Журнал «Микробиология» публикует экспериментальные и теоретические статьи по всем фундаментальным проблемам микробиологии. Издание размещает краткие сообщения и обзоры современных достижений в различных областях микробиологии, рецензии на новые книги, хронику научной жизни микробиологического сообщества.

  • Объем номера (уч.-изд. л.): 15,5
  • ISSN (print): 0026-3656
  • Год основания: 1932
  • Рубрика: Биологические науки
  • Импакт-фактор (2020): 1,156
  • Подписной индекс: 70540
  • Периодичность: 6

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Vol 92, No 3 (2023)

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Glycoside Hydrolases of the Obligate Methanotroph : an Unusual Evolutionary Strategy not Involving Distant Lateral Transfers
Naumoff D.G., Dedysh S.N.

The genome of the obligately methanotrophic bacterium Methyloferula stellata AR4 encodes thirty glycoside hydrolases. The closest homologues for most of these proteins belong to other members of the class Alphaproteobacteria. Two exceptions are represented by the genes encoding glycoside hydrolases of the families GH39 and GH65, which presumably appeared in M. stellata AR4 due to the lateral transfer from distantly related bacteria. This work was devoted to the study of the evolutionary history of these two genes. In the case of a member of the GH65 family of glycoside hydrolases, this scenario was not confirmed. Kojibiose phosphorylase encoded by this gene is common among Alphaproteobacteria. The suggested lateral transfer of the corresponding gene had an opposite direction, into one of the evolutionary lineages of the class Betaproteobacteria. The potential glycoside hydrolase of the GH39 family was shown to be the only one which gene is not of proteobacterial origin. The role of lateral transfers in the evolution of glycoside hydrolases and their homologues in methanotrophs and other bacteria is discussed.

Microbiology. 2023;92(3):243-249
pages 243-249 views
Adaptation of the Acidophilic Fungus to the pH Factor
Ianutsevich E.A., Danilova O.A., Grum-Grzhimailo O.A., Groza N.V., Tereshina V.M.

Investigation of the growth rate of Sistotrema brinkmannii at different values of pH values, temperature, and NaCl concentration showed that this fungus was a mesophile, preferred a salt-free medium, and was an obligate acidophile, since it had a pronounced growth optimum at pH 3.0–4.0 and did not grow at pH 7.0. To reveal the protective mechanisms allowing this fungus to develop under acidic conditions, the composition of its osmolytes and lipids was studied. This is the first report on occurrence of a large amount of trehalose (4.0‒6.6% of dry weight) in the mycelium of the fungus during its growth under optimal conditions, confirming the use of osmolytes by acidophiles for adaptation. At the same time, at the borders of the growth range (pH 2.6 and 6.0), the amount of trehalose in the mycelium of the fungus decreased by 2.5 times, which was in agreement with a narrow growth optimum of the fungus in its natural environments (pH 3.0–4.0). The composition of membrane lipids of the fungus was characterized by a high proportion of sphingolipids (up to 60% of the total), which decreased twofold in the course of growth under optimal conditions. The main membrane lipids, apart from sphingolipids, were phosphatidic acids, phosphatidylethanolamines, and sterols; the proportion of these lipids increased with time. The composition of membrane lipids of the fungus at pH 2.6 did not differ much from the optimal conditions, while in the near-neutral region there was a twofold increase in the proportion of sphingolipids, indicating their adaptive value. The simultaneous decrease in the proportion of sphingolipids and the increase in the level of trehalose in the growth dynamics suggest association of these compounds in the protection of cell membranes.

Microbiology. 2023;92(3):279-288
pages 279-288 views
Effect of the AZOBR_p60123 Plasmid Gene, Encoding the Wzt Protein, on Lipopolysaccharide Synthesis and Biofilm Formation in the Bacterium Sp245
Petrova L.P., Evstigneeva S.S., Filip’echeva Y.A., Volokhina I.V., Burygin G.L., Matora .Y., Shelud’ko A.V.

Inactivation of one of the genes (CDS AZOBR_p60123) of the ABC transporter ATP-binding protein Wzt in the p60123::aphAI mutant of Azospirillum baldaniorum Sp245 and the introduction of an additional copy of this gene into the parent or mutant strain affected the chain-length heterogeneity of O polysaccharides (OPSs) and lipopolysaccharides (LPSs), the OPS and LPS immunochemical characteristics, and the strain properties related to polysaccharide production (biofilm construction). Biofilms of the p60123::aphAI mutant Sp245.4-1-1 accumulated two times less biomass than those of Sp245. Introduction of pRK415-p60123 into the cells of Sp245.4-1-1 or Sp245 resulted in a respective increase or decrease in the ability of the resulting derivative strains to accumulate biofilm biomass, as compared with the original strains.

Microbiology. 2023;92(3):289-299
pages 289-299 views
Biodegradation of Phthalic Acid Esters by the White Rot Fungus
Savinova O.S., Shabaev A.V., Fedorova T.V.

The ability of the white rot fungus Peniophora lycii to degrade such phthalic acid esters (PAEs) as diethyl phthalate (DEP), dibutyl phthalate (DBP), di(2-ethylhexyl) phthalate (DEHP), diisobutyl phthalate (DiBP), and n-butylbenzyl phthalate (BBP) was studied. It was shown that DEHP was most efficiently biodegraded by the fungus (over 98% on day 6 of cultivation). The residual content of DBP and DiBP in the culture liquid of the fungus at the end of cultivation (10 days) was ~17–18%. BBP turned out to be the most difficult-to-degrade compound: its residual content on day 10 of P. lycii cultivation was ~40%. DEP was resistant to fungal biodegradation, and exhibited a toxic effect at 1.5 g/L: the rate of radial growth of the fungus on agar decreased threefold compared to the control, and the amount of fungal biomass during liquid-phase deep cultivation decreased by about 1.5 times. During the cultivation of P. lycii on media with PAEs, an increase in esterase activity by about 2 times and a significant decrease (by 2–4 times) in oxidase activity was shown compared to the control medium without phthalates.

Microbiology. 2023;92(3):310-317
pages 310-317 views
Biological Activity and Composition of Metabolites of Potential Agricultural Application from K-11 RCAM04697 (SCPM-O-B-9993)
Bataeva Y.V., Grigoryan L.N., Bogun A.G., Kislichkina A.A., Platonov M.E., Kurashov E.A., Krylova J.V., Fedorenko A.G., Andreeva M.P.

Strain K-11 was isolated from the highly saline brown semi-desert soil of the Astrakhan region. Based on analysis of the 16S rRNA gene sequence, this strain was identified as Streptomyces carpaticus K-11 RCAM04697 (SCPM-O-B-9993). Whole genome sequencing of the strain was performed. Phytotoxicity, antiviral, antioxidant, antifungal, and insecticidal activities of the strain were studied. All extracts and suspensions of S. carpaticus strain RCAM04697 had plant-stimulating activity. Antiviral properties was exhibited as suppression of development and propagation of viral pathogens in laboratory conditions: Tomato Mosaic Virus (ToMV) – 26.3%, Cucumber Mosaic Virus (CMV) – 33.8%, Y-Potato Virus (YVK) (Potato Y potyvirus, PVY) – 51.3%, Potato X-Virus (PVX) (Potato X potyvirus, PVX) – 41.3%. The highest antioxidant activity was shown by a suspension of S. carpaticus strain RCAM04697 (88.8%) and its aqueous-alcoholic (20 : 80) extract (76.0%). The strain inhibited growth of the phytopathogenic fungus Fusarium sporotrichioides to varying degrees. The insecticidal activity against Aphis fabae after 6 h of treatment was 100% in the variants with suspension treatment, water-alcohol (80 : 20, 50 : 50), methanol, and hexane extracts. The metabolites of the S. carpaticus RCAM04697 strain included flavonoids, alkaloids, glycosides, organic acids (isocitric, acetic, fumaric, lactic, pyruvic, and malic), alcohols, aldehydes, hydrocarbons, ethers, sulfur-containing compounds, and other groups of low-molecular weight organic compounds.

Microbiology. 2023;92(3):318-328
pages 318-328 views


Anaerobic and Aerobic Coexist in Deep Thermal Water
Lukina A.P., Kadniko V.V., Rusanov I.I., Avakyan M.R., Beletsky A.V., Mardanov A.V., Pimenov N.V., Ravin N.V., Karnachuk O.V.

Research on the microorganisms inhabiting deep aquifers is based on sampling the water released from deep wells and is seldom concerned with the physicochemical processes of the water-rock system. The issue of metabolism of aerobic prokaryotes revealed in deep habitats by molecular techniques remains unclear. Cultivation is required for direct determination of relation of prokaryotes to oxygen. In the present work, aerobic and anaerobic bacteria, which were revealed in thermal radon baths of the Belokurikha resort by molecular techniques, were isolated. Profiling by the 16S rRNA gene revealed predominance of members of the Deionococcus-Thermus group belonging to the genus Meiothermus (17.6% reads) and considered strictly aerobic. Anaerobic sulfate-reducing Thermodesulfovibrio were also present in the sample. The habitat was characterized by reductive, alkaline conditions. Target-oriented cultivation revealed aerobically growing Meiothermus sp. 1165, which was closely related to Meiothermus cerbereus. An alkaliphilic anaerobic sulfate reducer Thermodesulfovibrio sp. 1176 was also isolated. The rate of sulfate reduction measured in the Belokurikha water using yielded the value of 41.4 ± 1.06 µm Sred L–1 day–1, or 1.29 nmol S mL–1 day–1. Analysis of the genome of strain 1176 revealed the presence of various mechanisms responsible for its relative resistance to oxygen and oxidative stress, which included superoxide reductase, rubredoxin, a Fe-Mn family superoxide dismutase, a KatG catalase-peroxidase, and a cytochrome bd ubiquinol oxidase. The low redox potential and intense anaerobic sulfate reduction provide evidence for the generally reduced conditions in the Belokurikha deep horizons. Spatial separation of aerobes and anaerobes in the water-rock system, similar to the one occurring in the terrestrial microbial mats, may be hypothesized, as well as occurring of aerobic processes in microniches.

Microbiology. 2023;92(3):250-260
pages 250-260 views
Search for Novel Halophilic and Halotolerant Producers of Antimicrobial Compounds in Various Extreme Ecosystems
Gavrilov S.N., Barashkova A.S., Cherdyntseva T.A., Prokofeva M.I., Tresvyatskii O.V., Lukianov D.A., Nikandrova A.A., Haertle T., Merkel A.Y., Bonch-Osmolovskaya E.A., Rogozhin E.A.

The recent increase of antibiotic resistance in pathogenic microorganisms stimulated interest in the search for new antimicrobial compounds and their producers. Among the latter, halophilic microorganisms are considered to be the most promising group, since actinomycetes, producers of the majority of the known clinically important classes of antibiotics, are widely represented in this group. The present work reports the results of the search with three different approaches for new antimicrobial compounds in halophilic and halotolerant microorganisms inhabiting three different types of extreme ecosystems. Metagenomic analysis of microbial communities of subsurface thermal mineral waters revealed biosynthetic clusters of putative antimicrobial compounds, which belong to bacteria and archaea of uncultured lineages. Enrichment cultures with antimicrobial activity were obtained from the cold, deep oceanic sediments; analysis of their phylogenetic diversity resulted in identification of the potential producers of antimicrobial compounds as the members of class Desulfuromonadia. Finally, antimicrobial activity of a new species of soil natronophilic streptomycetes, Streptomyces sp. ACA25, was characterized; it was active only against gram-positive bacteria. The genome of this organism was sequenced, and the pathways for biosynthesis of polypeptide, polyketide, and beta-lactam antibiotics were identified. Active fractions of the ACA25 culture, containing antimicrobial compounds of polyketide and beta-lactam nature, were obtained. The active polyketide was identified as rosamycin, an antibiotic of the macrolide structural group. However, the fact that it did not inhibit bacterial translation highlighted structural differences between the new polyketide and rosamycin.

Microbiology. 2023;92(3):261-278
pages 261-278 views
Microbial Communities Associated with the White Sea Red Algae as a Source of Xylanolytic Microorganisms
Salova V.D., Kholdina A.M., Mel’nik A.D., Zayulina K.S., El’cheninov A.G., Klyukina A.A., Kublanov I.V.

—Microorganisms associated with algae and able to utilize complex substrates (e.g., plant heteropolysaccharides) may be important producers of hydrolytic enzymes. The microbial communities of the red algae Corallina sp. and Phyllophora sp. sampled in the Kandalaksha Gulf basin of the White Sea were analyzed using high-throughput sequencing of the V4-variable region of the 16S rRNA gene. The dominant phyla in microbiomes of both samples were Pseudomonadota and Bacteroidota (GTDB classification, https://gtdb.ecogenomic.org/). For the Corallina sp. sample, dominance of the Vibrio, Agarivorans, and Photobacterium genera was shown, while Granulosicoccus and Aliivibrio dominated in the Phyllophora sp. sample. The analyzed red macroalgae with associated microbiota were used as an inocula to obtain microbial enrichment cultures growing on β-1,4-xylan or β-1,3-glucan (сurdlan). It was shown that, similar to environmental samples Pseudomonadota and Bacteroidota phyla representatives were prevalent in all enrichment cultures. However, unlike the environmental samples, in the enrichment cultures the dominant genera were Marinomonas, Reinekea, Polaribacter, and Pseudoalteromonas. The latter, as well as the representatives of Vibrio sp., were isolated in pure cultures for which the xylanolytic activity was shown.

Microbiology. 2023;92(3):300-309
pages 300-309 views


Effect of Mutations in the Extracytosolic Domain of the H-ATPase on Its Activity and Regulation
Petrov V.V.

Plasma membrane H+-ATPase (PMA1), the key enzyme of yeast metabolism, undergoes multiple phosphorylation during biogenesis and functioning. In the course of this process, the ATPase is getting activated (glucose effect). We have employed site-directed mutagenesis to determine the functional role of potentially phosphorylable amino acid residues located in the extracytosolic L9-10 loop (846-SENWTD). The mutant enzyme forms were expressed at the plasma membrane to examine the effect of substitutions on biogenesis and ATPase activity. Immunobloting revealed that the mutant ATPase expression was not significantly impaired. In the absence of glucose, basal activity of the mutant enzymes differed insignificantly from that of the wild type. At the same time, regulation of the mutant E847A, T850A, and D851A enzymes has been impaired; the level of enzyme activation by glucose was lower by 2.0−2.5-fold. On the contrary, the S846A mutant displayed elevated basal activity, maintaining the ability to undergo further activation. These data indicate that these residues (especially, Ser-846, Thr-850, and Asp-851) are essential for the normal functioning of the PMA1 and its regulation by glucose.

Microbiology. 2023;92(3):329-334
pages 329-334 views
Calcinating Bacteria in Extreme Ecosystems of the Southern Aral Region
Kondrasheva K.V., Umruzokov A.A., Kalenov S.V., Merkel A.Y., Chernykh N.A., Slobodkin A.I., Gavrilov S.N., Davranov K.D.

The processes of microbially induced precipitation of calcium carbonates are widespread in natural environments and are an important part of the biogeochemical carbon cycle. These processes comprised the basis of new “biocementation” technologies, which are extensively developing worldwide during the last decade. These technologies are aimed at the construction of novel “self-healing” construction materials, as well as at maintaining the strength of various buildings and structures. Since the optimal conditions for calcite formation are high salinity and alkalinity of the environment, the search for calcifying microorganisms in a variety of ecosystems, including extreme ones, is of interest. At present, many strains of halophilic and halotolerant bacteria, that induce calcination, have already been isolated and tested in pilot industrial processes. Most of these bacteria possess urease activity, which is the main contributor to the binding of calcium ions to insoluble calcium carbonate. A wide variety of natural ecosystems with optimal conditions for the development of calcifying urobacteria, as well as the economic demand for biocementation technologies, stimulate interest in the search for more and more novel strains of these microorganisms. One of the promising resources to be screened for such organisms is the ecosystem of the drying Aral Sea and the adjacent desert and semi-desert Aral region. Here we present the results of screening various extreme ecosystems of the Aral region for the presence of calcifying microorganisms. We obtained 28 pure cultures of heterotrophic aerobic bacteria from samples of plant residues and soils of the Aral Sea region, 4 of which had urease and calcifying activities. Their activities were compared with those of the strains presently used to produce biocementing mixtures. We have identified the phylotypes of putative calcifying microorganisms in microbial communities of desert soil, thermal waters, and bottom sediments of a salt lake, and described the phylogenetic diversity of these communities. Our results indicated the wide distribution of calcifying microorganisms in the ecosystems of the South Aral region and highlighted the expediency of screening them for the new biotechnologically relevant strains of these organisms.

Microbiology. 2023;92(3):335-344
pages 335-344 views

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