria d AFam 1.00 1.00 1.00 1.00 1.00 1.00 1.00 0.70 0.81 0.98 0.86 0.690.89 1.001.00 1.00 1.00 0.99 0.97 0.61 1.00 0.94 AFam d Bacteria p Desulfobacterota B c Binatia o UTPRO1 f UTPRO1 g UTPRO1 s UTPRO1 sp002050235 WGS ID MWST01 2 1.00 1.00 AFam d Bacteria p Desulfobacterota c Desulfobulbia o Desulfobulbales f Desulfocapsaceae g Desulforhopalus s Desulforhopalus sp005116645 WGS ID SWCM01 1 AFam d Bacteria p Desulfobacterota B c Binatia o Binatales f Binataceae g Binatus s Binatus soli WGS ID DLMJ01 1 AFam d Bacteria p Desulfobacterota B c Binatia o UTPRO1 f UTPRO1 g DP-19 s DP-19 sp005879405 WGS ID VBKW01 2 AFamAFam d Bacteria d Bacteria p Desulfobacterota p Desulfobacterota B c Binatia B c Binatia o UTPRO1 o UTPRO1 f DP-6 gf DP-6DP-3 gs DP-3DP-6 sp005888095s DP-6 sp005879795 WGS ID VBKF01WGS ID 1VBKJ01 1 AFam d Bacteria p Desulfobacterota B c Binatia o Bin18 f Bin18 g Bin18 s Bin18 sp002238415 WGS ID MPMI01 1 AFam d Bacteria p Desulfobacterota B c Binatia o UBA9968 f UBA9968 g DP-1 s DP-1 sp005879605 WGS ID VBKE01 1 AFam d Bacteria p Desulfobacterota c Desulfobulbia o Desulfobulbales f Desulfocapsaceae g UBA2775 s UBA2775 sp002352445 WGS ID DEIL01 1 AFam d Bacteria p Desulfobacterota B c Binatia o UBA9968 f UBA9968 g DP-20 s DP-20 sp005879255 WGS ID VBKY01 1 AFamAFam d Bacteria d Bacteria p Desulfobacterota p Desulfobacterota B c BinatiaB c Binatia o UBA9968 o UBA9968 f UBA9968 f UBA9968 g 2-12-FULL-60-19 g UBA9968 s UBA9968s 2-12-FULL-60-19 sp001799045 sp001798595 WGS ID WGSMGRY01 ID MGSS01 1 1 AFam d Bacteria p Desulfobacterota B c Binatia o UBA9968 f UBA9968 g 2-12-FULL-57-22 s 2-12-FULL-57-22 sp001798455 WGS ID MGSQ01 1 AFam d Bacteria p Desulfobacterota c Desulfobulbia o Desulfobulbales f Desulfocapsaceae g SZUA-575 s SZUA-575 sp003249645 WGS ID QKIH01 1 AFam d Bacteria p Desulfobacterota c Desulfobulbia o Desulfobulbales f Desulfocapsaceae g Tol-SR s Tol-SR sp000769715 WGS ID JROS01 1 AFam d Bacteria AFamp Desulfobacterota Desulfopila inferna B c Binatia DSM19738 o Binatales 2 f Binataceae g Binatus s Binatus soli WGS ID DLMJ01 2 AFam dAFam Bacteria d Bacteria p Desulfobacterota p Desulfobacterota c Desulfobulbia c Desulfobacteria o Desulfobulbales o Desulfatiglandales f Desulfocapsaceae f NaphS2 g Desulforhopalus g NaphS2 s NaphS2 s Desulforhopalus sp000179315 sp005116645 WGS ID ADZZ01 WGS ID 1SWCM01 2 AFam d Bacteria p Desulfobacterota c Desulfomonilia o Desulfomonilales f Desulfomonilaceae g Desulfomonile s Desulfomonile tiedjei RS GCF
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  • Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities

    Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities

    Provided for non-commercial research and educational use only. Not for reproduction, distribution or commercial use. This chapter was originally published in the book Advances in Applied Microbiology, Vol 66, published by Elsevier, and the attached copy is provided by Elsevier for the author's benefit and for the benefit of the author's institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who know you, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier's permissions site at: http://www.elsevier.com/locate/permissionusematerial From: Noha Youssef, Mostafa S. Elshahed, and Michael J. McInerney, Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities. In Allen I. Laskin, Sima Sariaslani, and Geoffrey M. Gadd, editors: Advances in Applied Microbiology, Vol 66, Burlington: Academic Press, 2009, pp. 141-251. ISBN: 978-0-12-374788-4 © Copyright 2009 Elsevier Inc. Academic Press. Author's personal copy CHAPTER 6 Microbial Processes in Oil Fields: Culprits, Problems, and Opportunities Noha Youssef, Mostafa S. Elshahed, and Michael J. McInerney1 Contents I. Introduction 142 II. Factors Governing Oil Recovery 144 III. Microbial Ecology of Oil Reservoirs 147 A. Origins of microorganisms recovered from oil reservoirs 147 B. Microorganisms isolated from oil reservoirs 148 C. Culture-independent analysis of microbial communities in oil reservoirs 155 IV.
  • Reclassification of Desulfobacterium Phenolicum As Desulfobacula Phenolica Comb. Nov. and Description of Strain Saxt As Desulfot

    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.
  • Compile.Xlsx

    Compile.Xlsx

    Silva OTU GS1A % PS1B % Taxonomy_Silva_132 otu0001 0 0 2 0.05 Bacteria;Acidobacteria;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un;Acidobacteria_un; otu0002 0 0 1 0.02 Bacteria;Acidobacteria;Acidobacteriia;Solibacterales;Solibacteraceae_(Subgroup_3);PAUC26f; otu0003 49 0.82 5 0.12 Bacteria;Acidobacteria;Aminicenantia;Aminicenantales;Aminicenantales_fa;Aminicenantales_ge; otu0004 1 0.02 7 0.17 Bacteria;Acidobacteria;AT-s3-28;AT-s3-28_or;AT-s3-28_fa;AT-s3-28_ge; otu0005 1 0.02 0 0 Bacteria;Acidobacteria;Blastocatellia_(Subgroup_4);Blastocatellales;Blastocatellaceae;Blastocatella; otu0006 0 0 2 0.05 Bacteria;Acidobacteria;Holophagae;Subgroup_7;Subgroup_7_fa;Subgroup_7_ge; otu0007 1 0.02 0 0 Bacteria;Acidobacteria;ODP1230B23.02;ODP1230B23.02_or;ODP1230B23.02_fa;ODP1230B23.02_ge; otu0008 1 0.02 15 0.36 Bacteria;Acidobacteria;Subgroup_17;Subgroup_17_or;Subgroup_17_fa;Subgroup_17_ge; otu0009 9 0.15 41 0.99 Bacteria;Acidobacteria;Subgroup_21;Subgroup_21_or;Subgroup_21_fa;Subgroup_21_ge; otu0010 5 0.08 50 1.21 Bacteria;Acidobacteria;Subgroup_22;Subgroup_22_or;Subgroup_22_fa;Subgroup_22_ge; otu0011 2 0.03 11 0.27 Bacteria;Acidobacteria;Subgroup_26;Subgroup_26_or;Subgroup_26_fa;Subgroup_26_ge; otu0012 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_5;Subgroup_5_or;Subgroup_5_fa;Subgroup_5_ge; otu0013 1 0.02 13 0.32 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_or;Subgroup_6_fa;Subgroup_6_ge; otu0014 0 0 1 0.02 Bacteria;Acidobacteria;Subgroup_6;Subgroup_6_un;Subgroup_6_un;Subgroup_6_un; otu0015 8 0.13 30 0.73 Bacteria;Acidobacteria;Subgroup_9;Subgroup_9_or;Subgroup_9_fa;Subgroup_9_ge;
  • Polyamine Distribution Profiles Among Some Members Within Delta-And Epsilon-Subclasses of Proteobacteria

    Polyamine Distribution Profiles Among Some Members Within Delta-And Epsilon-Subclasses of Proteobacteria

    Microbiol. Cult. Coll. June. 2004. p. 3 ― 8 Vol. 20, No. 1 Polyamine Distribution Profiles among Some Members within Delta-and Epsilon-Subclasses of Proteobacteria Koei Hamana1）＊, Tomoko Saito1）, Mami Okada1）, and Masaru Niitsu2） 1）Department of Laboratory Sciences, School of Health Sciences, Faculty of Medicine, Gunma University, 39- 15 Showa-machi 3-chome, Maebashi, Gunma 371-8514, Japan 2）Faculty of Pharmaceutical Sciences, Josai University, Keyakidai 1-chome-1, Sakado, Saitama 350-0295, Japan Cellular polyamines of 18 species（13 genera）belonging to the delta and epsilon subclasses of the class Proteobacteria were analyzed by HPLC and GC. In the delta subclass, the four marine myxobacteria（the order Myxococcales）, Enhygromyxa salina, Haliangium ochroceum, Haliangium tepidum and Plesiocystis pacifica contained spermidine. Fe（III）-reducing two Geobacter species and two Pelobacter species belonging to the order Desulfuromonadales con- tained spermidine. Bdellovibrio bacteriovorus was absent in cellular polyamines. Bacteriovorax starrii contained putrescine and spermidine. Bacteriovorax stolpii contained spermidine and homo- spermidine. Spermidine was the major polyamine in the sulfate-reducing delta proteobacteria belonging to the genera Desulfovibrio, Desulfacinum, Desulfobulbus, Desulfococcus and Desulfurella, and some species of them contained cadaverine. Within the epsilon subclass, three Sulfurospirillum species ubiquitously contained spermidine and one of the three contained sper- midine and cadaverine. Thiomicrospora denitrificans contained cadaverine and spermidine as the major polyamine. These data show that cellular polyamine profiles can be used as a chemotaxonomic marker within delta and epsilon subclasses. Key words: polyamine, spermidine, homospermidine, Proteobacteria The class Proteobacteria is a major taxon of the 18, 26）. Fe（Ⅲ）-reducing members belonging to the gen- domain Bacteria and is phylogenetically divided into the era Pelobacter, Geobacter, Desulfuromonas and alpha, beta, gamma, delta and epsilon subclasses.