Afam D Bacteria P Desulfobacterota C Desulfobacteria O

Total Page:16

File Type:pdf, Size:1020Kb

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 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
Recommended publications
  • Table 1. Overview of Reactions Examined in This Study. ΔG Values Were Obtained from Thauer Et Al., 1977
    Supplemental Information: Table 1. Overview of reactions examined in this study. ΔG values were obtained from Thauer et al., 1977. No. Equation ∆G°' (kJ/reaction)* Acetogenic reactions – – – + 1 Propionate + 3 H2O → Acetate + HCO3 + 3 H2 + H +76.1 Sulfate-reducing reactions – 2– – – – + 2 Propionate + 0.75 SO4 → Acetate + 0.75 HS + HCO3 + 0.25 H –37.8 2– + – 3 4 H2 + SO4 + H → HS + 4 H2O –151.9 – 2– – – 4 Acetate + SO4 → 2 HCO3 + HS –47.6 Methanogenic reactions – – + 5 4 H2 + HCO3 + H → CH4 + 3 H2O –135.6 – – 6 Acetate + H2O → CH4 + HCO3 –31.0 Syntrophic propionate conversion – – – + 1+5 Propionate + 0.75 H2O → Acetate + 0.75 CH4 + 0.25 HCO3 + 0.25 H –25.6 Complete propionate conversion by SRB – 2– – – + 2+4 Propionate + 1.75 SO4 → 1.75 HS + 3 HCO3 + 0.25 H –85.4 Complete propionate conversion by syntrophs and methanogens 1+5+6 Propionate– + 1.75 H O → 1.75 CH + 1.25 HCO – + 0.25 H+ –56.6 2 4 3 1 Table S2. Overview of all enrichment slurries fed with propionate and the total amounts of the reactants consumed and products formed during the enrichment period. The enrichment slurries consisted of sediment from either the sulfate zone (SZ), sulfate-methane transition zone (SMTZ) or methane zone (MZ) and were incubated at 25°C or 10°C, with 3 mM, 20 mM or without (-) sulfate amendments along the study. The slurries P1/P2, P3/P4, P5/P6, P7/P8 from each sediment zone are biological replicates. Slurries with * are presented in the propionate conversion graphs and used for molecular analysis.
    [Show full text]
  • Microbial Fe(III) Oxide Reduction Potential in Chocolate Pots Hot Spring, Yellowstone National Park N
    Geobiology (2016), 14, 255–275 DOI: 10.1111/gbi.12173 Microbial Fe(III) oxide reduction potential in Chocolate Pots hot spring, Yellowstone National Park N. W. FORTNEY,1 S. HE,1 B. J. CONVERSE,1 B. L. BEARD,1 C. M. JOHNSON,1 E. S. BOYD2 ANDE.E.RODEN1 1Department of Geoscience, NASA Astrobiology Institute, University of Wisconsin-Madison, Madison, WI, USA 2Department of Microbiology and Immunology, NASA Astrobiology Institute, Montana State University, Bozeman, MT, USA ABSTRACT Chocolate Pots hot springs (CP) is a unique, circumneutral pH, iron-rich, geothermal feature in Yellowstone National Park. Prior research at CP has focused on photosynthetically driven Fe(II) oxidation as a model for mineralization of microbial mats and deposition of Archean banded iron formations. However, geochemical and stable Fe isotopic data have suggested that dissimilatory microbial iron reduction (DIR) may be active within CP deposits. In this study, the potential for microbial reduction of native CP Fe(III) oxides was inves- tigated, using a combination of cultivation dependent and independent approaches, to assess the potential involvement of DIR in Fe redox cycling and associated stable Fe isotope fractionation in the CP hot springs. Endogenous microbial communities were able to reduce native CP Fe(III) oxides, as documented by most probable number enumerations and enrichment culture studies. Enrichment cultures demonstrated sus- tained DIR driven by oxidation of acetate, lactate, and H2. Inhibitor studies and molecular analyses indicate that sulfate reduction did not contribute to observed rates of DIR in the enrichment cultures through abi- otic reaction pathways. Enrichment cultures produced isotopically light Fe(II) during DIR relative to the bulk solid-phase Fe(III) oxides.
    [Show full text]
  • 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.
    [Show full text]
  • Supplementary Information for Microbial Electrochemical Systems Outperform Fixed-Bed Biofilters for Cleaning-Up Urban Wastewater
    Electronic Supplementary Material (ESI) for Environmental Science: Water Research & Technology. This journal is © The Royal Society of Chemistry 2016 Supplementary information for Microbial Electrochemical Systems outperform fixed-bed biofilters for cleaning-up urban wastewater AUTHORS: Arantxa Aguirre-Sierraa, Tristano Bacchetti De Gregorisb, Antonio Berná, Juan José Salasc, Carlos Aragónc, Abraham Esteve-Núñezab* Fig.1S Total nitrogen (A), ammonia (B) and nitrate (C) influent and effluent average values of the coke and the gravel biofilters. Error bars represent 95% confidence interval. Fig. 2S Influent and effluent COD (A) and BOD5 (B) average values of the hybrid biofilter and the hybrid polarized biofilter. Error bars represent 95% confidence interval. Fig. 3S Redox potential measured in the coke and the gravel biofilters Fig. 4S Rarefaction curves calculated for each sample based on the OTU computations. Fig. 5S Correspondence analysis biplot of classes’ distribution from pyrosequencing analysis. Fig. 6S. Relative abundance of classes of the category ‘other’ at class level. Table 1S Influent pre-treated wastewater and effluents characteristics. Averages ± SD HRT (d) 4.0 3.4 1.7 0.8 0.5 Influent COD (mg L-1) 246 ± 114 330 ± 107 457 ± 92 318 ± 143 393 ± 101 -1 BOD5 (mg L ) 136 ± 86 235 ± 36 268 ± 81 176 ± 127 213 ± 112 TN (mg L-1) 45.0 ± 17.4 60.6 ± 7.5 57.7 ± 3.9 43.7 ± 16.5 54.8 ± 10.1 -1 NH4-N (mg L ) 32.7 ± 18.7 51.6 ± 6.5 49.0 ± 2.3 36.6 ± 15.9 47.0 ± 8.8 -1 NO3-N (mg L ) 2.3 ± 3.6 1.0 ± 1.6 0.8 ± 0.6 1.5 ± 2.0 0.9 ± 0.6 TP (mg
    [Show full text]
  • 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]
  • Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin, M
    Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin, M. Goñi-Urriza, C. Gassie, E. Carlier, M. Monperrus, R. Guyoneaud To cite this version: Yannick Colin, M. Goñi-Urriza, C. Gassie, E. Carlier, M. Monperrus, et al.. Distribution of Sulfate- Reducing Communities from Estuarine to Marine Bay Waters. Microbial Ecology, Springer Verlag, 2017, 73 (1), pp.39-49. 10.1007/s00248-016-0842-5. hal-01499135 HAL Id: hal-01499135 https://hal.archives-ouvertes.fr/hal-01499135 Submitted on 26 Sep 2017 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution - ShareAlike| 4.0 International License Microb Ecol (2017) 73:39–49 DOI 10.1007/s00248-016-0842-5 MICROBIOLOGY OF AQUATIC SYSTEMS Distribution of Sulfate-Reducing Communities from Estuarine to Marine Bay Waters Yannick Colin 1,2 & Marisol Goñi-Urriza1 & Claire Gassie1 & Elisabeth Carlier 1 & Mathilde Monperrus3 & Rémy Guyoneaud1 Received: 23 May 2016 /Accepted: 17 August 2016 /Published online: 31 August 2016 # Springer Science+Business Media New York 2016 Abstract Estuaries are highly dynamic ecosystems in which gradient. The concentration of cultured sulfidogenic microor- freshwater and seawater mix together.
    [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]
  • 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.
    [Show full text]
  • 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.
    [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]
  • 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;
    [Show full text]
  • 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.
    [Show full text]