Evaluation of Antibiotic Resistance of Salmonella Serotypes and Whole-Genome Sequencing of Multiresistant Strains Isolated from Food Products in Russia

Food products may be a source of Salmonella, one of the main causal agents of food poisoning, especially after the emergence of strains resistant to antimicrobial preparations. The present work dealt with investigation of the occurrence of resistance to antimicrobial preparations among S. enterica strains isolated from food. The isolates belonged to 11 serovars, among which Infantis (28%), Enteritidis (19%), and Typhimurium (13.4%) predominated. The isolates were most commonly resistant to trimethoprim/sulfamethoxazole (n = 19, 59.38%), cefazolin (n = 15, 46.86%), tetracycline (n = 13, 40.63%), and amikacin (n = 9, 28.13%). Most of the strains (68.75%) exhibited multiple resistance to commonly used antibiotics. High-throughput sequencing was used to analyse three multidrug-resistant strains (resistant to six or more antibiotics). Two of them (SZL 30 and SZL 31) belonged to S. Infantis, while one strain belonged to S. Typhimurium (SZL 38). Analysis of the genomes of the sequenced strains revealed the genes responsible for antibiotic resistance. In the genomes of strains SZL 30 and SZL 31 the genes of antibiotic resistance were shown to be localized mostly in integrons within plasmids, while most of the antibiotic resistance genes of strain SZL 38 were localized in a chromosomal island (17,949 nt). Genomes of the Salmonella strains SZL 30, SZL 31, and SZL 38 were shown to contain full-size pathogenicity islands: SPI-1, SPI-2, SPI-4, SPI-5, SPI-9, SPI-11, SPI-13, SPI-14, and CS54. Moreover, the genome of strain SZL 38 was also found to contain the full-size pathogenicity islands SPI-3, SPI-6, SPI-12, and SPI-16. The emergence of multidrug-resistant strains of various Salmonella serovars indicates that further research on the transmission pathways for these genetic determinants and monitoring of the distribution of these microorganisms are necessary.

[Diversity of magnetotactic bacteria of the Moskva River]

Diversity of magnetotactic bacteria in the Moskva River at the Strogino area was studied using microscopy and phylogenetic analysis. Magnetotactic cocci were the predominant morphotype. Phylogenetic analysis of the 16S rRNA gene sequences revealed 13 OTUs of the orders Magnetococcales and Rhodospirillales, class Alphaproteobacteria. The shares of the relevant sequences were 90 and 10%, respectively. An axenic culture of magnetotactic spirilla was isolated from the studied community. According to the results of the 16S rRNA gene sequencing, the isolate was identified as a new Magnetospirillum species.

Ornatilinea apprima gen. nov., sp. nov., a cellulolytic representative of the class Anaerolineae

A novel obligately anaerobic, mesophilic, organotrophic bacterium, strain P3M-1(T), was isolated from a microbial mat formed in a wooden bath filled with hot water emerging from a 2775 m-deep well in the Tomsk region of western Siberia, Russia. Cells of strain P3M-1(T) were rod-shaped, 0.3-0.7 µm in width and formed multicellullar filaments that reached up to 400 µm in length. Strain P3M-1(T) grew optimally at 42-45 °C, pH 7.5-8.0, and with 0.1% (w/v) NaCl. Under optimal conditions, the doubling time was 6 h. The isolate was able to ferment a variety of proteinaceous substrates and sugars, including microcrystalline cellulose. Acetate, ethanol and H(2) were the main products of glucose fermentation. The genomic DNA G+C content was 55 mol%. 16S rRNA gene sequence-based phylogenetic analyses showed that strain P3M-1(T) was a member of the class Anaerolinea, with 92.8 % sequence similarity to Levilinea saccharolytica KIBI-1(T). Based on phylogenetic analysis and physiological properties, strain P3M-1(T) represents a novel species in a new genus, for which the name Ornatilinea apprima gen. nov., sp. nov. is proposed; the type strain of O. apprima is P3M-1(T) (= DSM 23815(T)=VKM B-2669(T)).

Caloribacterium cisternae gen. nov., sp. nov., an anaerobic thermophilic bacterium from an underground gas storage reservoir

A novel anaerobic, moderately thermophilic bacterium (strain SGL43(T)) was isolated from Severo-Stavropolskoye underground gas storage reservoir (Russia). Cells of strain SGL43(T) were motile straight rods, 0.4 µm in diameter and 2.0-3.0 µm in length. The temperature range for growth was 28-65 °C, with optimum growth at 50 °C. The pH range for growth was 5.5-8.0, with optimum growth at pH 7.0-7.5. Growth of strain SGL43(T) was observed at NaCl concentrations of 0-4.0% (w/v) with optimum growth at 1.0% (w/v) NaCl. Substrates utilized by strain SGL43(T) included peptone, yeast extract, glucose, fructose, maltose, galactose, pyruvate and citrate. Products of glucose or citrate fermentation were acetate, hydrogen and CO(2). Thiosulfate was reduced to sulfide. The DNA G+C content of strain SGL43(T) was 43.1 mol%. 16S rRNA gene sequence analysis revealed that strain SGL43(T) belongs to the order Thermoanaerobacterales (phylum 'Firmicutes'). The closest relative of strain SGL43(T) was Thermoanaerobacterium saccharolyticum (86.2% 16S rRNA gene sequence similarity with the type strain). Based on the data presented here, strain SGL43(T) is considered to represent a novel species of a new genus, for which the name Caloribacterium cisternae gen. nov., sp. nov. is proposed. The type strain of Caloribacterium cisternae, the type species of the genus, is SGL43(T) (=DSM 23830(T)=VKM B-2670(T)).

Culturable diversity of lithotrophic haloalkaliphilic sulfate-reducing bacteria in soda lakes and the description of Desulfonatronum thioautotrophicum sp. nov., Desulfonatronum thiosulfatophilum sp. nov., Desulfonatronovibrio thiodismutans sp. nov., and Desulfonatronovibrio magnus sp. nov

Soda lake sediments usually contain high concentrations of sulfide indicating active sulfate reduction. Monitoring of sulfate-reducing bacteria (SRB) in soda lakes demonstrated a dominance of two groups of culturable SRB belonging to the order Desulfovibrionales specialized in utilization of inorganic electron donors, such as formate, H₂ and thiosulfate. The most interesting physiological trait of the novel haloalkaliphilic SRB isolates was their ability to grow lithotrophically by dismutation of thiosulfate and sulfite. All isolates were obligately alkaliphilic with a pH optimum at 9.5–10 and moderately salt tolerant. Among the fifteen newly isolated strains, four belonged to the genus Desulfonatronum and the others to the genus Desulfonatronovibrio. None of the isolates were closely related to previously described species of these genera. On the basis of phylogenetic, genotypic and phenotypic characterization of the novel soda lake SRB isolates, two novel species each in the genera Desulfonatronum and Desulfonatronovibrio are proposed.

Geoglobus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent

A hyperthermophilic, anaerobic, dissimilatory Fe(III)-reducing, facultatively chemolithoautotrophic archaeon (strain SBH6(T)) was isolated from a hydrothermal sample collected from the deepest of the known World Ocean hydrothermal fields, Ashadze field (1 degrees 58' 21'' N 4 degrees 51' 47'' W) on the Mid-Atlantic Ridge, at a depth of 4100 m. The strain was enriched using acetate as the electron donor and Fe(III) oxide as the electron acceptor. Cells of strain SBH6(T) were irregular cocci, 0.3-0.5 mum in diameter. The temperature range for growth was 50-85 degrees C, with an optimum at 81 degrees C. The pH range for growth was 5.0-7.5, with an optimum at pH 6.8. Growth of SBH6(T) was observed at NaCl concentrations ranging from 1 to 6 % (w/v) with an optimum at 2.5 % (w/v). The isolate utilized acetate, formate, pyruvate, fumarate, malate, propionate, butyrate, succinate, glycerol, stearate, palmitate, peptone and yeast extract as electron donors for Fe(III) reduction. It was also capable of growth with H(2) as the sole electron donor, CO(2) as a carbon source and Fe(III) as an electron acceptor without the need for organic substances. Fe(III) [in the form of poorly crystalline Fe(III) oxide or Fe(III) citrate] was the only electron acceptor that supported growth. 16S rRNA gene sequence analysis revealed that the closest relative of the isolated organism was Geoglobus ahangari 234(T) (97.0 %). On the basis of its physiological properties and phylogenetic analyses, the isolate is considered to represent a novel species, for which the name Geoglobus acetivorans sp. nov. is proposed. The type strain is SBH6(T) (=DSM 21716(T) =VKM B-2522(T)).

[Evaluation of the effect of late blight-resistant potato plants on the structure of bacterial associations in soil]

We studied the compositions of microbial associations isolated from soils where nontransgenic and transgenic late blight-resistant lines of potato varieties Lugovskoi, Charodei, and Golubizna had been grown. The analysis was based on denaturing gradient gel electrophoresis of total amplificates of 16S rRNA gene fragments and analysis of libraries of nifH gene fragments. Neither method revealed significant differences in the structure of the microbial associations isolated from soils with control or transgenic plants. The minor differences detected in the microflora ranges were no greater than those in the rhizospheres of different nontransgenic potato varieties.

[Roseococcus suduntuyensis sp. nov., a new aerobic bacteriochlorophyll A-containing bacterium isolated from a low-mineralized soda lake of Eastern Siberia]

A novel strain, SHET, of aerobic bacteriochlorophyll a-containing bacteria was isolated from the surface layer of bottom sediments from the soda lake Shuluutai-Ekhe-Torom (Chita oblast, Eastern Siberia, Russia). The lake water has a total mineralization of 3.0 g/l and a pH of 9.2. The cells of strain SHET are cocci or short rods, which reproduce by uniform division. The cells are motile by means of flagella. The cell wall structure is of the gram-negative type. Sparse intracytoplasmic membrane vesicles are located close to the cell wall. The new isolate is an obligate aerobe and facultative alkaliphile which grows in a pH range of 7.5-9.5 (with an optimum at pH 8.5-9.0). The best growth of strain SHET occurred at 2.0 g/l NaCl and 23-28 degrees C. Photosynthetic pigments are represented by bacteriochlorophyll a, with the maximum absorption at 865 nm in the in vivo spectrum, and carotenoids (spirilloxanthin derivatives). Analysis of the 16S rRNA gene sequences demonstrated that strain SHET is closely related to Roseococcus thiosulfatophilus of the alpha-1 subclass of Proteobacteria (98.6 % similarity). The DNA G + C base content is 69.1 mol %. Unlike Rsc. thiosulfatophilus, strain SHET grows well on sugars and glycerol and is not capable of utilizing thiosulfate as an energy source. The new isolate is a facultative alkaliphile and reduces nitrates to nitrites. On the basis of its phenotypic and genetic characteristics, strain SHET was described as a new species of the genus Roseococcus, Rsc. suduntuyensis sp. nov.

[Chlorobaculum macestae sp. nov., a new green sulfur bacterium]

The investigated green sulfur bacterium, strain M, was isolated from a sulfidic spring on the Black Sea Coast of the Caucasus. The cells of strain M are straight or curved rods 0.6-0.9 x 1.8-4.2 microm in size. According to the cell wall structure, the bacteria are gram-negative. Chlorosomes are located along the cell periphery. Strain M is an obligate anaerobe capable of photoautotrophic growth on sulfide, thiosulfate, and H2. It utilizes ammonium, urea, casein hydrolysate, and N2 as nitrogen sources and sulfide, thiosulfate, and elemental sulfur as sulfur sources. Bacteriochlorophyll c and the carotenoid chlorobactene are the main pigments. The optimal growth temperature is 25-28 degrees C; the optimal pH is 6.8. The strain does not require NaCl. Vitamin B12 stimulates growth. The content of the G+C base pairs in the DNA of strain M is 58.3 mol %. In the phylogenetic tree constructed on the basis of analysis of nucleotide sequences of 16S rRNA genes, strain M forms a separate branch, which occupies an intermediate position between the phylogenetic cluster containing representatives of the genus Chlorobaculum (94.9-96.8%) and the cluster containing species of the genus Chlorobium (94.1-96.5%). According to the results of analysis of the amino acid sequence corresponding to the fmo gene, strain M represents a branch which, unlike that in the "ribosomal" tree, falls into the cluster of the genus Chlorobaculum (95.8-97.2%). Phylogenetic analysis of the amino acid sequence corresponding to the nifH gene placed species of the genera Chlorobaculum and Chlorobium into a single cluster, whereas strain M formed a separate branch. The results obtained allow us to describe strain M as a new species of the genus Chlorobaculum. Chlorobaculum macestae sp. nov.

[Halomonas mongoliensis sp. nov. and Halomonas kenyensis sp. nov., new haloalkaliphilic denitrifiers capable of reducing N2O, isolated from soda lakes]

In the course of the search for N2O-utilizing microorganisms, two novel strains of haloalkaliphilic denitrifying bacteria, Z-7009 and AIR-2, were isolated from soda lakes of Mongolia and Kenya. These microorganisms are true alkaliphiles and grow in the pH ranges of 8.0-10.5 and 7.5-10.6, respectively. They are facultative anaerobes with an oxidative type of metabolism, able to utilize a wide range of organic substrates and reduce nitrate, nitrous oxide, and, to a lesser extent, nitrite to gaseous nitrogen. They can oxidize sulfide in the presence of acetate as the carbon source and nitrous oxide (strain Z-7009) or nitrate (strain AIR-2) as the electron acceptor. The strains require Na+ ions. They grow at medium mineralization levels of 0.16-2.2 M Na+ (Z-7009) and 0.04-2.2 M Na+ (AIR-2). The G+C contents of the DNA of strains Z-7009 and AIR-2 are 67.9 and 65.5 mol %, respectively. According to the results of 16S rRNA gene sequencing and DNA-DNA hybridization, as well as on the basis of physiological properties, the strains were classified as new species of the genus Halomonas: Halomonas mongoliensis, with the type strain Z-7009T (=DSM 17332, =VKM B2353), and Halomonas kenyensis, with the type strain AIR-2T (=DSM 17331, =VKM B2354).

Thermoanaerobacterium aciditolerans sp. nov., a moderate thermoacidophile from a Kamchatka hot spring

An anaerobic, moderately thermoacidophilic bacterium, strain 761-119T, was isolated from an acidic hot spring in the Orange Field of the Uzon Caldera (Kamchatka, far-eastern Russia). Cells were spore-forming, Gram-positive rods, possessing one polar flagellum. Growth of strain 761-119Twas observed between 37 and 68 °C and in the pH20 °Crange 3.2–7.1. No growth was observed within 5 days of incubation at or below 35 °C and at or above 70 °C, as well as at or below pH20 °C2.8 and at or above pH20 °C7.5. The optimal temperature and pH20 °Cfor growth were 55 °C and pH20 °C5.7, respectively. A wide range of carbohydrates and polysaccharides were fermented, as well as peptides and proteinaceous substrates. The main products of glucose fermentation were acetate, ethanol, lactate, H2and CO2. The DNA G+C content was 34 (±0.5) mol%. 16S rRNA gene sequence analysis indicated that strain 761-119Tbelonged to the genusThermoanaerobacterium. The level of 16S rRNA gene sequence similarity with otherThermoanaerobacteriumspecies was 86.5–97.8 %, with the only moderately acidophilic member of this genus,Thermoanaerobacterium aotearoense, being one of its closest relatives. DNA–DNA hybridization withT. aotearoenseshowed 33 % relatedness. Thus, morphological (one polar flagellum) and physiological characteristics (lower pH limit of growth at pH20 °C3.2 compared withT. aotearoense) and 16S rRNA gene sequence analyses revealed that strain 761-119Trepresents a novel species in the genusThermoanaerobacterium, for which the nameThermoanaerobacterium aciditoleranssp. nov. is proposed, with the type strain 761-119T(=DSM 16487T=VKM B-2363T).

[Analysis of nucleotide sequences polymorphism of chloroplast trnL-trnF spacer of tRNA genes in giant duckweed Spirodela polyrrhiza (L.) Schleiden]

Chloroplast DNA trnL-trnF spacer sequences of tRNA genes of 14 specimens of the fam. Lemnaceae have been characterized. Nucleotide polymorphism analysis of the spacer trnL-trnF of geographically isolated and morphologically differing accessions of S. polyrrhiza that is the most widespread species of Spirodela genus showed the low level of intraspecific variability. Five trnL-trnF haplotypes of S. polyrrhiza are identified. Both mono-, and polynucleotide repeats, and also extensive indels, specific to representatives Spirodela polyrrhiza, Landoltia punctata and Lemna sp. are revealed. Competency of Landoltia genus allocation as separate entity was confirmed.

[Geoalkalibacter ferrihydriticus gen. nov., sp. nov., the first alkaliphilic representative of the family Geobacteraceae, isolated from a soda lake]

Investigation of iron reduction in bottom sediments of alkaline soda lakes resulted in the isolation of a new obligately anaerobic iron-reducing bacterium, strain Z-0531, from Lake Khadyn (Tuva Republic, Russia) sediment samples. The cells of strain Z-0531 are short (1.0-1.5 by 0.3-0.5 microm), motile, non-spore-forming, gram-negative rods. The isolate is an obligate alkaliphile, developing in the pH range of 7.8-10.0, with an optimum at pH 8.6. It does not require NaCl but grows at NaCl concentrations of 0-50 g/1l. It can oxidize acetate with such electron acceptors as amorphous Fe(llI) hydroxide (AFH), EDTA-Fe(III), anthraquinone-2,6-disulfonate (quinone), Mn(IV), and S(0). On media with EDTA-Fe(III), the isolate can oxidize, apart from acetate, ethanol, pyruvate, oxalate, arginine, tartrate, lactate, propionate, and serine. H2 is not utilized. The reduced products formed during growth with AFH are siderite or magnetite, depending on the growth conditions. The isolate is incapable of fermenting sugars, peptides, and amino acids. Yeast extract or vitamins are required as growth factors. The organism is capable of dinitrogen fixation and harbors the nifH gene. The DNA G+C content is 55.3 mol %. 16S rRNA analysis places strain Z-0531 into the family Geobacteraceae. Its closest relative (93% similarity) is Desulfuromonas palmitatis. Based on phenotypic distinctions and phylogenetic position, it is proposed that strain Z-0531 be assigned to the new genus and species Geoalkalibacter ferrihydriticus gen. nov., sp. nov.

[Thiobacillus sajanensis sp. nov., a new obligately autotrophic sulfur-oxidizing bacterium isolated from Khoito-Gol hydrogen-sulfide springs, Buryatia]

Four strains of rod-shaped gram-negative sulfur-oxidizing bacteria were isolated from Khoito-Gol hydrogen-sulfide springs in the eastern Sayan Mountains (Buryatia). The cells of the new isolates were motile by means of a single polar flagellum. The strains were obligately chemolithoautotrophic aerobes that oxidized thiosulfate (with the production of sulfur and sulfates) and hydrogen sulfide. They grew in a pH range of 6.8-9.5, with an optimum at pH 9.3 and in a temperature range of 5-39 degrees C, with an optimum at 28-32 degrees C. The cells contained ubiquinone Q-8. The DNA G+C content of the new strains was 62.3-64.2 mol %. According to the results of analysis of their 16S rRNA genes, the isolates belong to the genus Thiobacillus within the subclass Betaproteobacteria. However, the similarity level of nucleotide sequences of the 16S rRNA genes was insufficient to assign the isolates to known species of this genus. The affiliation to the genus Thiobacillus was confirmed by DNA-DNA hybridization of the isolates with the type strain of the type species of the genus Thiobacillus, T. thioparus DSM 505T (= ATCC 8158T). Despite the phenotypic similarity, the hybridization level was as low as 21-29%. In addition, considerable differences were revealed in the structure of the genes encoding RuBPC, the key enzyme of autotrophic CO2 assimilation, between the known Thiobacillus species and the new isolates. Based on molecular-biological features and certain phenotypic distinctions, the new isolates were assigned to a new Thiobacillus species, T. sajanensis sp. nov., with the type strain 4HGT (= VKM B-2365T).

[Comparative characterization of cultured methane-oxidizing bacteria by serological and molecular methods]

Three stable methane-oxidizing enrichment cultures, SB26, SB31, and SB31A were analyzed by transmission electron microscopy and by serological and molecular techniques. Electron microscopy revealed the presence of both type I and type II methanotrophs in SB31 and SB31A enrichments; only type II methanotrophs were found in SB26 enrichment. Methylosinus trichosporium was detected in all three enrichments by the application of species-specific antibodies. Additionally, Methylocystis echinoides was found in SB26 culture; Methylococcus capsulatus, in SB31 and SB31A; and Methylomonas methanica, in SB31. The analysis with pmoA and nifH gene sequences as phylogenetic markers revealed the presence of Methylosinus/Methylocystis group in all communities. Moreover, the analysis of pmoA sequences revealed the presence of Methylomonas in SB31. Methylocella was detected in SB31 and SB31A enrichments only by nifH analysis. It was concluded that the simultaneous application of different approaches reveals more reliable information on the diversity of methanotrophs.

[Raoultella planticola, a new strain degrading 2,4,5-trichlorophenoxyacetic acid]

A new strain that degrades the herbicide 2,4,5-trichlorophenoxyacetic acid (2,4,5-T) was isolated from soil, which was exposed to factors related to the petrochemical industry. According to its physiological, biochemical, cultural, and morphological traits, together with the sequence of the 16S rRNA gene, the strain was identified as Raoultella planticola 33-4ch. The strain could consume 2,4,5-T as a sole source of carbon and energy. The amount of 2,4,5-T in the culture medium decreased by 51% after five days of incubation. Raoultella planticola 33-4ch consumes 2,4,5-T to produce 4-chlorophenoxyacetic, phenoxyacetic, and 3-methyl-2,6-dioxo-4-hexenoic acids.

[Two new species of microaerophilic sulfur spirilla, Spirillum winogradskii sp. nov. and Spirillum kriegii sp. nov]

New microaerophilic sulfur-oxidizing spirilla were isolated from hydrogen sulfide sludge of wastewater treatment plants. Strains D-427 and D-430 have spiral cells that are highly motile due to bipolar flagellum bundles covered with mucous sheaths. Under a phase-contrast microscope, these bundles are visible as single polar flagella. Spheroplasts are formed in the stationary growth phase. Both strains are obligate organotrophs able to oxidize a number of reduced sulfur compounds. The oxidation of sulfide and polysulfide leads to the formation of intracellular globules of elemental sulfur; thiosulfate oxidation results in tetrathionate accumulation in the medium. The cells are unable to utilize reduced sulfur compounds in the energy metabolism; their oxidation is caused by a chemical interaction with H2O2 and O2, synthesized in the electron transport chain. Both strains are obligate microaerophiles with an optimal oxygen concentration in the gas phase of 2 and 0.8% for strains D-427 and D-430, respectively. The strains utilize a limited number of organic acids as growth substrates, mainly tricarboxylic-acid-cycle intermediates. The DNA G+C content is 38.0 mol % (T(m)) for strain D-427 and 38.9 mol % for strain D-430. Phylogenetic analysis, based on the comparison of 16S rRNA gene sequences, revealed that the new isolates of sulfur spirilla are the most closely related to Spirillum volutans, the type species of the genus (97.4% similarity). They were assigned to the genus Spirillum within the class Beta-proteobacteria as two new species, S. winogradskii sp. nov. (D-427T = DSM 12756T) and S. kriegii sp. nov. (B-430T = BKM B-2372T). The emended description of the genus Spirillum is provided.

["Candidatus contubernalis alkalaceticum," an obligately syntrophic alkaliphilic bacterium capable of anaerobic acetate oxidation in a coculture with Desulfonatronum cooperativum]

From the silty sediments of the Khadyn soda lake (Tuva), a binary sulfidogenic bacterial association capable of syntrophic acetate oxidation at pH 10.0 was isolated. An obligately syntrophic, gram-positive, spore-forming alkaliphilic rod-shaped bacterium performs acetate oxidation in a syntrophic association with a hydrogenotrophic, alkaliphilic sulfate-reducing bacterium; the latter organism was previously isolated and characterized as the new species Desulfonatronum cooperativum. Other sulfate-reducing bacteria of the genera Desulfonatronum and Desulfonatronovibrio can also act as the hydrogenotrophic partner. Apart from acetate, the syntrophic culture can oxidize ethanol, propanol, isopropanol, serine, fructose, and isobutyric acid. Selective amplification of 16S rRNA gene fragments of the acetate-utilizing syntrophic component of the binary culture was performed; it was found to cluster with clones of uncultured gram-positive bacteria within the family Syntrophomonadaceae. The acetate-oxidizing bacterium is thus the first representative of this cluster obtained in a laboratory culture. Based on its phylogenetic position, the new acetate-oxidizing syntrophic bacterium is proposed to be assigned, in a Candidate status, to a new genus and species: "Candidatus Contubernalis alkalaceticum."

[Microbacterium oxydans, a symbiont of Djungarian hamster, displaying probiotic properties]

A resident microorganism (strain Kho-17) was isolated from secretions of the specific glandular structures at the angles of mouth of Djungarian hamster (Phodopus campbelli). According to cultural, morphological, and physiological properties as well as to the phylogenetic analysis basing on the sequences of 16S rRNA gene and analysis of the cell wall the strain was assigned to the species Microbacterium oxydans. The bacterium isolated displayed probiotic properties when administered orally as a suspension of live cells for 20 days to Syrian hamster (Mesocricetus auratus), which manifested themselves in increased body weight and weights of several organs and stimulation of both cell-mediated and humoral immunities.

[Halomonas campisalis, an obligatorily alkaliphilic, nitrous oxide-reducing denitrifier with a Mo-cofactor-lacking nitrate reductase]

We isolated eight strains of denitrifying bacteria that reduce nitrate and nitrous oxide at pH 10 from Lake Magadi (Kenya). Despite certain differences between the strains, they are similar in terms of G+C content (66.1-68.1 mol %) and DNA-DNA homology (75-92%) and represent different morphotypes of the same species. Based on the results of partial 16S rRNA sequencing, strain Z-7398-2 was most closely related to the Halomonas campisalis isolate from Alkali Lake (USA). The DNA-DNA homology level between the tested strain and the type strain of H. campisalis 4A was 88%. These two strains were also similar phenotypically. However, the culture isolated by us was characterized by peculiar properties, such as obligate alkaliphily, which manifested itself in the culture dependence on carbonates and lack of growth at pH values below 7, a nitrous oxide-reducing capacity, and an unusual nitrate reductase that lacked molybdenum and a Mo cofactor.

[An oligonucleotide primer system for amplification of the ribulose-1,5-bisphosphate carboxylase/oxygenase genes of bacteria of various taxonomic groups]

Based on the analysis of GenBank nucleotide sequences of the cbbL and cbbM genes, coding for the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBPC), the key enzyme of the Calvin cycle, a primer system was designed that allows about 800-bp-long fragments of these genes to be PCR-ampliflied in various photo- and chemotrophic bacteria. The efficiency of the designed primer system in detection of RuBPC genes was demonstrated in PCR with DNA of taxonomically diverse bacteria possessing RuBPC genes with a known primary structure. Nucleotide sequences of RuBPC gene fragments of bacteria belonging to the genera Acidithiobacillus. Ectothiorhodospira, Magnetospirillum, Methylocapsa, Thioalkalispira, Rhodobacter, and Rhodospirillum were determined to be deposited with GenBank and to be translated into amino acid sequences and subjected to phylogenetic analysis.

[Ectothiorhodosinus mongolicum gen. nov., sp. nov.,--a new purple sulfur bacterium from soda lake in Mongolia]

A new purple sulfur bacterium (strain M9) was isolated from the steppe soda Lake Dzun Uldziin Nur (pH 9.4; mineralization, 3.3%) situated in southeastern Mongolia. Individual cells appear as vibrios 0.3-0.5 x 0.7-1 micron in size. The dividing cells often do not separate from each other, forming an almost closed ring. The internal photosynthetic membranes are represented by concentric lamellae lining the cell wall. Photosynthetic pigments are bacteriochlorophyll a and carotenoids of the spirilloxanthin series. The main carotenoid (> 96%) is spirilloxanthin. Two typical light-harvesting complexes (LH1 and LH2) are present in the membranes in a 1:1 ratio. The bacterium is an anaerobe and facultative photoorganoheterotroph. Photolithoautotrophic growth on sulfide is scarce. Thiosulfate is utilized as an electron donor only in the presence of organic matter. Globules of elemental sulfur are formed as an intermediary product of sulfide and thiosulfate oxidation and are deposited outside the cells. The end product of oxidation is sulfate. In the presence of sulfide and carbonates, acetate, lactate, malate, pyruvate, propionate, succinate, and fumarate are used as the additional sources of carbon in anoxygenic photosynthesis. Vitamin are not required. The bacterium is an alkaliphile the pH optimum is at 8.3-9.1, the pH range is 7.6-10.1. The optimum NaCl concentration in the medium is 1 to 7%; the range is 0.5 to 0.9%. The optimum carbonate content in the medium is 2%; the range is 1 to 10%. The best growth occurs at 30-35 degrees C. The DNA G + C content is 57.5 mol%. According to the results of analysis of the 16S rRNA gene sequences, the new isolate M9 belongs to the phylogenetic cluster containing representatives of the family Ectothiorhodospiraceae within the class "Gammaproteobacteria." In this class, the new isolate forms a new branch, which occupies an intermediate position between the representatives of the genera Ectothiorhodospira and Thiorhodospira. Based on the phenotypic and genetic characteristics, the new purple sulfurbacterium was assigned to a new species of a new genus of the family Ectothiorhodospiraceae, Ectothiorhodosinus mongolicum gen. nov., sp. nov.

[Sulfobacillus sibiricus sp. nov., a new moderately thermophilic bacterium]

In the course of pilot industrial testing of a biohydrometallurgical technology for processing goldarsenic concentrate obtained from the Nezhdaninskoe ore deposit (East Siberia, Sakha, Yakutiya), a new gram-positive rod-shaped spore-forming moderately thermophilic bacterium (designated as strain N1) oxidizing Fe2+, S0, and sulfide minerals in the presence of yeast extract (0.02%) was isolated from a dense pulp. Physiologically, strain N1 differs from previously described species of the genus Sulfobacillus in having a somewhat higher optimal growth temperature (55 degrees C). Unlike the type strain of S. thermosulfidooxidans, strain N1 could grow on medium with 1 mM thiosulfate or sodium tetrathionate as a source of energy only within several passages and failed to grow, in the absence of an inorganic energy source, on media with sucrose, fructose, glucose, reduced glutathione, alanine, cysteine, sorbitol, sodium acetate, or pyruvate. The G + C content of the DNA of strain N1 was 48.2 mol %. The strain showed 42% homology after DNA-DNA hybridization with the type strain of S. thermosulfidooxidans and 10% homology with the type strain of S. acidophilus. The isolate differed from previously studied strains of S. thermosulfidooxidans in the structure of its chromosomal DNA (determined by the method of pulsed-field gel electrophoresis) which remained stable as growth conditions were changed. According to the results of the 16S rRNA gene analysis, the new strain forms a single cluster with the bacteria of the species Sulfobacillus thermosulfidooxidans (sequence similarity of 97.9-98.6%). Based on these genetic and physiological features, strain N1 is described as a new species Sulfobacillus sibiricus sp. nov.

[Cellulose decomposition under nitrogen deficiency by bacteria isolated from the intestines of phytophagous vertebrates]

A nitrogen-fixing strain identified as Klebsiella pneumonia 402-2 and two endoglucanase-synthesizing Bacillus strains were isolated from the intestines of phytophagous animals. One of the Bacillus strains was identified as Bacillus subtilis GL. Klebsiella pneumoniae 402-2 increased the endoglucanase activity of both Bacillus strains in mixed cultures. The data on the taxonomic position of strains 402-2 and GL and on the nitrogen-fixing capacity of strain 402-2 were confirmed by sequencing and analyzing their 16S rRNA genes and by amplifying the nitrogenase gene nifH.

[Identification of a new steroid transforming strain of mycobacteria as Mycobacterium neoaurum]

The ability to utilize sterols as a sole source of carbon was studied in 80 strains and consortia of hydrocarbon-oxidizing bacteria. One of the strains, which efficiently transformed both individual sterols and their mixtures, was identified as Mycobacterium neoaurum, based on the analysis of the sequence of the 16S rRNA gene.

Carboxydocella thermautotrophica gen. nov., sp. nov., a novel anaerobic, CO-utilizing thermophile from a Kamchatkan hot spring

A novel anaerobic, thermophilic, CO-utilizing bacterium, strain 41(T), was isolated from a terrestrial hot vent on the Kamchatka Peninsula. Strain 41(T) was found to be a Gram-positive bacterium, its cells being short, straight, motile rods. Chains of three to five cells were often observed. The isolate grew only chemolithoautotrophically on CO, producing equimolar quantities of H2 and CO2 (according to the equation CO+H2O --> CO2+H2). Growth was observed in the temperature range 40-68 degrees C, with an optimum at 58 degrees C, and in the pH range 6.5-7.6, with an optimum at pH 7.0. The generation time under optimal conditions for chemolithotrophic growth was 1.1 h. The DNA G+C content was 46 +/- 1 mol%. Growth was completely inhibited by penicillin, ampicillin, streptomycin, kanamycin and neomycin. On the basis of the phenotypic and phylogenetic features, it is proposed that this isolate represents a new genus and species, Carboxydocella thermautotrophica gen. nov., sp. nov. (type strain 41(T) = DSM 12356(T) = VKM B-2282(T)).

[Study of nucleotide sequences of nifH genes in methanotrophic bacteria]

Using a previously developed primer system, nifH gene fragments 450 nucleotides long were amplified, cloned, and sequenced for representatives of nitrogen-fixing methanotrophic bacteria of the genera Methylococcus, Methylocystis and Methylosinus. Fragments of nifH genes were also detected and sequenced in representatives of the genera Methylomonas and Methylobacter, which were not considered diazotrophs until recently. Phylogenetic analysis revealed remoteness of nifH genes sequences of methanotroph types I and II. At the same time, close relationship was found between nifH of type I methanotrophs and representatives of gamma-proteobacteria and between nifH genes of type II methanotrophs and representatives of alpha-proteobacteria. The results obtained in this study are in good accordance with the data of phylogenetic analysis based on 16S rRNA sequence comparison with the only exception of Methylococcus capsulatus strains, whose nifH genes proved to be closely related to nifH genes of Methylocystis and Methylosinus representatives. Our findings extend the database of primary sequences of nifH genes and allow the contribution of methanotrophs to the process of nitrogen fixation to be estimated.

Combined effect of low-frequency laser and polyphenol oxidase on adhesive activity of Escherichia coli strains isolated from patients with urinary diseases

The effects of polyphenol oxidase and low-frequency laser irradiation on adhesion of pathogenic Escherichia coli to human erythrocytes and buccal epithelial cells were studied. The maximum decrease in adhesive activity of these strains was observed after complex exposure to laser and enzyme.

Complex effects of pulsed infrared laser and asparaginase on Escherichia coli strains isolated from patients with urinary diseases

Treatment with L-asparaginase and low-frequency laser decreased adhesion of uropathogenic Escherichia coli to human erythrocytes. The maximum effect was observed after combined treatment (laser exposure followed by enzyme treatment).

[Phylogenetic diversity of the archaeal component in microbial mats on coral-like structures associated with methane seeps in the Black Sea]

With the use of molecular ecology methods, the archaea component of microbial mats on coral-like structures associated with methane seeps occurring at a depth of about 200 m in the Black Sea was investigated without the isolation of pure cultures. Using archaea-specific 16S rRNA-targeted oligonucleotide primes, long fragments of genes were amplified, cloned, and sequenced and their phylogenetic analysis was carried out. It was shown that archaea in microbial mats on coral-like structures are represented by two dominant phylotypes that belong to the kingdoms Crenarchaeota and Euryarchaeota and are not specifically related to any described archaea species. The possible role of the revealed archaea in the process of anaerobic methane oxidation is discussed.

Effects of asparaginase and polyphenol oxidase on adhesive characteristics of microorganisms

We studied the effects of polyphenol oxidase and asparaginase on microorganism adhesion to buccal epithelial cells. These enzymes reduced adhesion of pathogenic microorganisms (uropathogenic and Escherichia coli, Salmonella enteritidis, Entamoeba spp., Influenza virus, Candida albicans, Streptococcus spp.) and had virtually no effect on adhesive characteristics of probiotic variants of Escherichia coli and Lactobacillus fermentum.

Methanosarcina lacustris sp. nov., a new psychrotolerant methanogenic archaeon from anoxic lake sediments

A new psychrotolerant methanogenic archaeon strain ZS was isolated from anoxic lake sediments (Switzerland). The cells of the organism were non-motile cocci, 1.5-3.5 microm in diameter. The cells aggregated and formed pseudoparenchyma. The cell wall was Gram-positive. The organism utilized methanol, mono-, di-, trimethylamine and H2/CO2 with methane production. The temperature range for growth was 1-35 degrees C with an optimum at 25 degrees C. The DNA G+C content of the organism was 43.4. mol%. Analysis of the 16S rRNA gene sequence showed that strain ZS was phylogenetically closely related to members of the genus Methanosarcina, but clearly differed from all described species of this genus (95.6-97.6% of sequence similarity). The level of DNA-DNA hybridization of strain ZS with Methanosarcina barkeri and Methanosarcina mazei was 15 and 31%, respectively. Based on the results of physiological and phylogenetic studies strain ZS can be assigned to a new species of the genus Methanasarcina. The name Methanosarcina lacustris sp. nov. is proposed. The type strain is ZS (= DSM 13486T, VKM B-2268).

[Desulfacinum subterraneum sp.nov.--a new thermophilic sulfate-reducing bacterium isolated from a high temperature oil field ]

A new thermophilic sulfate-reducing bacterium isolated from the high-temperature White Tiger oil field (Vietnam) is described. Cells of the bacterium are oval (0.4-0.6 by 0.6-1.8 microns), nonmotile, non-spore-forming, and gram-negative. Growth occurs at 45 to 65 degrees C (with an optimum at 60 degrees C) at NaCl concentrations of 0 to 50 g/l. In the course of sulfate reduction, the organism can utilize lactate, pyruvate, malate, fumarate, ethanol, salts of fatty acids (formate, acetate, propionate, butyrate, caproate, palmitate), yeast extract, alanine, serine, cysteine, and H2 + CO2 (autotrophically). In addition to sulfate, the bacterium can use sulfite, thiosulfate, and elemental sulfur as electron acceptors. In the absence of electron acceptors, the bacterium can ferment pyruvate and yeast extract (a yet unrecognized capacity of sulfate reducers) with the formation of acetate and H2. The G + C content of DNA is 60.8 mol %. The level of DNA-DNA hybridization of the isolate (strain 101T) and Desulfacinum infernum (strain B alpha G1T) is as low as 34%. Analysis of the nucleotide sequence of 16S rDNA places strain 101T in the phylogenetic cluster of the Desulfacinum species within the sulfate reducer subdivision of the delta subclass of Proteobacteria. All these results allowed the bacterium studied to be described as a new species, Desulfacinum subterraneum sp. nov., with strain 101 as the type strain.