Robertson LA, Gijs Kuenen J, Paster BJ, Dewhirst FE, Vandamme P Thiovulum. In: Brenner DJ, Krieg NR, Staley JT, Garrity GM (eds). Bergey’s Manual of Systematics of Archaea and Bacteria. 2015. Wiley, New York, pp 1–4.
Sylvestre M-N, Jean-Louis P, Grimonprez A, Bilas P, Collienne A, Azède C, et al. Candidatus Thiovulum sp. strain imperiosus: the largest free-living Epsilonproteobacteraeota Thiovulum strain lives in a marine mangrove environment. Can J Microbiol. 2022;68:17–30.
Google Scholar
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.
Lackey JB, Lackey EW. The habitat and description of a new genus of sulphur bacterium. J Gen Microbiol. 1961;26:29–39.
Google Scholar
Lauterborn R. Die sapropelische Lebewelt. Ein Beitrag zur Biologie des Faulschlamms natürlicher Gewässer. Verh Naturhist Med Ver Heidelb. 1915;13:395–481.
Wirsen CO, Jannasch HW. Physiological and morphological observations on Thiovulum sp. J Bacteriol. 1978;136:765–74.
Google Scholar
Garcia-Pichel F. Rapid bacterial swimming measured in swarming cells of Thiovulum majus. J Bacteriol. 1989;171:3560–3.
Google Scholar
Thar R, Fenchel T. True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus. Appl Environ Microbiol. 2001;67:3299–303.
Google Scholar
Petroff AP, Wu X-L, Libchaber A. Fast-moving bacteria self-organize into active two-dimensional crystals of rotating cells. Phys Rev Lett. 2015;114:158102.
Google Scholar
De Boer WE, La Rivière JWM, Houwink AL. Observations on the morphology of Thiovulum majus Hinze. Antonie Van Leeuwenhoek. 1961;27:447–56.
Google Scholar
Marshall IPG, Blainey PC, Spormann AM, Quake SR. A single-cell genome for Thiovulum sp. Appl Environ Microbiol. 2012;78:8555–63.
Google Scholar
Jorgensen BB, Revsbech NP. Colorless sulfur bacteria, Beggiatoa spp. and Thiovulum spp., in O2 and H2S microgradients. Appl Environ Microbiol. 1983;45:1261–70.
Google Scholar
Fenchel T, Glud RN. Veil architecture in a sulphide-oxidizing bacterium enhances countercurrent flux. Nature. 1998;394:367–9.
Google Scholar
Lascu C, Popa R, Sarbu SM. Le karst de Movile (Dobrogea de Sud). Rev Roum de Géographie. 1994;38:85–94.
Riess W, Giere O, Kohls O, Sarbu S. Anoxic thermomineral cave waters and bacterial mats as habitat for freshwater nematodes. Aquat Micro Ecol. 1999;18:157–64.
Google Scholar
Engel AS. Bringing microbes into focus for speleology: an introduction. In: Engel AS (ed). Microbial Life of Cave Systems. 2015. De Gruyter, Berlin, München, Boston, pp 1–22.
Kumaresan D, Wischer D, Stephenson J, Hillebrand-Voiculescu A, Murrell JC. Microbiology of Movile Cave-A chemolithoautotrophic ecosystem. Geomicrobiol J. 2014;31:186–93.
Google Scholar
Sarbu SM. Movile Cave: A chemoautotrophically based groundwater ecosystem. In: Wilken H, Culver DC, Humphreys WF (eds). Subterranean Ecosystems. 2000. Elsevier, Amsterdam, pp 319–43.
Rohwerder T, Sand W, Lascu C. Preliminary evidence for a sulphur cycle in movile cave, Romania. Acta Biotechnol. 2003;23:101–7.
Google Scholar
Chen Y, Wu L, Boden R, Hillebrand A, Kumaresan D, Moussard H, et al. Life without light: microbial diversity and evidence of sulfur- and ammonium-based chemolithotrophy in Movile Cave. ISME J. 2009;3:1093–104.
Google Scholar
Flot J-F, Bauermeister J, Brad T, Hillebrand-Voiculescu A, Sarbu SM, Dattagupta S. Niphargus-Thiothrix associations may be widespread in sulphidic groundwater ecosystems: evidence from southeastern Romania. Mol Ecol. 2014;23:1405–17.
Google Scholar
Hutchens E, Radajewski S, Dumont MG, McDonald IR, Murrell JC. Analysis of methanotrophic bacteria in Movile Cave by stable isotope probing. Environ Microbiol. 2004;6:111–20.
Google Scholar
Schirmack J, Mangelsdorf K, Ganzert L, Sand W, Hillebrand-Voiculescu A, Wagner D. Methanobacterium movilense sp. nov., a hydrogenotrophic, secondary-alcohol-utilizing methanogen from the anoxic sediment of a subsurface lake. Int J Syst Evol Microbiol. 2014;64:522–7.
Google Scholar
Ganzert L, Schirmack J, Alawi M, Mangelsdorf K, Sand W, Hillebrand-Voiculescu A, et al. Methanosarcina spelaei sp. nov., a methanogenic archaeon isolated from a floating biofilm of a subsurface sulphurous lake. Int J Syst Evol Microbiol. 2014;64:3478–84.
Google Scholar
Vlasceanu L, Popa R, Kinkle BK. Characterization of Thiobacillus thioparus LV43 and its distribution in a chemoautotrophically based groundwater ecosystem. Appl Environ Microbiol. 1997;63:3123.
Google Scholar
Gros O. First description of a new uncultured epsilon sulfur bacterium colonizing marine mangrove sediment in the caribbean: Thiovulum sp. strain karukerense. FEMS Microbiol Lett. 2017;364:fnx172.
Google Scholar
Nercessian O, Noyes E, Kalyuzhnaya MG, Lidstrom ME, Chistoserdova L. Bacterial populations active in metabolism of C1 compounds in the sediment of Lake Washington, a freshwater lake. Appl Environ Microbiol. 2005;71:6885–99.
Google Scholar
Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: Rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. 2020;5:521922.
Google Scholar
Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37:540–6.
Google Scholar
Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31:3350–2.
Google Scholar
Gertz EM, Yu Y-K, Agarwala R, Schäffer AA, Altschul SF. Composition-based statistics and translated nucleotide searches: improving the TBLASTN module of BLAST. BMC Biol. 2006;4:41.
Google Scholar
Luo J, Lyu M, Chen R, Zhang X, Luo H, Yan C. SLR: a scaffolding algorithm based on long reads and contig classification. BMC Bioinforma. 2019;20:539.
Google Scholar
Wick RR, Judd LM, Gorrie CL, Holt KE. Unicycler: resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol. 2017;13:e1005595.
Google Scholar
Walker BJ, Abeel T, Shea T, Priest M, Abouelliel A, Sakthikumar S, et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS One. 2014;9:e112963.
Google Scholar
Vaser R, Sović I, Nagarajan N, Šikić M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017;27:737–46.
Google Scholar
Garrison E, Marth G. Haplotype-based variant detection from short-read sequencing. ArXiv 2012;1207.
Clark SC, Egan R, Frazier PI, Wang Z. ALE: a generic assembly likelihood evaluation framework for assessing the accuracy of genome and metagenome assemblies. Bioinformatics. 2013;29:435–43.
Google Scholar
Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Li D, Liu C-M, Luo R, Sadakane K, Lam T-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics. 2015;31:1674–6.
Google Scholar
Kang DD, Froula J, Egan R, Wang Z. MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ. 2015;3:e1165.
Google Scholar
Chaumeil P-A, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics. 2019;36:1925–7.
Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 2015;25:1043–55.
Google Scholar
Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9.
Google Scholar
Shaffer M, Borton MA, McGivern BB, Zayed AA, La Rosa SL, Solden LM, et al. DRAM for distilling microbial metabolism to automate the curation of microbiome function. Nucleic Acids Res. 2020;48:8883–8900.
Google Scholar
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res. 2016;44:D457–62.
Google Scholar
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2019;47:D309–D314.
Google Scholar
Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, et al. The PATRIC Bioinformatics Resource Center: Expanding data and analysis capabilities. Nucleic Acids Res. 2020;48:D606–12.
Google Scholar
Brettin T, Davis JJ, Disz T, Edwards RA, Gerdes S, Olsen GJ, et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci Rep. 2015;5:8365.
Google Scholar
Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, Edwards RA, et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics. 2008;9:75.
Google Scholar
Overbeek R, Olson R, Pusch GD, Olsen GJ, Davis JJ, Disz T, et al. The SEED and the Rapid Annotation of microbial genomes using Subsystems Technology (RAST). Nucleic Acids Res. 2014;42:D206–14.
Google Scholar
Tatusov RL, Galperin MY, Natale DA, Koonin EV. The COG database: a tool for genome-scale analysis of protein functions and evolution. Nucleic Acids Res. 2000;28:33–36.
Google Scholar
Eren AM, Esen ÖC, Quince C, Vineis JH, Morrison HG, Sogin ML, et al. Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319.
Google Scholar
Taboada B, Estrada K, Ciria R, Merino E. Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes. Bioinformatics. 2018;34:4118–20.
Google Scholar
Grissa I, Vergnaud G, Pourcel C. CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res. 2007;35:W52–7.
Google Scholar
Karp PD, Midford PE, Billington R, Kothari A, Krummenacker M, Latendresse M, et al. Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology. Brief Bioinform. 2021;22:109–26.
Google Scholar
Abby SS, Néron B, Ménager H, Touchon M, Rocha EPC. MacSyFinder: a program to mine genomes for molecular systems with an application to CRISPR-Cas systems. PLoS One. 2014;9:e110726.
Google Scholar
Denise R, Abby SS, Rocha EPC. Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility. PLoS Biol. 2019;17:e3000390.
Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:1–8. 2018 9:1
Google Scholar
Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol. 2021;59:476–80. 2021 59:5
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490.
Google Scholar
Patro R, Duggal G, Love MI, Irizarry RA, Kingsford C. Salmon provides fast and bias-aware quantification of transcript expression. Nat Methods. 2017;14:417–9.
Google Scholar
Ge SX, Son EW, Yao R. iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data. BMC Bioinform. 2018;19:534.
Google Scholar
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550.
Google Scholar
Ritchie ME, Phipson B, Wu D, Hu Y, Law CW, Shi W, et al. Limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43:e47.
Google Scholar
Guo J, Bolduc B, Zayed AA, Varsani A, Dominguez-Huerta G, Delmont TO, et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome. 2021;9:37.
Google Scholar
O’Leary NA, Wright MW, Brister JR, Ciufo S, Haddad D, McVeigh R, et al. Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation. Nucleic Acids Res. 2016;44:D733–D745.
Google Scholar
Brad T, Bizic M, Ionescu D, Chiriac CM, Kenesz M, Roba C, et al. Potential for natural attenuation of domestic and agricultural pollution in karst groundwater environments. Water. 2022;14:1597.
Google Scholar
Fenchel T. Motility and chemosensory behaviour of the sulphur bacterium Thiovulum majus. Microbiol-sgm. 1994;140:3109–16.
Google Scholar
Hamilton T, Jones DS, Schaperdoth I, Macalady J. Metagenomic insights into S(0) precipitation in a terrestrial subsurface lithoautotrophic ecosystem. Front Microbiol. 2014;5:756.
Porter M, Summers Engel A, Kane T, Kinkle B. Productivity-diversity relationships from chemolithoautotrophically based sulfidic karst systems. Int J Speleol. 2009;38:27–40.
Google Scholar
Zhou Z, Tran PQ, Kieft K, Anantharaman K. Genome diversification in globally distributed novel marine Proteobacteria is linked to environmental adaptation. ISME J. 2020;14:2060.
Google Scholar
Parrello B, Butler R, Chlenski P, Olson R, Overbeek J, Pusch GD, et al. A machine learning-based service for estimating quality of genomes using PATRIC. BMC Bioinform. 2019;20:1–9.
Google Scholar
Haase D, Hermann B, Einsle O, Simon J. Epsilonproteobacterial hydroxylamine oxidoreductase (εHao): characterization of a ‘missing link’ in the multihaem cytochrome c family. Mol Microbiol. 2017;105:127–38.
Google Scholar
Waite DW, Chuvochina MS, Hugenholtz P. Road map of the phylum Campylobacterota. Bergey’s Manual of Systematics of Archaea and Bacteria. 2019. pp 1–11.
Hoffman AA, Hercus MJ. Environmental stress as an evolutionary force. Bioscience. 2000;50:217–26.
Google Scholar
Logares R, Brte J, Heinrich F, Shalchian-Tabrizi K, Bertilsson S. Infrequent transitions between saline and fresh waters in one of the most abundant microbial lineages (SAR11). Mol Biol Evol. 2010;27:347–57.
Google Scholar
Rodriguez-R LM, Konstantinidis KT. Bypassing cultivation to identify bacterial species. Microbe. 2014;9:111–8.
Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil PA, et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol. 2018;36:996–1004. 2018 36:10
Google Scholar
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.
Birky CW, Adams J, Gemmel M, Perry J. Using population genetic theory and DNA sequences for species detection and identification in asexual organisms. PLoS One. 2010;5:e10609.
Google Scholar
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.
Volland J-M, Schintlmeister A, Zambalos H, Reipert S, Mozetič P, Espada-Hinojosa S, et al. NanoSIMS and tissue autoradiography reveal symbiont carbon fixation and organic carbon transfer to giant ciliate host. ISME J. 2018;12:714–27.
Google Scholar
Sarbu SM, Kane TC, Kinkle BK. A chemoautotrophically based cave ecosystem. Science. 1996;272:1953–5.
Google Scholar
Poser A, Vogt C, Knöller K, Ahlheim J, Weiss H, Kleinsteuber S, et al. Stable sulfur and oxygen isotope fractionation of anoxic sulfide oxidation by two different enzymatic pathways. Environ Sci Technol. 2014;48:9094–102.
Google Scholar
Slobodkina GB, Mardanov AV, Ravin NV, Frolova AA, Chernyh NA, Bonch-Osmolovskaya EA, et al. Respiratory ammonification of nitrate coupled to anaerobic oxidation of elemental sulfur in deep-sea autotrophic thermophilic bacteria. Front Microbiol. 2017;8:87.
Google Scholar
Eisenmann E, Beuerle J, Sulger K, Kroneck PMH, Schumacher W. Lithotrophic growth of Sulfurospirillum deleyianum with sulfide as electron donor coupled to respiratory reduction of nitrate to ammonia. Arch Microbiol. 1995;164:180–5.
Google Scholar
Pandey CB, Kumar U, Kaviraj M, Minick KJ, Mishra AK, Singh JS. DNRA: A short-circuit in biological N-cycling to conserve nitrogen in terrestrial ecosystems. Sci Total Environ. 2020;738:139710.
Google Scholar
Kern M, Simon J. Electron transport chains and bioenergetics of respiratory nitrogen metabolism in Wolinella succinogenes and other Epsilonproteobacteria. Biochimica et Biophysica Acta (BBA) – Bioenerg. 2009;1787:646–56.
Google Scholar
Meyer JL, Huber JA. Strain-level genomic variation in natural populations of Lebetimonas from an erupting deep-sea volcano. ISME J. 2014;8:867–80.
Google Scholar
Shu D, Guo J, Zhang B, He Y, Wei G. rDNA- and rRNA-derived communities present divergent assemblage patterns and functional traits throughout full-scale landfill leachate treatment process trains. Sci Tot Environ. 2019;646:1069–79.
Google Scholar
Bižic-Ionescu M, Ionescu D, Grossart HP. Organic particles: Heterogeneous hubs for microbial interactions in aquatic ecosystems. Front Microbiol. 2018;9:2569.
Google Scholar
Millman A, Bernheim A, Stokar-Avihail A, Fedorenko T, Voichek M, Leavitt A, et al. Bacterial retrons function in anti-phage defense. Cell. 2020;183:1551–.e12.
Google Scholar
Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases—a historical perspective and more. Nucleic Acids Res. 2014;42:7489–527.
Google Scholar
Fauré-Fremiet E, Rouiller CH. Étude au microscope électronique d’une bactérie sulfureuse, Thiovulum majus Hinze. Exp Cell Res. 1958;14:29–46.
Google Scholar
Renault TT, Abraham AO, Bergmiller T, Paradis G, Rainville S, Charpentier E, et al. Bacterial flagella grow through an injection-diffusion mechanism. Elife. 2017;6:e23136.
Google Scholar
Karami Y, López-Castilla A, Ori A, Thomassin JL, Bardiaux B, Malliavin T, et al. Computational and biochemical analysis of type IV pilus dynamics and stability. Structure. 2021;29:1397–.e6.
Google Scholar
Biais N, Ladoux B, Higashi D, So M, Sheetz M. Cooperative retraction of bundled type IV pili enables nanonewton force generation. PLoS Biol. 2008;6:e87.
Google Scholar
Higashi DL, Biais N, Weyand NJ, Agellon A, Sisko JL, Brown LM, et al. N. elongata produces type IV pili that mediate interspecies gene transfer with N. gonorrhoeae. PLoS One. 2011;6:e21373.
Google Scholar
Craig L, Forest KT, Maier B. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol. 2019;17:429–40.
Google Scholar
Gao Y, Neubauer M, Yang A, Johnson N, Morse M, Li G, et al. Altered motility of Caulobacter crescentus in viscous and viscoelastic media. BMC Microbiol. 2014;14:322.
Google Scholar
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.
Brad T, Iepure S, Sarbu SM. The chemoautotrophically based movile cave groundwater ecosystem, a hotspot of subterranean biodiversity. Diversity. 2021;13:128.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: Improved data processing and web-based tools. Nucleic Acids Res. 2013;41:D590–6.
Google Scholar
Grote J, Schott T, Bruckner CG, Glöckner FO, Jost G, Teeling H, et al. Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proc Natl Acad Sci USA. 2012;109:506–10.
Google Scholar
Credit: Source link
