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Vol 86, No 3 (2017)

Reviews

Microbial communities of lichens

Kachalkin A.V., Korchikov E.S., Dobrovol’skaya T.G., Pankratov T.A.

Abstract

The current state of scientific researches in lichen microbiology was reviewed. Analysis of the literature revealed the main areas and fundamental issues which refer to investigation of microbial consortia in lichen bodies. Special attention was focused on analysis of the prokaryotic community which plays a structural and functional role and is involved in metabolism and regulation of activity of the lichen symbiosis as a whole. In the review, for the first time the information on the yeast community, of which some members do not occur presently in other environmental substrates, was summarized. The data on the protozoa inhabiting lichen thalli were also provided. The reviewed literature enabled us to consider the growing and decaying thallus as a complex ecosystem with specific levels of regulation of abundance, taxonomic diversity, and activity of the members of five kingdoms: fungi, plants, protozoa, eubacteria, and archaea.

Microbiology. 2017;86(3):293-309
pages 293-309 views

Experimental Articles

Effect of O-acetylation of O antigen of Escherichia coli lipopolysaccharide on the nonspecific barrier function of the outer membrane

Kulikov E.E., Majewska J., Prokhorov N.S., Golomidova A.K., Tatarskiy E.V., Letarov A.V.

Abstract

Comparison of the methods for determination of permeability of the outer membrane of Escherichia coli strain 4s and its mutants was carried out. The studied isogenic strains E. coli 4s were obtained by selection of spontaneous mutants according to their sensitivity to bacteriophages recognizing the surface O antigen of the outer membrane lipopolysaccharide as a primary receptor. The variants differed in the presence and (de)acetylation of the lipopolysaccharide O antigen. A peptide antibiotic polymyxin, plasmid DNA, and lysozyme were used as probes. The role of acetylation of the O antigen of the lipopolysaccaride of E. coli outer membrane in modification of its permeability (correlating with bacteriophage sensitivity of the cells) was confirmed. Kinetic analysis using lysozyme was shown to be the optimal method for determination of the barrier function of E. coli outer membrane.

Microbiology. 2017;86(3):310-316
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Characterization of biofilm-forming marine bacteria and their effect on attachment and germination of algal spores

Beleneva I.A., Skriptsova A.V., Svetashev V.I.

Abstract

In this work, 37 bacterial strains isolated from biofouling of marine organisms and from the Museum of Heterotrophic Bacteria of the National Scientific Center of Marine Biology were studied. The strains were identified based on their phenotypic characteristics and on the fatty acid composition of their cell wall lipids. Members of the genus Pseudoalteromonas prevailed both in associated microflora of two dinoflagellate clones and in the biofilms from marine hydrobionts. Associated microflora included also members of the CFB cluster, Bacillus, Sulfitobacter, Acinetobacter, Shewanella, and Psychrobacter. A considerable portion of strains (48.6%) exhibited antimicrobial activity. Antifouling activity against algal spores was studied using single-species bacterial biofilms and the spores of Ulva lactuca и Undaria pinnatifida, the algae most common in the Sea of Japan. Strong inhibitory effect on attachment of Ulva and Undaria spores was observed for 75 and 51% of the strains, respectively. Attached spores were, however, less sensitive to the inhibitory action of biofilms. Species specificity of algal response to bacteria was shown, with a strain having different effect on the spores of different algal species. Biotechnologically promising strains were determined, which exhibited high activity against the spores of macroalgae and could probably be used as producers of antifouling substances and as components of antifouling coatings. No relation was found between antifouling activity of bacteria and the source of their isolation. Our results indicate wide occurrence of bacteria with antifouling activity among associated microflora of marine hydrobionts and demonstrate the extent of complexity and diversity of relations between bacterial biofilms and algal spores.

Microbiology. 2017;86(3):317-329
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Aerobic degradation of adamantanes at highly acidic conditions

Ivanova A.E., Kanat’eva A.Y., Kurganov A.A., Selifanova M.V., Purygin P.P.

Abstract

Biodegradation of alkyl-substituted adamantane derivatives (1-methyl, 1,3-dimethyl-, and 1,3,5-trimethyladamantane) by slow-growing bacteria Mycobacterium AGS10 was studied. The process was carried out under extremely acidic conditions (pH 2.5). Bacterial strain AGS10 was able to utilize these alicyclic hydrocarbons with a high degree of condensation and diamond-like structure, which are usually resistant to microbial transformation. Efficiency of alkyaldamantane biodegradation by the cells growing with these substrates as the sole carbon and energy sources was affected significantly by their aggregate state, which depended on molecular structure. Compared to the solid 1-methyladamantane, 1,3-dimethyladamantane, which is liquid under normal conditions, was a preferable substrate. Adamantanes in the gas condensate were generally more resistant to bacterial degradation than such markers as normal and isoprenoid alkanes. Moreover, biodegradation had no significant effect on relative distribution of the tested С11–С13 alkyladamantanes.

Microbiology. 2017;86(3):330-337
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Oil-oxidizing activity of bacteria isolated from south Sakhalin coastal waters

Buzoleva L.S., Bogatyrenko E.A., Repina M.A., Belkova N.L.

Abstract

Ability of bacteria isolated from the southern coastal waters of the Sakhalin Island to degrade various hydrocarbons was studied. The population of marine microorganisms grown on oil was heterogeneous in terms of hydrocarbon degradation. The rate of bacterial degradation of oil hydrocarbons was shown to correlate with their growth rate on the model medium. The degradation rates were higher for aromatic hydrocarbons than for alkanes. Based on our data, the studied bacteria were conditionally assigned to three groups: active, intermediately active, and passive degraders. Ability to oxidize oil was previously not reported for members of the genus Cobetia.

Microbiology. 2017;86(3):338-345
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Evaluation of antioxidant and antiproliferative metabolites of Penicillium flavigenum isolated from hypersaline environment: Tuz (Salt) Lake by Xcelligence technology

Canturk Z., Kocabiyik E., Ozturk N., İlhan S.

Abstract

The aim of the study is the determination of antioxidant and antiproliferative activities of fungal isolates’ metabolites belonging to Penicillium flavigenum isolated from Lake Tuz, Turkey. Evaluation of the antioxidant activity, the total phenolic content and antiproliferative effect were evaluated with DPPH (2,2-diphenyl-1-picrylhydrazyl) radical scavenging assay, Folin-ciocalteu method, Xcelligence real-time cell analysis. The total phenolic content of these isolates were found 62–82 mg/GAE. Ethyl acetate extracts from identified isolates, P. flavigenum, showed cytotoxic effects on A549, MCF7, Caco-2 cell lines. IC50 values of P. flavigenum ethyl acetate extracts were found 96.7 μg/mL for A549, 33.4 μg/mL for MCF7, 43.4 μg/mL for Caco-2 and 97.3 μg/mL for 3T3. Phenolic acids in the extracts from P. flavigenum were identified with HPLC and GC-MS. Penicillium flavigenum is a new report for Turkey. According to these findings, fungi-related secondary metabolites are very important sources in terms of antioxidant and antiproliferative effects.

Microbiology. 2017;86(3):346-354
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Formation of silver nanoparticles in water samples from Antarctic Lake Untersee

Skladnev D.A., Sorokin V.V., Gal’chenko V.F.

Abstract

Comparative integral assessment of the biological characteristics of the water samples of ice-covered Antarctic Lake Untersee was carried out using a new nanobiotechnological approach based on registration of biogenic nanoparticles of reduced silver Ag0. Formation of reduced silver nanoparticles occurred in all samples containing aboriginal microorganisms, while nanoparticles were not formed in the samples from which bacterial cells were removed. Size distribution of biogenic silver nanoparticles varied in the samples from five water horizons. The method proposed provides for rapid detection of live microbiological objects in the samples by detection of formation of biogenic nanoparticles of reduced silver. The method was termed OBNG (Observation of Biogenic Nanoparticles Growth).

Microbiology. 2017;86(3):355-362
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Polymorphism of lactose genes in the dairy yeasts Kluyveromyces marxianus, potential probiotic microorganisms

Naumova E.S., Sadykova A.Z., Michailova Y.V., Naumov G.I.

Abstract

Molecular karyotyping and Southern blot hybridization were used to investigate chromosomal polymorphism of the LAC genes controlling lactose fermentation in Kluyveromyces marxianus strains isolated from various dairy products and natural sources in Russia and CIS countries. Profound polymorphism of karyotype patterns and accumulation of LAC genes were observed in dairy K. marxianus strains. K. marxianus strains isolated from dairy products intensively fermented lactose at 37°C after one day of cultivation, while non-dairy strains exhibited delayed lactose fermentation or did not ferment it at all. Based on the fermentation tests, twelve K. marxianus strains were selected, which are of interest as potential probiotic microorganisms suitable for further molecular genetic studies and breeding.

Microbiology. 2017;86(3):363-369
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Myrothecium verrucaria F-3851, a producer of laccases transforming phenolic compounds at neutral and alkaline conditions

Podieiablonskaia E.V., Kolomytseva M.P., Myasoedova N.M., Baskunov B.P., Chernykh A.M., Classen T., Pietruszka J., Golovleva L.A.

Abstract

The conditions of submerged cultivation of the ascomycete Myrothecium verrucaria strain F-3851 were optimized in order to increase the yield of laccase in the culture liquid using the natural sources of carbon and energy (fresh rubbed potato tuber or floured grains of buckwheat, barley, oat, wheat, rye, rice, pea, or haricot). The pH-optima of oxidation of a number of laccase substrates (ABTS, 2,6-dimethoxyphenol, syringaldazine, ferulic acid, p-coumaryl alcohol, and coniferyl alcohol) by laccases of the culture liquid as well as substrate selectivity of laccases were investigated. The intermediates of transformation of phenylpropanoids (ferulic acid, p-coumaryl alcohol and coniferyl alcohol) by laccases of the culture liquid at neutral conditions were purified and identified. The ability of laccases of the culture liquid of M. verrucaria strain F-3851 to catalyze polymer compound formation during phenylpropanoid transformation was shown that offers the prospects of application of the laccases of M. verrucaria strain F-3851 for production of pharmacologically valuable polymers in a number of cellular biotechnologies carried out in neutral or alkaline environments.

Microbiology. 2017;86(3):370-376
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Long-term survival and resistance of submerged pseudomonad cultures in the exopolymer mass

Mulyukin A.L., Smirnova T.A., Shevlyagina N.V., Didenko L.V.

Abstract

An issue on the cellular forms that ensure survival of pseudomonads is important due to wide occurrence of these bacteria in the environment and their role for clinical microbiology. The present work demonstrates the high survival potential of Pseudomonas aurantiaca and P. аeruginosa in the mass of exopolymers produced by cells. Exopolymer formation occurred only during incubation of the post-stationary phase cultures of P. aurantiaca (at 4°C) and P. aeruginosa (at 4 and 20°C). After storage for 1.5–12 months, the number of colony-forming units in the exopolymer was 30 to 68% of the viable cell titer in stationary-phase cultures. Antibiotic-tolerant persister cells that were revealed in the exopolymer cultures after treatment with ciprofloxacin (2.5–100 μg/mL) were more resistant to the antibiotic than persisters in suspension cultures, with the threshold doses of 25 and 2.5 μg/mL, respectively. The cells embedded in the exopolymer were found to be more resistant to 5-min heating at 60–70°C than the vegetative cells of suspension cultures, which did not survive such heat treatment conditions. Electron microscopic investigation revealed morphological heterogeneity of exopolymer-embedded pseudomonads, including the presence of the cells similar to cystlike dormant forms. The populations developing on solid media inoculated with the exopolymer mass with cells were found to contain 1.5 to 2 orders of magnitude more persisters tolerant to high ciprofloxacin doses (25 μg/mL for P. aurantiaca and 100 μg/mL for P. aeruginosa) than the populations developing after inoculation with second-transfer vegetative cells of the cells of planktonic cultures. The results obtained improve our understanding of pseudomonad survival in the environment.

Microbiology. 2017;86(3):377-386
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Production characteristics of bacteria and phytoplankton in the Sea of Okhotsk and Bering Sea during spring–summer

Zakharkov S.P., Vladimirov A.S., Shtraikhert E.A., Shi X., Gladkich R.V., Buzoleva L.S.

Abstract

Production parameters for bacterioplankton were assessed during the spring–summer period in the western parts of the Sea of Okhotsk and the Bering Sea, as well as in northwestern Pacific Ocean. The lowest values of bacterial production were observed in early June during the spring phytoplankton bloom (0.08 mg C day–1 m–3), while the maximum values (up to 55 mg C day–1 m–3) occurred in late July‒early August, 1.5 to 2 months after the bloom. The concentration of dissolved organic matter, the substrate for bacterioplankton, was assessed using satellite data. The ratio between bacterial and primary production in the surface samples varied from 0.5% at the peak of phytoplankton bloom to 180% at the peak of bacterioplankton development.

Microbiology. 2017;86(3):387-394
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Molecular analysis of the hydrolytic component of petroleum-contaminated soils and of soils remediated with chitin

Manucharova N.A., Kuteinikova Y.V., Ivanov P.V., Nikolaeva S.K., Trofimov V.T., Stepanov P.Y., Tyapkina E.V., Lipatov D.N., Stepanov A.L.

Abstract

Molecular genetic techniques (FISH and metagenomic analysis) were used to investigate prokaryotic complexes in native soils (gray forest soil and urbostratozema typical), soils contaminated by petroleum products (gasoline or diesel fuel), and soils subject to remediation by addition of a nitrogen-containing polysaccharide biopolymer chitin. The share of metabolically active prokaryotic cells in the hydrolytic complex of soil microcosms was determined, as well as their biomass and biodiversity. Compared to the control, in the pollutant-containing experimental microcosms, a decrease in the share of metabolically active prokaryotic cells was observed, as well as changes of the hydrolytic complex structure, such as an increase in the share of the phylum Actinobacteria (specifically of the genera Galiella and Nocardioides in the samples contaminated with gasoline and diesel fuel, respectively). Supplementing the hydrocarbon-contaminated system the biopolymer chitin resulted in processing of mixed-minerals with an increase in the number of layers of the smectite type and, as a result, in formation of aggregates and improved aeration. An increase in the number of metabolically active prokaryotic cells and decreased diversity of the soil prokaryotic complex were observed, which were probably associated with the development of a selective group of the hydrolytic complex of chitindegrading microorganisms.

Microbiology. 2017;86(3):395-402
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Isolation of extremely halophilic Archaea from a saline river in the Lut Desert of Iran, moderately resistant to desiccation and gamma radiation

Shirsalimian M.S., Amoozegar M.A., Sepahy A.A., Kalantar S.M., Dabbagh R.

Abstract

Admittedly, the Lut Desert of Iran has been remained as an unexplored region from a microbiological standpoint. Domain Archaea contains extremophiles that can live in harsh habitats. Extremely halophilic archaea are exposed to different environmental stresses in the hypersaline environments such as high solar irradiance and periodic desiccation. Haloarchaeal diversity in Shoor River, a saline river in the Lut Desert (a salinity of 134.3 g L–1 of dissolved salts), was investigated by a culture-dependent method. A large number of extremely halophilic isolates were obtained and a subset of 59 isolates was considered distinct. Firstly, the isolates were screened for their resistance under desiccation stress in 35 days. Eleven of these strains remained viable during the period in a desiccator containing silica gel. Then, three of them were randomly selected and their resistance against desiccation and ionizing radiation were determined. The isolates MS2, MS17, and MS50 were still recovered after 8 weeks in a desiccator and were moderately resistant to gamma radiation with D10 value between 2 and 3 kGy. Strains MS2, MS17, and MS50 were affiliated with three species in the family Halobacteriaceae using 16S rRNA gene sequence analysis as well as morphological and biochemical characteristics—Haloterrigena jeotgali A29T (99.6% similarity), Natrialba aegyptia 40T (99.4% similarity) and Natrinema pallidum NCIMB 777T (99.3% similarity), respectively. Although resistance to desiccation did not follow the sigmoid survival curve pattern of Deinococcus radiodurans, apparently haloarchaea can show a more resistance to desiccation in more long-term periods of time. This is the first report on isolation of extremely halophilic archaea belonged to the family Halobacteriaceae and their radioresistance and desiccation tolerance properties isolated from the Shoor River.

Microbiology. 2017;86(3):403-411
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Short Communications

Uncultured bacteria and methanogenic archaea predominate in the microbial community of Western Siberian deep subsurface aquifer

Kadnikov V.V., Frank Y.A., Mardanov A.V., Beletskii A.V., Ivasenko D.A., Pimenov N.V., Karnachuk O.V., Ravin N.V.
Microbiology. 2017;86(3):412-415
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