دورية أكاديمية
Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species.
| العنوان: | Cave Thiovulum (Candidatus Thiovulum stygium) differs metabolically and genomically from marine species. |
|---|---|
| المؤلفون: | Bizic M; Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany. mina.bizic@igb-berlin.de.; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany. mina.bizic@igb-berlin.de., Brad T; 'Emil Racoviţă' Institute of Speleology, Clinicilor 5-7, 400006, Cluj-Napoca Romania, Romania. traian.brad@academia-cj.ro., Ionescu D; Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany. danny.ionescu@igb-berlin.de.; Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany. danny.ionescu@igb-berlin.de., Barbu-Tudoran L; Center for Electron Microscopy, 'Babeș-Bolyai' University, Clinicilor 5, 400006, Cluj-Napoca, Romania., Zoccarato L; Leibniz Institute for Freshwater Ecology and Inland Fisheries, IGB, Dep 3, Plankton and Microbial Ecology, Zur Alte Fischerhütte 2, OT Neuglobsow, 16775, Stechlin, Germany.; Institute of Computational Biology, University of Natural Resources and Life Sciences, Gregor-Mendel-Straße 3, 31180, Vienna, Austria., Aerts JW; Department of Molecular Cell Physiology, Faculty of Earth and Life sciences, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands., Contarini PE; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 97110, Pointe-à-Pitre, France.; Laboratory for Research in Complex Systems, Menlo Park, CA, USA., Gros O; Institut de Systématique, Evolution, Biodiversité (ISYEB), Muséum National d'Histoire Naturelle, CNRS, Sorbonne Université, EPHE, Université des Antilles, 97110, Pointe-à-Pitre, France., Volland JM; Laboratory for Research in Complex Systems, Menlo Park, CA, USA.; Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, 94720, Berkeley, CA, USA., Popa R; River Road Research, 62 Leslie St, Buffalo, NY, 1421, USA., Ody J; Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium., Vellone D; Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, VT, 05405, USA., Flot JF; Evolutionary Biology and Ecology, Université libre de Bruxelles (ULB), C.P. 160/12, Avenue F.D. Roosevelt 50, 1050, Brussels, Belgium.; Interuniversity Institute of Bioinformatics in Brussels-(IB)², Brussels, Belgium., Tighe S; Vermont Integrative Genomics Lab, University of Vermont Cancer Center, Health Science Research Facility, Burlington, Vermont, VT, 05405, USA., Sarbu SM; 'Emil Racoviţă' Institute of Speleology, Frumoasă 31-B, 010986, Bucureşti, Romania.; Department of Biological Sciences, California State University, Chico, CA, 95929, USA. |
| المصدر: | The ISME journal [ISME J] 2023 Mar; Vol. 17 (3), pp. 340-353. Date of Electronic Publication: 2022 Dec 17. |
| نوع المنشور: | Journal Article; Research Support, Non-U.S. Gov't; Research Support, U.S. Gov't, Non-P.H.S. |
| اللغة: | English |
| بيانات الدورية: | Publisher: Oxford University Press Country of Publication: England NLM ID: 101301086 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1751-7370 (Electronic) Linking ISSN: 17517362 NLM ISO Abbreviation: ISME J Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: 2024- : Oxford : Oxford University Press Original Publication: London : Nature Pub. Group |
| مواضيع طبية MeSH: | Caves*/chemistry , Epsilonproteobacteria*/metabolism, Sulfur/metabolism ; Romania ; Phylogeny |
| مستخلص: | 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 (© 2022. The Author(s).) |
| References: | 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. (PMID: 10.1139/cjm-2021-0101) 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. (PMID: 1446139610.1099/00221287-26-1-29) 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. (PMID: 10153121860310.1128/jb.136.2.765-774.1978) Garcia-Pichel F. Rapid bacterial swimming measured in swarming cells of Thiovulum majus. J Bacteriol. 1989;171:3560–3. (PMID: 249829321008710.1128/jb.171.6.3560-3563.1989) Thar R, Fenchel T. True chemotaxis in oxygen gradients of the sulfur-oxidizing bacterium Thiovulum majus. Appl Environ Microbiol. 2001;67:3299–303. (PMID: 114257579301610.1128/AEM.67.7.3299-3303.2001) 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. (PMID: 2593334210.1103/PhysRevLett.114.158102) De Boer WE, La Rivière JWM, Houwink AL. Observations on the morphology of Thiovulum majus Hinze. Antonie Van Leeuwenhoek. 1961;27:447–56. (PMID: 1387049310.1007/BF02538470) Marshall IPG, Blainey PC, Spormann AM, Quake SR. A single-cell genome for Thiovulum sp. Appl Environ Microbiol. 2012;78:8555–63. (PMID: 23023751350292810.1128/AEM.02314-12) Jorgensen BB, Revsbech NP. Colorless sulfur bacteria, Beggiatoa spp. and Thiovulum spp., in O Fenchel T, Glud RN. Veil architecture in a sulphide-oxidizing bacterium enhances countercurrent flux. Nature. 1998;394:367–9. (PMID: 10.1038/28609) 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. (PMID: 10.3354/ame018157) 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. (PMID: 10.1080/01490451.2013.839764) 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. (PMID: 10.1002/abio.200390000) 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. (PMID: 1947481310.1038/ismej.2009.57) 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. (PMID: 2404465310.1111/mec.12461) 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. (PMID: 1475687610.1046/j.1462-2920.2003.00543.x) 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. (PMID: 2410832510.1099/ijs.0.057224-0) 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. (PMID: 2505239410.1099/ijs.0.064956-0) 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. (PMID: 925119916861010.1128/aem.63.8.3123-3127.1997) 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. (PMID: 10.1093/femsle/fnx172) 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. (PMID: 16269723128769210.1128/AEM.71.11.6885-6899.2005) Gruber-Vodicka HR, Seah BKB, Pruesse E. phyloFlash: Rapid small-subunit rRNA profiling and targeted assembly from metagenomes. mSystems. 2020;5:521922. (PMID: 10.1128/mSystems.00920-20) Kolmogorov M, Yuan J, Lin Y, Pevzner PA. Assembly of long, error-prone reads using repeat graphs. Nat Biotechnol. 2019;37:540–6. (PMID: 3093656210.1038/s41587-019-0072-8) Wick RR, Schultz MB, Zobel J, Holt KE. Bandage: interactive visualization of de novo genome assemblies. Bioinformatics. 2015;31:3350–2. (PMID: 26099265459590410.1093/bioinformatics/btv383) 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. (PMID: 17156431177936510.1186/1741-7007-4-41) 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. (PMID: 10.1186/s12859-019-3114-9) 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. (PMID: 28594827548114710.1371/journal.pcbi.1005595) 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. (PMID: 25409509423734810.1371/journal.pone.0112963) 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. (PMID: 28100585541176810.1101/gr.214270.116) 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. (PMID: 2330350910.1093/bioinformatics/bts723) Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20. (PMID: 24695404410359010.1093/bioinformatics/btu170) 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. (PMID: 2560979310.1093/bioinformatics/btv033) 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. (PMID: 26336640455615810.7717/peerj.1165) 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. (PMID: 317301927703759) 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. (PMID: 25977477448438710.1101/gr.186072.114) Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics. 2014;30:2068–9. (PMID: 2464206310.1093/bioinformatics/btu153) 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. (PMID: 32766782749832610.1093/nar/gkaa621) 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. (PMID: 2647645410.1093/nar/gkv1070) 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. (PMID: 3041861010.1093/nar/gky1085) 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. (PMID: 31667520) 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. (PMID: 25666585432235910.1038/srep08365) 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. (PMID: 18261238226569810.1186/1471-2164-9-75) 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. (PMID: 2429365410.1093/nar/gkt1226) 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. (PMID: 1059217510239510.1093/nar/28.1.33) 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. (PMID: 26500826461481010.7717/peerj.1319) 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. (PMID: 29931111624793910.1093/bioinformatics/bty496) 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. (PMID: 17537822193323410.1093/nar/gkm360) 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. (PMID: 3181396410.1093/bib/bbz104) 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. (PMID: 25330359420157810.1371/journal.pone.0110726) 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. (PMID: 31323028666883510.1371/journal.pbio.3000390) 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. (PMID: 10.1038/s41467-018-07641-9) 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. (PMID: 3390797310.1007/s12275-021-1154-0) Price MN, Dehal PS, Arkin AP. FastTree 2-approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5:e9490. (PMID: 20224823283573610.1371/journal.pone.0009490) 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. (PMID: 28263959560014810.1038/nmeth.4197) 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. (PMID: 10.1186/s12859-018-2486-6) Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. (PMID: 25516281430204910.1186/s13059-014-0550-8) 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. (PMID: 25605792440251010.1093/nar/gkv007) 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. (PMID: 33522966785210810.1186/s40168-020-00990-y) 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. (PMID: 2655380410.1093/nar/gkv1189) 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. (PMID: 10.3390/w14101597) Fenchel T. Motility and chemosensory behaviour of the sulphur bacterium Thiovulum majus. Microbiol-sgm. 1994;140:3109–16. (PMID: 10.1099/13500872-140-11-3109) 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. (PMID: 25620962) 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. (PMID: 10.5038/1827-806X.38.1.4) 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. (PMID: 32393808736789110.1038/s41396-020-0669-4) 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. (PMID: 10.1186/s12859-019-3068-y) 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. (PMID: 2838883410.1111/mmi.13690) 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. (PMID: 10.1641/0006-3568(2000)050[0217:ESAAEF]2.3.CO;2) 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. (PMID: 1980886410.1093/molbev/msp239) 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. (PMID: 3014850310.1038/nbt.4229) 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. (PMID: 20498705286935410.1371/journal.pone.0010609) 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. (PMID: 29426952585425310.1038/s41396-018-0069-1) Sarbu SM, Kane TC, Kinkle BK. A chemoautotrophically based cave ecosystem. Science. 1996;272:1953–5. (PMID: 866249710.1126/science.272.5270.1953) 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. (PMID: 2500349810.1021/es404808r) 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. (PMID: 28194142527681810.3389/fmicb.2017.00087) 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. (PMID: 10.1007/BF02529969) 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. (PMID: 3254470410.1016/j.scitotenv.2020.139710) 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. (PMID: 10.1016/j.bbabio.2008.12.010) 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. (PMID: 2425744310.1038/ismej.2013.206) 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. (PMID: 10.1016/j.scitotenv.2018.07.388) Bižic-Ionescu M, Ionescu D, Grossart HP. Organic particles: Heterogeneous hubs for microbial interactions in aquatic ecosystems. Front Microbiol. 2018;9:2569. (PMID: 30416497621248810.3389/fmicb.2018.02569) 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. (PMID: 3315703910.1016/j.cell.2020.09.065) Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases—a historical perspective and more. Nucleic Acids Res. 2014;42:7489–527. (PMID: 24878924408107310.1093/nar/gku447) Fauré-Fremiet E, Rouiller CH. Étude au microscope électronique d’une bactérie sulfureuse, Thiovulum majus Hinze. Exp Cell Res. 1958;14:29–46. (PMID: 1351230210.1016/0014-4827(58)90211-8) 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. (PMID: 28262091538659210.7554/eLife.23136) 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. (PMID: 3452073810.1016/j.str.2021.07.008) 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. (PMID: 18416602229275410.1371/journal.pbio.0060087) 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. (PMID: 21731720312087310.1371/journal.pone.0021373) Craig L, Forest KT, Maier B. Type IV pili: dynamics, biophysics and functional consequences. Nat Rev Microbiol. 2019;17:429–40. (PMID: 3098851110.1038/s41579-019-0195-4) 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. (PMID: 25539737430259810.1186/s12866-014-0322-3) 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. (PMID: 10.3390/d13030128) 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. (PMID: 2319328310.1093/nar/gks1219) 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. (PMID: 2220398210.1073/pnas.1111262109) |
| المشرفين على المادة: | 70FD1KFU70 (Sulfur) |
| تواريخ الأحداث: | Date Created: 20221217 Date Completed: 20230223 Latest Revision: 20230512 |
| رمز التحديث: | 20230513 |
| مُعرف محوري في PubMed: | PMC9938260 |
| DOI: | 10.1038/s41396-022-01350-4 |
| PMID: | 36528730 |
| قاعدة البيانات: | MEDLINE |
Find this article in full text from Springer Verlag. 
Full Text Finder | تدمد: | 1751-7370 |
|---|---|
| DOI: | 10.1038/s41396-022-01350-4 |