Alcock BP, Raphenya AR, Lau TTY, Tsang KK, Bouchard M, Edalatmand A, Huynh W, Nguyen ALV, Cheng AA, Liu S, Min SY, Miroshnichenko A, Tran HK, Werfalli RE, Nasir JA, Oloni M, Speicher DJ, Florescu A, Singh B. et al. (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48(D1):D517–D525. https://doi.org/10.1093/NAR/GKZ935

Article  PubMed  Google Scholar 

Anandkumar B, George RP, Maruthamuthu S, Parvathavarthini N, Mudali UK (2016) Corrosion characteristics of sulfate-reducing bacteria (SRB) and the role of molecular biology in SRB studies: an overview. Corros Rev 34(1–2):41–63. https://doi.org/10.1515/CORRREV-2015-0055/XML

Article  Google Scholar 

Atack JM, Kelly DJ (2006) Structure, mechanism and physiological roles of bacterial cytochrome c peroxidases. Adv Microb Physiol 52:73–106

Google Scholar 

Bai H, Kang Y, Quan H, Han Y, Sun J, Feng Y (2013) Bioremediation of copper-containing wastewater by sulfate reducing bacteria coupled with iron. J Environ Manage 129:350–356. https://doi.org/10.1016/J.JENVMAN.2013.06.050

Article  PubMed  Google Scholar 

Bazin A, Gautreau G, Médigue C, Vallenet D, Calteau A (2020) PanRGP: a pangenome-based method to predict genomic Islands and explore their diversity. Bioinformatics 36(Supplement2):i651–i658. https://doi.org/10.1093/BIOINFORMATICS/BTAA792

Article  PubMed  Google Scholar 

Bertelli C, Tilley KE, Brinkman FSL (2019) Microbial genomic Island discovery, visualization and analysis. Brief Bioinform 20(5):1685–1698. https://doi.org/10.1093/BIB/BBY042

Article  PubMed  Google Scholar 

Borisov VB, Gennis RB, Hemp J, Verkhovsky MI (2011) The cytochrome Bd respiratory oxygen reductases. Biochim Et Biophys Acta (BBA)-Bioenergetics 1807(11):1398–1413

PubMed  Google Scholar 

Bosi E, Fondi M, Orlandini V, Perrin E, Maida I, de Pascale D, Tutino ML, Parrilli E, Giudice L, Filloux A, A., Fani R (2017) The pangenome of (Antarctic) pseudoalteromonas bacteria: evolutionary and functional insights. BMC Genomics 18(1):1–18. https://doi.org/10.1186/S12864-016-3382-Y/FIGURES/8

Article  Google Scholar 

Brioukhanov AL, Kadnikov VV, Beletsky AV, Savvichev AS (2023) Aerotolerant thiosulfate-reducing bacterium Fusibacter sp. strain WBS isolated from littoral bottom sediments of the White Sea—biochemical and genome analysis. Microorganisms 11(7): 1642

Carneiro AR, Ramos RTJ, Barbosa HPM, Schneider MPC, Barh D, Azevedo V, Silva A (2012) Quality of prokaryote genome assembly: indispensable issues of factors affecting prokaryote genome assembly quality. Gene 505(2):365–367. https://doi.org/10.1016/J.GENE.2012.06.016

Article  PubMed  Google Scholar 

Castro HF, Williams NH, Ogram A (2000) Phylogeny of sulfate-reducing bacteria. FEMS Microbiol Ecol 31(1):1–9. https://doi.org/10.1111/J.1574-6941.2000.TB00665.X

Article  PubMed  Google Scholar 

Chen YR, Zhou LZ, Fang ST, Long HY, Chen JY, Zhang GX (2019) Isolation of desulfovibrio spp. From human gut microbiota using a next-generation sequencing directed culture method. Lett Appl Microbiol 68(6):553–561. https://doi.org/10.1111/LAM.13149

Article  PubMed  Google Scholar 

Cross KL, Chirania P, Xiong W, Beall CJ, Elkins JG, Giannone RJ, Griffen AL, Guss AM, Hettich RL, Joshi SS (2018) Insights into the evolution of host association through the isolation and characterization of a novel human periodontal pathobiont. Desulfobulbus Oralis MBio 9(2). https://doi.org/10.1128/mbio02061–02017

Das T, Al-Tawaha AR, Pandey DK, Nongdam P, Shekhawat MS, Dey A, Choudhary K, Sahay S (2022) Halophilic, acidophilic, alkaliphilic, metallophilic, and radioresistant fungi: habitats and their living strategies. Ecology, Physiology and Applications, Springer, Extremophilic Fungi, pp 171–193

Google Scholar 

de Crécy-Lagard V, Yacoubi E, de la Garza B, Noiriel RD, A., Hanson AD (2007) Comparative genomics of bacterial and plant folate synthesis and salvage: predictions and validations. BMC Genomics 8(1):1–15. https://doi.org/10.1186/1471-2164-8-245/FIGURES/8

Article  Google Scholar 

Dev S, Galey M, Chun CL, Novotny C, Ghosh T, Aggarwal S (2021) Enrichment of psychrophilic and acidophilic sulfate-reducing bacterial consortia–a solution toward acid mine drainage treatment in cold regions. Environ Science: Processes Impacts 23(12):2007–2020

Google Scholar 

Dyksma S, Pester M (2024) Growth of sulfate-reducing Desulfobacterota and bacillota at periodic oxygen stress of 50% air-O2 saturation. Microbiome 12(1):191

PubMed  PubMed Central  Google Scholar 

Edwards MJ, Richardson DJ, Paquete CM, Clarke TA (2020) Role of multiheme cytochromes involved in extracellular anaerobic respiration in bacteria. Protein Sci 29(4):830–842

PubMed  Google Scholar 

Ettema TJG, Huynen MA, De Vos WM, n Der Oost J (2003) TRASH: a novel metal-binding domain predicted to be involved in heavy-metal sensing, trafficking and resistance. Trends Biochem Sci 28(4):170–173. https://doi.org/10.1016/S0968-0004(03)00037-9

Article  PubMed  Google Scholar 

Fassler J, Cooper P (2011), July 14 Blast Glossary. In: BLAST® Help [Internet]. Bethesda (MD): National Center for Biotechnology Information (US). https://www.ncbi.nlm.nih.gov/books/NBK62051/

Fournier M, Aubert C, Dermoun Z, Durand MC, Moinier D, Dolla A (2006) Response of the anaerobe desulfovibrio vulgaris Hildenborough to oxidative conditions: proteome and transcript analysis. Biochimie 88(1):85–94. https://doi.org/10.1016/J.BIOCHI.2005.06.012

Article  PubMed  Google Scholar 

Gao SH, Ho JY, Fan L, Nouwens A, Hoelzle RD, Schulz B, Guo J, Zhou J, Yuan Z, Bond PL (2019) A comparative proteomic analysis of desulfovibrio vulgaris Hildenborough in response to the antimicrobial agent free nitrous acid. Sci Total Environ 672:625–633. https://doi.org/10.1016/J.SCITOTENV.2019.03.442

Article  PubMed  Google Scholar 

Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Médigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC, Vallenet D (2020) PPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol 16(3):e1007732. https://doi.org/10.1371/JOURNAL.PCBI.1007732

Article  PubMed  PubMed Central  Google Scholar 

Goñi-Urriza M, Klopp C, Ranchou-Peyruse M, Ranchou-Peyruse A, Monperrus M, Khalfaoui-Hassani B, Guyoneaud R (2020) Genome insights of mercury methylation among desulfovibrio and Pseudodesulfovibrio strains. Res Microbiol 171(1):3–12. https://doi.org/10.1016/J.RESMIC.2019.10.003

Article  PubMed  Google Scholar 

Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and ghostkoala: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428(4):726–731. https://doi.org/10.1016/J.JMB.2015.11.006

Article  PubMed  Google Scholar 

Keller KL, Wall JD, Hanson TE, Barton LL, Stahl DA (2011) Genetics and molecular biology of the electron flow for sulfate respiration in desulfovibrio. https://doi.org/10.3389/fmicb.2011.00135

Kim SY, Jeong HJ, Kim M, Choi AR, Kim MS, Kang SG, Lee SJ (2019) Characterization of the copper-sensing transcriptional regulator CopR from the hyperthermophilic Archeaon Thermococcus onnurineus NA1. BioMetals. 32(6):923–937. https://doi.org/10.1007/S10534-019-00223-2

Kleindienst S, Herbst FA, Stagars M, Von Netzer F, Von Bergen M, Seifert J, Peplies J, Amann R, Musat F, Lueders T, Knittel K (2014) Diverse sulfate-reducing bacteria of the desulfosarcina/desulfococcus clade are the key alkane degraders at marine seeps. ISME J 2014 8(10):10. https://doi.org/10.1038/ismej.2014.51

Article  Google Scholar 

Knop R, Keweloh S, Pukall J, Dittmann S, Zühlke D, Sievers S (2025) A rubrerythrin locus of Clostridioides difficile encodes enzymes that efficiently detoxify reactive oxygen species. Anaerobe 102941

Koch G, Varney J, Bowman E, Thompson N, Gl D, Moghissi O, Gould M, Payer J (2016) International measures of prevention, application, and economics of corrosion technologies study. http://impact.nace.org/documents/Nace-International-Report.pdf

Köseoǧlu VK, Agaissea H (2019) Evolutionary perspectives on the moonlighting functions of bacterial factors that support Actin-Based motility. MBio 10(4). https://doi.org/10.1128/MBIO.01520-19

Koul B, Chaudhary R, Taak P (2021) Extremophilic microbes and their application in bioremediation of environmental contaminants. Microbe mediated remediation of environmental contaminants. Elsevier, pp 115–128

Kumari K, Rawat V, Shadan A, Sharma PK, Deb S, Singh RP (2023) In-depth genome and pan-genome analysis of a metal-resistant bacterium Pseudomonas Parafulva OS-1. Front Microbiol 14:1140249. https://doi.org/10.3389/FMICB.2023.1140249/BIBTEX

Article  PubMed  PubMed Central  Google Scholar 

Kushkevych I. V. - Dissimilatory sulfate reduction in the intestinal sulfate-reducing bacteria (2016). (n.d.). Retrieved April 19, 2022, from http://www.irbis-nbuv.gov.ua/cgi-bin/irbis_nbuv/cgiirbis_64.exe?I21DBN=LINK%26P21DBN=UJRN%26Z21ID=%26S21REF=10%26S21CNR=20%26S21STN=1%26S21FMT=ASP_meta%26C21COM=S%262_S21P03=FILA=%262_S21STR=bist_2016_10_1_19

Kushkevych I, Cejnar J, Treml J, Dordević D, Kollar P, Vítězová M (2020) Recent advances in metabolic pathways of sulfate reduction in intestinal bacteria. Cells 9(3). https://doi.org/10.3390/CELLS9030698/CELLS_09_00698_PDF.PDF

Lallemand T, Leduc M, Landès C, Rizzon C, Lerat E (2020) An overview of duplicated gene detection methods: Why the duplication mechanism has to be accounted for in their choice. Genes 11(9): 1046

Lapierre P, Gogarten JP (2009) Estimating the size of the bacterial pan-genome. In Trends in Genetics 25(3):107 -110. Elsevier Current Trends. https://doi.org/10.1016/j.tig.2008.12.004

Little BJ, Blackwood DJ, Hinks J, Lauro FM, Marsili E, Okamoto A, Rice SA, Wade SA, Flemming HC (2020) Microbially influenced corrosion—Any progress? Corros Sci 170. https://doi.org/10.1016/J.CORSCI.2020.108641

Liu N, Qiu L, Qiu L (2024) Carbon steel corrosion induced by Sulfate-Reducing bacteria: A review of electrochemical mechanisms and pathways in biofilms. Coatings 14(9):1105

Google Scholar 

Marietou A, Røy H, Jørgensen BB, Kjeldsen KU (2018) Sulfate transporters in dissimilatory sulfate reducing microorganisms: A comparative genomics analysis. Front Microbiol 9(MAR):309. https://doi.org/10.3389/FMICB.2018.00309/BIBTEX

Article  PubMed  PubMed Central  Google Scholar 

Meehan BM, Malamy MH (2012) Fumarate reductase is a major contributor to the generation of reactive oxygen species in the anaerobe bacteroides fragilis. Microbiology 158(2):539–546

PubMed  PubMed Central  Google Scholar 

Mehta-Kolte MG, Stoeva MK, Mehra A, Redford SA, Youngblut MD, Zane G, Grégoire P, Carlson HK, Wall J, Coates JD (2019) Adaptation of desulfovibrio alaskensis G20 to perchlorate, a specific inhibitor of sulfate reduction. Environ Microbiol 21(4):1395–1406. https://doi.org/10.1111/1462-2920.14570

Article  PubMed  Google Scholar 

Mogensen GL, Kjeldsen KU, Ingvorsen K (2005) Desulfovibrio aerotolerans sp. nov., an oxygen tolerant sulphate-reducing bacterium isolated from activated sludge. Anaerobe 11(6):339–349

PubMed  Google Scholar 

Novichkov PS, Li X, Kuehl JV, Deutschbauer AM, Arkin AP, Price MN, Rodionov DA (2014) Control of methionine metabolism by the SahR transcriptional regulator in Proteobacteria. Environ Microbiol 16(1):1–8. https://doi.org/10.1111/1462-2920.12273

Article  PubMed