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Complete genome sequence of Thioalkalivibrio sp. K90mix.

Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC - Stand Genomic Sci (2011)

Bottom Line: Thioalkalivibrio sp.The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method.The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.

View Article: PubMed Central - PubMed

ABSTRACT
Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.

No MeSH data available.


Related in: MedlinePlus

Phylogenetic tree based on protein sequences of different flagellar motors. The sequences of the proton-driven flagellar motor MotAB from E. coli (ECDH10B_2031, ECDH10B_2030) and of the sodium-driven flagellar motor PomAB from V. cholerae (VC0892, VC0893) were used as reference proteins. Other proteins were selected after BLAST analysis. Subsequently, the selected protein sequences were aligned used Clustal W, and a neighbor joining tree was drawn using MEGA 5. Ac, Acidithiobacillus caldus ATCC 51756; Ae, Alkalilimnicolaehrlichei MLHE-1; Av, Allochromatium vinosum DSM 180; Bh, Bacillus halodurans C125; Bs, Bacillus subtilis strain 168; Ec, Escherichia coli DH10B; Hh, Halorhodospirahalophila SL1; Nm, Nitrococcus mobilis NB-231; Ts, Thioalkalivibrio sulfidophilus HLEbGR7; Tv-K90, Thioalkalivibrio sp. K90mix; Va, Vibrio alginolyticus 12G01; Vc, Vibriocholera O1; Vp, Vibrio parahaemolyticus RIMD2210633. The sequences of Thioalkalivibrio sp. K90mix are shown in bold type. The bar indicates 20% sequence difference. Numbers on the branches indicate percentage bootstrap values from 1000 iterations; only those values are shown that distinguish the different flagellar motors. The CheW sequence of Thioalkalivibrio sp. K90mix (TK90_1183) was used as an outgroup, but was pruned from the tree.
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f7: Phylogenetic tree based on protein sequences of different flagellar motors. The sequences of the proton-driven flagellar motor MotAB from E. coli (ECDH10B_2031, ECDH10B_2030) and of the sodium-driven flagellar motor PomAB from V. cholerae (VC0892, VC0893) were used as reference proteins. Other proteins were selected after BLAST analysis. Subsequently, the selected protein sequences were aligned used Clustal W, and a neighbor joining tree was drawn using MEGA 5. Ac, Acidithiobacillus caldus ATCC 51756; Ae, Alkalilimnicolaehrlichei MLHE-1; Av, Allochromatium vinosum DSM 180; Bh, Bacillus halodurans C125; Bs, Bacillus subtilis strain 168; Ec, Escherichia coli DH10B; Hh, Halorhodospirahalophila SL1; Nm, Nitrococcus mobilis NB-231; Ts, Thioalkalivibrio sulfidophilus HLEbGR7; Tv-K90, Thioalkalivibrio sp. K90mix; Va, Vibrio alginolyticus 12G01; Vc, Vibriocholera O1; Vp, Vibrio parahaemolyticus RIMD2210633. The sequences of Thioalkalivibrio sp. K90mix are shown in bold type. The bar indicates 20% sequence difference. Numbers on the branches indicate percentage bootstrap values from 1000 iterations; only those values are shown that distinguish the different flagellar motors. The CheW sequence of Thioalkalivibrio sp. K90mix (TK90_1183) was used as an outgroup, but was pruned from the tree.

Mentions: Thioalkalivibrio sp. K90mix has all the genes that are indispensable for the production of flagellar proteins (FlgA, TK90_0923; FlgB, TK90_0926; FlgC, TK90_0927; FlgD, TK90_0928; FlgE, TK90_0929; FlgF, TK90_0930; FlgG, TK90_0931; FlgH, TK90_0932; FlgI, TK90_0933; FlgK, TK90_0935; FlgL, TK90_0936; FlgM, TK90_0922; FlgN, TK90_0921; FliC, TK90_1400, 1448, 1450; FliD, TK90_1447; FliE, TK90_1157; FliF, TK90_1158; FliG, TK90_1159; FliH, TK90_1160; FliI, TK90_1161; FliJ, TK90_1162; FliK, TK90_1163; FliM, TK90_1165; FliN, TK90_1166; FliO, TK90_1167; FliP, TK90_1168; FliQ, TK90_1169; FliR, TK90_1170; FliS, TK90_1446; FlhA, TK90_1172; FlhB, TK90_1171; see Table 1 in [49]). Phylogenetic analysis of sequences encoding different flagellar motors showed, with significant bootstrap values, genes encoding both proton-driven motors (TK90_0578, TK90_0577) related to E. coli MotA and MotB, as well as sodium-driven motors (TK90_1180, TK1181) related to Vibriocholera PomA and PomB and Bacillus subtilis MotP and MotS (Figure 7). The results also show the presence of proton- and sodium-driven flagellar motors in the Ectothiorhodospiraceae, “Thioalkalivibrio sulfidophilus”, Halorhodospira halophila, and Alkalilimnicolaehrlichei, as well as in Achromatiumvinosum,Acidithiobacillus caldus, Vibrio alginolyticus and Vibrio parahaemolyticus. Vibrio cholerae, Bacillus subtilis, B. halodurans, and Nitrococcus mobilis only have sodium-driven flagellar motors. Grouping of the proton-driven MotA and sodium-driven PomA has also been found by Krulwich et al. [50].


Complete genome sequence of Thioalkalivibrio sp. K90mix.

Muyzer G, Sorokin DY, Mavromatis K, Lapidus A, Foster B, Sun H, Ivanova N, Pati A, D'haeseleer P, Woyke T, Kyrpides NC - Stand Genomic Sci (2011)

Phylogenetic tree based on protein sequences of different flagellar motors. The sequences of the proton-driven flagellar motor MotAB from E. coli (ECDH10B_2031, ECDH10B_2030) and of the sodium-driven flagellar motor PomAB from V. cholerae (VC0892, VC0893) were used as reference proteins. Other proteins were selected after BLAST analysis. Subsequently, the selected protein sequences were aligned used Clustal W, and a neighbor joining tree was drawn using MEGA 5. Ac, Acidithiobacillus caldus ATCC 51756; Ae, Alkalilimnicolaehrlichei MLHE-1; Av, Allochromatium vinosum DSM 180; Bh, Bacillus halodurans C125; Bs, Bacillus subtilis strain 168; Ec, Escherichia coli DH10B; Hh, Halorhodospirahalophila SL1; Nm, Nitrococcus mobilis NB-231; Ts, Thioalkalivibrio sulfidophilus HLEbGR7; Tv-K90, Thioalkalivibrio sp. K90mix; Va, Vibrio alginolyticus 12G01; Vc, Vibriocholera O1; Vp, Vibrio parahaemolyticus RIMD2210633. The sequences of Thioalkalivibrio sp. K90mix are shown in bold type. The bar indicates 20% sequence difference. Numbers on the branches indicate percentage bootstrap values from 1000 iterations; only those values are shown that distinguish the different flagellar motors. The CheW sequence of Thioalkalivibrio sp. K90mix (TK90_1183) was used as an outgroup, but was pruned from the tree.
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f7: Phylogenetic tree based on protein sequences of different flagellar motors. The sequences of the proton-driven flagellar motor MotAB from E. coli (ECDH10B_2031, ECDH10B_2030) and of the sodium-driven flagellar motor PomAB from V. cholerae (VC0892, VC0893) were used as reference proteins. Other proteins were selected after BLAST analysis. Subsequently, the selected protein sequences were aligned used Clustal W, and a neighbor joining tree was drawn using MEGA 5. Ac, Acidithiobacillus caldus ATCC 51756; Ae, Alkalilimnicolaehrlichei MLHE-1; Av, Allochromatium vinosum DSM 180; Bh, Bacillus halodurans C125; Bs, Bacillus subtilis strain 168; Ec, Escherichia coli DH10B; Hh, Halorhodospirahalophila SL1; Nm, Nitrococcus mobilis NB-231; Ts, Thioalkalivibrio sulfidophilus HLEbGR7; Tv-K90, Thioalkalivibrio sp. K90mix; Va, Vibrio alginolyticus 12G01; Vc, Vibriocholera O1; Vp, Vibrio parahaemolyticus RIMD2210633. The sequences of Thioalkalivibrio sp. K90mix are shown in bold type. The bar indicates 20% sequence difference. Numbers on the branches indicate percentage bootstrap values from 1000 iterations; only those values are shown that distinguish the different flagellar motors. The CheW sequence of Thioalkalivibrio sp. K90mix (TK90_1183) was used as an outgroup, but was pruned from the tree.
Mentions: Thioalkalivibrio sp. K90mix has all the genes that are indispensable for the production of flagellar proteins (FlgA, TK90_0923; FlgB, TK90_0926; FlgC, TK90_0927; FlgD, TK90_0928; FlgE, TK90_0929; FlgF, TK90_0930; FlgG, TK90_0931; FlgH, TK90_0932; FlgI, TK90_0933; FlgK, TK90_0935; FlgL, TK90_0936; FlgM, TK90_0922; FlgN, TK90_0921; FliC, TK90_1400, 1448, 1450; FliD, TK90_1447; FliE, TK90_1157; FliF, TK90_1158; FliG, TK90_1159; FliH, TK90_1160; FliI, TK90_1161; FliJ, TK90_1162; FliK, TK90_1163; FliM, TK90_1165; FliN, TK90_1166; FliO, TK90_1167; FliP, TK90_1168; FliQ, TK90_1169; FliR, TK90_1170; FliS, TK90_1446; FlhA, TK90_1172; FlhB, TK90_1171; see Table 1 in [49]). Phylogenetic analysis of sequences encoding different flagellar motors showed, with significant bootstrap values, genes encoding both proton-driven motors (TK90_0578, TK90_0577) related to E. coli MotA and MotB, as well as sodium-driven motors (TK90_1180, TK1181) related to Vibriocholera PomA and PomB and Bacillus subtilis MotP and MotS (Figure 7). The results also show the presence of proton- and sodium-driven flagellar motors in the Ectothiorhodospiraceae, “Thioalkalivibrio sulfidophilus”, Halorhodospira halophila, and Alkalilimnicolaehrlichei, as well as in Achromatiumvinosum,Acidithiobacillus caldus, Vibrio alginolyticus and Vibrio parahaemolyticus. Vibrio cholerae, Bacillus subtilis, B. halodurans, and Nitrococcus mobilis only have sodium-driven flagellar motors. Grouping of the proton-driven MotA and sodium-driven PomA has also been found by Krulwich et al. [50].

Bottom Line: Thioalkalivibrio sp.The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method.The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.

View Article: PubMed Central - PubMed

ABSTRACT
Thioalkalivibrio sp. K90mix is an obligately chemolithoautotrophic, natronophilic sulfur-oxidizing bacterium (SOxB) belonging to the family Ectothiorhodospiraceae within the Gammaproteobacteria. The strain was isolated from a mixture of sediment samples obtained from different soda lakes located in the Kulunda Steppe (Altai, Russia) based on its extreme potassium carbonate tolerance as an enrichment method. Here we report the complete genome sequence of strain K90mix and its annotation. The genome was sequenced within the Joint Genome Institute Community Sequencing Program, because of its relevance to the sustainable removal of sulfide from wastewater and gas streams.

No MeSH data available.


Related in: MedlinePlus