Alla V. Bryanskaya

Molecular analysis of the benthos microbial community in Zavarzin thermal spring (Uzon Caldera, Kamchatka, Russia)

BackgroundGeothermal areas are of great interest for the study of microbial communities. The results of such investigations can be used in a variety of fields (ecology, microbiology, medicine) to answer fundamental questions, as well as those with practical benefits. Uzon caldera is located in the Uzon-Geyser depression that is situated in the centre of the Karym-Semyachin region of the East Kamchatka graben-synclinorium. The microbial communities of Zavarzin spring are well studied; however, its benthic microbial mat has not been previously described.ResultsPyrosequencing of the V3 region of the 16S rRNA gene was used to study the benthic microbial community of the Zavarzin thermal spring (Uzon Caldera, Kamchatka). The community is dominated by bacteria (>95% of all sequences), including thermophilic, chemoorganotrophic Caldiserica (33.0%) and Dictyoglomi (24.8%). The benthic community and the previously examined planktonic community of Zavarzin spring have qualitatively similar, but quantitatively different, compositions.ConclusionsIn this study, we performed a metagenomic analysis of the benthic microbial mat of Zavarzin spring. We compared this benthic community to microbial communities found in the water and of an integral probe consisting of water and bottom sediments. Various phylogenetic groups of microorganisms, including potentially new ones, represent the full-fledged trophic system of Zavarzin. A thorough geochemical study of the spring was performed.

Identification of Bacillus strains by MALDI TOF MS using geometric approach.

Microorganism identification by MALDI TOF mass-spectrometry is based on the comparison of the mass spectrum of the studied organism with those of reference strains. It is a rapid and reliable method. However, commercial databases and programs are mostly designed for identification of clinically important strains and can be used only for particular mass spectrometer models. The need for open platforms and reference databases is obvious. In this study we describe a geometric approach for microorganism identification by mass spectra and demonstrate its capabilities by analyzing 24 strains belonging to the Bacillus pumilus group. This method is based on representing mass spectra as points on a multidimensional space, which allows us to use geometric distances to compare the spectra. Delimitation of microorganisms performed by geometric approach correlates well with the results of molecular phylogenetic analysis and clustering using Biotyper 3.1. All three methods used allowed us to reliably divide the strains into two groups corresponding to closely related species, Bacillus pumilus and Bacillus altitudinis. The method developed by us will be implemented in a Web interface designed for using open reference databases for microorganism identification. The data is available at http://www.bionet.nsc.ru/mbl/database/database.html.

Geobacillus icigianus sp. nov., a thermophilic bacterium isolated from a hot spring.

A Gram-reaction-positive, motile, thermophilic spore-forming strain, G1w1(T), was isolated from a hot spring of the Valley of Geysers, Kamchatka (Russia). Based on data from the present polyphasic taxonomic study, including phylogenetic analysis of 16S rRNA and spo0A gene sequences, the strain is considered to represent a novel species of the genus Geobacillus, for which the name Geobacillus icigianus sp. nov. is proposed. The type strain is G1w1(T) ( = VKM B-2853(T) = DSM 28325(T)).

Draft Genome Sequence of Geobacillus icigianus Strain G1w1T Isolated from Hot Springs in the Valley of Geysers, Kamchatka (Russian Federation).

ABSTRACT The Geobacillus icigianus G1w1T strain was isolated from sludge samples of unnamed vaporing hydrothermal (97°С) outlets situated in a geyser in the Troinoy region (Valley of Geysers, Kronotsky Nature Reserve, Kamchatka, Russian Federation; 54°25′51.40″N, 160°7′41.40″E). The sequenced and annotated genome is 3,457,810 bp and encodes 3,342 genes.

Draft Genome Sequence of Anoxybacillus flavithermus Strain 25, Isolated from the Garga Hot Spring in the Barguzin Valley, Baikal Region, Russian Federation

ABSTRACT Anoxybacillus flavithermus strain 25 was isolated from a sediment sample from the Garga hot spring in the Barguzin Valley, Baikal Region, Russian Federation (54°19′3.72″N, 110°59′38.4″E). The sequenced and annotated genome is 2,838,680 bp and encodes 3,009 genes.

Adaptive capabilities of microorganisms of salt lakes of the Altai Region under conditions of early Mars

Adaptive capacity of bacteria and archaea from salt lakes of the Altai Region are discussed. It is established that halophilic archaea (genus Halorubrum) and halotolerant bacteria (genus Halomonas) grow in a wide range of pH and mineralization (in the presence of Cl−, SO42−, ClO4−, Mg2+) and survive at low temperatures with a minor decrease in viability.

A quantitative method for determination of PPDK concentration in miscanthus leaves

In this study, we used ELISA for quantification of PPDK in photosynthesizing leaves of miscanthus. We cloned a fragment of the gene encoding PPDK, purified the resulting protein by affinity chromatography, identified it using MALDI mass spectrometry, and obtained monoclonal antibodies by immunizing BALB/c mice. Selectivity of monoclonal antibodies was assessed by Western blot using the protein extracts of Soranovskii. The presence of PPDK was again verified by MALDI mass spectrometry. Therefore, we developed and tested the method for determining PPDK quantity in miscanthus using ELISA.

2.3THz radiation: Absence of genotoxicity/mutagenicity in Escherichia coli and Salmonella typhimurium.

The mutagenicity and genotoxicity in bacteria of 2.3THz radiation (THz) produced by a free-electron laser (NovoFEL) were evaluated; exposures were 5, 10, or 15min at average power 1.4W/cm(2). Two Ames mutagenicity test strains of Salmonella typhimurium, TA98 and TA102, were used. For the genotoxicity test, we measured SOS induction in Escherichia coli PQ37. No significant differences were found between exposed and control cells, indicating that THz radiation is neither mutagenic nor genotoxic under these conditions. Nevertheless, a small increase in total cell number of S. typhimurium after 15min exposure, and an increase in β-galactosidase and alkaline phosphatase activities in E.coli PQ37, were observed, indicating some effect of THz radiation on cell metabolism. We also examined the combined effect of 4-NQO (8μM; positive control) and THz exposure (5min) on genotoxicity in E.coli PQ37. Unexpectedly, THz radiation decreased 4-NQO genotoxicity.

Theoretical and practical issues of hydrocarbon biological oxidation by microorganisms

This study is focused on the theoretical issues of biological oxidation of oil hydrocarbons varying from alkanes to polycyclic aromatic hydrocarbons. The biochemical mechanisms of the decomposition of the oil components are shown, as well as the review of data represented in the conventional data bases. The results of the microbial community studies, inhabiting the natural oil seeps of the Uzon caldera, are described in detail. It is the first study of the ecophysiological characteristics of oil-degrading microorganisms isolated from the thermal oil seeps of the caldera.

Bioinformatics analysis of the genome of Geobacillus stearothermophilus 22 Strain isolated from the Garga hot spring, Baikal Region

A new strain, Geobacillus stearothermophilus 22, was isolated from the Garga hot spring in the Bargusin Valley, Baikal Region, Russia. The morphology and biochemistry of the strain were analyzed, and full genome sequencing was conducted. The sequence was subjected to bioinformatics analysis. The nucleotide sequences (contigs) of the strain were found to be similar to the genome of the thermophilic strain G. kaustophilus Y412MC52. The proteome of the new strain was analyzed. Enzymes that belong to hemicellulases (endoxylanase, beta-xylosidase, and arabinofuranosidase) and the endocellulase enzyme were detected.