Том 88, № 5 (2019)

Microorganisms disproportionating inorganic sulfur compounds are involved in biogeochemical cycles of elements in the modern biosphere. Sulfur-disproportionating prokaryotes are represented by 30 species of the Bacteria domain and belong to the phyla Proteobacteria, Thermodesulfobacteria, and Firmicutes. Most of the sulfur-disproportionating bacteria belong to four orders of the class Deltaproteobacteria. The microorganisms responsible for dismutation of sulfur compounds inhabit freshwater and shallow marine sediments, hypersaline and soda lakes, anthropogenic environments, and various natural thermal ecosystems. Most sulfur-disproportionating organisms are able to use other processes for growth, primarily dissimilatory sulfate reduction. Ability to grow autotrophically was shown for 17 sulfur-disproportionating strains from different phylogenetic groups. The biochemical mechanisms involved in disproportionation of sulfur compounds remain uncertain, which hinders the application of the current omics techniques. Comparative analysis of available complete genomes of the microorganisms capable of elemental sulfur disproportionation is provided. The presence of the complete set of the dissimilatory sulfate reduction genes was found not to be necessary for S⁰ disproportionation. This process does not require dissimilatory sulfite reductase (Dsr) and adenylyl-sulfate reductase (Apr). Sulfur relay proteins and the elemental sulfur- and/or polysulfides-reducing enzymes are important in sulfur disproportionation, but different microorganisms probably employ different sulfur transferases and polysulfide reductases in these processes.

Mass spectrometry (MS) methods furnish the clue to many microbiological applications including advanced studies on the diversity and classification of prokaryotes. Mass spectral data contribute to the polyphasic taxonomy which considers genotypic characters together with structure-functional and ecological traits. Additionally, these methods contribute to reliable and rapid identification of microorganisms bypassing conventional manipulations which are materials and time consuming. MS based analyses of biomarkers can be performed at the level of whole cells, cell homogenates, subcellular fractions, and individual molecules. For this purpose, various MS methods can be employed, such as MALDI-TOF, ESI, SELDI, and BAMS. Of these, MALDI-TOF MS is the especially easy-to-use and rapid method with many analytical applications, primarily in proteomics which aims at comprehensive description of protein inventory in prokaryotes. An alternative for detection and comparison of biomarkers via MS is amplification and alignment of marker gene sequences. Two molecular approaches supplement each other under support of database resources. Microbiologists readily assimilate MS methods propelled by high performance analyzers and sensitive detectors. The review focuses at progressing application of MS methods in microbiology, with an emphasis on identification and comparative study of bacteria.

Aerobic methanotrophic bacteria are an ecologically important group of microorganisms, which are functionally specialized in oxidation of the greenhouse gas methane. Recent insights into the growing pool of available genome sequences from methanotrophs revealed a number of as-yet-unknown metabolic capabilities of these bacteria. Thus, the genes indicative of aerobic anoxygenic photosynthesis by means of the photosystem II characteristic of purple bacteria were revealed in the genome of an obligate methanotroph Methylocapsa palsarum NE2^T. Advanced search for genomic determinants of phototrophy in other methanotrophs confirmed their occurrence in a number of methanotrophic Alphaproteobacteria, including Methylocella silvestris BL2^T and TVC, Methylocystis rosea SV97^T and GW6, as well as Methylocystis spp. strains SB2 and MitZ-2018. Genomes of these methanotrophs contained the pufABCLM gene clusters encoding the light-harvesting complex, bch/chl genes responsible for bacteriochlorophyll biosynthesis, and the pucC gene essential for bacteriochlorophyll transport, as well as the crtFDC, crtL and crtB genes responsible for carotenoid biosynthesis. Organization of these gene clusters was conserved within each methanotroph species and was highly similar in Methylocapsa and Methylocella strains. A number of rearrangements, including inverse localization of the genes encoding bacteriochlorophyll and carotenoid biosynthesis, were observed in the genomes of Methylocystis species. The presence of pufLM genes was also revealed in a new isolate of Methylocapsa palsarum, strain NSB8, which was obtained in this study from a tundra wetland of European Northern Russia. The presence of phototrophy-related genes in all available strains of the abovementioned species indicates their functional importance for these bacteria and suggests realization of the phototrophic potential under certain environmental conditions.

3-Chlorobenzoic acid (3-CBA) is widely used as a precursor/preservative in industry and agriculture and is therefore a known environmental contaminant. The key stages of 3-CBA decomposition by Rhodococcus opacus strains 1CP and 6a were studied. Comparative characterization of the substrate specificity of 3-chlorobenzoate 1,2-dioxygenase (3-CBA 1,2-DO), induced in the strains grown in the presence of 3‑CBA, was carried out. These enzymes were established to have a wider substrate specificity than the benzoate 1,2-dioxygenase (1,2-BDO) of R. opacus strain 1CP, which is induced during growth of R. opacus strain 1CP in the presence of benzoate. Benzoate, 3-CBA, and 3,4-dihydroxybenzoate served as substrates for 3‑CBA 1,2-DO. During the degradation of 3-CBA by R. opacus 1CP cells, both 3-chloro- and 4-chlorocatechol (3-CCat and 4-CCat) were detected. R. opacus 6a efficiently degraded 3-CBA without accumulation of intermediates. The difference in the pathways of 3-CBA degradation by these strains was shown: via the pathway of ortho-cleavage of 3-chlorocatechol in R. opacus 1CP and of 4-chlorocatechol in R. opacus 6a. In the genome of the strain R. opacus 6a, the genes encoding chlorocatechol 1,2-dioxygenase and chloromuconate cycloisomerase were found, which were 98-99% identical to the genes of R. opacus 1CP encoding 4‑chlorocatechol 1,2-dioxygenase (4-CCat 1,2-DO) and 3-chloromuconate cycloisomerase (3-CMCI) of the modified ortho-cleavage pathway for conversion of 4-chlorocatechol (the intermediate of 4-chlorophenol degradation). It was shown for the strains under study that implementation of different pathways for 3-CBA decomposition was predestined not by the metabolic capabilities of bacteria, but by the substrate specificity of 3-CBA 1,2-DO, the enzyme that initiates 3-CBA degradation.

Conditions of formation and phylogenetic composition were studied for pigmented biofilms and microbial mats of the Kandalaksha Bay (White Sea) supralittoral and of the littoral of the lakes separated from the sea. During the sampling period, salinity was 15 to 26 g/L, except for several desalinated salt marsh sites (4‒11 g/L); the temperature was 9‒12°C. The species composition and structure of benthic phototrophic communities were affected by severe climatic conditions of the area, including low average annual temperature and freezing of the littoral zones. Application of Next-generation sequencing of the 16S rRNA gene V3-V4 regions combined with microscopy of the samples and obtained cultures for analysis of the biodiversity of microbial communities resulted in improved understanding of diversity of both oxygenic and anoxygenic bacteria in the Kandalaksha Bay littoral. No significant differences were revealed in species composition of microbial mats from salt marshes and shallow sites of the lakes of marine origin. Members of the phyla Bacteroidetes (up to 36%) and Proteobacteria (up to 67%) predominated in the mats and biofilms. The share of phototrophic bacteria was 0.3–18%. Oxygenic phototrophs (cyanobacteria Phormidium, Oscillatoria, Spirulina, and Anabaena, as well as diatoms) predominated in the phototrophic community. The species number of anoxygenic phototrophic bacteria did not exceed 5% of all prokaryotes. These were mainly mesophilic marine species of purple sulfur bacteria of the genera Thiorhodococcus and Thiocapsa. No members of the family Ectothiorhodospiraceae, which are typical of microbial mats from southern seas, were found in subpolar microbial mats. Nonsulfur purple bacteria and aerobic anoxygenic phototrophic bacteria were mostly similar to the known marine species. Green sulfur bacteria (salt-water Prosthecochloris and Сhlorobium species) were detected in two coastal mat samples from meromictic lakes. Anoxygenic filamentous phototrophic bacteria, which occurred in almost all benthic phototrophic communities, were represented by new phylotypes.

Bacterial communities of the six Ericaceae bog plants were studied. The total number of bacteria on the vegetative organs of the Ericaceae plants was high and comparable to the one on Sphagnum mosses. Members of bacterial taxa colonizing both heather plants and Sphagnum mosses were identified. According to their 16S rRNA gene sequences, predominant bacteria of the epiphytic-saprotrophic complex were identified as Pseudomonas, Stenotrophomonas, Serratia, and Chryseobacterium species. The physiological diversity of the hydrolytic bacterial complex was significantly higher in the Ericaceae plants than in the Sphagnum mosses. Analysis of the taxonomic position and functions of identified bacteria indicated that the studied bacteria were capable of stimulating the growth of plants inhabiting ombotrophic bogs.