A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

Alneberg, J., Bjarnason, B. S., de Bruijn, I., Schirmer, M., Quick, J., Ijaz, U. Z., Lahti, L., Loman, N. J., Andersson, A. F., & Quince, C. (2014). Binning metagenomic contigs by coverage and composition. Nature Methods, 11(11), 1144-1146. https://doi.org/10.1038/nmeth.3103

Alneberg, J., Karlsson, C. M. G., Divne, A.-M., Bergin, C., Homa, F., Lindh, M. V., Hugerth, L. W., Ettema, T. J. G., Bertilsson, S., Andersson, A. F., & Pinhassi, J. (2018). Genomes from uncultivated prokaryotes: A comparison of metagenome-assembled and single-amplified genomes. Microbiome, 6(1), 173. https://doi.org/10.1186/s40168-018-0550-0

Altschul, S. F., Gish, W., Miller, W., Myers, E. W., & Lipman, D. J. (1990). Basic local alignment search tool. Journal of Molecular Biology, 215(3), 403-410. https://doi.org/10.1016/S0022-2836(05)80360-2

Anantharaman, K., Brown, C. T., Hug, L. A., Sharon, I., Castelle, C. J., Probst, A. J., Thomas, B. C., Singh, A., Wilkins, M. J., Karaoz, U., Brodie, E. L., Williams, K. H., Hubbard, S. S., & Banfield, J. F. (2016). Thousands of microbial genomes shed light on interconnected biogeochemical processes in an aquifer system. Nature Communications, 7(1), 13219. https://doi.org/10.1038/ncomms13219

Bankevich, A., Nurk, S., Antipov, D., Gurevich, A. A., Dvorkin, M., Kulikov, A. S., Lesin, V. M., Nikolenko, S. I., Pham, S., Prjibelski, A. D., Pyshkin, A. V., Sirotkin, A. V., Vyahhi, N., Tesler, G., Alekseyev, M. A., & Pevzner, P. A. (2012). SPAdes: A new genome assembly algorithm and its applications to single-cell sequencing. Journal of Computational Biology, 19(5), 455-477. https://doi.org/10.1089/cmb.2012.0021

Bell, E., Lamminmäki, T., Alneberg, J., Andersson, A. F., Qian, C., Xiong, W., Hettich, R. L., Frutschi, M., & Bernier-Latmani, R. (2020). Active sulfur cycling in the terrestrial deep subsurface. The ISME Journal, 14(5), 1260-1272. https://doi.org/10.1038/s41396-020-0602-x

Berben, T., Overmars, L., Sorokin, D. Y., & Muyzer, G. (2019). Diversity and distribution of sulfur oxidation-related genes in Thioalkalivibrio, a genus of Chemolithoautotrophic and Haloalkaliphilic sulfur-oxidizing bacteria. Frontiers in Microbiology, 10, 160. https://doi.org/10.3389/fmicb.2019.00160

Berg, J. S., Jézéquel, D., Duverger, A., Lamy, D., Laberty-Robert, C., & Miot, J. (2019). Microbial diversity involved in iron and cryptic sulfur cycling in the ferruginous, low-sulfate waters of Lake Pavin. PLoS One, 14(2), e0212787. https://doi.org/10.1371/journal.pone.0212787

Biderre-Petit, C., Boucher, D., Kuever, J., Alberic, P., Jézéquel, D., Chebance, B., Borrel, G., Fonty, G., & Peyret, P. (2011). Identification of sulfur-cycle prokaryotes in a low-sulfate Lake (Lake Pavin) using aprA and 16S rRNA gene markers. Microbial Ecology, 61(2), 313-327. https://doi.org/10.1007/s00248-010-9769-4

Biderre-Petit, C., Dugat-Bony, E., Mege, M., Parisot, N., Adrian, L., Moné, A., Denonfoux, J., Peyretaillade, E., Debroas, D., Boucher, D., & Peyret, P. (2016). Distribution of Dehalococcoidia in the anaerobic deep water of a remote meromictic crater Lake and detection of Dehalococcoidia-derived reductive dehalogenase homologous genes. PLoS One, 11(1), e0145558. https://doi.org/10.1371/journal.pone.0145558

Biderre-Petit, C., Jézéquel, D., Dugat-Bony, E., Lopes, F., Kuever, J., Borrel, G., Viollier, E., Fonty, G., & Peyret, P. (2011). Identification of microbial communities involved in the methane cycle of a freshwater meromictic lake: Methane cycle in a stratified freshwater ecosystem. FEMS Microbiology Ecology, 77(3), 533-545. https://doi.org/10.1111/j.1574-6941.2011.01134.x

Biderre-Petit, C., Taib, N., Gardon, H., Hochart, C., & Debroas, D. (2019). New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics. FEMS Microbiology Ecology, 95(3), fiy183. https://doi.org/10.1093/femsec/fiy183

Block, K. R., O'Brien, J. M., Edwards, W. J., & Marnocha, C. L. (2021). Vertical structure of the bacterial diversity in meromictic Fayetteville green Lake. MicrobiologyOpen, 10(4), e1228. https://doi.org/10.1002/mbo3.1228

Bolger, A. M., Lohse, M., & Usadel, B. (2014). Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, 30(15), 2114-2120. https://doi.org/10.1093/bioinformatics/btu170

Booker, A. E., Borton, M. A., Daly, R. A., Welch, S. A., Nicora, C. D., Hoyt, D. W., Wilson, T., Purvine, S. O., Wolfe, R. A., Sharma, S., Mouser, P. J., Cole, D. R., Lipton, M. S., Wrighton, K. C., & Wilkins, M. J. (2017). Sulfide generation by dominant Halanaerobium microorganisms in hydraulically fractured shales. MSphere, 2(4), e00257-17. https://doi.org/10.1128/mSphereDirect.00257-17

Bowers, R. M., Stepanauskas, R., Harmon-Smith, M., Doud, D., Reddy, T. B. K., Schulz, F., Jarett, J., Rivers, A. R., Eloe-Fadrosh, E. A., Tringe, S. G., Ivanova, N. N., Copeland, A., Clum, A., Becraft, E. D., Malmstrom, R. R., Birren, B., Podar, M., Bork, P., Weinstock, G. M., … Woyke, T. (2017). Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea. Nature Biotechnology, 35(8), 725-731. https://doi.org/10.1038/nbt.3893

Bradley, J. M., Svistunenko, D. A., Wilson, M. T., Hemmings, A. M., Moore, G. R., & Le Brun, N. E. (2020). Bacterial iron detoxification at the molecular level. Journal of Biological Chemistry, 295(51), 17602-17623. https://doi.org/10.1074/jbc.REV120.007746

Buchfink, B., Reuter, K., & Drost, H.-G. (2021). Sensitive protein alignments at 321 tree-of-life scale using DIAMOND. Nature Methods, 18, 366-368. https://doi.org/10.1038/s41592-021-01101-x

Bura-Nakić, E., Viollier, E., & Ciglenečki, I. (2012). Electrochemical and colorimetric measurements show the dominant role of FeS in a permanently anoxic Lake. Environmental Science & Technology, 47(2), 741-749. https://doi.org/10.1021/es303603j

Callbeck, C. M., Canfield, D. E., Kuypers, M. M. M., Yilmaz, P., Lavik, G., Thamdrup, B., Schubert, C. J., & Bristow, L. A. (2021). Sulfur cycling in oceanic oxygen minimum zones. Limnology and Oceanography, 66(6), 2360-2392. https://doi.org/10.1002/lno.11759

Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., & Madden, T. L. (2009). BLAST+: Architecture and applications. BMC Bioinformatics, 10(1), 421. https://doi.org/10.1186/1471-2105-10-421

Campbell, B. J., Engel, A. S., Porter, M. L., & Takai, K. (2006). The versatile ε-proteobacteria: Key players in sulphidic habitats. Nature Reviews Microbiology, 4(6), 458-468. https://doi.org/10.1038/nrmicro1414

Capella-Gutiérrez, S., Silla-Martínez, J. M., & Gabaldón, T. (2009). trimAl: A tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics, 25(15), 1972-1973. https://doi.org/10.1093/bioinformatics/btp348

Chaumeil, P.-A., Mussig, A. J., Hugenholtz, P., & Parks, D. H. (2020). GTDB-Tk: A toolkit to classify genomes with the genome taxonomy database. Bioinformatics, 36(6), 1925-1927. https://doi.org/10.1093/bioinformatics/btz848

Coluzzi, C., Guédon, G., Devignes, M.-D., Ambroset, C., Loux, V., Lacroix, T., Payot, S., & Leblond-Bourget, N. (2017). A glimpse into the world of integrative and Mobilizable elements in streptococci reveals an unexpected diversity and novel families of mobilization proteins. Frontiers in Microbiology, 8, 443. https://doi.org/10.3389/fmicb.2017.00443

Crutcher, F. K., Puckhaber, L. S., Stipanovic, R. D., Bell, A. A., Nichols, R. L., Lawrence, K. S., & Liu, J. (2017). Microbial resistance mechanisms to the antibiotic and Phytotoxin Fusaric acid. Journal of Chemical Ecology, 43(10), 996-1006. https://doi.org/10.1007/s10886-017-0889-x

Dahl, C. (2015). Cytoplasmic sulfur trafficking in sulfur-oxidizing prokaryotes. IUBMB Life, 67(4), 268-274. https://doi.org/10.1002/iub.1371

Diao, M., Huisman, J., & Muyzer, G. (2018). Spatio-temporal dynamics of sulfur bacteria during oxic-Anoxic regime shifts in a seasonally stratified lake. FEMS Microbiology Ecology, 94(4), fiy040. https://doi.org/10.1093/femsec/fiy040

Dy, R. L., Przybilski, R., Semeijn, K., Salmond, G. P. C., & Fineran, P. C. (2014). A widespread bacteriophage abortive infection system functions through a Type IV toxin-antitoxin mechanism. Nucleic Acids Research, 42(7), 4590-4605. https://doi.org/10.1093/nar/gkt1419

Edgar, R. C. (2004). MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics, 5(1), 113. https://doi.org/10.1186/1471-2105-5-113

Edgar, R. C. (2022). Muscle5: High-accuracy alignment ensembles enable unbiased assessments of sequence homology and phylogeny. BMC Bioinformatics, 13(1), 6968. https://doi.org/10.1038/s41467-022-34630-w

Eren, A. M., Esen, Ö. C., Quince, C., Vineis, J. H., Morrison, H. G., Sogin, M. L., & Delmont, T. O. (2015). Anvi'o: An advanced analysis and visualization platform for 'omics data. PeerJ, 3, e1319. https://doi.org/10.7717/peerj.1319

Fang, Y., Liu, J., Yang, J., Wu, G., Hua, Z., Dong, H., Hedlund, B. P., Baker, B. J., & Jiang, H. (2022). Compositional and metabolic responses of autotrophic microbial community to salinity in lacustrine environments. MSystems, 7(4), e00335-22. https://doi.org/10.1128/msystems.00335-22

Fraikin, N., Goormaghtigh, F., & Van Melderen, L. (2020). Type II toxin-antitoxin systems: Evolution and revolutions. Journal of Bacteriology, 202(7), e00763. https://doi.org/10.1128/JB.00763-19

French, C. E., Bell, J. M. L., & Ward, F. B. (2008). Diversity and distribution of hemerythrin-like proteins in prokaryotes. FEMS Microbiology Letters, 279(2), 131-145. https://doi.org/10.1111/j.1574-6968.2007.01011.x

Goris, J., Konstantinidis, K. T., Klappenbach, J. A., Coenye, T., Vandamme, P., & Tiedje, J. M. (2007). DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. International Journal of Systematic and Evolutionary Microbiology, 57(1), 81-91. https://doi.org/10.1099/ijs.0.64483-0

Götz, F., Longnecker, K., Kido Soule, M. C., Becker, K. W., McNichol, J., Kujawinski, E. B., & Sievert, S. M. (2018). Targeted metabolomics reveals proline as a major osmolyte in the chemolithoautotroph Sulfurimonas denitrificans. MicrobiologyOpen, 7(4), e00586. https://doi.org/10.1002/mbo3.586

Grein, F., Ramos, A. R., Venceslau, S. S., & Pereira, I. A. C. (2013). Unifying concepts in anaerobic respiration: Insights from dissimilatory sulfur metabolism. Biochimica et Biophysica Acta (BBA) - Bioenergetics, 1827(2), 145-160. https://doi.org/10.1016/j.bbabio.2012.09.001

Grote, J., Schott, T., Bruckner, C. G., Glöckner, F. O., Jost, G., Teeling, H., Labrenz, M., & Jürgens, K. (2012). Genome and physiology of a model Epsilonproteobacterium responsible for sulfide detoxification in marine oxygen depletion zones. Proceedings of the National Academy of Sciences, 109(2), 506-510. https://doi.org/10.1073/pnas.1111262109

Gwak, J.-H., Awala, S. I., Nguyen, N.-L., Yu, W.-J., Yang, H.-Y., von Bergen, M., Jehmlich, N., Kits, K. D., Loy, A., Dunfield, P. F., Dahl, C., Hyun, J.-H., & Rhee, S.-K. (2022). Sulfur and methane oxidation by a single microorganism. Proceedings of the National Academy of Sciences, 119(32), e2114799119. https://doi.org/10.1073/pnas.2114799119

Hahn, C. R., Farag, I. F., Murphy, C. L., Podar, M., Elshahed, M. S., & Youssef, N. H. (2022). Microbial diversity and sulfur cycling in an early earth analogue: From ancient novelty to modern commonality. MBio, 13(2), e00016-22. https://doi.org/10.1128/mbio.00016-22

Hamilton, T. L., Bovee, R. J., Thiel, V., Sattin, S. R., Mohr, W., Schaperdoth, I., Vogl, K., Gilhooly, W. P., III, Lyons, T. W., Tomsho, L. P., Schuster, S. C., Overmann, J., Bryant, D. A., Pearson, A., & Macalady, J. L. (2014). Coupled reductive and oxidative sulfur cycling in the phototrophic plate of a meromictic lake. Geobiology, 12(5), 451-468. https://doi.org/10.1111/gbi.12092

Han, Y., & Perner, M. (2015). The globally widespread genus Sulfurimonas: Versatile energy metabolisms and adaptations to redox clines. Frontiers in Microbiology, 6, 989. https://doi.org/10.3389/fmicb.2015.00989

Henkel, J. V., Vogts, A., Werner, J., Neu, T. R., Spröer, C., Bunk, B., & Schulz-Vogt, H. N. (2021). Candidatus Sulfurimonas marisnigri sp. Nov. and Candidatus Sulfurimonas baltica sp. Nov., thiotrophic manganese oxide reducing chemolithoautotrophs of the class Campylobacteria isolated from the pelagic redoxclines of the Black Sea and the Baltic Sea. Systematic and Applied Microbiology, 44(1), 126155. https://doi.org/10.1016/j.syapm.2020.126155

Hu, Q., Wang, S., Lai, Q., Shao, Z., & Jiang, L. (2021). Sulfurimonas indica sp. Nov., a hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal sulfide chimney in the Northwest Indian Ocean. International Journal of Systematic and Evolutionary Microbiology, 71(1), e004575. https://doi.org/10.1099/ijsem.0.004575

Huang, Y., Gilna, P., & Li, W. (2009). Identification of ribosomal RNA genes in metagenomic fragments. Bioinformatics, 25(10), 1338-1340. https://doi.org/10.1093/bioinformatics/btp161

Huerta-Cepas, J., Szklarczyk, D., Heller, D., Hernández-Plaza, A., Forslund, S. K., Cook, H., Mende, D. R., Letunic, I., Rattei, T., Jensen, L. J., von Mering, C., & Bork, P. (2019). eggNOG 5.0: A hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Research, 47(D1), D309-D314. https://doi.org/10.1093/nar/gky1085

Hyatt, D., Chen, G.-L., LoCascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11(1), 119. https://doi.org/10.1186/1471-2105-11-119

Jaffe, A. L., Bardot, C., Lejeune, A. L., Liu, J., Colombet, J., Perrière, F., Billard, H., Castelle, C. J., Lehours, A.-C., & Banfield, J. F. (2023). Variable impact of geochemical gradients on the functional potential of bacteria, archaea, and phages from the permanently stratified lac Pavin. Microbiome, 11(1), 14. https://doi.org/10.1186/s40168-022-01416-7

Johnson, L. A., & Hug, L. A. (2019). Distribution of reactive oxygen species defense mechanisms across domain bacteria. Free Radical Biology and Medicine, 140, 93-102. https://doi.org/10.1016/j.freeradbiomed.2019.03.032

Kamruzzaman, M., Wu, A. Y., & Iredell, J. R. (2021). Biological functions of type II toxin-antitoxin Systems in Bacteria. Microorganisms, 9(6), 1276. https://doi.org/10.3390/microorganisms9061276

Kang, D. K., Froula, J., Egan, R., & Wang, Z. (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ, 27(3), e1165. https://doi.org/10.7717/peerj.1165

Kim, M., Oh, H.-S., Park, S.-C., & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64(Pt_2), 346-351. https://doi.org/10.1099/ijs.0.059774-0

Kumar, S., Stecher, G., & Tamura, K. (2016). MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Molecular Biology and Evolution, 33(7), 1870-1874. https://doi.org/10.1093/molbev/msw054

Lahme, S., Callbeck, C. M., Eland, L. E., Wipat, A., Enning, D., Head, I. M., & Hubert, C. R. J. (2020). Comparison of sulfide-oxidizing Sulfurimonas strains reveals a new mode of thiosulfate formation in subsurface environments. Environmental Microbiology, 22(5), 1784-1800. https://doi.org/10.1111/1462-2920.14894

Lahme, S., Enning, D., Callbeck, C. M., Menendez Vega, D., Curtis, T. P., Head, I. M., & Hubert, C. R. J. (2019). Metabolites of an oil field sulfide-oxidizing, nitrate-reducing Sulfurimonas sp. cause severe corrosion. Applied and Environmental Microbiology, 85(3), e01891-18. https://doi.org/10.1128/AEM.01891-18

Lee, M. D. (2019). GToTree: A user-friendly workflow for phylogenomics. Bioinformatics, 35(20), 4162-4164. https://doi.org/10.1093/bioinformatics/btz188

Li, H., & Durbin, R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25(14), 1754-1760. https://doi.org/10.1093/bioinformatics/btp324

Li, D., Liu, C.-M., Luo, R., Sadakane, K., & Lam, T.-W. (2015). MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, 31(10), 1674-1676. https://doi.org/10.1093/bioinformatics/btv033

Li, W., & Godzik, A. (2006). Cd-hit: A fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics, 22(13), 1658-1659. https://doi.org/10.1093/bioinformatics/btl158

Lin, S.-H., & Liao, Y.-C. (2013). CISA: Contig integrator for sequence assembly of bacterial genomes. PLoS One, 8(3), e60843. https://doi.org/10.1371/journal.pone.0060843

Liu, B., Zheng, D., Jin, Q., Chen, L., & Yang, J. (2019). VFDB 2019: A comparative pathogenomic platform with an interactive web interface. Nucleic Acids Research, 47(D1), D687-D692. https://doi.org/10.1093/nar/gky1080

Liu, L.-J., Stockdreher, Y., Koch, T., Sun, S.-T., Fan, Z., Josten, M., Sahl, H.-G., Wang, Q., Luo, Y.-M., Liu, S.-J., Dahl, C., & Jiang, C.-Y. (2014). Thiosulfate transfer mediated by DsrE/TusA homologs from Acidothermophilic sulfur-oxidizing archaeon Metallosphaera cuprina. Journal of Biological Chemistry, 289(39), 26949-26959. https://doi.org/10.1074/jbc.M114.591669

Liu, M., Li, X., Xie, Y., Bi, D., Sun, J., Li, J., Tai, C., Deng, Z., & Ou, H.-Y. (2019). ICEberg 2.0: An updated database of bacterial integrative and conjugative elements. Nucleic Acids Research, 47(D1), D660-D665. https://doi.org/10.1093/nar/gky1123

Lushchak, V. I. (2011). Adaptive response to oxidative stress: Bacteria, fungi, plants and animals. Comparative Biochemistry and Physiology Part C: Toxicology & Pharmacology, 153(2), 175-190. https://doi.org/10.1016/j.cbpc.2010.10.004

Marietou, A., Røy, H., Jørgensen, B. B., & Kjeldsen, K. U. (2018). Sulfate transporters in dissimilatory sulfate reducing microorganisms: A comparative genomics analysis. Frontiers in Microbiology, 9, 309. https://doi.org/10.3389/fmicb.2018.00309

Maschmann, Z. A., Chua, T. K., Chandrasekaran, S., Ibáñez, H., & Crane, B. R. (2022). Redox properties and PAS domain structure of the Escherichia coli energy sensor Aer indicate a multistate sensing mechanism. Journal of Biological Chemistry, 298(12), 102598. https://doi.org/10.1016/j.jbc.2022.102598

Meier, D. V., Pjevac, P., Bach, W., Hourdez, S., Girguis, P. R., Vidoudez, C., Amann, R., & Meyerdierks, A. (2017). Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents. The ISME Journal, 11(7), 1545-1558. https://doi.org/10.1038/ismej.2017.37

Miot, J., Jézéquel, D., Benzerara, K., Cordier, L., Rivas-Lamelo, S., Skouri-Panet, F., Férard, C., Poinsot, M., & Duprat, E. (2016). Mineralogical diversity in Lake Pavin: Connections with water column chemistry and biomineralization processes. Minerals, 6(2), 24. https://doi.org/10.3390/min6020024

Molari, M., Hassenrueck, C., Laso-Pérez, R., Wegener, G., Offre, P., Scilipoti, S., & Boetius, A. (2023). A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes. Nature Microbiology, 8(4), 651-665. https://doi.org/10.1038/s41564-023-01342-w

Möller, L., Laas, P., Rogge, A., Goetz, F., Bahlo, R., Leipe, T., & Labrenz, M. (2019). Sulfurimonas subgroup GD17 cells accumulate polyphosphate under fluctuating redox conditions in the Baltic Sea: Possible implications for their ecology. The ISME Journal, 13(2), 482-493. https://doi.org/10.1038/s41396-018-0267-x

Nosalova, L., Piknova, M., Kolesarova, M., & Pristas, P. (2023). Cold Sulfur Springs-Neglected niche for autotrophic sulfur-oxidizing bacteria. Microorganisms, 11(6), 1436. https://doi.org/10.3390/microorganisms11061436

Parks, D. H., Chuvochina, M., Rinke, C., Mussig, A. J., Chaumeil, P.-A., & Hugenholtz, P. (2022). GTDB: An ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy. Nucleic Acids Research, 50(D1), D785-D794. https://doi.org/10.1093/nar/gkab776

Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P., & Tyson, G. W. (2015). CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Research, 25(7), 1043-1055. https://doi.org/10.1101/gr.186072.114

Peng, Y., Leung, H. C. M., Yiu, S. M., & Chin, F. Y. L. (2012). IDBA-UD: A de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics, 28(11), 1420-1428. https://doi.org/10.1093/bioinformatics/bts174

Price, M. N., Dehal, P. S., & Arkin, A. P. (2010). FastTree 2 - Approximately maximum-likelihood trees for large alignments. PLoS One, 5(3), e9490. https://doi.org/10.1371/journal.pone.0009490

Pritchard, L., Glover, R. H., Humphris, S., Elphinstone, J. G., & Toth, I. K. (2015). Genomics and taxonomy in diagnostics for food security: Soft-rotting enterobacterial plant pathogens. Analytical Methods, 8(1), 12-24. https://doi.org/10.1039/C5AY02550H

Probst, A. J., Ladd, B., Jarett, J. K., Geller-McGrath, D. E., Sieber, C. M. K., Emerson, J. B., Anantharaman, K., Thomas, B. C., Malmstrom, R. R., Stieglmeier, M., Klingl, A., Woyke, T., Ryan, M. C., & Banfield, J. F. (2018). Differential depth distribution of microbial function and putative symbionts through sediment-hosted aquifers in the deep terrestrial subsurface. Nature Microbiology, 3(3), 328-336. https://doi.org/10.1038/s41564-017-0098-y

Ratnikova, N. M., Slobodkin, A. I., Merkel, A. Y., Kopitsyn, D. S., Kevbrin, V. V., Bonch-Osmolovskaya, E. A., & Slobodkina, G. B. (2020). Sulfurimonas crateris sp. Nov., a facultative anaerobic sulfur-oxidizing chemolithoautotrophic bacterium isolated from a terrestrial mud volcano. International Journal of Systematic and Evolutionary Microbiology, 70(1), 487-492. https://doi.org/10.1099/ijsem.0.003779

Ravot, G., Magot, M., Ollivier, B., Patel, B. K. C., Ageron, E., Grimont, P. A. D., Thomas, P., & Garcia, J.-L. (2006). Haloanaerobium congolense sp. Nov., an anaerobic, moderately halophilic, thiosulfate- and sulfur-reducing bacterium from an African oil field. FEMS Microbiology Letters, 147(1), 81-88. https://doi.org/10.1111/j.1574-6968.1997.tb10224.x

Rivas-Lamelo, S., Benzerara, K., Lefèvre, C. T., Monteil, C. L., Jézéquel, D., Menguy, N., Viollier, E., Guyot, F., Férard, C., Poinsot, M., Skouri-Panet, F., Trcera, N., Miot, J., & Duprat, E. (2017). Magnetotactic bacteria as a new model for P sequestration in the ferruginous Lake Pavin. Geochemical Perspectives Letters, 5, 35-41. https://doi.org/10.7185/geochemlet.1743

Rogge, A., Vogts, A., Voss, M., Jürgens, K., Jost, G., & Labrenz, M. (2017). Success of chemolithoautotrophic SUP05 and Sulfurimonas GD17 cells in pelagic Baltic Sea redox zones is facilitated by their lifestyles as K- and r -strategists: SUP05 and Sulfurimonas in sulfidic redox zones. Environmental Microbiology, 19(6), 2495-2506. https://doi.org/10.1111/1462-2920.13783

Römling, U., Galperin, M. Y., & Gomelsky, M. (2013). Cyclic di-GMP: The first 25 years of a universal bacterial second messenger. Microbiology and Molecular Biology Reviews, 77(1), 1-52. https://doi.org/10.1128/MMBR.00043-12

Salmaso, N. (2019). Effects of habitat partitioning on the distribution of Bacterioplankton in Deep Lakes. Frontiers in Microbiology, 10, 2257. https://doi.org/10.3389/fmicb.2019.02257

Sikorski, J., Munk, C., Lapidus, A., Djao, O. D. N., Tapia, R., Goodwin, L., Pitluck, S., Liolios, K., Ivanova, N., Mavromatis, K., Mikhailova, N., Pati, A., Sims, D., Meincke, L., Brettin, T., Detter, J. C., Chen, A., Palaniappan, K., Land, M., … Klenk, H.-P. (2010). Sulfurimonas autotrophica type strain (OK10). Standards in Genomic Sciences, 3(2), 194-202. https://doi.org/10.4056/sigs.1173118

Soto-Jimenez, L., Estrada, K., & Sanchez-Flores, A. (2014). GARM: Genome assembly, reconciliation and merging pipeline. Current Topics in Medicinal Chemistry, 14(3), 418-424. https://doi.org/10.2174/1568026613666131204110628

Takai, K., Suzuki, M., Nakagawa, S., Miyazaki, M., Suzuki, Y., Inagaki, F., & Horikoshi, K. (2006). Sulfurimonas paralvinellae sp. Nov., a novel mesophilic, hydrogen- and sulfur-oxidizing chemolithoautotroph within the Epsilonproteobacteria isolated from a deep-sea hydrothermal vent polychaete nest, reclassification of Thiomicrospira denitrificans as Sulfurimonas denitrificans comb. Nov. And emended description of the genus Sulfurimonas. International Journal of Systematic and Evolutionary Microbiology, 56(8), 1725-1733. https://doi.org/10.1099/ijs.0.64255-0

Tanaka, Y., Yoshikaie, K., Takeuchi, A., Ichikawa, M., Mori, T., Uchino, S., Sugano, Y., Hakoshima, T., Takagi, H., Nonaka, G., & Tsukazaki, T. (2020). Crystal structure of a YeeE/YedE family protein engaged in thiosulfate uptake. Science. Advances, 6(35), eaba7637. https://doi.org/10.1126/sciadv.aba7637

Taviti, A. C., & Beuria, T. K. (2019). Bacterial min proteins beyond the cell division. Critical Reviews in Microbiology, 45(1), 22-32. https://doi.org/10.1080/1040841X.2018.1538932

Taylor, G. T., Suter, E. A., Pachiadaki, M. G., Astor, Y., Edgcomb, V. P., & Scranton, M. I. (2018). Temporal shifts in dominant sulfur-oxidizing chemoautotrophic populations across the Cariaco Basin's redoxcline. Deep Sea Research Part II: Topical Studies in Oceanography, 156, 80-96. https://doi.org/10.1016/j.dsr2.2017.11.016

Thompson, C. C., Chimetto, L., Edwards, R. A., Swings, J., Stackebrandt, E., & Thompson, F. L. (2013). Microbial genomic taxonomy. BMC Genomics, 23(14), 913. https://doi.org/10.1186/1471-2164-14--913

Tian, H., Gao, P., Chen, Z., Li, Y., Li, Y., Wang, Y., Zhou, J., Li, G., & Ma, T. (2017). Compositions and abundances of sulfate-reducing and sulfur-oxidizing microorganisms in water-flooded petroleum reservoirs with different temperatures in China. Frontiers in Microbiology, 8, 143. https://doi.org/10.3389/fmicb.2017.00143

Tully, B. J., Wheat, C. G., Glazer, B. T., & Huber, J. A. (2018). A dynamic microbial community with high functional redundancy inhabits the cold, oxic subseafloor aquifer. The ISME Journal, 12(1), 1-16. https://doi.org/10.1038/ismej.2017.187

Van Dongen, S. (2008). Graph clustering via a discrete uncoupling process. SIAM Journal on Matrix Analysis and Applications, 30, 1. https://doi.org/10.1137/040608635

van Vliet, D. M., von Meijenfeldt, F. A. B., Dutilh, B. E., Villanueva, L., Sinninghe Damsté, J. S., Stams, A. J. M., & Sánchez-Andrea, I. (2021). The bacterial sulfur cycle in expanding dysoxic and euxinic marine waters. Environmental Microbiology, 23(6), 2834-2857. https://doi.org/10.1111/1462-2920.15265

Wacey, D., Kilburn, M. R., Saunders, M., Cliff, J., & Brasier, M. D. (2011). Microfossils of Sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia. Nature Geoscience, 4(10), 698-702. https://doi.org/10.1038/ngeo1238

Wang, L., Cheung, M. K., Liu, R., Wong, C. K., Kwan, H. S., & Hwang, J.-S. (2017). Diversity of Total bacterial communities and chemoautotrophic populations in sulfur-rich sediments of shallow-water hydrothermal vents off Kueishan Island. Taiwan. Microbial Ecology, 73(3), 571-582. https://doi.org/10.1007/s00248-016-0898-2

Wang, S., Jiang, L., Hu, Q., Cui, L., Zhu, B., Fu, X., Lai, Q., Shao, Z., & Yang, S. (2021). Characterization of Sulfurimonas hydrogeniphila sp. Nov., a novel bacterium predominant in Deep-Sea hydrothermal vents and comparative genomic analyses of the genus Sulfurimonas. Frontiers in Microbiology, 12, 626705. https://doi.org/10.3389/fmicb.2021.626705

Wang, S., Jiang, L., Xie, S., Alain, K., Wang, Z., Wang, J., Liu, D., & Shao, Z. (2023). Disproportionation of inorganic sulfur compounds by mesophilic Chemolithoautotrophic Campylobacterota. MSystems, 8(1), e00954-22. https://doi.org/10.1128/msystems.00954-22

Wang, S., Shao, Z., Lai, Q., Liu, X., Xie, S., Jiang, L., & Yang, S. (2021). Sulfurimonas sediminis sp. Nov., a novel hydrogen- and sulfur-oxidizing chemolithoautotroph isolated from a hydrothermal vent at the Longqi system, southwestern Indian ocean. Antonie Van Leeuwenhoek, 114(6), 813-822. https://doi.org/10.1007/s10482-021-01560-4

Wang, X., Preston, J. F., & Romeo, T. (2004). The pgaABCD locus of Escherichia coli promotes the synthesis of a polysaccharide Adhesin required for biofilm formation. Journal of Bacteriology, 186(9), 2724-2734. https://doi.org/10.1128/JB.186.9.2724-2734.2004

Wang, Z., Wang, S., Lai, Q., Wei, S., Jiang, L., & Shao, Z. (2022). Sulfurimonas marina sp. Nov., an obligately chemolithoautotrophic, Sulphur-oxidizing bacterium isolated from a deep-sea sediment sample from the South China Sea. International Journal of Systematic and Evolutionary Microbiology, 72(10), 005582. https://doi.org/10.1099/ijsem.0.005582

Waskom, M. (2021). seaborn: Statistical data visualization. Journal of Open Source Software, 6(60), 3021. https://doi.org/10.21105/joss.03021

Whelan, S., & Goldman, N. (2001). A general empirical model of protein evolution derived from multiple protein families using a maximum-likelihood approach. Molecular Biology and Evolution, 18(5), 691-699. https://doi.org/10.1093/oxfordjournals.molbev.a003851

Xie, Y., Wei, Y., Shen, Y., Li, X., Zhou, H., Tai, C., Deng, Z., & Ou, H.-Y. (2018). TADB 2.0: An updated database of bacterial type II toxin-antitoxin loci. Nucleic Acids Research, 46(D1), D749-D753. https://doi.org/10.1093/nar/gkx1033

Yarza, P., Yilmaz, P., Pruesse, E., Glöckner, F. O., Ludwig, W., Schleifer, K.-H., Whitman, W. B., Euzéby, J., Amann, R., & Rosselló-Móra, R. (2014). Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nature Reviews Microbiology, 12(9), 635-645. https://doi.org/10.1038/nrmicro3330

Yeo, C. C. (2018). GNAT toxins of bacterial toxin-antitoxin systems: Acetylation of charged tRNAs to inhibit translation: GNAT toxins of bacterial toxin-antitoxin systems. Molecular Microbiology, 108(4), 331-335. https://doi.org/10.1111/mmi.13958

Zankari, E., Hasman, H., Cosentino, S., Vestergaard, M., Rasmussen, S., Lund, O., Aarestrup, F. M., & Larsen, M. V. (2012). Identification of acquired antimicrobial resistance genes. Journal of Antimicrobial Chemotherapy, 67(11), 2640-2644. https://doi.org/10.1093/jac/dks261

Zeng, X., Alain, K., & Shao, Z. (2021). Microorganisms from deep-sea hydrothermal vents. Marine Life Science & Technology, 3(2), 204-230. https://doi.org/10.1007/s42995-020-00086-4

A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

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Corinne Biderre-Petit (C)

Damien Courtine (D)

Claire Hennequin (C)

Pierre E Galand (PE)

Stefan Bertilsson (S)

Didier Debroas (D)

Arthur Monjot (A)

Cécile Lepère (C)

Anna-Maria Divne (AM)

Corentin Hochart (C)

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