TY - JOUR AU - Wacey, D. AU - Kilburn, M. R. AU - Saunders, M. AU - Cliff, J. AU - Brasier, M. D. PY - 2011 DA - 2011// TI - Microfossils of sulphur-metabolizing cells in 3.4-billion-year-old rocks of Western Australia JO - Nat Geosci. VL - 4 UR - https://doi.org/10.1038/ngeo1238 DO - 10.1038/ngeo1238 ID - Wacey2011 ER - TY - JOUR AU - Martin, W. AU - Baross, J. AU - Kelley, D. AU - Russell, M. J. PY - 2008 DA - 2008// TI - Hydrothermal vents and the origin of life JO - Nat Rev Microbiol. VL - 6 UR - https://doi.org/10.1038/nrmicro1991 DO - 10.1038/nrmicro1991 ID - Martin2008 ER - TY - JOUR AU - Canfield, D. E. PY - 1999 DA - 1999// TI - The evolution of the sulfur cycle JO - Am J Sci. VL - 299 UR - https://doi.org/10.2475/ajs.299.7-9.697 DO - 10.2475/ajs.299.7-9.697 ID - Canfield1999 ER - TY - JOUR AU - Meier, D. V. AU - Pjevac, P. AU - Bach, W. AU - Hourdez, S. AU - Girguis, P. R. AU - Vidoudez, C. PY - 2017 DA - 2017// TI - Niche partitioning of diverse sulfur-oxidizing bacteria at hydrothermal vents JO - ISME J. VL - 11 UR - https://doi.org/10.1038/ismej.2017.37 DO - 10.1038/ismej.2017.37 ID - Meier2017 ER - TY - JOUR AU - Jørgensen, B. B. PY - 1982 DA - 1982// TI - Mineralization of organic matter in the sea bed—the role of sulphate reduction JO - Nature. VL - 296 UR - https://doi.org/10.1038/296643a0 DO - 10.1038/296643a0 ID - Jørgensen1982 ER - TY - BOOK PY - 2016 DA - 2016// TI - Soda Lakes of East Africa PB - Springer International Publishing CY - Cham ID - ref6 ER - TY - JOUR AU - Sorokin, D. Y. AU - Berben, T. AU - Melton, E. D. AU - Overmars, L. AU - Vavourakis, C. D. AU - Muyzer, G. PY - 2014 DA - 2014// TI - Microbial diversity and biogeochemical cycling in soda lakes JO - Extremophiles. VL - 18 UR - https://doi.org/10.1007/s00792-014-0670-9 DO - 10.1007/s00792-014-0670-9 ID - Sorokin2014 ER - TY - JOUR AU - Sorokin, D. Y. AU - Kuenen, J. G. AU - Muyzer, G. PY - 2011 DA - 2011// TI - The microbial sulfur cycle at extremely haloalkaline conditions of soda lakes JO - Front Microbiol. VL - 2 UR - https://doi.org/10.3389/fmicb.2011.00044 DO - 10.3389/fmicb.2011.00044 ID - Sorokin2011 ER - TY - CHAP AU - Sorokin, D. Y. AU - Banciu, H. AU - Robertson, L. A. AU - Kuenen, J. G. AU - Muntyan, M. S. AU - Muyzer, G. PY - 2013 DA - 2013// TI - Halophilic and haloalkaliphilic sulfur-oxidizing bacteria BT - The prokaryotes PB - Springer Berlin Heidelberg CY - Berlin UR - https://doi.org/10.1007/978-3-642-30141-4_77 DO - 10.1007/978-3-642-30141-4_77 ID - Sorokin2013 ER - TY - JOUR AU - Sorokin, D. Y. AU - Banciu, H. L. AU - Muyzer, G. PY - 2015 DA - 2015// TI - Functional microbiology of soda lakes JO - Curr Opin Microbiol. VL - 25 UR - https://doi.org/10.1016/J.MIB.2015.05.004 DO - 10.1016/J.MIB.2015.05.004 ID - Sorokin2015 ER - TY - CHAP AU - Sorokin, D. Y. PY - 2017 DA - 2017// TI - Anaerobic haloalkaliphiles BT - Encyclopedia of life sciences PB - Wiley CY - Chichester UR - https://doi.org/10.1002/9780470015902.a0027654 DO - 10.1002/9780470015902.a0027654 ID - Sorokin2017 ER - TY - CHAP AU - Oren, A. PY - 2014 DA - 2014// TI - The family Ectothiorhodospiraceae BT - The prokaryotes PB - Springer Berlin Heidelberg CY - Berlin UR - https://doi.org/10.1007/978-3-642-38922-1_248 DO - 10.1007/978-3-642-38922-1_248 ID - Oren2014 ER - TY - JOUR AU - Sorokin, D. Y. AU - Messina, E. AU - Cono, V. AU - Ferrer, M. AU - Ciordia, S. AU - Mena, M. C. PY - 2018 DA - 2018// TI - Sulfur respiration in a group of facultatively anaerobic natronoarchaea ubiquitous in hypersaline soda lakes JO - Front Microbiol. VL - 9 UR - https://doi.org/10.3389/fmicb.2018.02359 DO - 10.3389/fmicb.2018.02359 ID - Sorokin2018 ER - TY - JOUR AU - Koch, T. AU - Dahl, C. PY - 2018 DA - 2018// TI - A novel bacterial sulfur oxidation pathway provides a new link between the cycles of organic and inorganic sulfur compounds JO - ISME J. VL - 12 UR - https://doi.org/10.1038/s41396-018-0209-7 DO - 10.1038/s41396-018-0209-7 ID - Koch2018 ER - TY - JOUR AU - Brito, J. A. AU - Sousa, F. L. AU - Stelter, M. AU - Bandeiras, T. M. AU - Vonrhein, C. AU - Teixeira, M. PY - 2009 DA - 2009// TI - Structural and functional insights into sulfide:quinone oxidoreductase JO - Biochemistry. VL - 48 UR - https://doi.org/10.1021/bi9003827 DO - 10.1021/bi9003827 ID - Brito2009 ER - TY - JOUR AU - Thorup, C. AU - Schramm, A. AU - Findlay, A. J. AU - Finster, K. W. AU - Schreiber, L. PY - 2017 DA - 2017// TI - Disguised as a sulfate reducer: growth of the deltaproteobacterium Desulfurivibrio alkaliphilus by sulfide oxidation with nitrate JO - MBio. VL - 8 UR - https://doi.org/10.1128/mBio.00671-17 DO - 10.1128/mBio.00671-17 ID - Thorup2017 ER - TY - JOUR AU - Wasmund, K. AU - Mußmann, M. AU - Loy, A. PY - 2017 DA - 2017// TI - The life sulfuric: microbial ecology of sulfur cycling in marine sediments JO - Environ Microbiol Rep. VL - 9 UR - https://doi.org/10.1111/1758-2229.12538 DO - 10.1111/1758-2229.12538 ID - Wasmund2017 ER - TY - JOUR AU - Poser, A. AU - Lohmayer, R. AU - Vogt, C. AU - Knoeller, K. AU - Planer-Friedrich, B. AU - Sorokin, D. PY - 2013 DA - 2013// TI - Disproportionation of elemental sulfur by haloalkaliphilic bacteria from soda lakes JO - Extremophiles. VL - 17 UR - https://doi.org/10.1007/s00792-013-0582-0 DO - 10.1007/s00792-013-0582-0 ID - Poser2013 ER - TY - JOUR AU - Friedrich, C. G. AU - Rother, D. AU - Bardischewsky, F. AU - Quentmeier, A. AU - Fischer, J. PY - 2001 DA - 2001// TI - Oxidation of reduced inorganic sulfur compounds by bacteria: emergence of a common mechanism? JO - Appl Environ Microbiol. VL - 67 UR - https://doi.org/10.1128/AEM.67.7.2873-2882.2001 DO - 10.1128/AEM.67.7.2873-2882.2001 ID - Friedrich2001 ER - TY - JOUR AU - Ghosh, W. AU - Dam, B. PY - 2009 DA - 2009// TI - Biochemistry and molecular biology of lithotrophic sulfur oxidation by taxonomically and ecologically diverse bacteria and archaea JO - FEMS Microbiol Rev. VL - 33 UR - https://doi.org/10.1111/j.1574-6976.2009.00187.x DO - 10.1111/j.1574-6976.2009.00187.x ID - Ghosh2009 ER - TY - JOUR AU - Friedrich, C. G. AU - Quentmeier, A. AU - Bardischewsky, F. AU - Rother, D. AU - Kraft, R. AU - Kostka, S. PY - 2000 DA - 2000// TI - Novel genes coding for lithotrophic sulfur oxidation of Paracoccus pantotrophus GB17 JO - J Bacteriol. VL - 182 UR - https://doi.org/10.1128/JB.182.17.4677-4687.2000 DO - 10.1128/JB.182.17.4677-4687.2000 ID - Friedrich2000 ER - TY - JOUR AU - Dahl, C. AU - Engels, S. AU - Pott-Sperling, A. S. AU - Schulte, A. AU - Sander, J. AU - Lubbe, Y. PY - 2005 DA - 2005// TI - Novel genes of the dsr gene cluster and evidence for close interaction of Dsr proteins during sulfur oxidation in the phototrophic sulfur bacterium Allochromatium vinosum JO - J Bacteriol. VL - 187 UR - https://doi.org/10.1128/JB.187.4.1392-1404.2005 DO - 10.1128/JB.187.4.1392-1404.2005 ID - Dahl2005 ER - TY - JOUR AU - Müller, F. H. AU - Bandeiras, T. M. AU - Urich, T. AU - Teixeira, M. AU - Gomes, C. M. AU - Kletzin, A. PY - 2004 DA - 2004// TI - Coupling of the pathway of sulphur oxidation to dioxygen reduction: characterization of a novel membrane-bound thiosulphate:quinone oxidoreductase JO - Mol Microbiol. VL - 53 UR - https://doi.org/10.1111/j.1365-2958.2004.04193.x DO - 10.1111/j.1365-2958.2004.04193.x ID - Müller2004 ER - TY - JOUR AU - Brito, J. A. AU - Denkmann, K. AU - Pereira, I. A. C. AU - Archer, M. AU - Dahl, C. PY - 2015 DA - 2015// TI - Thiosulfate dehydrogenase (TsdA) from Allochromatium vinosum JO - J Biol Chem. VL - 290 UR - https://doi.org/10.1074/jbc.M114.623397 DO - 10.1074/jbc.M114.623397 ID - Brito2015 ER - TY - JOUR AU - Denkmann, K. AU - Grein, F. AU - Zigann, R. AU - Siemen, A. AU - Bergmann, J. AU - Helmont, S. PY - 2012 DA - 2012// TI - Thiosulfate dehydrogenase: a widespread unusual acidophilic c-type cytochrome JO - Environ Microbiol. VL - 14 UR - https://doi.org/10.1111/j.1462-2920.2012.02820.x DO - 10.1111/j.1462-2920.2012.02820.x ID - Denkmann2012 ER - TY - JOUR AU - Sorokin, D. Y. PY - 2003 DA - 2003// TI - Oxidation of inorganic sulfur compounds by obligately organotrophic bacteria JO - Microbiology. VL - 72 UR - https://doi.org/10.1023/B:MICI.0000008363.24128.e5 DO - 10.1023/B:MICI.0000008363.24128.e5 ID - Sorokin2003 ER - TY - JOUR AU - Burns, J. L. AU - DiChristina, T. J. PY - 2009 DA - 2009// TI - Anaerobic respiration of elemental sulfur and thiosulfate by Shewanella oneidensis MR-1 requires psrA, a homolog of the phsA gene of Salmonella enterica Serovar Typhimurium LT2 JO - Appl Environ Microbiol. VL - 75 UR - https://doi.org/10.1128/AEM.00888-09 DO - 10.1128/AEM.00888-09 ID - Burns2009 ER - TY - JOUR AU - Hedderich, R. AU - Klimmek, O. AU - Kröger, A. AU - Dirmeier, R. AU - Keller, M. AU - Stetter, K. O. PY - 1998 DA - 1998// TI - Anaerobic respiration with elemental sulfur and with disulfides JO - FEMS Microbiol Rev. VL - 22 UR - https://doi.org/10.1111/J.1574-6976.1998.TB00376.X DO - 10.1111/J.1574-6976.1998.TB00376.X ID - Hedderich1998 ER - TY - JOUR AU - Berks, B. C. AU - Hinsley, A. P. PY - 2002 DA - 2002// TI - Specificity of respiratory pathways involved in the reduction of sulfur compounds by Salmonella enterica JO - Microbiology. VL - 148 UR - https://doi.org/10.1099/00221287-148-11-3631 DO - 10.1099/00221287-148-11-3631 ID - Berks2002 ER - TY - JOUR AU - Melton, E. D. AU - Sorokin, D. Y. AU - Overmars, L. AU - Chertkov, O. AU - Clum, A. AU - Pillay, M. PY - 2016 DA - 2016// TI - Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2T, a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes JO - Stand Genomic Sci. VL - 11 UR - https://doi.org/10.1186/s40793-016-0184-4 DO - 10.1186/s40793-016-0184-4 ID - Melton2016 ER - TY - JOUR AU - Foti, M. J. AU - Sorokin, D. Y. AU - Zacharova, E. E. AU - Pimenov, N. V. AU - Kuenen, J. G. AU - Muyzer, G. PY - 2008 DA - 2008// TI - Bacterial diversity and activity along a salinity gradient in soda lakes of the Kulunda Steppe (Altai, Russia) JO - Extremophiles. VL - 12 UR - https://doi.org/10.1007/s00792-007-0117-7 DO - 10.1007/s00792-007-0117-7 ID - Foti2008 ER - TY - JOUR AU - Tourova, T. P. AU - Slobodova, N. V. AU - Bumazhkin, B. K. AU - Kolganova, T. V. AU - Muyzer, G. AU - Sorokin, D. Y. PY - 2013 DA - 2013// TI - Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes using soxB as a functional molecular marker JO - FEMS Microbiol Ecol. VL - 84 UR - https://doi.org/10.1111/1574-6941.12056 DO - 10.1111/1574-6941.12056 ID - Tourova2013 ER - TY - JOUR AU - Edwardson, C. F. AU - Hollibaugh, J. T. PY - 2017 DA - 2017// TI - Metatranscriptomic analysis of prokaryotic communities active in sulfur and arsenic cycling in Mono Lake, California, USA JO - ISME J. VL - 11 UR - https://doi.org/10.1038/ismej.2017.80 DO - 10.1038/ismej.2017.80 ID - Edwardson2017 ER - TY - JOUR AU - Vavourakis, C. D. AU - Ghai, R. AU - Rodriguez-Valera, F. AU - Sorokin, D. Y. AU - Tringe, S. G. AU - Hugenholtz, P. PY - 2016 DA - 2016// TI - Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines JO - Front Microbiol. VL - 7 UR - https://doi.org/10.3389/fmicb.2016.00211 DO - 10.3389/fmicb.2016.00211 ID - Vavourakis2016 ER - TY - JOUR AU - Vavourakis, C. D. AU - Andrei, A. -. S. AU - Mehrshad, M. AU - Ghai, R. AU - Sorokin, D. Y. AU - Muyzer, G. PY - 2018 DA - 2018// TI - A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments JO - Microbiome. VL - 6 UR - https://doi.org/10.1186/s40168-018-0548-7 DO - 10.1186/s40168-018-0548-7 ID - Vavourakis2018 ER - TY - JOUR AU - Breugel, F. AU - Dickinson, M. H. PY - 2017 DA - 2017// TI - Superhydrophobic diving flies (Ephydra hians) and the hypersaline waters of Mono Lake JO - Proc Natl Acad Sci. VL - 114 UR - https://doi.org/10.1073/pnas.1714874114 DO - 10.1073/pnas.1714874114 ID - Breugel2017 ER - TY - JOUR AU - Borsodi, A. K. AU - Korponai, K. AU - Schumann, P. AU - Spröer, C. AU - Felföldi, T. AU - Márialigeti, K. PY - 2017 DA - 2017// TI - Nitrincola alkalilacustris sp. nov. and Nitrincola schmidtii sp. nov., alkaliphilic bacteria isolated from soda pans, and emended description of the genus Nitrincola JO - Int J Syst Evol Microbiol. VL - 67 UR - https://doi.org/10.1099/ijsem.0.002437 DO - 10.1099/ijsem.0.002437 ID - Borsodi2017 ER - TY - JOUR AU - Boden, R. AU - Scott, K. M. AU - Williams, J. AU - Russel, S. AU - Antonen, K. AU - Rae, A. W. PY - 2017 DA - 2017// TI - An evaluation of Thiomicrospira, Hydrogenovibrio and Thioalkalimicrobium: reclassification of four species of Thiomicrospira to each Thiomicrorhabdus gen. nov. and Hydrogenovibrio, and reclassification of all four species of Thioalkalimicrobium to Thiomic JO - Int J Syst Evol Microbiol. VL - 67 UR - https://doi.org/10.1099/ijsem.0.001855 DO - 10.1099/ijsem.0.001855 ID - Boden2017 ER - TY - JOUR AU - Wasmund, K. AU - Schreiber, L. AU - Lloyd, K. G. AU - Petersen, D. G. AU - Schramm, A. AU - Stepanauskas, R. PY - 2014 DA - 2014// TI - Genome sequencing of a single cell of the widely distributed marine subsurface Dehalococcoidia, phylum Chloroflexi JO - ISME J. VL - 8 UR - https://doi.org/10.1038/ismej.2013.143 DO - 10.1038/ismej.2013.143 ID - Wasmund2014 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2019 DA - 2019// TI - MAGs from Cock Soda Lake ID - Vavourakis2019 ER - TY - JOUR AU - Timmers, P. H. A. AU - Vavourakis, C. D. AU - Kleerebezem, R. AU - Damsté, J. S. S. AU - Muyzer, G. AU - Stams, A. J. M. PY - 2018 DA - 2018// TI - Metabolism and occurrence of methanogenic and sulfate-reducing syntrophic acetate oxidizing communities in haloalkaline environments JO - Front Microbiol. VL - 9 UR - https://doi.org/10.3389/fmicb.2018.03039 DO - 10.3389/fmicb.2018.03039 ID - Timmers2018 ER - TY - JOUR AU - Namsaraev, Z. AU - Samylina, O. AU - Sukhacheva, M. AU - Borisenko, G. AU - Sorokin, D. Y. AU - Tourova, T. PY - 2018 DA - 2018// TI - Effect of salinity on diazotrophic activity and microbial composition of phototrophic communities from Bitter-1 soda lake (Kulunda Steppe, Russia) JO - Extremophiles. VL - 22 UR - https://doi.org/10.1007/s00792-018-1026-7 DO - 10.1007/s00792-018-1026-7 ID - Namsaraev2018 ER - TY - JOUR AU - Samylina, O. S. AU - Sapozhnikov, F. V. AU - Gainanova, O. Y. AU - Ryabova, A. V. AU - Nikitin, M. A. AU - Sorokin, D. Y. PY - 2014 DA - 2014// TI - Algo-bacterial communities of the Kulunda steppe (Altai Region, Russia) Soda Lakes JO - Microbiology. VL - 83 UR - https://doi.org/10.1134/S0026261714060162 DO - 10.1134/S0026261714060162 ID - Samylina2014 ER - TY - JOUR AU - Sorokin, D. Y. AU - Pelt, S. AU - Tourova, T. P. AU - Evtushenko, L. I. PY - 2009 DA - 2009// TI - Nitriliruptor alkaliphilus gen. nov., sp. nov., a deep-lineage haloalkaliphilic actinobacterium from soda lakes capable of growth on aliphatic nitriles, and proposal of Nitriliruptoraceae fam. nov. and Nitriliruptorales ord. nov JO - Int J Syst Evol Microbiol. VL - 59 UR - https://doi.org/10.1099/ijs.0.002204-0 DO - 10.1099/ijs.0.002204-0 ID - Sorokin2009 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2019 DA - 2019// TI - MAGs from hypersaline soda lake sediments ID - Vavourakis2019 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2018 DA - 2018// TI - Raw sequence reads metagenomes, metatranscriptome and 16S rRNA gene and transcript amplicon sequencing ID - Vavourakis2018 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2019 DA - 2019// TI - Assembled contigs metatranscriptome ID - Vavourakis2019 ER - TY - JOUR AU - Pereira, I. A. C. AU - Ramos, A. R. AU - Grein, F. AU - Marques, M. C. AU - Silva, S. M. AU - Venceslau, S. S. PY - 2011 DA - 2011// TI - A comparative genomic analysis of energy metabolism in sulfate reducing Bacteria and Archaea JO - Front Microbiol. VL - 2 UR - https://doi.org/10.3389/fmicb.2011.00069 DO - 10.3389/fmicb.2011.00069 ID - Pereira2011 ER - TY - JOUR AU - Czyzewski, B. r. y. a. n. K. AU - Wang, D. a. -. N. e. n. g. PY - 2012 DA - 2012// TI - Identification and characterization of a bacterial hydrosulphide ion channel JO - Nature VL - 483 UR - https://doi.org/10.1038/nature10881 DO - 10.1038/nature10881 ID - Czyzewski2012 ER - TY - JOUR AU - Sorokin, D. Y. AU - Tourova, T. P. AU - Braker, G. AU - Muyzer, G. PY - 2007 DA - 2007// TI - Thiohalomonas denitrificans gen. nov., sp. nov. and Thiohalomonas nitratireducens sp. nov., novel obligately chemolithoautotrophic, moderately halophilic, thiodenitrifying Gammaproteobacteria from hypersaline habitats JO - Int J Syst Evol Microbiol. VL - 57 UR - https://doi.org/10.1099/ijs.0.65112-0 DO - 10.1099/ijs.0.65112-0 ID - Sorokin2007 ER - TY - JOUR AU - Kopejtka, K. AU - Tomasch, J. AU - Zeng, Y. AU - Tichý, M. AU - Sorokin, D. Y. AU - Koblížek, M. PY - 2017 DA - 2017// TI - Genomic analysis of the evolution of phototrophy among haloalkaliphilic Rhodobacterales JO - Genome Biol Evol. VL - 9 UR - https://doi.org/10.1093/gbe/evx141 DO - 10.1093/gbe/evx141 ID - Kopejtka2017 ER - TY - JOUR AU - Hensel, M. AU - Hinsley, A. P. AU - Nikolaus, T. AU - Sawers, G. AU - Berks, B. C. PY - 1999 DA - 1999// TI - The genetic basis of tetrathionate respiration in Salmonella typhimurium JO - Mol Microbiol. VL - 32 UR - https://doi.org/10.1046/j.1365-2958.1999.01345.x DO - 10.1046/j.1365-2958.1999.01345.x ID - Hensel1999 ER - TY - STD TI - Nolla-Ardèvol V, Strous M, Tegetmeyer HE. Anaerobic digestion of the microalga Spirulina at extreme alkaline conditions: biogas production, metagenome, and metatranscriptome. Front Microbiol. 2015:1–21. doi:https://doi.org/10.3389/fmicb.2015.00597. ID - ref53 ER - TY - JOUR AU - Sorokin, D. Y. AU - Kuenen, J. G. PY - 2005 DA - 2005// TI - Chemolithotrophic haloalkaliphiles from soda lakes JO - FEMS Microbiol Ecol. VL - 52 UR - https://doi.org/10.1016/j.femsec.2005.02.012 DO - 10.1016/j.femsec.2005.02.012 ID - Sorokin2005 ER - TY - STD TI - Sorokin DY, Rusanov II, Pimenov N V., Tourova TP, Abbas B, Muyzer G. Sulfidogenesis under extremely haloalkaline conditions in soda lakes of Kulunda Steppe (Altai, Russia). FEMS Microbiol Ecol. 2010;73:no-no. doi:https://doi.org/10.1111/j.1574-6941.2010.00901.x. ID - ref55 ER - TY - JOUR AU - Spang, A. AU - Saw, J. H. AU - Jørgensen, S. L. AU - Zaremba-Niedzwiedzka, K. AU - Martijn, J. AU - Lind, A. E. PY - 2015 DA - 2015// TI - Complex archaea that bridge the gap between prokaryotes and eukaryotes JO - Nature. VL - 521 UR - https://doi.org/10.1038/nature14447 DO - 10.1038/nature14447 ID - Spang2015 ER - TY - JOUR AU - Zeng, Y. AU - Feng, F. AU - Medova, H. AU - Dean, J. AU - Kobli ek, M. PY - 2014 DA - 2014// TI - Functional type 2 photosynthetic reaction centers found in the rare bacterial phylum Gemmatimonadetes JO - Proc Natl Acad Sci. VL - 111 UR - https://doi.org/10.1073/pnas.1400295111 DO - 10.1073/pnas.1400295111 ID - Zeng2014 ER - TY - JOUR AU - Dachev, M. AU - Bína, D. AU - Sobotka, R. AU - Moravcová, L. AU - Gardian, Z. AU - Kaftan, D. PY - 2017 DA - 2017// TI - Unique double concentric ring organization of light harvesting complexes in Gemmatimonas phototrophica JO - PLOS Biol. VL - 15 UR - https://doi.org/10.1371/journal.pbio.2003943 DO - 10.1371/journal.pbio.2003943 ID - Dachev2017 ER - TY - JOUR AU - Chernousova, E. AU - Gridneva, E. AU - Grabovich, M. AU - Dubinina, G. AU - Akimov, V. AU - Rossetti, S. PY - 2009 DA - 2009// TI - Thiothrix caldifontis sp. nov. and Thiothrix lacustris sp. nov., gammaproteobacteria isolated from sulfide springs JO - Int J Syst Evol Microbiol. VL - 59 UR - https://doi.org/10.1099/ijs.0.009456-0 DO - 10.1099/ijs.0.009456-0 ID - Chernousova2009 ER - TY - JOUR AU - König, S. AU - Gros, O. AU - Heiden, S. E. AU - Hinzke, T. AU - Thürmer, A. AU - Poehlein, A. PY - 2017 DA - 2017// TI - Nitrogen fixation in a chemoautotrophic lucinid symbiosis JO - Nat Microbiol. VL - 2 UR - https://doi.org/10.1038/nmicrobiol.2016.193 DO - 10.1038/nmicrobiol.2016.193 ID - König2017 ER - TY - JOUR AU - Anantharaman, K. AU - Hausmann, B. AU - Jungbluth, S. P. AU - Kantor, R. S. AU - Lavy, A. AU - Warren, L. A. PY - 2018 DA - 2018// TI - Expanded diversity of microbial groups that shape the dissimilatory sulfur cycle JO - ISME J. VL - 12 UR - https://doi.org/10.1038/s41396-018-0078-0 DO - 10.1038/s41396-018-0078-0 ID - Anantharaman2018 ER - TY - JOUR AU - Ma, K. AU - Schicho, R. N. AU - Kelly, R. M. AU - Adams, M. W. PY - 1993 DA - 1993// TI - Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor JO - Proc Natl Acad Sci. VL - 90 UR - https://doi.org/10.1073/pnas.90.11.5341 DO - 10.1073/pnas.90.11.5341 ID - Ma1993 ER - TY - JOUR AU - Liu, X. AU - Li, M. AU - Castelle, C. J. AU - Probst, A. J. AU - Zhou, Z. AU - Pan, J. PY - 2018 DA - 2018// TI - Insights into the ecology, evolution, and metabolism of the widespread Woesearchaeotal lineages JO - Microbiome. VL - 6 UR - https://doi.org/10.1186/s40168-018-0488-2 DO - 10.1186/s40168-018-0488-2 ID - Liu2018 ER - TY - JOUR AU - Sorokin, D. Y. AU - Abbas, B. AU - Geleijnse, M. AU - Pimenov, N. V. AU - Sukhacheva, M. V. AU - Loosdrecht, M. C. M. PY - 2015 DA - 2015// TI - Methanogenesis at extremely haloalkaline conditions in the soda lakes of Kulunda Steppe (Altai, Russia) JO - FEMS Microbiol Ecol. VL - 91 UR - https://doi.org/10.1093/femsec/fiv016 DO - 10.1093/femsec/fiv016 ID - Sorokin2015 ER - TY - JOUR AU - Lee, K. M. AU - Adams, M. AU - Klassen, J. L. PY - 2019 DA - 2019// TI - Evaluation of DESS as a storage medium for microbial community analysis JO - PeerJ. VL - 7 UR - https://doi.org/10.7717/peerj.6414 DO - 10.7717/peerj.6414 ID - Lee2019 ER - TY - JOUR AU - Wesemael, J. C. PY - 1955 DA - 1955// TI - De bepaling van het calciumcarbonaatgehalte van gronden JO - Chem Weekbl. VL - 51 ID - Wesemael1955 ER - TY - CHAP AU - Zopfi, J. AU - Ferdelman, T. G. AU - Fossing, H. ED - Amend, J. P. ED - Edwards, K. J. ED - Lyons, T. W. PY - 2004 DA - 2004// TI - Distribution and fate of sulfur intermediates—sulfite, tetrathionate, thiosulfate, and elemental sulfur—in marine sediments BT - Sulfur biogeochemistry: past and present PB - Geological Society of America CY - Boulder UR - https://doi.org/10.1130/0-8137-2379-5.97 DO - 10.1130/0-8137-2379-5.97 ID - Zopfi2004 ER - TY - JOUR AU - Parada, A. E. AU - Needham, D. M. AU - Fuhrman, J. A. PY - 2016 DA - 2016// TI - Every base matters: assessing small subunit rRNA primers for marine microbiomes with mock communities, time series and global field samples JO - Environ Microbiol. VL - 18 UR - https://doi.org/10.1111/1462-2920.13023 DO - 10.1111/1462-2920.13023 ID - Parada2016 ER - TY - STD TI - Joshi NA, Fass J. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files. 2011. github.com/najoshi/sickle. ID - ref69 ER - TY - JOUR AU - Quast, C. AU - Pruesse, E. AU - Yilmaz, P. AU - Gerken, J. AU - Schweer, T. AU - Yarza, P. PY - 2012 DA - 2012// TI - The SILVA ribosomal RNA gene database project: improved data processing and web-based tools JO - Nucleic Acids Res. VL - 41 UR - https://doi.org/10.1093/nar/gks1219 DO - 10.1093/nar/gks1219 ID - Quast2012 ER - TY - STD TI - Andersen KSS, Kirkegaard RH, Karst SM, Albertsen M. ampvis2: an R package to analyse and visualise 16S rRNA amplicon data. bioRxiv. 2018:299537. doi:https://doi.org/10.1101/299537. ID - ref71 ER - TY - STD TI - DOE JGI. BBDuk (BBDuk version 36.19). jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide/. Accessed 20 June 2017. UR - http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/bbduk-guide ID - ref72 ER - TY - JOUR AU - Li, D. AU - Liu, C. -. M. AU - Luo, R. AU - Sadakane, K. AU - Lam, T. -. W. PY - 2015 DA - 2015// TI - MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph JO - Bioinformatics. VL - 31 UR - https://doi.org/10.1093/bioinformatics/btv033 DO - 10.1093/bioinformatics/btv033 ID - Li2015 ER - TY - JOUR AU - Hyatt, D. AU - Chen, G. -. L. AU - LoCascio, P. F. AU - Land, M. L. AU - Larimer, F. W. AU - Hauser, L. J. PY - 2010 DA - 2010// TI - Prodigal: prokaryotic gene recognition and translation initiation site identification JO - BMC Bioinformatics. VL - 11 UR - https://doi.org/10.1186/1471-2105-11-119 DO - 10.1186/1471-2105-11-119 ID - Hyatt2010 ER - TY - JOUR AU - Lowe, T. M. AU - Eddy, S. R. PY - 1997 DA - 1997// TI - tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence JO - Nucleic Acids Res. VL - 25 UR - https://doi.org/10.1093/nar/25.5.0955 DO - 10.1093/nar/25.5.0955 ID - Lowe1997 ER - TY - JOUR AU - Kanehisa, M. AU - Sato, Y. AU - Morishima, K. PY - 2016 DA - 2016// TI - BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences JO - J Mol Biol. VL - 428 UR - https://doi.org/10.1016/j.jmb.2015.11.006 DO - 10.1016/j.jmb.2015.11.006 ID - Kanehisa2016 ER - TY - JOUR AU - Kang, D. D. AU - Froula, J. AU - Egan, R. AU - Wang, Z. PY - 2015 DA - 2015// TI - MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities JO - PeerJ. VL - 3 UR - https://doi.org/10.7717/peerj.1165 DO - 10.7717/peerj.1165 ID - Kang2015 ER - TY - STD TI - Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei A-S, Ghai R, et al. Raw sequence reads metagenomes soda lakes - T1Sed10. 2015. https://www.ncbi.nlm.nih.gov/sra/SRX143969[accn]. UR - https://www.ncbi.nlm.nih.gov/sra/SRX143969 ID - ref78 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - B1-Sed10 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Ghai, R. AU - Rodriguez-Valera, F. AU - Sorokin, D. Y. AU - Tringe, S. G. AU - Hugenholtz, P. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - T5-Br10 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Ghai, R. AU - Rodriguez-Valera, F. AU - Sorokin, D. Y. AU - Tringe, S. G. AU - Hugenholtz, P. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - PL-Br10 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Ghai, R. AU - Rodriguez-Valera, F. AU - Sorokin, D. Y. AU - Tringe, S. G. AU - Hugenholtz, P. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - Tc-Br11 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Ghai, R. AU - Rodriguez-Valera, F. AU - Sorokin, D. Y. AU - Tringe, S. G. AU - Hugenholtz, P. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - B1-Br10 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - CSSed10 ID - Vavourakis2015 ER - TY - BOOK AU - Vavourakis, C. D. AU - Mehrshad, M. AU - Balkema, C. AU - Hall, R. AU - Andrei, A. -. S. AU - Ghai, R. PY - 2015 DA - 2015// TI - Raw sequence reads metagenomes soda lakes - CSSed11 ID - Vavourakis2015 ER - TY - STD TI - Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei A-S, Ghai R, et al. Raw sequence reads metagenomes soda lakes - T3-Sed10. 2015. https://www.ncbi.nlm.nih.gov/sra/SRX143967[accn]. UR - https://www.ncbi.nlm.nih.gov/sra/SRX143967 ID - ref86 ER - TY - STD TI - Bushnell B, Egan R, Copeland A, Foster B, Clum A, Sun H, et al. BBMap: a fast, accurate, splice-aware aligner. 2014. https://doi.org/10.1186/1471-2105-13-238. ID - ref87 ER - TY - JOUR AU - Eren, A. M. AU - Esen, Ö. C. AU - Quince, C. AU - Vineis, J. H. AU - Morrison, H. G. AU - Sogin, M. L. PY - 2015 DA - 2015// TI - Anvi’o: an advanced analysis and visualization platform for ‘omics data JO - PeerJ. VL - 3 UR - https://doi.org/10.7717/peerj.1319 DO - 10.7717/peerj.1319 ID - Eren2015 ER - TY - JOUR AU - Parks, D. H. AU - Chuvochina, M. AU - Waite, D. W. AU - Rinke, C. AU - Skarshewski, A. AU - Chaumeil, P. -. A. PY - 2018 DA - 2018// TI - A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life JO - Nat Biotechnol. VL - 36 UR - https://doi.org/10.1038/nbt.4229 DO - 10.1038/nbt.4229 ID - Parks2018 ER - TY - JOUR AU - Klappenbach, J. A. AU - Goris, J. AU - Vandamme, P. AU - Coenye, T. AU - Konstantinidis, K. T. AU - Tiedje, J. M. PY - 2007 DA - 2007// TI - DNA–DNA hybridization values and their relationship to whole-genome sequence similarities JO - Int J Syst Evol Microbiol VL - 57 UR - https://doi.org/10.1099/ijs.0.64483-0 DO - 10.1099/ijs.0.64483-0 ID - Klappenbach2007 ER - TY - JOUR AU - Huerta-Cepas, J. AU - Szklarczyk, D. AU - Forslund, K. AU - Cook, H. AU - Heller, D. AU - Walter, M. C. PY - 2016 DA - 2016// TI - eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences JO - Nucleic Acids Res. VL - 44 UR - https://doi.org/10.1093/nar/gkv1248 DO - 10.1093/nar/gkv1248 ID - Huerta-Cepas2016 ER - TY - JOUR AU - Müller, A. L. AU - Kjeldsen, K. U. AU - Rattei, T. AU - Pester, M. AU - Loy, A. PY - 2015 DA - 2015// TI - Phylogenetic and environmental diversity of DsrAB-type dissimilatory (bi) sulfite reductases JO - ISME J. VL - 9 UR - https://doi.org/10.1038/ismej.2014.208 DO - 10.1038/ismej.2014.208 ID - Müller2015 ER - TY - STD TI - Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei A-S, Ghai R, et al. Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake: Supplementary Electronic Files Online. 2019. doi:https://doi.org/10.21942/uva.c.4594961. ID - ref93 ER - TY - JOUR AU - Langmead, B. AU - Salzberg, S. L. PY - 2012 DA - 2012// TI - Fast gapped-read alignment with Bowtie 2 JO - Nat Methods. VL - 9 UR - https://doi.org/10.1038/nmeth.1923 DO - 10.1038/nmeth.1923 ID - Langmead2012 ER - TY - JOUR AU - Kopylova, E. AU - Noé, L. AU - Touzet, H. PY - 2012 DA - 2012// TI - SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data JO - Bioinformatics. VL - 28 UR - https://doi.org/10.1093/bioinformatics/bts611 DO - 10.1093/bioinformatics/bts611 ID - Kopylova2012 ER - TY - JOUR AU - Griffiths-Jones, S. AU - Moxon, S. AU - Marshall, M. AU - Khanna, A. AU - Eddy, S. R. AU - Bateman, A. PY - 2004 DA - 2004// TI - Rfam: annotating non-coding RNAs in complete genomes JO - Nucleic Acids Res. VL - 33 UR - https://doi.org/10.1093/nar/gki081 DO - 10.1093/nar/gki081 ID - Griffiths-Jones2004 ER - TY - STD TI - Doe JGI. dedupe.sh. jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/dedupe-guide/. Accessed 20 June 2017. UR - http://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/dedupe-guide ID - ref97 ER - TY - JOUR AU - Hug, L. A. AU - Baker, B. J. AU - Anantharaman, K. AU - Brown, C. T. AU - Probst, A. J. AU - Castelle, C. J. PY - 2016 DA - 2016// TI - A new view of the tree of life JO - Nat Microbiol. VL - 1 UR - https://doi.org/10.1038/nmicrobiol.2016.48 DO - 10.1038/nmicrobiol.2016.48 ID - Hug2016 ER - TY - JOUR AU - Harris, K. A. AU - Zhou, Z. AU - Peters, M. L. AU - Wilkins, S. G. AU - Breaker, R. R. PY - 2018 DA - 2018// TI - A second RNA-binding protein is essential for ethanol tolerance provided by the bacterial OLE ribonucleoprotein complex JO - Proc Natl Acad Sci. VL - 115 UR - https://doi.org/10.1073/pnas.1803191115 DO - 10.1073/pnas.1803191115 ID - Harris2018 ER -