25 research outputs found
Influence of salts and pH on growth and activity of a novel facultatively alkaliphilic, extremely salt-tolerant, obligately chemolithoautotrophic sufur-oxidizing Gammaproteobacterium Thioalkalibacter halophilus gen. nov., sp. nov. from South-Western Siberian soda lakes
S11.28 The finding of the CBB3-oxidase gene and the evidence for enzyme expression in extremely alkaliphilic bacteria
Sodium Energetic Cycle in the Natronophilic Bacterium: Thioalkalivibrio versutus
As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na+-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Ds) as high as -270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Ds consumers has not been proven. We obtained motile cells and used them to study the supposed Na+ energeticcycle in these bacteria. The resulting motility was activated in the presence of the protonophore2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, andwas fully blocked by amilorideâan inhibitor of Na+-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na+-translocating CO and Na+-motive flagella operate in the Na+ energetic cycle mode. Our research may shed light on the energetic reasonfor how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes
Phenotypic and genomic properties of a novel deep-lineage haloalkaliphilic member of the phylum Balneolaeota from soda lakes possessing Na<sup>+</sup>-translocating proteorhodopsin
Stable development of a heterotrophic bacterial satellite with a peculiar cell morphology has been observed in several enrichment cultures of haloalkaliphilic benthic filamentous cyanobacteria from a hypersaline soda lake in Kulunda Steppe (Altai, Russia). The organism was isolated in pure culture (strain Omega) using sonicated cyanobacterial cells as substrate and it was identified as a deep phylogenetic lineage within the recently proposed phylum Balneolaeota. It is an obligately aerobic heterotroph utilizing proteins and peptides for growth. The cell morphology significantly varied from semicircles to long filaments depending on the growth conditions. The cultures are red-orange colored due to a presence of carotenoids. The isolate is an obligate alkaliphile with a pH range for growth from 8.5 to 10.5 (optimum at 9.5-10) and moderately salt-tolerant with a range from 0.3 to 3 M total Na+ (optimum at 1 M). The genome analysis of strain Omega demonstrated a presence of gene, encoding a proteorhodopsin forming a separate branch in the sodium-translocating proteorhodopsin family. Experiments with washed cells of Omega confirmed light-dependent sodium export. A possible physiological role of the sodium proteorhodopsin in strain Omega is discussed. Phylogenomic analysis demostrated that strain Omega forms an deep, independent branch of a new genus and family level within a recently established phylum Balneolaeota.BT/Environmental Biotechnolog
Sodium Energetic Cycle in the Natronophilic Bacterium: Thioalkalivibrio versutus
As inhabitants of soda lakes, Thioalkalivibrio versutus are halo- and alkaliphilic bacteria that have previously been shown to respire with the first demonstrated Na+-translocating cytochrome-c oxidase (CO). The enzyme generates a sodium-motive force (Ds) as high as -270 mV across the bacterial plasma membrane. However, in these bacteria, operation of the possible Ds consumers has not been proven. We obtained motile cells and used them to study the supposed Na+ energeticcycle in these bacteria. The resulting motility was activated in the presence of the protonophore2-heptyl-4-hydroxyquinoline N-oxide (HQNO), in line with the same effect on cell respiration, andwas fully blocked by amilorideâan inhibitor of Na+-motive flagella. In immotile starving bacteria, ascorbate triggered CO-mediated respiration and motility, both showing the same dependence on sodium concentration. We concluded that, in T. versutus, Na+-translocating CO and Na+-motive flagella operate in the Na+ energetic cycle mode. Our research may shed light on the energetic reasonfor how these bacteria are confined to a narrow chemocline zone and thrive in the extreme conditions of soda lakes.BT/Environmental Biotechnolog
Metagenomics Revealed a New Genus â<i>Candidatus</i> Thiocaldithrix dubininisâ gen. nov., sp. nov. and a New Species â<i>Candidatus</i> Thiothrix puteiâ sp. nov. in the Family <i>Thiotrichaceae</i>, Some Members of Which Have Traits of Both Na<sup>+</sup>- and H<sup>+</sup>-Motive Energetics
Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1â55.6%). We proposed to assign GKL-01 to a new species and genus âCandidatus Thiocaldithrix dubininisâ gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name âCandidatus Thiothrix puteiâ sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na+-ATPases and H+-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically
A Temperate <i>Sinorhizobium</i> Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis
Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960sâ1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place
Thioalkalivibrio sulfidiphilus sp. nov., a haloalkaliphilic, sulfur-oxidizing gammaproteobacterium from alkaline habitats
<i>Ensifer meliloti</i> L6-AK89, an Effective Inoculant of <i>Medicago lupulina</i> Varieties: Phenotypic and Deep-Genome Screening
This paper presents a deep analysis of the accessory genome of an economically promising strain of Ensifer (Sinorhizobium) meliloti, L6-AK89, obtained as a result of next-generation high-throughput sequencing (MiSeq, MinIon). Strain L6-AK89 is a StrR mutant of the native strain CIAM1775, a symbiont of Medicago lupulina that adapted to a saline and arid habitat in NW Kazakhstan. CIAM1775 is an effective inoculant of M. lupulina cv. Mira (fodder type standard), cultivated on moderately acid soils in the NW agricultural region of Russia. Strain L6-AK89 makes it possible to obtain the expected high (>150%) increases in dry mass of the same plant variety in plant tests. The L6-AK89 genome has an increased proportion of sequences related to the accessory elements relative to reference strain Rm1021, 7.4% versus 4.8%. A set of 53 nod/noe/nol/nif/fdx/fix genes and 32 genes involved in stress tolerance together with 16S rRNA and recAâatpDâglnIIâgyrBâdnaJ were evaluated. The high symbiotic efficiency of L6-ĐĐ89 with hop clover is most likely due to unique features of its genome, in combination with structural differences in its nod and stress-related genes, as well as unique clusters of quorum-sensing genes and osmoprotector synthesis