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Dynamics of Thioalkalivibrio species in a co-culture under selective pressure of ampicillin

Ahn, Anne Catherine (author), Schuurmans, J. Merijn (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria belonging to the genus Thioalkalivibrio are highly abundant in microbial communities found in soda lakes and dominant in full-scale bioreactors removing sulfide from industrial waste gases. Despite certain soda lakes being remote and unaffected by anthropogenic activities,...

journal article 2023

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Molecular and physiological adaptations to low temperature in thioalkalivibrio strains isolated from soda lakes with different temperature regimes

Ahn, Anne Catherine (author), Jongepier, Evelien (author), Merijn Schuurmans, J. (author), Irene, W. (author), Sinninghe Damsté, Jaap S. (author), Galinski, Erwin A. (author), Roman, Pawel (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

The genus Thioalkalivibrio comprises sulfur-oxidizing bacteria thriving in soda lakes at high pH and salinity. Depending on the geographical location and the season, these lakes can strongly vary in temperature. To obtain a comprehensive understanding of the molecular and physiological adaptations to low temperature, we compared the responses...

journal article 2021

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Trinuclear copper biocatalytic center forms an active site of thiocyanate dehydrogenase

Tikhonova, Tamara V. (author), Sorokin, Dimitry Y. (author), Hagen, W.R. (author), Khrenova, Maria G. (author), Muyzer, Gerard (author), Rakitina, Tatiana V. (author), Shabalin, Ivan G. (author), Trofimov, Anton A. (author), Tsallagov, Stanislav I. (author), Popov, Vladimir O. (author)

Biocatalytic copper centers are generally involved in the activation and reduction of dioxygen, with only few exceptions known. Here we report the discovery and characterization of a previously undescribed copper center that forms the active site of a copper-containing enzyme thiocyanate dehydrogenase (suggested EC 1.8.2.7) that was purified...

journal article 2020

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Comparative genomics of Thiohalobacter thiocyanaticus HRh1T and guyparkeriasp. SCN-R1, halophilic chemolithoautotrophic sulfur-oxidizing gammaproteobacteria capable of using thiocyanate as energy source

Tsallagov, Stanislav I. (author), Sorokin, Dimitry Y. (author), Tikhonova, Tamara V. (author), Popov, Vladimir O. (author), Muyzer, Gerard (author)

The genomes of Thiohalobacter thiocyanaticus and Guyparkeria (formerly known as Halothiobacillus) sp. SCN-R1, two gammaproteobacterial halophilic sulfur-oxidizing bacteria (SOB) capable of thiocyanate oxidation via the "cyanate pathway", have been analyzed with a particular focus on their thiocyanate-oxidizing potential and sulfur oxidation...

journal article 2019

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Transcriptomic analysis of two thioalkalivibriospecies under arsenite stress revealed a potential candidate gene for an alternative arsenite oxidation pathway

Ahn, Anne Catherine (author), Cavalca, L. (author), Colombo, Milena (author), Schuurmans, J.M.A. (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

The genus Thioalkalivibrio includes haloalkaliphilic chemolithoautotrophic sulfur-oxidizing bacteria isolated from various soda lakes worldwide. Some of these lakes possess in addition to their extreme haloalkaline environment also other harsh conditions, to which Thioalkalivibrio needs to adapt. An example is arsenic in soda lakes in eastern...

journal article 2019

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Diversity and distribution of sulfur oxidation-related genes in thioalkalivibrio, a genus of chemolithoautotrophic and haloalkaliphilic sulfur-oxidizing bacteria

Berben, Tom (author), Overmars, Lex (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Soda lakes are saline alkaline lakes characterized by high concentrations of sodium carbonate/bicarbonate which lead to a stable elevated pH (>9), and moderate to extremely high salinity. Despite this combination of extreme conditions, biodiversity in soda lakes is high, and the presence of diverse microbial communities provides a driving...

journal article 2019

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

Vavourakis, Charlotte D. (author), Mehrshad, Maliheh (author), Balkema, Cherel (author), Van Hall, Rutger (author), Andrei, Adrian Ştefan (author), Ghai, Rohit (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Background: The planetary sulfur cycle is a complex web of chemical reactions that can be microbial-mediated or can occur spontaneously in the environment, depending on the temperature and pH. Inorganic sulfur compounds can serve as energy sources for specialized prokaryotes and are important substrates for microbial growth in general. Here,...

journal article 2019

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Metabolism and occurrence of methanogenic and sulfate-reducing syntrophic acetate oxidizing communities in haloalkaline environments

Timmers, Peer H.A. (author), Vavourakis, Charlotte D. (author), Kleerebezem, R. (author), Sinninghe Damsté, Jaap S. (author), Muyzer, Gerard (author), Stams, Alfons J.M. (author), Sorokin, Dimitry Y. (author), Plugge, Caroline M. (author)

Anaerobic syntrophic acetate oxidation (SAO) is a thermodynamically unfavorable process involving a syntrophic acetate oxidizing bacterium (SAOB) that forms interspecies electron carriers (IECs). These IECs are consumed by syntrophic partners, typically hydrogenotrophic methanogenic archaea or sulfate reducing bacteria. In this work, the...

journal article 2018

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

Vavourakis, Charlotte D. (author), Andrei, Adrian Stefan (author), Mehrshad, Maliheh (author), Ghai, Rohit (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Background: Hypersaline soda lakes are characterized by extreme high soluble carbonate alkalinity. Despite the high pH and salt content, highly diverse microbial communities are known to be present in soda lake brines but the microbiome of soda lake sediments received much less attention of microbiologists. Here, we performed metagenomic...

journal article 2018

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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, Tom (author), Balkema, Cherel (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Thiocyanate (N=C-S-) is a moderately toxic, inorganic sulfur compound. It occurs naturally as a by-product of the degradation of glucosinolatecontaining plants and is produced industrially in a number of mining processes. Currently, two pathways for the primary degradation of thiocyanate in bacteria are recognized, the carbonyl sulfide...

journal article 2017

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Draft genome sequence of Dethiobacter alkaliphilus strain AHT1^T, a gram-positive sulfidogenic polyextremophile

Melton, Emily Denise (author), Sorokin, Dimitry Y. (author), Overmars, Lex (author), Lapidus, Alla L. (author), Pillay, Manoj (author), Ivanova, Natalia (author), del Rio, Tijana Glavina (author), Kyrpides, Nikos C. (author), Woyke, Tanja (author), Muyzer, Gerard (author)

Dethiobacter alkaliphilus strain AHT1^T is an anaerobic, sulfidogenic, moderately salt-tolerant alkaliphilic chemolithotroph isolated from hypersaline soda lake sediments in northeastern Mongolia. It is a Gram-positive bacterium with low GC content, within the phylum Firmicutes. Here we report its draft genome sequence, which...

journal article 2017

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Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

Ahn, Anne Catherine (author), Meier-Kolthoff, Jan P. (author), Overmars, Lex (author), Richter, Michael (author), Woyke, Tanja (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world,...

journal article 2017

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Comparative genome analysis of three thiocyanate oxidizing Thioalkalivibrio species isolated from soda lakes

Berben, Tom (author), Overmars, Lex (author), Sorokin, Dimitry Y. (author), Muyzer, Gerard (author)

Thiocyanate is a C1 compound containing carbon, nitrogen, and sulfur. It is a (by)product in a number of natural and industrial processes. Because thiocyanate is toxic to many organisms, including humans, its removal from industrial waste streams is an important problem. Although a number of bacteria can use thiocyanate as a nitrogen source,...

journal article 2017

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

Melton, Emily Denise (author), Sorokin, Dimitry Y. (author), Overmars, Lex (author), Chertkov, Olga (author), Clum, Alicia (author), Pillay, Manoj (author), Ivanova, Natalia (author), Shapiro, Nicole (author), Kyrpides, Nikos C. (author), Woyke, Tanja (author), Lapidus, Alla L. (author), Muyzer, Gerard (author)

Desulfurivibrio alkaliphilus strain AHT2^T is a strictly anaerobic sulfidogenic haloalkaliphile isolated from a composite sediment sample of eight hypersaline alkaline lakes in the Wadi al Natrun valley in the Egyptian Libyan Desert. D. alkaliphilus AHT2^T is Gram-negative and belongs to the family Desulfobulbaceae within...

journal article 2016

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Metagenomic insights into the uncultured diversity and physiology of microbes in four hypersaline soda lake brines

Vavourakis, Charlotte D. (author), Ghai, Rohit (author), Rodriguez-Valera, Francisco (author), Sorokin, Dimitry Y. (author), Tringe, Susannah G. (author), Hugenholtz, Philip (author), Muyzer, Gerard (author)

Soda lakes are salt lakes with a naturally alkaline pH due to evaporative concentration of sodium carbonates in the absence of major divalent cations. Hypersaline soda brines harbor microbial communities with a high species- and strain-level archaeal diversity and a large proportion of still uncultured poly-extremophiles compared to neutral...

journal article 2016

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

Berben, Tom (author), Sorokin, Dimitry Y. (author), Ivanova, Natalia (author), Pati, Amrita (author), Kyrpides, Nikos (author), Goodwin, Lynne A. (author), Woyke, Tanja (author), Muyzer, Gerard (author)

Thioalkalivibrio thiocyanodenitrificans strain ARhD 1^T is a motile, Gram-negative bacterium isolated from soda lakes that belongs to the Gammaproteobacteria. It derives energy for growth and carbon fixation from the oxidation of sulfur compounds, most notably thiocyanate, and so is a chemolithoautotroph. It is capable of complete...

journal article 2015

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

Suzuki, S. (author), Kuenen, J.G. (author), Schipper, K. (author), Van der Velde, S. (author), Ishii, S. (author), Wu, A. (author), Sorokin, D.Y. (author), Tenney, A. (author), Meng, X.Y. (author), Morrill, P.L. (author), Kamagata, Y. (author), Muyzer, G. (author), Nealson, K.H. (author)

Serpentinization, or the aqueous alteration of ultramafic rocks, results in challenging environments for life in continental sites due to the combination of extremely high pH, low salinity and lack of obvious electron acceptors and carbon sources. Nevertheless, certain Betaproteobacteria have been frequently observed in such environments. Here...

journal article 2014

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Desulfuribacillus alkaliarsenatis gen. nov. sp. nov., a deep-lineage, obligately anaerobic, dissimilatory sulfur and arsenate-reducing, haloalkaliphilic representative of the order Bacillales from soda lakes

Sorokin, D.Y. (author), Tourova, T.P. (author), Sukhacheva, M.V. (author), Muyzer, G. (author)

An anaerobic enrichment culture inoculated with a sample of sediments from soda lakes of the Kulunda Steppe with elemental sulfur as electron acceptor and formate as electron donor at pH 10 and moderate salinity inoculated with sediments from soda lakes in Kulunda Steppe (Altai, Russia) resulted in the domination of a Gram-positive, spore...

journal article 2012

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Desulfonatronovibrio halophilus sp. nov., a novel moderately halophilic sulfate-reducing bacterium from hypersaline chloride–sulfate lakes in Central Asia

Sorokin, D.Y. (author), Tourova, T.P. (author), Abbas, B. (author), Suhacheva, M.V. (author), Muyzer, G. (author)

Four strains of lithotrophic sulfate-reducing bacteria (SRB) have been enriched and isolated from anoxic sediments of hypersaline chloride–sulfate lakes in the Kulunda Steppe (Altai, Russia) at 2 M NaCl and pH 7.5. According to the 16S rRNA gene sequence analysis, the isolates were closely related to each other and belonged to the genus...

journal article 2012

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Anaerobic utilization of pectinous substrates at extremely haloalkaline conditions by Natranaerovirga pectinivora gen. nov., sp. nov., and Natranaerovirga hydrolytica sp. nov., isolated from hypersaline soda lakes

Sorokin, D.Y. (author), Tourova, T.P. (author), Panteleeva, A.N. (author), Kaparullina, E.N. (author), Muyzer, G. (author)

Anaerobic enrichments at pH 10, with pectin and polygalacturonates as substrates and inoculated with samples of sediments of hypersaline soda lakes from the Kulunda Steppe (Altai, Russia) demonstrated the potential for microbial pectin degradation up to soda-saturating conditions. The enrichments resulted in the isolation of six strains of...

journal article 2012