Nitrogen Metabolism of an Anoxygenic Filamentous Phototrophic Bacterium Oscillocholris trichoides Strain DG-6

Abstract—

The possible nitrogen sources for Osc. trichoides DG6, a typical strain of the Oscillochloridaceae family, are ammonium, N2, glutamate, asparagine, glycine, and glutamine. The assimilation of molecular nitrogen occurs with the participation of nitrogenase, the structural gene of which, nifH, is located in the gene cluster which also includes the genes of the nifD and nifK nitrogenase subunits and the auxiliary nifB gene. Considering that nifHBDK clusters have been also annotated in the genomes of other members of the Oscillochloridaceae family, including uncultured and candidate taxa, it can be assumed that the ability to fix nitrogen is a property immanent for this entire family. The pathways for assimilating ammonium in the cells grown using different nitrogen sources may differ. Osc. trichoides DG6 growing in a medium containing ammonium assimilated it with the participation of glutamate dehydrogenase, which is determined by a single gene. The expression product of this gene has dual functionality and can be used to implement the reaction with both NAD and NADP. With the growth of Osc. trichoides DG6 on a medium with glutamate as the only nitrogen source all the enzymes necessary for the implementation of the GS‑GOGAT pathway were found in the cells. However, for the glutamine synthetase reaction, ammonium, which was absent in the growth medium, was required. The source of ammonium may be glutamate metabolized through glutamate dehydrogenase.

[Identification of Hydrocarbon-Oxidizing Dietzia Bacteria from Petroleum Reservoirs Based on Phenotypic Properties and Analysis of the 16S rRNA and gyrB Genes]

The taxonomic position of hydrocarbon-oxidizing bacterial strains 263 and 32d isolated from formation water of the Daqing petroleum reservoir (PRC) was determined by polyphasic taxonomy techniques, including analysis of the 16S rRNA and the gyrB genes. The major chemotaxonomic characteristics of both strains, including the IV type cell wall, composition of cell wall fatty acids, mycolic acids, and menaquinones, agreed with those typical of Dietzia strains. The DNA G+C content of strains 263 and 32d were 67.8 and 67.6 mol%, respectively. Phylogenetic analysis of the 16S rRNA gene of strain 32d revealed 99.7% similarity to the gene of D. maris, making it possible to identify strain 32d as belonging to this species. The 16S rRNA gene sequence of strain 263 exhibited 99.7 and 99.9% similarity to those of D. natronolimnaea and D. cercidiphylli YIM65002(T), respectively. Analysis of the gyrB genes of the subterranean isolates and of a number of Dietzia type strains confirmed classiffication of strain 32d as a D. maris strain and of strain 263, as a D. natronolimnaea strain. A conclusion was made concerning higher resolving power of phylogenetic analysis of the gyrB gene compared to the 16S rRNA gene analysis in the case of determination of the species position of Dietzia isolates.

[Sulfate-Reducing Bacterial Communities in the Water Column of the Gdansk Deep (Baltic Sea)]

Biodiversity of sulfate-reducing bacterial communities in the water column of the Gdansk Deep, Baltic Sea, where H2S had been detected in near-bottom layers, was analyzed by PCR with primers for the 16S rRNA genes of six major phylogenetic subgroups of sulfate-reducing bacteria (SRB). Using denaturing gradient gel electrophoresis followed by sequencing, the nucleotide sequences of reamplified dsrB gene fragments from investigated water samples were determined. For the first time the presence of nucleotide sequences of the dsrB gene was detected by PCR in the water samples from all hydrochemical layers, including subsurface oxic waters. The presence of the 16S rRNA genes of representatives of Desulfotomaculum, Desulfococcus-Desulfonema-Desulfosarcina, and Desulfovibrio-Desulfomicrobium SRB subgroups was also revealed throughout the water column of the Gdansk Deep. Analysis of translated amino acid sequences encoded by the dsrB gene demonstrated the highest homology with the relevant sequences of uncultured SRB from various marine habitats.

[Phylogenetic diversity of bacteria in soda lake stratified sediments]

Various previously developed techniques for DNA extraction from the samples with complex physicochemical structure (soils, silts, and sediments) and modifications of these techniques developed in the present work were tested. Their usability for DNA extraction from the sediments of the Kulunda Steppe hypersaline soda lakes was assessed, and the most efficient procedure for indirect (two-stage) DNA extraction was proposed. Almost complete separation of the cell fraction was shown, as well as the inefficiency of nested PCR for analysis of the clone libraries obtained from washed sediments by amplification of the 16S rRNA gene fragments. Analysis of the clone library obtained from the cell fractions of stratified sediments (upper, medium, and lower layers) revealed that in the sediments of Lake Gorchina-3 most eubacterial phylotypes belonged to the class Clostridia, phylum Firmicutes. They were probably specific for this habitatand formed a new, presently unknown high-rank taxon. The data obtained revealed no pronounced stratification of the spe- cies diversity of the eubacterial component of the microbial community inhabiting the sediments (0-20 cm) in the inshore zone of Lake Gorchina-3.

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

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 Desulfonatronovibrio, which, so far, included only obligately alkaliphilic members found exclusively in soda lakes. The isolates utilized formate, H₂ and pyruvate as electron donors and sulfate, sulfite and thiosulfate as electron acceptors. In contrast to the described species of the genus Desulfonatronovibrio, the salt lake isolates could only tolerate high pH (up to pH 9.4), while they grow optimally at a neutral pH. They belonged to the moderate halophiles growing between 0.2 and 2 M NaCl with an optimum at 0.5 M. On the basis of their distinct phenotype and phylogeny, the described halophilic SRB are proposed to form a novel species within the genus Desulfonatronovibrio, D. halophilus (type strain HTR1^T = DSM24312^T = UNIQEM U802^T).

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

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 obligately anaerobic fermentative bacteria, which represented a novel deep lineage within the order Clostridiales loosely associated with the family Lachnospiraceae. The isolates were rod-shaped and formed terminal round endospores. One of the striking features of the novel group is a very narrow substrate spectrum for growth, restricted to galacturonic acid and its polymers (e.g. pectin). Acetate and formate were the final fermentation products. Growth was possible in a pH range from 8 to 10.5, with an optimum at pH 9.5-10, and in a salinity range from 0.2 to 3.5 M Na(+). On the basis of unique phenotypic properties and distinct phylogeny, the pectinolytic isolates are proposed to be assigned to a new genus Natranaerovirga with two species N. hydrolytica (APP2(T)=DSM24176(T)=UNIQEM U806(T)) and N. pectinivora (AP3(T)=DSM24629(T)=UNIQEM U805(T)).

Natronoflexus pectinivorans gen. nov. sp. nov., an obligately anaerobic and alkaliphilic fermentative member of Bacteroidetes from soda lakes

Anaerobic enrichment with pectin at pH 10 and moderate salinity inoculated with sediments from soda lakes of the Kulunda Steppe (Altai, Russia) resulted in the isolation of a novel member of the Bacteroidetes, strain AP1(T). The cells are long, flexible, Gram-negative rods forming pink carotenoids. The isolate is an obligate anaerobe, fermenting various carbohydrates to acetate and succinate. It can hydrolyze and utilize pectin, xylan, starch, laminarin and pullulan as growth substrates. Growth is possible in a pH range from 8 to 10.5, with an optimum at pH 9.5, and at a salinity range from 0.1 to 2 M Na(+). Phylogenetic analysis based on 16S rRNA sequences placed the isolate into the phylum Bacteroidetes as a separate lineage within the family Marinilabilaceae. On the basis of distinct phenotype and phylogeny, the soda lake isolate AP1(T) is proposed to be assigned in a new genus and species Natronoflexus pectinivorans (=DSM24179(T) = UNIQEM U807(T)).

Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov

Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H₂ and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.