Vol 85, No 2 (2016)

The processes of speciation and macroevolution of root nodule bacteria (rhizobia), based on deep rearrangements of their genomes and occurring in the N₂-fixing symbiotic system, are reconstructed. At the first stage of rhizobial evolution, transformation of free-living diazotrophs (related to Rhodopseudomonas) to symbiotic N₂-fixers (Bradyrhizobium) occurred due to the acquisition of the fix gene system, which is responsible for providing nitrogenase with electrons and redox potentials, as well as for oxygen-dependent regulation of nitrogenase synthesis in planta, and then of the nod genes responsible for the synthesis of the lipo-chitooligosaccharide Nod factors, which induce root nodule development. The subsequent rearrangements of bacterial genomes included (1) increased volume of hereditary information supported by species, genera (pangenome), and individual strains; (2) transition from the unitary genome to a multicomponent one; and (3) enhanced levels of bacterial genetic plasticity and horizontal gene transfer, resulting in formation of new genera—of which Mesorhizobium, Rhizobium, and Sinorhizobium are the largest—and of over 100 species. Rhizobial evolution caused by development and diversification of the Nod factor-synthesizing systems may result in either relaxed host specificity range (transition of Bradyrhizobium from autotrophic to symbiotrophic carbon metabolism in interaction with a broad spectrum of legumes) or narrowed host specificity range (transition of Rhizobium and Sinorhizobium to “altruistic” interaction with legumes of the galegoid clade). Reconstruction of the evolutionary pathway from symbiotic N₂-fixers to their free-living ancestors makes it possible to initiate the studies based on up-to-date genome screening technologies and aimed at the issues of genetic integration of organisms into supraspecies complexes, ratios of the macro- and microevolutionary mechanisms, and development of cooperative adaptations based on altruistic interaction between the symbiotic partners.

Exometabolites of 22 strains of the genus Penicillium, section Chrysogena isolated from low-temperature ecotopes of various geographical regions were analyzed. The ecotopes included permafrost deposits, frozen volcanic ash, a fossil horse, cryopeg, and water from an Antarctic lake. The studied strains were found to contain exometabolites belonging to the groups of penicillins (penicillin G), chrysogines (chrysogine, 3-acetyl-quinazolin-4(3H)-one, 2-pyruvoylaminobenzamide, 2-(2-hydroxypropionylamino)-benzamide, and questiomycin A), roquefortines (3,12-dihydroroquefortine, roquefortine, glandicolines A and B, and meleagrine), xanthocillins (xanthocillin X), and simple tryptophan derivatives (N-acetyltriptamine and indoleacetic acid). In five P. chrysogenum strains and three P. nalgiovense strains, a correlation was found between exometabolite spectra and morphological characteristics of the cultures isolated from modern ecotopes. For other strains species, identification was based on morphological features due to the absence of biosynthesis of penicillin G on the major chemotaxonomic markers for these species.

The previously obtained insertion mutants of Azospirillum brasilense Sp245 in the genes mmsB1 and fabG1 (strains SK039 and Sp245.1610, respectively) were characterized by impaired flagellation and motility. The putative products of expression of these genes are 3-hydroxyisobutyrate dehydrogenase and 3-oxoacyl-[acyl-carrier protein] reductase, respectively. In the present work, A. brasilense strains Sp245, SK039, and Sp245.1610 were found to have differences in the content of 3-hydroxyhexadecanoic, hexadecanoic, 3-hydroxytetradecanoic, hexadecenoic, octadecenoic, and nonadecanoic acids in their lipopolysaccharide preparations, as well as in cell hydrophobicity and hemagglutination activity and dynamics of cell aggregation, in biomass amount, and in the relative content of lipopolysaccharide antigens in mature biofilms formed on hydrophilic or hydrophobic surfaces.

Trichoderma species are widely used in agriculture as biofungicides. These fungi are rich source of secondary metabolites and the mycoparasitic species are enriched in genes for biosynthesis of secondary metabolites. Most often, genes for secondary metabolism are clustered in fungal genomes. Previously, no systematic study was undertaken to identify the secondary-metabolism related gene clusters in Trichoderma genomes. In the present study, a survey of the three Trichoderma genomes viz. T. reesei, T. atroviride and T. virens, was made to identify the putative gene clusters associated with secondary metabolism. In T. reesei genome, we identified one new NRPS and 6 new PKS clusters, which is much less than that found in T. atroviride (4 and 8) and T. virens (8 and 7). This work would pave the way for discovery of novel secondary metabolites and pathways in Trichoderma.

A comparative analysis of the four commercially available and laboratory luminescent sensor strains to the toxic effect of 10 carbon-based nanomaterials (CBNs) and 10 metal nanoparticles (MNPs) was carried out in this study. The bioluminescence inhibition assays with marine Photobacterium phosphoreum and recombinant Escherichia coli strains were varied in minimal toxic concentrations and EC₅₀ values but led to well-correlated biotoxicity evaluation for the most active compounds, which were ranked as Cu > (MgO, CuO) > (fullerenol, graphene oxide). The novel sensor strain Bacillus subtilis EG168-1 exhibited the highest sensitivity to CBNs and MNPs, which increased significantly the number of toxic compounds causing the bacterial bioluminescence inhibition effect.

Microbial diversity in the sediments of the Kara Sea shelf and the southern Yenisei Bay, differing in pore water mineralization, was studied using massive parallel pyrosequencing according to the 454 (Roche) technology. Members of the same phyla (Cyanobacteria, Verrucomicrobia, Actinobacteria, Proteobacteria, and Bacteroidetes) predominated in bacterial communities of the sediments, while their ratio and taxonomic composition varied within the phyla and depended on pore water mineralization. Increasing salinity gradient was found to coincide with increased share of the γ-Proteobacteria and decreased abundance of α- and β-Proteobacteria, as well as of the phyla Verrucomicrobia, Chloroflexi, Chlorobi, and Acidobacteria. Archaeal diversity was lower, with Thaumarchaeota predominant in the sediments with high and low mineralization, while Crenarchaeota predominated in moderately mineralized sediments. Microbial communities of the Kara Sea shelf and Yenisei Bay sediments were found to contain the organisms capable of utilization of a broad spectrum of carbon sources, including gaseous and petroleum hydrocarbons.

Quantitative ratios of the biomasses of bacterio- and phytoplankton, interrelation of their production characteristics, and association of the functional characteristics with environmental factors were studied for Lake Khanka, the Yenisei River, and the Krasnoyarsk Reservoir. The ratio between the biomasses of bacterioplankton (B_b) and phytoplankton (B_p) in these water bodies was shown to vary within the range exceeding three orders of magnitude. Bacterioplankton biomass was relatively stable and varied from sample to sample by an order of magnitude. In more than 50% of the samples (total sample number, 495), bacterioplankton biomass exceeded that of the phytoplankton. The average B_b/B_p ratios for Lake Khanka, Yenisei River, and Krasnoyarsk Reservoir were 5.1, 2, and 1.4, respectively. Increased B_b/B_p ratios were found to correlate with elevated specific (per unit biomass) phytoplankton production. This finding indicated additional supply of biogenic elements to phytoplankton due to their recycling by bacterial communities. The ratio between bacterioplankton and phytoplankton production for Lake Khanka varied from year to year (0.07 to 0.76). For the Yenisei River and the Krasnoyarsk Reservoir these ratios were on average 0.19 and 0.27, respectively. According to the literature data for other water bodies, bacterial production may reach from 10 to over 100% of the primary production. The equilibrium density of bacterioplankton (maximal density of the population) in Lake Khanka was ~1.5 times higher than in the Yenisei River and the Krasnoyarsk Reservoir due to higher content of suspended mineral matter and associated organo-mineral detritus in the lake. The interaction between dissolved organic compounds sorbed on the surface of mineral particles results in chemical alteration of biochemically stable substrate into compounds which may be assimilated by aquatic microorganisms.