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Temperature as competitive strategy determining factor in pulse-fed aerobic bioreactors.

Stouten GR, Hogendoorn C, Douwenga S, Kilias ES, Muyzer G, Kleerebezem R.

ISME J. 2019 Sep 2. doi: 10.1038/s41396-019-0495-8. [Epub ahead of print]


Metagenomes and metatranscriptomes shed new light on the microbial-mediated sulfur cycle in a Siberian soda lake.

Vavourakis CD, Mehrshad M, Balkema C, van Hall R, Andrei AŞ, Ghai R, Sorokin DY, Muyzer G.

BMC Biol. 2019 Aug 22;17(1):69. doi: 10.1186/s12915-019-0688-7.


Transcriptomic Analysis of Two Thioalkalivibrio Species Under Arsenite Stress Revealed a Potential Candidate Gene for an Alternative Arsenite Oxidation Pathway.

Ahn AC, Cavalca L, Colombo M, Schuurmans JM, Sorokin DY, Muyzer G.

Front Microbiol. 2019 Jul 4;10:1514. doi: 10.3389/fmicb.2019.01514. eCollection 2019.


Exploring Biodiversity and Arsenic Metabolism of Microbiota Inhabiting Arsenic-Rich Groundwaters in Northern Italy.

Cavalca L, Zecchin S, Zaccheo P, Abbas B, Rotiroti M, Bonomi T, Muyzer G.

Front Microbiol. 2019 Jul 2;10:1480. doi: 10.3389/fmicb.2019.01480. eCollection 2019.


Comparative Genomics of Thiohalobacter thiocyanaticus HRh1T and Guyparkeria sp. SCN-R1, Halophilic Chemolithoautotrophic Sulfur-Oxidizing Gammaproteobacteria Capable of Using Thiocyanate as Energy Source.

Tsallagov SI, Sorokin DY, Tikhonova TV, Popov VO, Muyzer G.

Front Microbiol. 2019 May 1;10:898. doi: 10.3389/fmicb.2019.00898. eCollection 2019.


Coexistence of sulfate reducers with the other oil bacterial groups in Diyarbakır oil fields.

Tüccar T, Ilhan-Sungur E, Abbas B, Muyzer G.

Anaerobe. 2019 Oct;59:19-31. doi: 10.1016/j.anaerobe.2019.04.008. Epub 2019 Apr 25.


Diversity and Distribution of Sulfur Oxidation-Related Genes in Thioalkalivibrio, a Genus of Chemolithoautotrophic and Haloalkaliphilic Sulfur-Oxidizing Bacteria.

Berben T, Overmars L, Sorokin DY, Muyzer G.

Front Microbiol. 2019 Feb 14;10:160. doi: 10.3389/fmicb.2019.00160. eCollection 2019.


Wide diversity of methane and short-chain alkane metabolisms in uncultured archaea.

Borrel G, Adam PS, McKay LJ, Chen LX, Sierra-García IN, Sieber CMK, Letourneur Q, Ghozlane A, Andersen GL, Li WJ, Hallam SJ, Muyzer G, de Oliveira VM, Inskeep WP, Banfield JF, Gribaldo S.

Nat Microbiol. 2019 Apr;4(4):603-613. doi: 10.1038/s41564-019-0363-3. Epub 2019 Mar 4.


Seaweed Loads Cause Stronger Bacterial Community Shifts in Coastal Lagoon Sediments Than Nutrient Loads.

Aires T, Muyzer G, Serrão EA, Engelen AH.

Front Microbiol. 2019 Jan 9;9:3283. doi: 10.3389/fmicb.2018.03283. eCollection 2018.


Metabolism and Occurrence of Methanogenic and Sulfate-Reducing Syntrophic Acetate Oxidizing Communities in Haloalkaline Environments.

Timmers PHA, Vavourakis CD, Kleerebezem R, Damsté JSS, Muyzer G, Stams AJM, Sorokin DY, Plugge CM.

Front Microbiol. 2018 Dec 10;9:3039. doi: 10.3389/fmicb.2018.03039. eCollection 2018.


A metagenomics roadmap to the uncultured genome diversity in hypersaline soda lake sediments.

Vavourakis CD, Andrei AS, Mehrshad M, Ghai R, Sorokin DY, Muyzer G.

Microbiome. 2018 Sep 19;6(1):168. doi: 10.1186/s40168-018-0548-7.


Spatio-temporal dynamics of sulfur bacteria during oxic--anoxic regime shifts in a seasonally stratified lake.

Diao M, Huisman J, Muyzer G.

FEMS Microbiol Ecol. 2018 Apr 1;94(4). doi: 10.1093/femsec/fiy040.


Succession of Bacterial Communities in a Seasonally Stratified Lake with an Anoxic and Sulfidic Hypolimnion.

Diao M, Sinnige R, Kalbitz K, Huisman J, Muyzer G.

Front Microbiol. 2017 Dec 14;8:2511. doi: 10.3389/fmicb.2017.02511. eCollection 2017.


Analysis of the Genes Involved in Thiocyanate Oxidation during Growth in Continuous Culture of the Haloalkaliphilic Sulfur-Oxidizing Bacterium Thioalkalivibrio thiocyanoxidans ARh 2T Using Transcriptomics.

Berben T, Balkema C, Sorokin DY, Muyzer G.

mSystems. 2017 Dec 26;2(6). pii: e00102-17. doi: 10.1128/mSystems.00102-17. eCollection 2017 Nov-Dec.


Oxic-anoxic regime shifts mediated by feedbacks between biogeochemical processes and microbial community dynamics.

Bush T, Diao M, Allen RJ, Sinnige R, Muyzer G, Huisman J.

Nat Commun. 2017 Oct 6;8(1):789. doi: 10.1038/s41467-017-00912-x.


Draft genome sequence of Dethiobacter alkaliphilus strain AHT1T, a gram-positive sulfidogenic polyextremophile.

Melton ED, Sorokin DY, Overmars L, Lapidus AL, Pillay M, Ivanova N, Del Rio TG, Kyrpides NC, Woyke T, Muyzer G.

Stand Genomic Sci. 2017 Sep 21;12:57. doi: 10.1186/s40793-017-0268-9. eCollection 2017.


Comparative Genome Analysis of Three Thiocyanate Oxidizing Thioalkalivibrio Species Isolated from Soda Lakes.

Berben T, Overmars L, Sorokin DY, Muyzer G.

Front Microbiol. 2017 Feb 28;8:254. doi: 10.3389/fmicb.2017.00254. eCollection 2017.


Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio.

Ahn AC, Meier-Kolthoff JP, Overmars L, Richter M, Woyke T, Sorokin DY, Muyzer G.

PLoS One. 2017 Mar 10;12(3):e0173517. doi: 10.1371/journal.pone.0173517. eCollection 2017.


Isolation of a sulfide-producing bacterial consortium from cooling-tower water: Evaluation of corrosive effects on galvanized steel.

Ilhan-Sungur E, Ozuolmez D, Çotuk A, Cansever N, Muyzer G.

Anaerobe. 2017 Feb;43:27-34. doi: 10.1016/j.anaerobe.2016.11.005. Epub 2016 Nov 18.


Complete genome sequence of Desulfurivibrio alkaliphilus strain AHT2(T), a haloalkaliphilic sulfidogen from Egyptian hypersaline alkaline lakes.

Melton ED, Sorokin DY, Overmars L, Chertkov O, Clum A, Pillay M, Ivanova N, Shapiro N, Kyrpides NC, Woyke T, Lapidus AL, Muyzer G.

Stand Genomic Sci. 2016 Sep 8;11(1):67. doi: 10.1186/s40793-016-0184-4. eCollection 2016.


Rhizosphere Microbiomes of European + Seagrasses Are Selected by the Plant, But Are Not Species Specific.

Cúcio C, Engelen AH, Costa R, Muyzer G.

Front Microbiol. 2016 Mar 31;7:440. doi: 10.3389/fmicb.2016.00440. eCollection 2016.


Metagenomic Insights into the Uncultured Diversity and Physiology of Microbes in Four Hypersaline Soda Lake Brines.

Vavourakis CD, Ghai R, Rodriguez-Valera F, Sorokin DY, Tringe SG, Hugenholtz P, Muyzer G.

Front Microbiol. 2016 Feb 25;7:211. doi: 10.3389/fmicb.2016.00211. eCollection 2016.


Bacterial community structure and variation in a full-scale seawater desalination plant for drinking water production.

Belila A, El-Chakhtoura J, Otaibi N, Muyzer G, Gonzalez-Gil G, Saikaly PE, van Loosdrecht MCM, Vrouwenvelder JS.

Water Res. 2016 May 1;94:62-72. doi: 10.1016/j.watres.2016.02.039. Epub 2016 Feb 18.


Complete genome sequence of Thioalkalivibrio paradoxus type strain ARh 1(T), an obligately chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium isolated from a Kenyan soda lake.

Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G.

Stand Genomic Sci. 2015 Nov 19;10:105. doi: 10.1186/s40793-015-0097-7. eCollection 2015.


Partial genome sequence of the haloalkaliphilic soda lake bacterium Thioalkalivibrio thiocyanoxidans ARh 2(T).

Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G.

Stand Genomic Sci. 2015 Oct 26;10:85. doi: 10.1186/s40793-015-0078-x. eCollection 2015.


Partial genome sequence of Thioalkalivibrio thiocyanodenitrificans ARhD 1(T), a chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacterium capable of complete denitrification.

Berben T, Sorokin DY, Ivanova N, Pati A, Kyrpides N, Goodwin LA, Woyke T, Muyzer G.

Stand Genomic Sci. 2015 Oct 26;10:84. doi: 10.1186/s40793-015-0080-3. eCollection 2015.


Characterization of the arsenite oxidizer Aliihoeflea sp. strain 2WW and its potential application in the removal of arsenic from groundwater in combination with Pf-ferritin.

Corsini A, Colombo M, Muyzer G, Cavalca L.

Antonie Van Leeuwenhoek. 2015 Sep;108(3):673-84. doi: 10.1007/s10482-015-0523-2. Epub 2015 Jul 7.


Cytochrome cbb3 of Thioalkalivibrio is a Na+-pumping cytochrome oxidase.

Muntyan MS, Cherepanov DA, Malinen AM, Bloch DA, Sorokin DY, Severina II, Ivashina TV, Lahti R, Muyzer G, Skulachev VP.

Proc Natl Acad Sci U S A. 2015 Jun 23;112(25):7695-700. doi: 10.1073/pnas.1417071112. Epub 2015 Jun 8.


Tracking the dynamics of heterotrophs and nitrifiers in moving-bed biofilm reactors operated at different COD/N ratios.

Bassin JP, Abbas B, Vilela CL, Kleerebezem R, Muyzer G, Rosado AS, van Loosdrecht MC, Dezotti M.

Bioresour Technol. 2015 Sep;192:131-41. doi: 10.1016/j.biortech.2015.05.051. Epub 2015 May 19.


Functional microbiology of soda lakes.

Sorokin DY, Banciu HL, Muyzer G.

Curr Opin Microbiol. 2015 Jun;25:88-96. doi: 10.1016/j.mib.2015.05.004. Epub 2015 May 27. Review.


Genome analysis of Desulfotomaculum gibsoniae strain Groll(T) a highly versatile Gram-positive sulfate-reducing bacterium.

Kuever J, Visser M, Loeffler C, Boll M, Worm P, Sousa DZ, Plugge CM, Schaap PJ, Muyzer G, Pereira IA, Parshina SN, Goodwin LA, Kyrpides NC, Detter J, Woyke T, Chain P, Davenport KW, Rohde M, Spring S, Klenk HP, Stams AJ.

Stand Genomic Sci. 2014 Mar 20;9(3):821-39. doi: 10.4056/sigs.5209235. eCollection 2014 Jun 15.


Genome analyses of the carboxydotrophic sulfate-reducers Desulfotomaculum nigrificans and Desulfotomaculum carboxydivorans and reclassification of Desulfotomaculum caboxydivorans as a later synonym of Desulfotomaculum nigrificans.

Visser M, Parshina SN, Alves JI, Sousa DZ, Pereira IA, Muyzer G, Kuever J, Lebedinsky AV, Koehorst JJ, Worm P, Plugge CM, Schaap PJ, Goodwin LA, Lapidus A, Kyrpides NC, Detter JC, Woyke T, Chain P, Davenport KW, Spring S, Rohde M, Klenk HP, Stams AJ.

Stand Genomic Sci. 2014 Mar 1;9(3):655-75. doi: 10.4056/sigs.4718645. eCollection 2014 Jun 15.


Microbial diversity and biogeochemical cycling in soda lakes.

Sorokin DY, Berben T, Melton ED, Overmars L, Vavourakis CD, Muyzer G.

Extremophiles. 2014 Sep;18(5):791-809. doi: 10.1007/s00792-014-0670-9. Epub 2014 Aug 26. Review.


Physiological and genomic features of highly alkaliphilic hydrogen-utilizing Betaproteobacteria from a continental serpentinizing site.

Suzuki S, Kuenen JG, Schipper K, van der Velde S, Ishii S, Wu A, Sorokin DY, Tenney A, Meng X, Morrill PL, Kamagata Y, Muyzer G, Nealson KH.

Nat Commun. 2014 May 21;5:3900. doi: 10.1038/ncomms4900.


Isolation and characterization of an obligately chemolithoautotrophic Halothiobacillus strain capable of growth on thiocyanate as an energy source.

Sorokin DY, Abbas B, van Zessen E, Muyzer G.

FEMS Microbiol Lett. 2014 May;354(1):69-74. doi: 10.1111/1574-6968.12432. Epub 2014 Apr 11.


Nitrolancea hollandica gen. nov., sp. nov., a chemolithoautotrophic nitrite-oxidizing bacterium isolated from a bioreactor belonging to the phylum Chloroflexi.

Sorokin DY, Vejmelkova D, Lücker S, Streshinskaya GM, Rijpstra WI, Sinninghe Damsté JS, Kleerbezem R, van Loosdrecht M, Muyzer G, Daims H.

Int J Syst Evol Microbiol. 2014 Jun;64(Pt 6):1859-65. doi: 10.1099/ijs.0.062232-0. Epub 2014 Feb 26.


Draft genome sequence of Rhodococcus rhodochrous strain ATCC 17895.

Chen BS, Otten LG, Resch V, Muyzer G, Hanefeld U.

Stand Genomic Sci. 2013 Oct 5;9(1):175-84. doi: 10.4056/sigs.4418165. eCollection 2013 Oct 16.


Sulfate-dependent acetate oxidation under extremely natron-alkaline conditions by syntrophic associations from hypersaline soda lakes.

Sorokin DY, Abbas B, Tourova TP, Bumazhkin BK, Kolganova TV, Muyzer G.

Microbiology. 2014 Apr;160(Pt 4):723-32. doi: 10.1099/mic.0.075093-0. Epub 2014 Jan 30.


Identification of key factors in Accelerated Low Water Corrosion through experimental simulation of tidal conditions: influence of stimulated indigenous microbiota.

Marty F, Gueuné H, Malard E, Sánchez-Amaya JM, Sjögren L, Abbas B, Quillet L, van Loosdrecht MC, Muyzer G.

Biofouling. 2014;30(3):281-97. doi: 10.1080/08927014.2013.864758. Epub 2014 Jan 23.


Arsenic transforming abilities of groundwater bacteria and the combined use of Aliihoeflea sp. strain 2WW and goethite in metalloid removal.

Corsini A, Zaccheo P, Muyzer G, Andreoni V, Cavalca L.

J Hazard Mater. 2014 Mar 30;269:89-97. doi: 10.1016/j.jhazmat.2013.12.037. Epub 2013 Dec 27.


Draft Genome Sequence of the Arsenite-Oxidizing Strain Aliihoeflea sp. 2WW, Isolated from Arsenic-Contaminated Groundwater.

Cavalca L, Corsini A, Andreoni V, Muyzer G.

Genome Announc. 2013 Dec 19;1(6). pii: e01072-13. doi: 10.1128/genomeA.01072-13.


Diversity and distribution of Halomonas in Rambla Salada, a hypersaline environment in the southeast of Spain.

Oueriaghli N, González-Domenech CM, Martínez-Checa F, Muyzer G, Ventosa A, Quesada E, Béjar V.

FEMS Microbiol Ecol. 2014 Feb;87(2):460-74. doi: 10.1111/1574-6941.12237. Epub 2013 Nov 18.


Genetic diversity of inorganic carbon uptake systems causes variation in CO2 response of the cyanobacterium Microcystis.

Sandrini G, Matthijs HC, Verspagen JM, Muyzer G, Huisman J.

ISME J. 2014 Mar;8(3):589-600. doi: 10.1038/ismej.2013.179. Epub 2013 Oct 17.


Genome analysis of Chitinivibrio alkaliphilus gen. nov., sp. nov., a novel extremely haloalkaliphilic anaerobic chitinolytic bacterium from the candidate phylum Termite Group 3.

Sorokin DY, Gumerov VM, Rakitin AL, Beletsky AV, Damsté JS, Muyzer G, Mardanov AV, Ravin NV.

Environ Microbiol. 2014 Jun;16(6):1549-65. doi: 10.1111/1462-2920.12284. Epub 2013 Oct 21.


Genome analysis of Desulfotomaculum kuznetsovii strain 17(T) reveals a physiological similarity with Pelotomaculum thermopropionicum strain SI(T).

Visser M, Worm P, Muyzer G, Pereira IA, Schaap PJ, Plugge CM, Kuever J, Parshina SN, Nazina TN, Ivanova AE, Bernier-Latmani R, Goodwin LA, Kyrpides NC, Woyke T, Chain P, Davenport KW, Spring S, Klenk HP, Stams AJ.

Stand Genomic Sci. 2013 Apr 15;8(1):69-87. doi: 10.4056/sigs.3627141. eCollection 2013 Apr 15.


Microbial transformations of arsenic: perspectives for biological removal of arsenic from water.

Cavalca L, Corsini A, Zaccheo P, Andreoni V, Muyzer G.

Future Microbiol. 2013 Jun;8(6):753-68. doi: 10.2217/fmb.13.38. Epub 2013 Apr 16. Review.


Isolation and characterization of two novel alkalitolerant sulfidogens from a Thiopaq bioreactor, Desulfonatronum alkalitolerans sp. nov., and Sulfurospirillum alkalitolerans sp. nov.

Sorokin DY, Tourova TP, Muyzer G.

Extremophiles. 2013 May;17(3):535-43. doi: 10.1007/s00792-013-0538-4. Epub 2013 Apr 7.


Temporal and spatial coexistence of archaeal and bacterial amoA genes and gene transcripts in Lake Lucerne.

Vissers EW, Anselmetti FS, Bodelier PL, Muyzer G, Schleper C, Tourna M, Laanbroek HJ.

Archaea. 2013;2013:289478. doi: 10.1155/2013/289478. Epub 2013 Mar 5.


Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DL(T)).

Spring S, Visser M, Lu M, Copeland A, Lapidus A, Lucas S, Cheng JF, Han C, Tapia R, Goodwin LA, Pitluck S, Ivanova N, Land M, Hauser L, Larimer F, Rohde M, Göker M, Detter JC, Kyrpides NC, Woyke T, Schaap PJ, Plugge CM, Muyzer G, Kuever J, Pereira IA, Parshina SN, Bernier-Latmani R, Stams AJ, Klenk HP.

Stand Genomic Sci. 2012 Dec 19;7(2):304-19. doi: 10.4056/sigs.3226659. Epub 2012 Dec 11.


Analysis of community composition of sulfur-oxidizing bacteria in hypersaline and soda lakes using soxB as a functional molecular marker.

Tourova TP, Slobodova NV, Bumazhkin BK, Kolganova TV, Muyzer G, Sorokin DY.

FEMS Microbiol Ecol. 2013 May;84(2):280-9. doi: 10.1111/1574-6941.12056. Epub 2012 Dec 31.

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