Том 88, № 4 (2019)

Extremophilic prokaryotes, inhabitants of hot, cold, acidic, alkaline, saline, and deep-sea ecosystems, are classified as mono- and polyextremophilic or extreme-tolerant. Under conditions of heating, acidification, or salinization, thermophilic saprotrophic archaea are capable of maintaining endogenous homeostasis and high growth rates by biosynthesis of heat shock enzymes (proteins ofgeneral stress response), C₄₀C₄₀ membrane tetraesters with different numbers of cyclopentane rings, trehalose, and other hyperosmolytes. Small size of reduced genomes (0.5–3.0 Mb) of archaeal thermoacidophiles and hyperthermophiles was shown to reflect their adaptability mainly due to phenotypic changes and probably to have a reduced potential for speciation. In contrast, psychrophilic heterotrophic bacteria respond to sublethal temperature decrease by increased conformational flexibility of the macromolecules and elevated content of unsaturated fatty acids in the composition of their membrane lipids, synthesize membrane-associated glycoproteins, anti-freeze proteins, a group of general stress response proteins, specific and inducible cold shock proteins, which increase the growth rate. When slowing down and stopping the growth, psychrophiles switch on the processes of secondary metabolism and sharply increasing the biosynthesis of adaptogenic exopolysaccharides. Thus, they ameliorate the direct effects of salinity and hydrostatic pressure on viable cells, block the viral attack, and affect the microstructure and physicochemical properties of ice. Marine psychrophilic and piezopsychrophilic bacteria havelarger genomes of 2.6–6.4 Mb, which reflects their adaptability due to genotypic changes and an increased potential for speciation.

The molecular mechanisms of stress response of Planktothrix agardhii, one of the dominant cya-nobacteria in the basins of the Northwestern Russia and other regions during “blooming,” on the effect of 4-tert-octylphenol (OP), a hormone-like xenobiotic of anthropogenic origin, were studied. In the presence of OP, an increase in the permeability of P. agardhii cell membranes occurred, one of the reasons for which was the oxidation of membrane lipids under conditions of oxidative stress caused by generation of reactive oxygen species. A dose-dependent increase of the activities of enzymatic and non-enzymatic antioxidants in P. agardhii was registered in response to octylphenol-induced oxidative stress, indicating OP action as an activator of expression of stress regulons genes. Due to the structural similarity of 4-tert-octylphenol and alkylresorcinols (AR), the natural microbial regulators controlling development of microbial populations, OP released into the environment may imitate the functions of AR, interfering with the communication process of microbial cells in the population, which may adversely affect the succession and stability of functioning of microbial communities.

Molecular biological and cultivation-based approaches were used to investigate the microbial community of tehnogenic soil contaminated with poorly degradable toxic (chlorinated) aromatic compounds. Diversity of the bphA1 genes, the key genes for the degradation of biphenyl/polychlorinated biphenyls (PCB) was assessed, and new bacterial degraders of biphemyl/PCB were isolated. Cloning of the PCR product obtained using the DNA isolated from soil as a template and the primers to the biphenyl 2,3-dioxygenase α-subunit gene (bphA1) revealed two types of the genes of aromatic dioxygenases (DO) with the highest similarity (97.8‒99.5%) to the genes encoding the Rieske cluster of DO α-subunits (bphA1) from uncultured bacteria. Two biphenyl-degrading isolates obtained from an enrichment culture of a soil sample incubated with biphenyl were identified as Pseudomonas (VRP2-6 and VRP2-2). According to their 16S rRNA gene sequences, they exhibited the highest similarity to the type strain of P. taiwanensis (99%) and P. alcaligenes (100%), respectively. Analysis of the bphA1 sequences of strains VRP2-6 and VRP2-2 revealed the similarity to those of the known biphenyl-degrading pseudomonads not exceeding 97.3%. The isolate VRP2-6 efficiently utilized ortho- and para-monochlorinated biphenyls and degraded dichlorinated biphenyl oxidizing both the ortho- and para-chlorinated rings of the biphenyl molecule. New pseudomonad strains may be of interest for development of biotechnologies aimed at monitoring and remediation of biphenyl/PCB-contaminated soils.

Phages of the phytopathogenic Pectobacteriaceae species causing black leg and soft rot of potato were investigated. These phages are promising as biocontrol agents to prevent the loss of seed and ware potato tubers. The present work characterizes a new podovirus PP16, infecting a broad range of Pectobacterium carotovorum strains. Based on its genomic composition, phage PP16 was assigned to a separate phylogenetic branch of the genus Phimunavirus, subfamily Autographivirinae. Bacteriophage PP16 efficiently inhibited development of bacterial infection both in vitro and in planta. The field experiment demonstrated a substantial increase of plant germination after the treatment of seed potato with phage PP16.

The genus Clostridium includes a group of anaerobic bacteria, which have remarkable application prospects in cellulose degradation and industrial production or are important pathogens. In this study, the phylogeny of Clostridium spp., whose complete genomes were reported, was inferred based on concatenation of 49 conservative genes, including ribosomal protein genes. The results indicated that the topology of the genomic tree was consistent with the clusters of the species in the ribosomal protein tree and 16S rRNA trees. Based on the alignment and phylogenetic analysis of 49 conservative selected genes and 27218 final nucleotide characters, the genomic tree supported classification results and reassignments of some species in previous works, including other genomic trees. The phylogenetic deduction was not only the classification skeleton of the genus Clostridium, but also the relationship of those species in genes involved in basic cell cycles.

Numbers of bacterial, archaeal, and fungal ribosomal gene copies and the taxonomic structure of prokaryotic communities in virgin tropical soils under weakly impacted monsoon forests at the CKat Tien National Park (Southern Vietnam) were determined, and their relation with the major physicochemical parameters of the studied soils were investigated. Samples were collected from genetic horizons of brown tropical (Cambisol) and dark-colored (Umbrisol) soils on volcanic deposits, red-yellow tropical soil (Regosol) on metamorphic slates, and alluvial sandy-loam soil (Fluvisol). The numbers of ribosomal gene copies in virgin soils of southern Vietnam tropical forests were up to 10¹¹–10¹² gene copies per 1 g, which was comparable to the richest soils of the temperate zone. The highest numbers of microbial genes were found in the upper horizons (4–10 cm). Higher abundance of microbial ribosomal genes was found in volcanic soils, compared to red-yellow tropical and alluvial ones. The dominant prokaryotic phyla were Proteobacteria and Acidobacteria (subgroup 1, Acidobacteriales; subgroup 2; and Solibacterales). The share of Acidobacteria in soils correlated with pH and was highest in the most acidic red-yellow tropical soil. The share of Verrucomicrobia was highest in the surface soil layers and decreased with depth. The share of Chloroflexi increased with depth. Members of the recently described bacterial phylum Rokubacteria were revealed. The differences in soil-forming rocks (volcanic deposits, meatmorphic slates, and alluvium) determined the differences in the chemical properties of soils and the taxonomic structure of their prokaryotic communities. Organic carbon content is probably the main factor determining both the abundance of microbial ribosomal genes and the taxonomic structure of prokaryotic communities from virgin forest tropical soils.