Vol 85, No 3 (2016)

Rare bacterial biosphere (RBB) is a large and probably predominant sector of bacterial diversity, which is specifically represented by small populations. Although some RBB components have been characterized phenotypically (actualistic objects), it has been mainly described as a set of virtual objects, i.e., of the 16S rRNA gene sequences from environmental DNA samples, which are grouped into phylotypes (operational taxonomic units, OTUs). The upper OTU threshold for RBB is presently not standardized. It is usually ~1% of the sum of OTU sequences in the metagenome library, or five sequences per OTU in absolute values. The analyzed RBB objects include (1) virtual and actualistic objects; (2) autochthonous and allochthonous forms; (3) vegetative and differentiated cells; (4) dead bacteria and free DNA; and (5) artifacts and informational gaps. The RBB phenomenon has not been sufficiently explained. According to some concepts, the RBB objects are rare due to restrictive action of unfavorable environmental factors. According to others, they utilize a successful adaptive strategy of low abundance, which facilitates higher genetic diversity, dispersal and colonization of new niches, and microbial conversion of specific substrates. Since RBB was revealed only in the early 2000s and is still poorly studied, its role in organic evolution and its place in the ecosystems should be determined by future research. The information on the RBB composition, distribution, and functions will be important for bacteriology, while some cultured species may be of basic or applied importance.

Comparative analysis of germination of asexual sporulation spores (conidia and sporangiospores) and of specific features of dormancy release was carried out for ascomycete mycelial fungi Aspergillus tamarii VKM F-64 and A. sydowii VKM F-441, as well as for zygomycete fungi Cunninghamella echinulata VKM F-663 and Umbelopsis ramanniana VKM F-582. The spores of these strains were shown to be in a state of exogenous dormancy and differed in lag phase duration and germination rate, which depended on the presence of nutrients in the medium. Only the strain C. echinulata VKM F-663 exhibited 100% spore germination, with the germination rate and lag phase duration not depending on the composition of the medium. While in A. tamarii strain VKM F-64, the total number of spores germinating on rich and poor media was also almost the same, in the absence of nutrients lag phase duration increased and the germination rate decreased. For strains U. ramanniana VKM F-582 and A. sydowii VKM F-441, the degree of spore germination in the absence of nutrients in the medium was considerably lower than on the rich medium, while the lag phase was longer. These data indicate that the spores of C. echinulata VKM F-663 are in the state of exogenous dormancy, which does not require for release any compounds except water. The spores of U. ramanniana strain VKM F-582 and of the Aspergillus strains exhibited another variant of exogenous dormancy, which required for release, apart from water, also the sources of carbon and nitrogen. Thus, the character of dormancy release may differ even within a single genus (Aspergillus).

The composition of the membrane lipids and cytosol soluble carbohydrates under three kinds of unfavorable impacts (osmotic, oxidative, and cold) was studied. Changes in the composition of the membrane lipids, specifically, increasing content of phosphatidic acids and decreasing levels of phosphatidylcholines and phosphatidylethanolamines, were the general response to the impacts. The degree of fatty acid unsaturation increased in all dominant phospholipids under osmotic shock, only in cardiolipins and phosphatidic acids under oxidative stress, and only in phosphatidylcholines under cold shock. Increased sterol content was observed only under cold and osmotic treatments. No general pattern was revealed in the composition of cytosol carbohydrates in response to stresses. Oxidative stress had almost no effect on the carbohydrate composition, while osmotic and cold treatments resulted in increased glycerol content and decreased total carbohydrate content. The mechanisms of fungal response to various stress impacts are discussed.

Production of biosurfactants by acidophilic mycobacteria was demonstrated in the course of aerobic degradation of hydrocarbons (n-tridecane, n-tricosane, n-hexacosane, model mixtures of С₁₄–С₁₇, С₁₂‒С₁₉, and С₉–С₂₁n-alkanes, 2,2,4,4,6,8,8-heptamethylnonane, squalane, and butylcyclohexane) and their complex mixtures (hydrocarbon gas condensate, kerosene, black oil, and paraffin oil) under extremely acidic conditions (pH 2.5). When grown on hydrocarbons, the studied bacterial culture AG_S10 caused a decrease in the surface and interfacial tension of the solutions (to the lowest observed values of 26.0 and 1.3 mN/m, respectively) compared to the bacteria-free control. The rheological characteristics of the culture changed only when mycobacteria were grown on hydrocarbons. Neither the medium nor the cell-free culture liquid had the surfactant activity, which indicated formation of an endotype biosurfactant by mycobacteria. Biodegradation of n-alkanes was accompanied by an increase in cell numbers, surfactant production, and changes in the hydrophobicity of bacterial cell surface and in associated phenomena of adsorption and desorption to the hydrocarbon phase. Research on AGS10 culture liquids containing the raw biosurfactant demonstrated the preservation of its activity within a broad range of pH, temperature, and salinity.

A bacterial strain IB-4, antagonistic to plant pathogenic fungi of the genera Fusarium, Bipolaris, and Alternaria, was isolated from arable soils of the Mechetlinskii district, Bashkortostan. Physiological, biochemical, and culture morphological properties of strain IB-4 supported its classification within the genus Pseudomonas. In spite of some discrepancies in the results of phenotypic and chemotaxonomic research, analysis of the 16S rRNA gene sequence, DNA–DNA hybridization, GC-content, and MALDI mass spectral data provide considerable evidence supporting its identification as a Pseudomonas koreensis strain. P. koreensis strain IB-4 was shown to possess the valuable features characteristic of PGPR microorganisms: antifungal and nitrogenase activities and ability to synthesize indole-3-acetic acid (IAA) and cytokinin-like compounds. Field test, in which potato plants were treated with the culture liquid of P. koreensis strain IB-4 revealed a positive effect on potato yield and resistance to plant pathogens.

Multidrug-resistant tuberculosis (MDR-TB) is caused by bacteria that are resistant to the most effective anti TB drugs (Isoniazid and Rifampicin) with or without resistance to other drugs. Novel intervention strategies to eliminate this disease based on finding proteins can be used for designing new drugs or new and reliable kits for diagnosis. The aim of this study was to compare the protein profile of MDR-TB with sensitive isolates. Two-dimensional gel electrophoresis (2DE) along with mass spectrometry is a powerful and effective tool to identification and characterization of Mycobacterium tuberculosis. Two-dimensional gel electrophoresis and matrix assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry was used for diagnosis and comparison of proteins. We identified 14 protein spots in MDR-TB isolates that 2DE analysis showed these spots absent in M. tuberculosis sensitive isolates (Rv1876, Rv0379, Rv0147, Rv2031c, Rv3597c, Rv1886c, MT0493, Rv0440, Rv3614c, Rv1626, Rv0443, Rv0475, Rv3057 and unknown protein. The results showed 22 protein spots which were up regulated (or expressed) by the MDR-TB isolates, (Rv1240, Rv3028c, Rv2971, Rv2114c, Rv3311, Rv3699, Rv1023, Rv1308, Rv3774, Rv0831c, Rv2890c, Rv1392, Rv0719, Rv0054, Rv3418c, Rv0462, Rv2215, Rv2986c, Rv3248c and Rv1908c)). Two up regulated protein spots were identified in sensitive isolate (Rv1133c and Rv0685). These data will provide valuable clues in further investigation for suitable TB rapid tests or drug targets against drug resistant and sensitive of M. tuberculosis.

Pyrosequencing of the 16S rRNA gene fragments was used to investigate the bacterial community of an Alla hot spring microbial mat. The mat community was mainly represented by the members of five phyla: Deinococcus-Thermus, Nitrospirae, Atribacteria (OP9), Proteobacteria, Chloroflexi, and Firmicutes, with other groups responsible for not more than 2% of the total number. From hot springs of the Baikal Rift Zone (Buryatia, Russia), 13 strains of aerobic alkaliphilic thermophilic organotrophic bacteria were isolated, and their morphology, ecology, physiology, and phylogenetic position were studied. Based on analysis of their 16S rRNA gene sequences, the isolates were identified as members of the family Bacillaceae. Strains Al-9-1, Se-1, Ga-1-1, Ga-9-2, and Se-1-10 were assigned to the genus Anoxybacillus; strains Ur-6, Br-2-2, А2, and Um-09m, to the genus Bacillus; strains Gor-10s and Gа-35, to the genus Paenabacillus. Secreted endopeptidases of the isolates were shown to have relatively narrow substrate specificity. The investigated enzymes were characterized by high pH (6.3–11.4) and temperature stability (23–70°C), which makes it possible to carry out organic matter degradation in the environment under variable ecological conditions.

The brine shrimp, Artemia is the dominant macrozooplankton present in many hypersaline environments. Artemia urmiana is the only macroscopic organism in Urmia Salt Lake (Iran), and the high salinity of the lake makes it a suitable environment for halophilic archaea too. Because of common environment for Artemia and extreme halophiles; this investigation is concentrated on studying the relationship between Artemia and halophilic archaea in Urmia Lake. In this study first the procedure of arhaea isolation was done. Then, isolated strains were sub-cultured and DNA was extracted and amplified by PCR using specific primers for amplifying archaeal 16S rRNA. The amplified archeal DNA fragments were purified, and sequenced. 16S rRNA sequences were compared to known sequences using the NCBI BLAST program. Sequences relating to Halorubrum, Haloarcula and Halobacterium species were identified in Urmia Salt Lake water and Artemia adults and the phylogenetic tree of different species was constructed. Only Halorubrum species were present in association with Artemia. They belong to Halobacteriaceae family of archeae which are isolated from different salt lakes in different parts of world and we could show their existence in adult Artemia, another organism living in hypersaline enviroments.