Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species

Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbi...

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Published inThe ISME Journal Vol. 17; no. 3; pp. 340 - 353
Main Authors Bizic, Mina, Brad, Traian, Ionescu, Danny, Barbu-Tudoran, Lucian, Zoccarato, Luca, Aerts, Joost W., Contarini, Paul-Emile, Gros, Olivier, Volland, Jean-Marie, Popa, Radu, Ody, Jessica, Vellone, Daniel, Flot, Jean-François, Tighe, Scott, Sarbu, Serban M.
Format Journal Article
LanguageEnglish
Published London Nature Publishing Group UK 01.03.2023
Nature Publishing Group
Subjects
14/28
14/63
38/91
45
45/22
45/23
45/90
631/181/757
631/326/171/1878
631/326/2565/855
631/326/41/2530
704/47
Ammonia
Aquatic environment
Bacteria
Biomedical and Life Sciences
Candidatus Thiovulum
Cavernicolous species
Caves
Caves - chemistry
Ecology
Electron microscopy
Environmental Sciences
Epsilonproteobacteria - metabolism
Evolutionary Biology
Genomes
Life Sciences
Microbial Ecology
Microbial Genetics and Genomics
Microbiology
Microorganisms
New species
Nitrate reduction
Oxidation
Phylogeny
Pili
Romania
Strains (organisms)
Sulfur
Sulfur - metabolism
Sulfur bacteria
Surface water
Romania
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Abstract Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum . We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum . We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca . T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
AbstractList Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum . We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum . We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca . T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum . We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum . We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca . T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O 2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum . We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum . We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca . T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O 2 and NO 3 - as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O (~7%). The cave's surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O and NO as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
Abstract Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed from the atmosphere for ~5 million years, has several aqueous chambers, some with low atmospheric O2 (~7%). The cave’s surface-water microbial community is dominated by bacteria we identified as Thiovulum. We show that this strain, and others from subsurface environments, are phylogenetically distinct from marine Thiovulum. We assembled a closed genome of the Movile strain and confirmed its metabolism using RNAseq. We compared the genome of this strain and one we assembled from public data from the sulfidic Frasassi caves to four marine genomes, including Candidatus Thiovulum karukerense and Ca. T. imperiosus, whose genomes we sequenced. Despite great spatial and temporal separation, the genomes of the Movile and Frasassi Thiovulum were highly similar, differing greatly from the very diverse marine strains. We concluded that cave Thiovulum represent a new species, named here Candidatus Thiovulum stygium. Based on their genomes, cave Thiovulum can switch between aerobic and anaerobic sulfide oxidation using O2 and NO3- as electron acceptors, the latter likely via dissimilatory nitrate reduction to ammonia. Thus, Thiovulum is likely important to both S and N cycles in sulfidic caves. Electron microscopy analysis suggests that at least some of the short peritrichous structures typical of Thiovulum are type IV pili, for which genes were found in all strains. These pili may play a role in veil formation, by connecting adjacent cells, and in the motility of these exceptionally fast swimmers.
Author Bizic, Mina
Brad, Traian
Tighe, Scott
Ody, Jessica
Flot, Jean-François
Gros, Olivier
Barbu-Tudoran, Lucian
Ionescu, Danny
Contarini, Paul-Emile
Volland, Jean-Marie
Popa, Radu
Aerts, Joost W.
Sarbu, Serban M.
Zoccarato, Luca
Vellone, Daniel
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  organization: Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB)
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  organization: “Emil Racoviţă” Institute of Speleology
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  surname: Flot
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  surname: Tighe
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  surname: Sarbu
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  organization: “Emil Racoviţă” Institute of Speleology, Frumoasă 31-B, Department of Biological Sciences, California State University
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Cites_doi 10.1016/j.scitotenv.2020.139710
10.1007/BF02538470
10.1021/es404808r
10.1093/nar/gky1085
10.1186/1741-7007-4-41
10.1371/journal.pone.0021373
10.1007/s12275-021-1154-0
10.1016/j.scitotenv.2018.07.388
10.1186/s12859-019-3068-y
10.1093/bioinformatics/btz848
10.1038/nmeth.4197
10.1038/s41579-019-0195-4
10.1103/PhysRevLett.114.158102
10.3389/fmicb.2018.02569
10.1128/jb.136.2.765-774.1978
10.1038/nbt.4229
10.1128/AEM.71.11.6885-6899.2005
10.1093/bioinformatics/btv383
10.1371/journal.pone.0009490
10.1101/gr.186072.114
10.1371/journal.pbio.0060087
10.7717/peerj.1165
10.1515/9783110339888
10.1016/j.cell.2020.09.065
10.1641/0006-3568(2000)050[0217:ESAAEF]2.3.CO;2
10.1038/s41587-019-0072-8
10.1099/ijs.0.064956-0
10.1016/0014-4827(58)90211-8
10.1093/nar/gkv1070
10.1371/journal.pbio.3000390
10.3354/ame018157
10.1371/journal.pone.0110726
10.1038/srep08365
10.1093/nar/gks1219
10.1046/j.1462-2920.2003.00543.x
10.1093/bioinformatics/bty496
10.1126/science.272.5270.1953
10.1128/aem.45.4.1261-1270.1983
10.1007/BF02529969
10.1093/nar/28.1.33
10.3390/d13030128
10.1128/mSystems.00920-20
10.1128/AEM.67.7.3299-3303.2001
10.1038/28609
10.1101/gr.214270.116
10.1093/nar/gkm360
10.1038/s41396-018-0069-1
10.1038/s41467-018-07641-9
10.1139/cjm-2021-0101
10.1093/nar/gkv1189
10.1371/journal.pone.0010609
10.7717/peerj.1319
10.1093/nar/gkv007
10.5038/1827-806X.38.1.4
10.1128/jb.171.6.3560-3563.1989
10.1093/nar/gkaa621
10.1093/bioinformatics/btv033
10.1093/bioinformatics/btu170
10.1093/nar/gkt1226
10.1093/femsle/fnx172
10.1186/1471-2164-9-75
10.1186/s13059-014-0550-8
10.1093/bioinformatics/bts723
10.1093/nar/gku447
10.1016/j.str.2021.07.008
10.1186/s12859-019-3114-9
10.1073/pnas.1111262109
10.1186/s12859-018-2486-6
10.1111/mmi.13690
10.1111/mec.12461
10.7554/eLife.23136
10.1038/ismej.2009.57
10.1371/journal.pone.0112963
10.3389/fmicb.2017.00087
10.1080/01490451.2013.839764
10.1099/13500872-140-11-3109
10.1016/j.bbabio.2008.12.010
10.1099/ijs.0.057224-0
10.1002/abio.200390000
10.1093/bioinformatics/btu153
10.1093/molbev/msp239
10.1038/s41396-020-0669-4
10.1093/bib/bbz104
10.1128/AEM.02314-12
10.1128/aem.63.8.3123-3127.1997
10.1371/journal.pcbi.1005595
10.3390/w14101597
10.1099/00221287-26-1-29
10.1186/s12866-014-0322-3
10.1038/ismej.2013.206
10.1186/s40168-020-00990-y
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References ShuDGuoJZhangBHeYWeiGrDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trainsSci Tot Environ20196461069791:CAS:528:DC%2BC1cXhsVahtLnJ10.1016/j.scitotenv.2018.07.388
GuoJBolducBZayedAAVarsaniADominguez-HuertaGDelmontTOVirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA virusesMicrobiome2021933522966785210810.1186/s40168-020-00990-y
Birky CW, Maughan H. Evolutionary genetic species detected in prokaryotes by applying the K/θ ratio to DNA sequences. bioRxiv 2021; 2020.04.27.062828.
LoveMIHuberWAndersSModerated estimation of fold change and dispersion for RNA-seq data with DESeq2Genome Biol20141525516281430204910.1186/s13059-014-0550-8
PorterMSummers EngelAKaneTKinkleBProductivity-diversity relationships from chemolithoautotrophically based sulfidic karst systemsInt J Speleol200938274010.5038/1827-806X.38.1.4
ZhouZTranPQKieftKAnantharamanKGenome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptationISME J20201420601:CAS:528:DC%2BB3cXptlehsr8%3D32393808736789110.1038/s41396-020-0669-4
GroteJSchottTBrucknerCGGlöcknerFOJostGTeelingHGenome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zonesProc Natl Acad Sci USA2012109506101:CAS:528:DC%2BC38Xht1ensLo%3D2220398210.1073/pnas.1111262109
WirsenCOJannaschHWPhysiological and morphological observations on Thiovulum spJ Bacteriol1978136765741:CAS:528:DyaE1MXltFWrtg%3D%3D10153121860310.1128/jb.136.2.765-774.1978
PriceMNDehalPSArkinAPFastTree 2-approximately maximum-likelihood trees for large alignmentsPLoS One20105e949020224823283573610.1371/journal.pone.0009490
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv 2012;1207.
Rodriguez-RLMKonstantinidisKTBypassing cultivation to identify bacterial speciesMicrobe201491118
HoffmanAAHercusMJEnvironmental stress as an evolutionary forceBioscience2000502172610.1641/0006-3568(2000)050[0217:ESAAEF]2.3.CO;2
PatroRDuggalGLoveMIIrizarryRAKingsfordCSalmon provides fast and bias-aware quantification of transcript expressionNat Methods20171441791:CAS:528:DC%2BC2sXltVWgtL8%3D28263959560014810.1038/nmeth.4197
SarbuSMKaneTCKinkleBKA chemoautotrophically based cave ecosystemScience1996272195351:CAS:528:DyaK28XjvVOisLs%3D866249710.1126/science.272.5270.1953
SlobodkinaGBMardanovAVRavinNVFrolovaAAChernyhNABonch-OsmolovskayaEARespiratory ammonification of nitrate coupled to anaerobic oxidation of elemental sulfur in deep-sea autotrophic thermophilic bacteriaFront Microbiol201788728194142527681810.3389/fmicb.2017.00087
Robertson LA, Kuenen JG, Paster BJ, Dewhirst FE, Vandamme P Thiovulum Hinze 1913, 195AL. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds). Bergey’s Manual of Systematic Bacteriology. 2006. Springer, New York, pp 1189–91.
MarshallIPGBlaineyPCSpormannAMQuakeSRA single-cell genome for Thiovulum spAppl Environ Microbiol2012788555631:CAS:528:DC%2BC38Xhslyjsr%2FI23023751350292810.1128/AEM.02314-12
PandeyCBKumarUKavirajMMinickKJMishraAKSinghJSDNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystemsSci Total Environ20207381397101:CAS:528:DC%2BB3cXhtFKisL3E3254470410.1016/j.scitotenv.2020.139710
DeniseRAbbySSRochaEPCDiversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motilityPLoS Biol201917e300039031323028666883510.1371/journal.pbio.3000390
BiaisNLadouxBHigashiDSoMSheetzMCooperative retraction of bundled type IV pili enables nanonewton force generationPLoS Biol20086e8718416602229275410.1371/journal.pbio.0060087
VlasceanuLPopaRKinkleBKCharacterization of Thiobacillus thioparus LV43 and its distribution in a chemoautotrophically based groundwater ecosystemAppl Environ Microbiol19976331231:CAS:528:DyaK2sXlt1Wisrw%3D925119916861010.1128/aem.63.8.3123-3127.1997
ChaumeilP-AMussigAJHugenholtzPParksDHGTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy DatabaseBioinformatics20193619257317301927703759
MillmanABernheimAStokar-AvihailAFedorenkoTVoichekMLeavittABacterial retrons function in anti-phage defenseCell20201831551.e121:CAS:528:DC%2BB3cXit12htr7K3315703910.1016/j.cell.2020.09.065
O’LearyNAWrightMWBristerJRCiufoSHaddadDMcVeighRReference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotationNucleic Acids Res201644D733D7452655380410.1093/nar/gkv1189
KernMSimonJElectron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other EpsilonproteobacteriaBiochimica et Biophysica Acta (BBA) - Bioenerg20091787646561:CAS:528:DC%2BD1MXntVSitrw%3D10.1016/j.bbabio.2008.12.010
KangDDFroulaJEganRWangZMetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communitiesPeerJ20153e116526336640455615810.7717/peerj.1165
SylvestreM-NJean-LouisPGrimonprezABilasPCollienneAAzèdeCCandidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environmentCan J Microbiol20226817301:CAS:528:DC%2BB3MXisVSrtrnN10.1139/cjm-2021-0101
BradTIepureSSarbuSMThe chemoautotrophically based movile cave groundwater ecosystem, a hotspot of subterranean biodiversityDiversity2021131281:CAS:528:DC%2BB3MXhvFCls7fF10.3390/d13030128
Fauré-FremietERouillerCHÉtude au microscope électronique d’une bactérie sulfureuse, Thiovulum majus HinzeExp Cell Res19581429461351230210.1016/0014-4827(58)90211-8
WalkerBJAbeelTSheaTPriestMAbouellielASakthikumarSPilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvementPLoS One20149e11296325409509423734810.1371/journal.pone.0112963
KanehisaMSatoYKawashimaMFurumichiMTanabeMKEGG as a reference resource for gene and protein annotationNucleic Acids Res201644D457621:CAS:528:DC%2BC2sXhtV2nsrrI2647645410.1093/nar/gkv1070
De BoerWELa RivièreJWMHouwinkALObservations on the morphology of Thiovulum majus HinzeAntonie Van Leeuwenhoek196127447561387049310.1007/BF02538470
BrettinTDavisJJDiszTEdwardsRAGerdesSOlsenGJRASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomesSci Rep2015525666585432235910.1038/srep08365
ParrelloBButlerRChlenskiPOlsonROverbeekJPuschGDA machine learning-based service for estimating quality of genomes using PATRICBMC Bioinform2019201910.1186/s12859-019-3068-y
GaoYNeubauerMYangAJohnsonNMorseMLiGAltered motility of Caulobacter crescentus in viscous and viscoelastic mediaBMC Microbiol20141432225539737430259810.1186/s12866-014-0322-3
WickRRSchultzMBZobelJHoltKEBandage: interactive visualization of de novo genome assembliesBioinformatics201531335021:CAS:528:DC%2BC28Xhs1Git7%2FJ26099265459590410.1093/bioinformatics/btv383
LiDLiuC-MLuoRSadakaneKLamT-WMEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graphBioinformatics201531167461:CAS:528:DC%2BC28XhtFyltL3N2560979310.1093/bioinformatics/btv033
RitchieMEPhipsonBWuDHuYLawCWShiWLimma powers differential expression analyses for RNA-sequencing and microarray studiesNucleic Acids Res201543e4725605792440251010.1093/nar/gkv007
Garcia-PichelFRapid bacterial swimming measured in swarming cells of Thiovulum majusJ Bacteriol1989171356031:STN:280:DyaL1M3lsFWgtg%3D%3D249829321008710.1128/jb.171.6.3560-3563.1989
BirkyCWAdamsJGemmelMPerryJUsing population genetic theory and DNA sequences for species detection and identification in asexual organismsPLoS One20105e1060920498705286935410.1371/journal.pone.0010609
SchirmackJMangelsdorfKGanzertLSandWHillebrand-VoiculescuAWagnerDMethanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lakeInt J Syst Evol Microbiol20146452271:CAS:528:DC%2BC2cXhtlClsrzE2410832510.1099/ijs.0.057224-0
Spöri Y, Stoch F, Dellicour S, Birky CW, Flot J-F KoT: an automatic implementation of the K/θ method for species delimitation. bioRxiv 2022; 2021.08.17.454531.
FenchelTGludRNVeil architecture in a sulphide-oxidizing bacterium enhances countercurrent fluxNature199839436791:CAS:528:DyaK1cXkvFKnsbo%3D10.1038/28609
Huerta-CepasJSzklarczykDHellerDHernández-PlazaAForslundSKCookHeggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 virusesNucleic Acids Res201947D309D3141:CAS:528:DC%2BC1MXhs1Gqtr%2FL3041861010.1093/nar/gky1085
GrosOFirst description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the caribbean: Thiovulum sp. strain karukerenseFEMS Microbiol Lett2017364fnx17210.1093/femsle/fnx172
WickRRJuddLMGorrieCLHoltKEUnicycler: resolving bacterial genome assemblies from short and long sequencing readsPLoS Comput Biol201713e100559528594827548114710.1371/journal.pcbi.1005595
Sarbu SM, Popa R. A unique chemoautotrophically based cave ecosystem. In: Camacho AI (ed). The natural history of biospeleology. 1992. Mus. Nat. de Hist. Naturales, Madrid, pp 637–66.
KarpPDMidfordPEBillingtonRKothariAKrummenackerMLatendresseMPathway Tools version 23.0 update: software for pathway/genome informatics and systems biologyBrief Bioinform202122109263181396410.1093/bib/bbz104
ClarkSCEganRFrazierPIWangZALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assembliesBioinformatics201329435431:CAS:528:DC%2BC3sXis1OjsLk%3D2330350910.1093/bioinformatics/bts723
EisenmannEBeuerleJSulgerKKroneckPMHSchumacherWLithotrophic growth of Sulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammoniaArch Microbiol199516418051:CAS:528:DyaK2MXovFyjsrc%3D10.1007/BF02529969
RenaultTTAbrahamAOBergmillerTParadisGRainvilleSCharpentierEBacterial flagella grow through an injection-diffusion mechanismElife20176e2313628262091538659210.7
Poser (2024011017301374100_CR84) 2014; 48
Bižic-Ionescu (2024011017301374100_CR91) 2018; 9
Price (2024011017301374100_CR60) 2010; 5
Lackey (2024011017301374100_CR4) 1961; 26
Kern (2024011017301374100_CR88) 2009; 1787
Wick (2024011017301374100_CR30) 2015; 31
Spöri (2024011017301374100_CR79) 2022; 2021.08.17.454531
Chaumeil (2024011017301374100_CR41) 2019; 36
Brad (2024011017301374100_CR102) 2021; 13
Grissa (2024011017301374100_CR54) 2007; 35
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Karami (2024011017301374100_CR96) 2021; 29
Kolmogorov (2024011017301374100_CR29) 2019; 37
Zhou (2024011017301374100_CR71) 2020; 14
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Pingoud (2024011017301374100_CR93) 2014; 42
Volland (2024011017301374100_CR82) 2018; 12
Millman (2024011017301374100_CR92) 2020; 183
Fauré-Fremiet (2024011017301374100_CR94) 1958; 14
Clark (2024011017301374100_CR37) 2013; 29
Jain (2024011017301374100_CR58) 2018; 9
Rodriguez-R (2024011017301374100_CR77) 2014; 9
Gao (2024011017301374100_CR100) 2014; 14
Sarbu (2024011017301374100_CR101) 1992
Walker (2024011017301374100_CR34) 2014; 9
Wirsen (2024011017301374100_CR6) 1978; 136
Ritchie (2024011017301374100_CR64) 2015; 43
Davis (2024011017301374100_CR47) 2020; 48
Love (2024011017301374100_CR63) 2014; 15
Garcia-Pichel (2024011017301374100_CR7) 1989; 171
Denise (2024011017301374100_CR57) 2019; 17
Grote (2024011017301374100_CR104) 2012; 109
Sylvestre (2024011017301374100_CR2) 2022; 68
Robertson (2024011017301374100_CR1) 2015
Huerta-Cepas (2024011017301374100_CR46) 2019; 47
O’Leary (2024011017301374100_CR66) 2016; 44
Rohwerder (2024011017301374100_CR19) 2003; 23
Jorgensen (2024011017301374100_CR12) 1983; 45
Birky (2024011017301374100_CR80) 2010; 5
Kumaresan (2024011017301374100_CR17) 2014; 31
Nercessian (2024011017301374100_CR27) 2005; 71
Petroff (2024011017301374100_CR9) 2015; 114
Riess (2024011017301374100_CR15) 1999; 18
Garrison (2024011017301374100_CR36) 2012; 1207
Eren (2024011017301374100_CR52) 2015; 3
Guo (2024011017301374100_CR65) 2021; 9
Abby (2024011017301374100_CR56) 2014; 9
Biais (2024011017301374100_CR97) 2008; 6
Lascu (2024011017301374100_CR14) 1994; 38
Thar (2024011017301374100_CR8) 2001; 67
Aziz (2024011017301374100_CR49) 2008; 9
Craig (2024011017301374100_CR99) 2019; 17
Pandey (2024011017301374100_CR87) 2020; 738
Hoffman (2024011017301374100_CR75) 2000; 50
Parrello (2024011017301374100_CR72) 2019; 20
Overbeek (2024011017301374100_CR50) 2014; 42
Hamilton (2024011017301374100_CR69) 2014; 5
Lauterborn (2024011017301374100_CR5) 1915; 13
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Porter (2024011017301374100_CR70) 2009; 38
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Gruber-Vodicka (2024011017301374100_CR28) 2020; 5
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Sarbu (2024011017301374100_CR83) 1996; 272
Meyer (2024011017301374100_CR89) 2014; 8
Fenchel (2024011017301374100_CR68) 1994; 140
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Bolger (2024011017301374100_CR38) 2014; 30
Chen (2024011017301374100_CR20) 2009; 3
Shu (2024011017301374100_CR90) 2019; 646
Schirmack (2024011017301374100_CR23) 2014; 64
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Tatusov (2024011017301374100_CR51) 2000; 28
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Eisenmann (2024011017301374100_CR86) 1995; 164
Ge (2024011017301374100_CR62) 2018; 19
De Boer (2024011017301374100_CR10) 1961; 27
Brettin (2024011017301374100_CR48) 2015; 5
Engel (2024011017301374100_CR16) 2015
Patro (2024011017301374100_CR61) 2017; 14
Kim (2024011017301374100_CR59) 2021; 59
Marshall (2024011017301374100_CR11) 2012; 78
Flot (2024011017301374100_CR21) 2014; 23
Birky (2024011017301374100_CR81) 2021; 2020.04.27.062828
Parks (2024011017301374100_CR42) 2015; 25
Renault (2024011017301374100_CR95) 2017; 6
References_xml – volume: 738
  start-page: 139710
  year: 2020
  ident: 2024011017301374100_CR87
  article-title: DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems
  publication-title: Sci Total Environ
  doi: 10.1016/j.scitotenv.2020.139710
  contributor:
    fullname: Pandey
– volume: 27
  start-page: 447
  year: 1961
  ident: 2024011017301374100_CR10
  article-title: Observations on the morphology of Thiovulum majus Hinze
  publication-title: Antonie Van Leeuwenhoek
  doi: 10.1007/BF02538470
  contributor:
    fullname: De Boer
– volume: 9
  start-page: 111
  year: 2014
  ident: 2024011017301374100_CR77
  article-title: Bypassing cultivation to identify bacterial species
  publication-title: Microbe
  contributor:
    fullname: Rodriguez-R
– volume: 48
  start-page: 9094
  year: 2014
  ident: 2024011017301374100_CR84
  article-title: Stable sulfur and oxygen isotope fractionation of anoxic sulfide oxidation by two different enzymatic pathways
  publication-title: Environ Sci Technol
  doi: 10.1021/es404808r
  contributor:
    fullname: Poser
– volume: 47
  start-page: D309
  year: 2019
  ident: 2024011017301374100_CR46
  article-title: eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gky1085
  contributor:
    fullname: Huerta-Cepas
– volume: 4
  start-page: 41
  year: 2006
  ident: 2024011017301374100_CR31
  article-title: Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST
  publication-title: BMC Biol
  doi: 10.1186/1741-7007-4-41
  contributor:
    fullname: Gertz
– volume: 6
  start-page: e21373
  year: 2011
  ident: 2024011017301374100_CR98
  article-title: N. elongata produces type IV pili that mediate interspecies gene transfer with N. gonorrhoeae
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0021373
  contributor:
    fullname: Higashi
– volume: 59
  start-page: 476
  year: 2021
  ident: 2024011017301374100_CR59
  article-title: Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity
  publication-title: J Microbiol
  doi: 10.1007/s12275-021-1154-0
  contributor:
    fullname: Kim
– volume: 646
  start-page: 1069
  year: 2019
  ident: 2024011017301374100_CR90
  article-title: rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains
  publication-title: Sci Tot Environ
  doi: 10.1016/j.scitotenv.2018.07.388
  contributor:
    fullname: Shu
– volume: 20
  start-page: 1
  year: 2019
  ident: 2024011017301374100_CR72
  article-title: A machine learning-based service for estimating quality of genomes using PATRIC
  publication-title: BMC Bioinform
  doi: 10.1186/s12859-019-3068-y
  contributor:
    fullname: Parrello
– volume: 36
  start-page: 1925
  year: 2019
  ident: 2024011017301374100_CR41
  article-title: GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btz848
  contributor:
    fullname: Chaumeil
– volume: 14
  start-page: 417
  year: 2017
  ident: 2024011017301374100_CR61
  article-title: Salmon provides fast and bias-aware quantification of transcript expression
  publication-title: Nat Methods
  doi: 10.1038/nmeth.4197
  contributor:
    fullname: Patro
– volume: 17
  start-page: 429
  year: 2019
  ident: 2024011017301374100_CR99
  article-title: Type IV pili: dynamics, biophysics and functional consequences
  publication-title: Nat Rev Microbiol
  doi: 10.1038/s41579-019-0195-4
  contributor:
    fullname: Craig
– volume: 114
  start-page: 158102
  year: 2015
  ident: 2024011017301374100_CR9
  article-title: Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells
  publication-title: Phys Rev Lett
  doi: 10.1103/PhysRevLett.114.158102
  contributor:
    fullname: Petroff
– volume: 48
  start-page: D606
  year: 2020
  ident: 2024011017301374100_CR47
  article-title: The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities
  publication-title: Nucleic Acids Res
  contributor:
    fullname: Davis
– volume: 2021.08.17.454531
  year: 2022
  ident: 2024011017301374100_CR79
  article-title: KoT: an automatic implementation of the K/θ method for species delimitation
  publication-title: bioRxiv
  contributor:
    fullname: Spöri
– volume: 9
  start-page: 2569
  year: 2018
  ident: 2024011017301374100_CR91
  article-title: Organic particles: Heterogeneous hubs for microbial interactions in aquatic ecosystems
  publication-title: Front Microbiol
  doi: 10.3389/fmicb.2018.02569
  contributor:
    fullname: Bižic-Ionescu
– volume: 136
  start-page: 765
  year: 1978
  ident: 2024011017301374100_CR6
  article-title: Physiological and morphological observations on Thiovulum sp
  publication-title: J Bacteriol
  doi: 10.1128/jb.136.2.765-774.1978
  contributor:
    fullname: Wirsen
– volume: 36
  start-page: 996
  year: 2018
  ident: 2024011017301374100_CR78
  article-title: A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
  publication-title: Nat Biotechnol
  doi: 10.1038/nbt.4229
  contributor:
    fullname: Parks
– volume: 71
  start-page: 6885
  year: 2005
  ident: 2024011017301374100_CR27
  article-title: Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake
  publication-title: Appl Environ Microbiol
  doi: 10.1128/AEM.71.11.6885-6899.2005
  contributor:
    fullname: Nercessian
– volume: 31
  start-page: 3350
  year: 2015
  ident: 2024011017301374100_CR30
  article-title: Bandage: interactive visualization of de novo genome assemblies
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv383
  contributor:
    fullname: Wick
– volume: 5
  start-page: e9490
  year: 2010
  ident: 2024011017301374100_CR60
  article-title: FastTree 2-approximately maximum-likelihood trees for large alignments
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0009490
  contributor:
    fullname: Price
– start-page: 637
  volume-title: The natural history of biospeleology
  year: 1992
  ident: 2024011017301374100_CR101
  contributor:
    fullname: Sarbu
– volume: 25
  start-page: 1043
  year: 2015
  ident: 2024011017301374100_CR42
  article-title: CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
  publication-title: Genome Res
  doi: 10.1101/gr.186072.114
  contributor:
    fullname: Parks
– volume: 6
  start-page: e87
  year: 2008
  ident: 2024011017301374100_CR97
  article-title: Cooperative retraction of bundled type IV pili enables nanonewton force generation
  publication-title: PLoS Biol
  doi: 10.1371/journal.pbio.0060087
  contributor:
    fullname: Biais
– volume: 3
  start-page: e1165
  year: 2015
  ident: 2024011017301374100_CR40
  article-title: MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
  publication-title: PeerJ
  doi: 10.7717/peerj.1165
  contributor:
    fullname: Kang
– start-page: 1
  volume-title: Microbial Life of Cave Systems
  year: 2015
  ident: 2024011017301374100_CR16
  doi: 10.1515/9783110339888
  contributor:
    fullname: Engel
– volume: 183
  start-page: 1551
  year: 2020
  ident: 2024011017301374100_CR92
  article-title: Bacterial retrons function in anti-phage defense
  publication-title: Cell
  doi: 10.1016/j.cell.2020.09.065
  contributor:
    fullname: Millman
– volume: 50
  start-page: 217
  year: 2000
  ident: 2024011017301374100_CR75
  article-title: Environmental stress as an evolutionary force
  publication-title: Bioscience
  doi: 10.1641/0006-3568(2000)050[0217:ESAAEF]2.3.CO;2
  contributor:
    fullname: Hoffman
– volume: 37
  start-page: 540
  year: 2019
  ident: 2024011017301374100_CR29
  article-title: Assembly of long, error-prone reads using repeat graphs
  publication-title: Nat Biotechnol
  doi: 10.1038/s41587-019-0072-8
  contributor:
    fullname: Kolmogorov
– volume: 64
  start-page: 3478
  year: 2014
  ident: 2024011017301374100_CR24
  article-title: Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake
  publication-title: Int J Syst Evol Microbiol
  doi: 10.1099/ijs.0.064956-0
  contributor:
    fullname: Ganzert
– volume: 14
  start-page: 29
  year: 1958
  ident: 2024011017301374100_CR94
  article-title: Étude au microscope électronique d’une bactérie sulfureuse, Thiovulum majus Hinze
  publication-title: Exp Cell Res
  doi: 10.1016/0014-4827(58)90211-8
  contributor:
    fullname: Fauré-Fremiet
– volume: 44
  start-page: D457
  year: 2016
  ident: 2024011017301374100_CR45
  article-title: KEGG as a reference resource for gene and protein annotation
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv1070
  contributor:
    fullname: Kanehisa
– volume: 17
  start-page: e3000390
  year: 2019
  ident: 2024011017301374100_CR57
  article-title: Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
  publication-title: PLoS Biol
  doi: 10.1371/journal.pbio.3000390
  contributor:
    fullname: Denise
– volume: 5
  start-page: 756
  year: 2014
  ident: 2024011017301374100_CR69
  article-title: Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem
  publication-title: Front Microbiol
  contributor:
    fullname: Hamilton
– volume: 18
  start-page: 157
  year: 1999
  ident: 2024011017301374100_CR15
  article-title: Anoxic thermomineral cave waters and bacterial mats as habitat for freshwater nematodes
  publication-title: Aquat Micro Ecol
  doi: 10.3354/ame018157
  contributor:
    fullname: Riess
– volume: 13
  start-page: 395
  year: 1915
  ident: 2024011017301374100_CR5
  article-title: Die sapropelische Lebewelt. Ein Beitrag zur Biologie des Faulschlamms natürlicher Gewässer
  publication-title: Verh Naturhist Med Ver Heidelb
  contributor:
    fullname: Lauterborn
– volume: 9
  start-page: e110726
  year: 2014
  ident: 2024011017301374100_CR56
  article-title: MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0110726
  contributor:
    fullname: Abby
– volume: 5
  start-page: 8365
  year: 2015
  ident: 2024011017301374100_CR48
  article-title: RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes
  publication-title: Sci Rep
  doi: 10.1038/srep08365
  contributor:
    fullname: Brettin
– volume: 41
  start-page: D590
  year: 2013
  ident: 2024011017301374100_CR103
  article-title: The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gks1219
  contributor:
    fullname: Quast
– volume: 6
  start-page: 111
  year: 2004
  ident: 2024011017301374100_CR22
  article-title: Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing
  publication-title: Environ Microbiol
  doi: 10.1046/j.1462-2920.2003.00543.x
  contributor:
    fullname: Hutchens
– volume: 34
  start-page: 4118
  year: 2018
  ident: 2024011017301374100_CR53
  article-title: Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bty496
  contributor:
    fullname: Taboada
– volume: 272
  start-page: 1953
  year: 1996
  ident: 2024011017301374100_CR83
  article-title: A chemoautotrophically based cave ecosystem
  publication-title: Science
  doi: 10.1126/science.272.5270.1953
  contributor:
    fullname: Sarbu
– volume: 45
  start-page: 1261
  year: 1983
  ident: 2024011017301374100_CR12
  article-title: Colorless sulfur bacteria, Beggiatoa spp. and Thiovulum spp., in O2 and H2S microgradients
  publication-title: Appl Environ Microbiol
  doi: 10.1128/aem.45.4.1261-1270.1983
  contributor:
    fullname: Jorgensen
– volume: 164
  start-page: 180
  year: 1995
  ident: 2024011017301374100_CR86
  article-title: Lithotrophic growth of Sulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia
  publication-title: Arch Microbiol
  doi: 10.1007/BF02529969
  contributor:
    fullname: Eisenmann
– volume: 28
  start-page: 33
  year: 2000
  ident: 2024011017301374100_CR51
  article-title: The COG database: a tool for genome-scale analysis of protein functions and evolution
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/28.1.33
  contributor:
    fullname: Tatusov
– volume: 13
  start-page: 128
  year: 2021
  ident: 2024011017301374100_CR102
  article-title: The chemoautotrophically based movile cave groundwater ecosystem, a hotspot of subterranean biodiversity
  publication-title: Diversity
  doi: 10.3390/d13030128
  contributor:
    fullname: Brad
– volume: 5
  start-page: 521922
  year: 2020
  ident: 2024011017301374100_CR28
  article-title: phyloFlash: Rapid small-subunit rRNA profiling and targeted assembly from metagenomes
  publication-title: mSystems
  doi: 10.1128/mSystems.00920-20
  contributor:
    fullname: Gruber-Vodicka
– volume: 67
  start-page: 3299
  year: 2001
  ident: 2024011017301374100_CR8
  article-title: True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus
  publication-title: Appl Environ Microbiol
  doi: 10.1128/AEM.67.7.3299-3303.2001
  contributor:
    fullname: Thar
– volume: 394
  start-page: 367
  year: 1998
  ident: 2024011017301374100_CR13
  article-title: Veil architecture in a sulphide-oxidizing bacterium enhances countercurrent flux
  publication-title: Nature
  doi: 10.1038/28609
  contributor:
    fullname: Fenchel
– volume: 27
  start-page: 737
  year: 2017
  ident: 2024011017301374100_CR35
  article-title: Fast and accurate de novo genome assembly from long uncorrected reads
  publication-title: Genome Res
  doi: 10.1101/gr.214270.116
  contributor:
    fullname: Vaser
– volume: 35
  start-page: W52
  year: 2007
  ident: 2024011017301374100_CR54
  article-title: CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkm360
  contributor:
    fullname: Grissa
– volume: 12
  start-page: 714
  year: 2018
  ident: 2024011017301374100_CR82
  article-title: NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host
  publication-title: ISME J
  doi: 10.1038/s41396-018-0069-1
  contributor:
    fullname: Volland
– volume: 38
  start-page: 85
  year: 1994
  ident: 2024011017301374100_CR14
  article-title: Le karst de Movile (Dobrogea de Sud)
  publication-title: Rev Roum de Géographie
  contributor:
    fullname: Lascu
– volume: 9
  start-page: 1
  year: 2018
  ident: 2024011017301374100_CR58
  article-title: High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
  publication-title: Nat Commun
  doi: 10.1038/s41467-018-07641-9
  contributor:
    fullname: Jain
– volume: 68
  start-page: 17
  year: 2022
  ident: 2024011017301374100_CR2
  article-title: Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment
  publication-title: Can J Microbiol
  doi: 10.1139/cjm-2021-0101
  contributor:
    fullname: Sylvestre
– start-page: 319
  volume-title: Subterranean Ecosystems
  year: 2000
  ident: 2024011017301374100_CR18
  contributor:
    fullname: Sarbu
– volume: 44
  start-page: D733
  year: 2016
  ident: 2024011017301374100_CR66
  article-title: Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv1189
  contributor:
    fullname: O’Leary
– volume: 5
  start-page: e10609
  year: 2010
  ident: 2024011017301374100_CR80
  article-title: Using population genetic theory and DNA sequences for species detection and identification in asexual organisms
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0010609
  contributor:
    fullname: Birky
– volume: 3
  start-page: e1319
  year: 2015
  ident: 2024011017301374100_CR52
  article-title: Anvi’o: an advanced analysis and visualization platform for ’omics data
  publication-title: PeerJ
  doi: 10.7717/peerj.1319
  contributor:
    fullname: Eren
– volume: 43
  start-page: e47
  year: 2015
  ident: 2024011017301374100_CR64
  article-title: Limma powers differential expression analyses for RNA-sequencing and microarray studies
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkv007
  contributor:
    fullname: Ritchie
– volume: 38
  start-page: 27
  year: 2009
  ident: 2024011017301374100_CR70
  article-title: Productivity-diversity relationships from chemolithoautotrophically based sulfidic karst systems
  publication-title: Int J Speleol
  doi: 10.5038/1827-806X.38.1.4
  contributor:
    fullname: Porter
– start-page: 1
  volume-title: Bergey’s Manual of Systematics of Archaea and Bacteria
  year: 2015
  ident: 2024011017301374100_CR1
  contributor:
    fullname: Robertson
– volume: 171
  start-page: 3560
  year: 1989
  ident: 2024011017301374100_CR7
  article-title: Rapid bacterial swimming measured in swarming cells of Thiovulum majus
  publication-title: J Bacteriol
  doi: 10.1128/jb.171.6.3560-3563.1989
  contributor:
    fullname: Garcia-Pichel
– volume: 48
  start-page: 8883
  year: 2020
  ident: 2024011017301374100_CR44
  article-title: DRAM for distilling microbial metabolism to automate the curation of microbiome function
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkaa621
  contributor:
    fullname: Shaffer
– volume: 31
  start-page: 1674
  year: 2015
  ident: 2024011017301374100_CR39
  article-title: MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btv033
  contributor:
    fullname: Li
– volume: 30
  start-page: 2114
  year: 2014
  ident: 2024011017301374100_CR38
  article-title: Trimmomatic: a flexible trimmer for Illumina sequence data
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu170
  contributor:
    fullname: Bolger
– volume: 42
  start-page: D206
  year: 2014
  ident: 2024011017301374100_CR50
  article-title: The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST)
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gkt1226
  contributor:
    fullname: Overbeek
– volume: 364
  start-page: fnx172
  year: 2017
  ident: 2024011017301374100_CR26
  article-title: First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the caribbean: Thiovulum sp. strain karukerense
  publication-title: FEMS Microbiol Lett
  doi: 10.1093/femsle/fnx172
  contributor:
    fullname: Gros
– volume: 9
  start-page: 75
  year: 2008
  ident: 2024011017301374100_CR49
  article-title: The RAST Server: rapid annotations using subsystems technology
  publication-title: BMC Genomics
  doi: 10.1186/1471-2164-9-75
  contributor:
    fullname: Aziz
– volume: 15
  start-page: 550
  year: 2014
  ident: 2024011017301374100_CR63
  article-title: Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
  publication-title: Genome Biol
  doi: 10.1186/s13059-014-0550-8
  contributor:
    fullname: Love
– volume: 29
  start-page: 435
  year: 2013
  ident: 2024011017301374100_CR37
  article-title: ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/bts723
  contributor:
    fullname: Clark
– volume: 42
  start-page: 7489
  year: 2014
  ident: 2024011017301374100_CR93
  article-title: Type II restriction endonucleases—a historical perspective and more
  publication-title: Nucleic Acids Res
  doi: 10.1093/nar/gku447
  contributor:
    fullname: Pingoud
– volume: 29
  start-page: 1397
  year: 2021
  ident: 2024011017301374100_CR96
  article-title: Computational and biochemical analysis of type IV pilus dynamics and stability
  publication-title: Structure
  doi: 10.1016/j.str.2021.07.008
  contributor:
    fullname: Karami
– volume: 1207
  year: 2012
  ident: 2024011017301374100_CR36
  article-title: Haplotype-based variant detection from short-read sequencing
  publication-title: ArXiv
  contributor:
    fullname: Garrison
– volume: 20
  start-page: 539
  year: 2019
  ident: 2024011017301374100_CR32
  article-title: SLR: a scaffolding algorithm based on long reads and contig classification
  publication-title: BMC Bioinforma
  doi: 10.1186/s12859-019-3114-9
  contributor:
    fullname: Luo
– volume: 109
  start-page: 506
  year: 2012
  ident: 2024011017301374100_CR104
  article-title: Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones
  publication-title: Proc Natl Acad Sci USA
  doi: 10.1073/pnas.1111262109
  contributor:
    fullname: Grote
– volume: 19
  start-page: 534
  year: 2018
  ident: 2024011017301374100_CR62
  article-title: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data
  publication-title: BMC Bioinform
  doi: 10.1186/s12859-018-2486-6
  contributor:
    fullname: Ge
– volume: 105
  start-page: 127
  year: 2017
  ident: 2024011017301374100_CR73
  article-title: Epsilonproteobacterial hydroxylamine oxidoreductase (εHao): characterization of a ‘missing link’ in the multihaem cytochrome c family
  publication-title: Mol Microbiol
  doi: 10.1111/mmi.13690
  contributor:
    fullname: Haase
– volume: 23
  start-page: 1405
  year: 2014
  ident: 2024011017301374100_CR21
  article-title: Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania
  publication-title: Mol Ecol
  doi: 10.1111/mec.12461
  contributor:
    fullname: Flot
– volume: 6
  start-page: e23136
  year: 2017
  ident: 2024011017301374100_CR95
  article-title: Bacterial flagella grow through an injection-diffusion mechanism
  publication-title: Elife
  doi: 10.7554/eLife.23136
  contributor:
    fullname: Renault
– volume: 3
  start-page: 1093
  year: 2009
  ident: 2024011017301374100_CR20
  article-title: Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave
  publication-title: ISME J
  doi: 10.1038/ismej.2009.57
  contributor:
    fullname: Chen
– volume: 2020.04.27.062828
  year: 2021
  ident: 2024011017301374100_CR81
  article-title: Evolutionary genetic species detected in prokaryotes by applying the K/θ ratio to DNA sequences
  publication-title: bioRxiv
  contributor:
    fullname: Birky
– ident: 2024011017301374100_CR74
– volume: 9
  start-page: e112963
  year: 2014
  ident: 2024011017301374100_CR34
  article-title: Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement
  publication-title: PLoS One
  doi: 10.1371/journal.pone.0112963
  contributor:
    fullname: Walker
– volume: 8
  start-page: 87
  year: 2017
  ident: 2024011017301374100_CR85
  article-title: Respiratory ammonification of nitrate coupled to anaerobic oxidation of elemental sulfur in deep-sea autotrophic thermophilic bacteria
  publication-title: Front Microbiol
  doi: 10.3389/fmicb.2017.00087
  contributor:
    fullname: Slobodkina
– start-page: 1189
  volume-title: Bergey’s Manual of Systematic Bacteriology
  year: 2006
  ident: 2024011017301374100_CR3
  contributor:
    fullname: Robertson
– volume: 31
  start-page: 186
  year: 2014
  ident: 2024011017301374100_CR17
  article-title: Microbiology of Movile Cave-A chemolithoautotrophic ecosystem
  publication-title: Geomicrobiol J
  doi: 10.1080/01490451.2013.839764
  contributor:
    fullname: Kumaresan
– volume: 140
  start-page: 3109
  year: 1994
  ident: 2024011017301374100_CR68
  article-title: Motility and chemosensory behaviour of the sulphur bacterium Thiovulum majus
  publication-title: Microbiol-sgm
  doi: 10.1099/13500872-140-11-3109
  contributor:
    fullname: Fenchel
– volume: 1787
  start-page: 646
  year: 2009
  ident: 2024011017301374100_CR88
  article-title: Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria
  publication-title: Biochimica et Biophysica Acta (BBA) - Bioenerg
  doi: 10.1016/j.bbabio.2008.12.010
  contributor:
    fullname: Kern
– volume: 64
  start-page: 522
  year: 2014
  ident: 2024011017301374100_CR23
  article-title: Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake
  publication-title: Int J Syst Evol Microbiol
  doi: 10.1099/ijs.0.057224-0
  contributor:
    fullname: Schirmack
– volume: 23
  start-page: 101
  year: 2003
  ident: 2024011017301374100_CR19
  article-title: Preliminary evidence for a sulphur cycle in movile cave, Romania
  publication-title: Acta Biotechnol
  doi: 10.1002/abio.200390000
  contributor:
    fullname: Rohwerder
– volume: 30
  start-page: 2068
  year: 2014
  ident: 2024011017301374100_CR43
  article-title: Prokka: rapid prokaryotic genome annotation
  publication-title: Bioinformatics
  doi: 10.1093/bioinformatics/btu153
  contributor:
    fullname: Seemann
– volume: 27
  start-page: 347
  year: 2010
  ident: 2024011017301374100_CR76
  article-title: Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11)
  publication-title: Mol Biol Evol
  doi: 10.1093/molbev/msp239
  contributor:
    fullname: Logares
– volume: 14
  start-page: 2060
  year: 2020
  ident: 2024011017301374100_CR71
  article-title: Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation
  publication-title: ISME J
  doi: 10.1038/s41396-020-0669-4
  contributor:
    fullname: Zhou
– volume: 22
  start-page: 109
  year: 2021
  ident: 2024011017301374100_CR55
  article-title: Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology
  publication-title: Brief Bioinform
  doi: 10.1093/bib/bbz104
  contributor:
    fullname: Karp
– volume: 78
  start-page: 8555
  year: 2012
  ident: 2024011017301374100_CR11
  article-title: A single-cell genome for Thiovulum sp
  publication-title: Appl Environ Microbiol
  doi: 10.1128/AEM.02314-12
  contributor:
    fullname: Marshall
– volume: 63
  start-page: 3123
  year: 1997
  ident: 2024011017301374100_CR25
  article-title: Characterization of Thiobacillus thioparus LV43 and its distribution in a chemoautotrophically based groundwater ecosystem
  publication-title: Appl Environ Microbiol
  doi: 10.1128/aem.63.8.3123-3127.1997
  contributor:
    fullname: Vlasceanu
– volume: 13
  start-page: e1005595
  year: 2017
  ident: 2024011017301374100_CR33
  article-title: Unicycler: resolving bacterial genome assemblies from short and long sequencing reads
  publication-title: PLoS Comput Biol
  doi: 10.1371/journal.pcbi.1005595
  contributor:
    fullname: Wick
– volume: 14
  start-page: 1597
  year: 2022
  ident: 2024011017301374100_CR67
  article-title: Potential for natural attenuation of domestic and agricultural pollution in karst groundwater environments
  publication-title: Water
  doi: 10.3390/w14101597
  contributor:
    fullname: Brad
– volume: 26
  start-page: 29
  year: 1961
  ident: 2024011017301374100_CR4
  article-title: The habitat and description of a new genus of sulphur bacterium
  publication-title: J Gen Microbiol
  doi: 10.1099/00221287-26-1-29
  contributor:
    fullname: Lackey
– volume: 14
  start-page: 322
  year: 2014
  ident: 2024011017301374100_CR100
  article-title: Altered motility of Caulobacter crescentus in viscous and viscoelastic media
  publication-title: BMC Microbiol
  doi: 10.1186/s12866-014-0322-3
  contributor:
    fullname: Gao
– volume: 8
  start-page: 867
  year: 2014
  ident: 2024011017301374100_CR89
  article-title: Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano
  publication-title: ISME J
  doi: 10.1038/ismej.2013.206
  contributor:
    fullname: Meyer
– volume: 9
  start-page: 37
  year: 2021
  ident: 2024011017301374100_CR65
  article-title: VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses
  publication-title: Microbiome
  doi: 10.1186/s40168-020-00990-y
  contributor:
    fullname: Guo
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Snippet Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed...
Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave (Romania), sealed...
Abstract Thiovulum spp. (Campylobacterota) are large sulfur bacteria that form veil-like structures in aquatic environments. The sulfidic Movile Cave...
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Ammonia
Aquatic environment
Bacteria
Biomedical and Life Sciences
Candidatus Thiovulum
Cavernicolous species
Caves
Caves - chemistry
Ecology
Electron microscopy
Environmental Sciences
Epsilonproteobacteria - metabolism
Evolutionary Biology
Genomes
Life Sciences
Microbial Ecology
Microbial Genetics and Genomics
Microbiology
Microorganisms
New species
Nitrate reduction
Oxidation
Phylogeny
Pili
Romania
Strains (organisms)
Sulfur
Sulfur - metabolism
Sulfur bacteria
Surface water
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Title Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species
URI https://link.springer.com/article/10.1038/s41396-022-01350-4
https://www.ncbi.nlm.nih.gov/pubmed/36528730
https://www.proquest.com/docview/2777534726
https://search.proquest.com/docview/2755580140
https://hal.univ-antilles.fr/hal-03998872
https://pubmed.ncbi.nlm.nih.gov/PMC9938260
Volume 17
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