E. Bonch-osmolovskaya - Academia.edu (original) (raw)

Papers by E. Bonch-osmolovskaya

Microbiome research reports, Feb 28, 2024

Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute ... more Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.

International journal of systematic and evolutionary microbiology, 2015

Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean... more Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1(T) was isolated from a hot spring (Kunashir Island, Russia) and strain SBP2(T) was isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30-60 °C and pH range 5.0-8.0. Strain R1(T) grew optimally at 60 °C and pH 6.0-6.5; for SBP2(T) optimal conditions were at 52 °C and pH 7.5-8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the order Planctomycetales, for which the names Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov. are proposed. The type strain of Thermogutta terrifontis, the type species of th...

Journal of Agricultural and Food Chemistry, 2004

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008

A moderately thermophilic, anaerobic bacterium (strain SG 508 T) was isolated from a hydrothermal... more A moderately thermophilic, anaerobic bacterium (strain SG 508 T) was isolated from a hydrothermal vent chimney located at 136 N on the East Pacific Rise at a depth of 2650 m. Cells of strain SG 508 T were straight to slightly curved rods, 0.4-0.6 mm in diameter and 2.0-3.0 mm in length. Spore formation was observed only below pH 5.5. The temperature range for growth was 22-60 6C, with optimum growth at 50 6C. The pH range for growth was 4.0-8.5, with optimum growth at pH 6.0-6.8. Growth of strain SG 508 T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v), with optimum growth at 2.5 % (w/v). Substrates utilized by strain SG 508 T included casein, peptone, tryptone, yeast extract, beef extract, starch, maltose and glucose. The products of glucose fermentation were ethanol, acetate, H 2 , formate and CO 2. Strain SG 508 T was able to reduce elemental sulfur to hydrogen sulfide. The DNA G+C content of strain SG 508 T was 30.9 mol%. 16S rRNA gene sequence analysis revealed that the isolated organism belonged to cluster I of the genus Clostridium. On the basis of its physiological properties and data from phylogenetic analyses, strain SG 508 T is considered to represent a novel species of the genus Clostridium, for which the name Clostridium tepidiprofundi sp. nov. is proposed. The type strain is SG 508 T (5DSM 19306 T 5VKM B-2459 T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of SG 508 T is EF197795.

Current Microbiology, 1999

Twenty-five samples of stratal fluids obtained from a high-temperature (60-84°C) deep subsurface ... more Twenty-five samples of stratal fluids obtained from a high-temperature (60-84°C) deep subsurface (1700-2500 m) petroleum reservoir of Western Siberia were investigated for the presence of dissimilatory Fe(III)-reducing microorganisms. Of the samples, 44% and 76% were positive for Fe(III) reduction with peptone and H 2 respectively as electron donors. In most of these samples, the numbers of culturable thermophilic H 2-utilizing iron reducers were in the order of 10-100 cells/ml. Nine strains of thermophilic anaerobic bacteria and archaea isolated from petroleum reservoirs were tested for their ability to reduce Fe(III). Eight strains belonging to the genera Thermoanaerobacter, Thermotoga, and Thermococcus were found capable of dissimilatory Fe(III) reduction, with peptone or H 2 as electron donor and amorphous Fe(III) oxide as electron acceptor. These results demonstrated that Fe(III) reduction may be a common feature shared by a wide range of anaerobic thermophiles and hyperthermophiles in deep subsurface petroleum reservoirs.

The interdiction of the use of MBM in animal feeding makes the elaboration of simple and economic... more The interdiction of the use of MBM in animal feeding makes the elaboration of simple and economically viable procedures of valorization and decontamination of substances containing pathogenic prions necessary. One of the possible solutions is the use of microorganisms. Hence, collections of microorganisms able to grow on keratin or on MBM, and secreting proteases able to degrade PrPsc were screened. Three strains of thermophilic bacteria, isolated initially from hot springs scattered on the planet, were able to degrade amyloids (some of them infectious) and to grow on media made of MBM. Their proteolytic activity, mostly of chymotryptic nature were maximal between 60 and 80 °C and were triggered towards the hydrolysis of peptide bonds between amino acids largely present in prion proteins. Their action cleaves the prion protein into short inoffensive fragments. The perspectives resulting from this work imply the use of such microorganisms, whose proteolytic potential allows to degrad...

Applied and Environmental Microbiology, 2004

A method for rapid detection and identification of hyperthermophilic archaea of the family Thermo... more A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5′-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3′) and TcPc 589R (5′-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3′) was developed and used for identification of new isolates.

FEMS Microbiology Ecology, 2001

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009

A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50 T) was isolate... more A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50 T) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 ° 58' 21'' N 4 ° 51' 47'' W) at a depth of 4100 m. Cells of strain SL50 T were motile, straight to bent rods with one polar flagellum, 0.5-0.6 µm in width and 3.0-3.5 µm in length. The temperature range for growth was 25-75 °C, with an optimum at 60 °C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50 T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50 T was 60 min. Strain SL50 T used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50 T was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50 T was Deferribacter abyssi JR T (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50 T (=DSM 21529 T =VKPM B-10097 T). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO 2 as the carbon source.

Frontiers in microbiology, 2017

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metaboli... more Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3 -type and canonical cbb3 -type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentrat...

Extremophiles : life under extreme conditions, Jan 27, 2016

Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular... more Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats. The highest rates of inorganic carbon assimilation determined by the in situ incubation of samples in the presence of (14)C-labeled bicarbonate were found in oxygen-dependent streamers; in two sediment samples ...

Herald of the Russian Academy of Sciences, 2010

Microbiology—a science of organisms, although microorganisms—belongs to classical biological dis�... more Microbiology—a science of organisms, although microorganisms—belongs to classical biological dis� ciplines. However, owing to the specifics of its objects, it had to develop a complex of methods that are uncharacteristic of other biological disciplines. The minimal diversity of morphological characters in microorganisms under a great diversity of functional characteristics has made the latter the main pheno� typic descriptors. At the

The FEBS journal, Jan 29, 2015

The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides ... more The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specifici...

International journal of systematic and evolutionary microbiology, 2015

A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon... more A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon Caldera, Kronotsky Nature Reserve, Kamchatka, Russia. The isolate, strain 1860(T), grew optimally at 90-95 °C and pH 6.0-7.0. The cells were non-motile straight rods, 1.5-5.0 µm in length, covered with surface-layer lattice. Strain 1860(T) utilized complex proteinaceous compounds as electron donors and ferrihydrite, Fe(III) citrate, nitrate, thiosulfate, selenite, selenate and arsenate as electron acceptors for growth. The sequence of the 16S rRNA gene of strain 1860(T) had 97.9-98.7 % similarity with those of members of the genus Pyrobaculum. On the basis of its physiological properties and phylogenetic analyses including in silico genome to genome hybridization, the isolate is considered to represent a novel species, for which the name Pyrobaculum ferrireducens sp. nov. is proposed. The type strain is 1860(T) ( = DSM 28942(T) = VKM B-2856(T)).

International journal of systematic and evolutionary microbiology, 2014

A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T),... more A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T), was isolated from a deep-sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of the novel isolate were rods, 0.3-0.8 µm in width and 1.5-10 µm in length, surrounded by a sheath-like structure (toga). Strain Rift-s3(T) grew at temperatures ranging from 44 to 75 °C, at pH 5.5 to 8.0, and with NaCl concentrations of 3 to 60 g l(-1). Under optimum conditions (65 °C, pH 6.0, NaCl 25 g l(-1)), the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan and pectin, and proteins including β-keratins, casein and gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. The G+C content of the DNA was 30 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed the affiliation of strain Rift-s3(T) with the genus Thermosipho, with Thermosipho atlant...

Microbiome research reports, Feb 28, 2024

Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute ... more Aim: Microbiomes influence the physiology and behavior of multicellular organisms and contribute to their adaptation to changing environmental conditions. However, yeast and bacterial microbiota have usually been studied separately; therefore, the interaction between bacterial and yeast communities in the gut of Drosophila melanogaster (D. melanogaster) is often overlooked. In this study, we investigate the correlation between bacterial and yeast communities in the gut of D. melanogaster. Methods: We studied the shifts in the joint microbiome of Drosophila melanogaster, encompassing both yeasts and bacteria, during adaptation to substrate with varying salt concentrations (0%, 2%, 4%, and 7%) using plating for both yeasts and bacteria and NGS-sequencing of variable 16S rRNA gene regions for bacteria. Results: The microbiome of flies and their substrates was gradually altered at moderate NaCl concentrations (2% and 4% compared with the 0% control) and completely transformed at high salt concentrations (7%). The relative whereas the relative abundance of the more halotolerant lactobacilli first increased, peaking at 4% NaCl, and then declined dramatically at 7%. At this salinity level, potentially pathogenic bacteria of the genera Leuconostoc and Providencia were dominant. The yeast microbiome of D. melanogaster also undergoes significant changes with an increase in salt concentration in the substrate. The total yeast abundance undergoes nonlinear changes: it is lowest at 0% salt concentration and highest at 2%-4%. At a 7% concentration, the yeast abundance in flies and their substrate is lower than at 2%-4% but significantly higher than at 0%. Conclusions: The abundance and diversity of bacteria that are potentially beneficial to the flies decreased, while the proportion of potential pathogens, Leuconostoc and Providencia, increased with an increase in salt concentration in the substrate. In samples with a relatively high abundance and/or diversity of yeasts, the corresponding indicators for bacteria were often lowered, and vice versa. This may be due to the greater halotolerance of yeasts compared to bacteria and may also indicate antagonism between these groups of microorganisms.

International journal of systematic and evolutionary microbiology, 2015

Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean... more Two novel strains of thermophilic planctomycetes were recovered from terrestrial and subterranean habitats. Strain R1(T) was isolated from a hot spring (Kunashir Island, Russia) and strain SBP2(T) was isolated from a deep gold mine (South Africa). Both isolates grew in the temperature range 30-60 °C and pH range 5.0-8.0. Strain R1(T) grew optimally at 60 °C and pH 6.0-6.5; for SBP2(T) optimal conditions were at 52 °C and pH 7.5-8.0. Both strains were capable of anaerobic respiration with nitrate and nitrite as electron acceptors as well as of microaerobic growth. They also could grow by fermentation of mono-, di- and polysaccharides. Based on their phylogenetic position and phenotypic features we suggest that the new isolates represent two novel species belonging to a new genus in the order Planctomycetales, for which the names Thermogutta terrifontis gen. nov., sp. nov. and Thermogutta hypogea sp. nov. are proposed. The type strain of Thermogutta terrifontis, the type species of th...

Journal of Agricultural and Food Chemistry, 2004

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2008

A moderately thermophilic, anaerobic bacterium (strain SG 508 T) was isolated from a hydrothermal... more A moderately thermophilic, anaerobic bacterium (strain SG 508 T) was isolated from a hydrothermal vent chimney located at 136 N on the East Pacific Rise at a depth of 2650 m. Cells of strain SG 508 T were straight to slightly curved rods, 0.4-0.6 mm in diameter and 2.0-3.0 mm in length. Spore formation was observed only below pH 5.5. The temperature range for growth was 22-60 6C, with optimum growth at 50 6C. The pH range for growth was 4.0-8.5, with optimum growth at pH 6.0-6.8. Growth of strain SG 508 T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v), with optimum growth at 2.5 % (w/v). Substrates utilized by strain SG 508 T included casein, peptone, tryptone, yeast extract, beef extract, starch, maltose and glucose. The products of glucose fermentation were ethanol, acetate, H 2 , formate and CO 2. Strain SG 508 T was able to reduce elemental sulfur to hydrogen sulfide. The DNA G+C content of strain SG 508 T was 30.9 mol%. 16S rRNA gene sequence analysis revealed that the isolated organism belonged to cluster I of the genus Clostridium. On the basis of its physiological properties and data from phylogenetic analyses, strain SG 508 T is considered to represent a novel species of the genus Clostridium, for which the name Clostridium tepidiprofundi sp. nov. is proposed. The type strain is SG 508 T (5DSM 19306 T 5VKM B-2459 T). The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of SG 508 T is EF197795.

Current Microbiology, 1999

Twenty-five samples of stratal fluids obtained from a high-temperature (60-84°C) deep subsurface ... more Twenty-five samples of stratal fluids obtained from a high-temperature (60-84°C) deep subsurface (1700-2500 m) petroleum reservoir of Western Siberia were investigated for the presence of dissimilatory Fe(III)-reducing microorganisms. Of the samples, 44% and 76% were positive for Fe(III) reduction with peptone and H 2 respectively as electron donors. In most of these samples, the numbers of culturable thermophilic H 2-utilizing iron reducers were in the order of 10-100 cells/ml. Nine strains of thermophilic anaerobic bacteria and archaea isolated from petroleum reservoirs were tested for their ability to reduce Fe(III). Eight strains belonging to the genera Thermoanaerobacter, Thermotoga, and Thermococcus were found capable of dissimilatory Fe(III) reduction, with peptone or H 2 as electron donor and amorphous Fe(III) oxide as electron acceptor. These results demonstrated that Fe(III) reduction may be a common feature shared by a wide range of anaerobic thermophiles and hyperthermophiles in deep subsurface petroleum reservoirs.

The interdiction of the use of MBM in animal feeding makes the elaboration of simple and economic... more The interdiction of the use of MBM in animal feeding makes the elaboration of simple and economically viable procedures of valorization and decontamination of substances containing pathogenic prions necessary. One of the possible solutions is the use of microorganisms. Hence, collections of microorganisms able to grow on keratin or on MBM, and secreting proteases able to degrade PrPsc were screened. Three strains of thermophilic bacteria, isolated initially from hot springs scattered on the planet, were able to degrade amyloids (some of them infectious) and to grow on media made of MBM. Their proteolytic activity, mostly of chymotryptic nature were maximal between 60 and 80 °C and were triggered towards the hydrolysis of peptide bonds between amino acids largely present in prion proteins. Their action cleaves the prion protein into short inoffensive fragments. The perspectives resulting from this work imply the use of such microorganisms, whose proteolytic potential allows to degrad...

Applied and Environmental Microbiology, 2004

A method for rapid detection and identification of hyperthermophilic archaea of the family Thermo... more A method for rapid detection and identification of hyperthermophilic archaea of the family Thermococcaceae based on PCR amplification of 16S rRNA gene fragments with primers TcPc 173F (5′-TCCCCCATAGGYCTGRGGTACTGGAAGGTC-3′) and TcPc 589R (5′-GCCGTGRGATTTCGCCAGGGACTTACGGGC-3′) was developed and used for identification of new isolates.

FEMS Microbiology Ecology, 2001

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, 2009

A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50 T) was isolate... more A thermophilic, anaerobic, chemolithoautotrophic bacterium (designated strain SL50 T) was isolated from a hydrothermal sample collected at the Mid-Atlantic Ridge from the deepest of the known World ocean hydrothermal fields, Ashadze field (1 ° 58' 21'' N 4 ° 51' 47'' W) at a depth of 4100 m. Cells of strain SL50 T were motile, straight to bent rods with one polar flagellum, 0.5-0.6 µm in width and 3.0-3.5 µm in length. The temperature range for growth was 25-75 °C, with an optimum at 60 °C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.5. Growth of strain SL50 T was observed at NaCl concentrations ranging from 1.0 to 6.0 % (w/v) with an optimum at 2.5 % (w/v). The generation time under optimal growth conditions for strain SL50 T was 60 min. Strain SL50 T used molecular hydrogen, acetate, lactate, succinate, pyruvate and complex proteinaceous compounds as electron donors, and Fe(III), Mn(IV), nitrate or elemental sulfur as electron acceptors. The G+C content of the DNA of strain SL50 T was 28.7 mol%. 16S rRNA gene sequence analysis revealed that the closest relative of strain SL50 T was Deferribacter abyssi JR T (95.5 % similarity). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Deferribacter autotrophicus sp. nov. is proposed. The type strain is SL50 T (=DSM 21529 T =VKPM B-10097 T). Deferribacter autotrophicus sp. nov. is the first described deep-sea bacterium capable of chemolithoautotrophic growth using molecular hydrogen as an electron donor and ferric iron as electron acceptor and CO 2 as the carbon source.

Frontiers in microbiology, 2017

Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metaboli... more Melioribacter roseus, a representative of recently proposed Ignavibacteriae phylum, is a metabolically versatile thermophilic bacterium, inhabiting subsurface biosphere of the West-Siberian megabasin and capable of growing on various substrates and electron acceptors. Genomic analysis followed by inhibitor studies and membrane potential measurements of aerobically grown M. roseus cells revealed the activity of aerobic respiratory electron transfer chain comprised of respiratory complexes I and IV, and an alternative complex III. Phylogeny reconstruction revealed that oxygen reductases belonged to atypical cc(o/b)o3 -type and canonical cbb3 -type cytochrome oxidases. Also, two molybdoenzymes of M. roseus were affiliated either with Ttr or Psr/Phs clades, but not with typical respiratory arsenate reductases of the Arr clade. Expression profiling, both at transcripts and protein level, allowed us to assign the role of the terminal respiratory oxidase under atmospheric oxygen concentrat...

Extremophiles : life under extreme conditions, Jan 27, 2016

Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular... more Microbial communities of Kamchatka Peninsula terrestrial hot springs were studied using molecular, radioisotopic and cultural approaches. Analysis of 16S rRNA gene fragments performed by means of high-throughput sequencing revealed that aerobic autotrophic sulfur-oxidizing bacteria of the genus Sulfurihydrogenibium (phylum Aquificae) dominated in a majority of streamers. Another widely distributed and abundant group was that of anaerobic bacteria of the genus Caldimicrobium (phylum Thermodesulfobacteria). Archaea of the genus Vulcanisaeta were abundant in a high-temperature, slightly acidic hot spring, where they were accompanied by numerous Nanoarchaeota, while the domination of uncultured Thermoplasmataceae A10 was characteristic for moderately thermophilic acidic habitats. The highest rates of inorganic carbon assimilation determined by the in situ incubation of samples in the presence of (14)C-labeled bicarbonate were found in oxygen-dependent streamers; in two sediment samples ...

Herald of the Russian Academy of Sciences, 2010

Microbiology—a science of organisms, although microorganisms—belongs to classical biological dis�... more Microbiology—a science of organisms, although microorganisms—belongs to classical biological dis� ciplines. However, owing to the specifics of its objects, it had to develop a complex of methods that are uncharacteristic of other biological disciplines. The minimal diversity of morphological characters in microorganisms under a great diversity of functional characteristics has made the latter the main pheno� typic descriptors. At the

The FEBS journal, Jan 29, 2015

The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides ... more The epoxide hydrolases (EHs) represent an attractive option for the synthesis of chiral epoxides and 1,2-diols which are valuable building blocks for the synthesis of several pharmaceutical compounds. A metagenomic approach has been used to identify two new members of the atypical EH limonene-1,2-epoxide hydrolase (LEH) family of enzymes. These two LEHs (Tomsk-LEH and CH55-LEH) show EH activities towards different epoxide substrates, differing in most cases from those previously identified for Rhodococcus erythropolis (Re-LEH) in terms of stereoselectivity. Tomsk-LEH and CH55-LEH, both from thermophilic sources, have higher optimal temperatures and apparent melting temperatures than Re-LEH. The new LEH enzymes have been crystallized and their structures solved to high resolution in the native form and in complex with the inhibitor valpromide for Tomsk-LEH and poly(ethylene glycol) for CH55-LEH. The structural analysis has provided insights into the LEH mechanism, substrate specifici...

International journal of systematic and evolutionary microbiology, 2015

A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon... more A novel hyperthermophilic, anaerobic, archaeon was isolated from a terrestrial hot spring at Uzon Caldera, Kronotsky Nature Reserve, Kamchatka, Russia. The isolate, strain 1860(T), grew optimally at 90-95 °C and pH 6.0-7.0. The cells were non-motile straight rods, 1.5-5.0 µm in length, covered with surface-layer lattice. Strain 1860(T) utilized complex proteinaceous compounds as electron donors and ferrihydrite, Fe(III) citrate, nitrate, thiosulfate, selenite, selenate and arsenate as electron acceptors for growth. The sequence of the 16S rRNA gene of strain 1860(T) had 97.9-98.7 % similarity with those of members of the genus Pyrobaculum. On the basis of its physiological properties and phylogenetic analyses including in silico genome to genome hybridization, the isolate is considered to represent a novel species, for which the name Pyrobaculum ferrireducens sp. nov. is proposed. The type strain is 1860(T) ( = DSM 28942(T) = VKM B-2856(T)).

International journal of systematic and evolutionary microbiology, 2014

A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T),... more A novel obligately anaerobic, extremely thermophilic, organotrophic bacterium, strain Rift-s3(T), was isolated from a deep-sea sample containing Riftia pachyptila sheath from Guaymas Basin, Gulf of California. Cells of the novel isolate were rods, 0.3-0.8 µm in width and 1.5-10 µm in length, surrounded by a sheath-like structure (toga). Strain Rift-s3(T) grew at temperatures ranging from 44 to 75 °C, at pH 5.5 to 8.0, and with NaCl concentrations of 3 to 60 g l(-1). Under optimum conditions (65 °C, pH 6.0, NaCl 25 g l(-1)), the doubling time was 30 min. The isolate was able to ferment mono-, oligo- and polysaccharides including cellulose, chitin, xylan and pectin, and proteins including β-keratins, casein and gelatin. Acetate, hydrogen and carbon dioxide were the main products of glucose fermentation. The G+C content of the DNA was 30 mol%. Phylogenetic analysis of 16S rRNA gene sequences showed the affiliation of strain Rift-s3(T) with the genus Thermosipho, with Thermosipho atlant...