Sulfobacillus sibiricus sp. nov., a New Moderately Thermophilic Bacterium

In the course of pilot industrial testing of a biohydrometallurgical technology for processing gold-arsenic 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°C). Unlike the type strain of S. thermosulfidooxidans, strain N1 could grow on a 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.     

Sulfobacillus thermosulfidooxidans: a new lineage of bacterial evolution?

The nucleotide sequence of 5 S ribosomal RNA (rRNA) of type strain Sulfobacillus thermosulfidooxidans VKM B-1269 was determined. This organism represents a group of moderately thermophilic acidophilic chemolithotrophic bacteria, able to use ferrous and sulfur compounds as the sole energy source. 5 S rRNA of this bacterium is drastically different from all other known bacterial 5 S rRNA sequences. It is suggested that S. thermosulfidooxidans represents a new lineage of bacterial evolution, that diverged from other bacteria at an early step of their evolution.     

Effect of the medium composition and cultivation conditions on sporulation in chemolithotrophic bacteria

The possibility of controlling endospore formation by changing cultivation conditions was for the first time shown in acidophilic chemolithotrophic bacteria Sulfobacillus thermosulfidooxidans type strain 1269 and the thermotolerant strain K1 formerly described as "S. thermosulfidooxidans subsp. thermotolerans". Suppression of sporulation occurred when these strains were cultured in Manning's liquid medium with yeast extract. This medium was optimized by gradually reducing the concentrations of ferrous iron salts (the source of energy), phosphorous, nitrogen, and yeast extract and simultaneously increasing the concentrations of calcium, magnesium, and manganese (the elements important for sporogenesis) to attain higher yields of endospores by strains 1269 and K1. As a result, a new medium A was proposed, in which the life cycle of the strains studied culminated in sporulation at a level of 45 and 60%, respectively, of the total cell number. In a series of additional tests, the growth temperature and medium pH were adjusted to obtain the maximum yield of endospores. The optimal ranges found were 40-50 degrees C and pH 1.8-2.2 for strain 1269 and 35-40 degrees C and pH 2.5-2.7 for strain K1. An even higher yield of endospores, amounting to 55 and 75% for strains 1269 and K1, respectively, was obtained when the above growth conditions were combined (growth on medium A at optimal temperatures and pH). Our results suggest a new approach to optimizing sporulation by acidophilic chemolithotrophs, which consists in limiting the energy and nutrient sources and using temperature and pH values within the tolerance bounds of these cultures but outside their growth of optimum ranges.     

Growth and carbohydrate metabolism of sulfobacilli]

The moderately thermophilic acidophilic bacteria Sulfobacillus thermosulfidooxidans, strain 1269, S. thermosulfidooxidans subsp. "asporogenes," strain 41, and the thermotolerant strain S. thermosulfidooxidans subsp. "thermotolerans" K1 prefer mixotrophic growth conditions (the concomitant presence of ferrous iron, thiosulfate, and organic compounds in the medium). In heterotrophic and autotrophic growth conditions, these sulfobacilli can grow over only a few culture transfers. In cell-free extracts of these sulfobacilli, key enzymes of the Embden-Meyerhof-Parnas, pentose-phosphate, and Entner-Doudoroff pathways were found. The role of a particular pathway depended on the cultivation conditions. All of the enzymes assayed were most active under mixotrophic conditions in the presence of Fe2+ and glucose, suggesting the operation of all of the three major pathways of carbohydrate metabolism under these conditions. However, the operation of the Entner-Doudoroff pathway in strain 41 was restricted under mixotrophic conditions. After the first culture transfer from mixotrophic to heterotrophic conditions, the utilization of glucose occurred only via the Embden-Meyerhof-Parnas and Entner-Doudoroff pathways. After the first culture transfer from mixotrophic to autotrophic conditions, the activity of carbohydrate metabolism enzymes decreased in all of the strains studied; in strain K1, only the glycolytic pathway remained operative. The high activity of fructose-bisphosphate aldolase, remaining in strain 41 cells under these conditions, suggests the involvement of this enzyme in the reactions of the Calvin cycle or of gluconeogenesis.     

Effect of cultivation conditions on the growth and activities of sulfur metabolism enzymes and carboxylases of Sulfobacillus thermosulfidooxidans subsp. asporogenes strain 41

The moderately thermophilic acidophilic bacterium Sulfobacillus thermosulfidooxidans subsp. asporogenes strain 41 is capable of utilizing sulfides of gold-arsenic concentrate and elemental sulfur as a source of energy. The growth in the presence of S0 under auto- or mixotrophic conditions was less stable compared with the media containing iron monoxide. The enzymes involved in oxidation of sulfur inorganic compounds--thiosulfate-oxidizing enzyme, tetrathionate hydrolase, rhodonase, adenylyl sulfate reductase, sulfite oxidase, and sulfur oxygenase--were discovered in the cells of Sulfobacillus grown in the mineral medium containing 0.02% yeast extract and either sulfur or iron monoxide and thiosulfate. Cell-free extracts of the cultures grown in the medium with sulfur under auto- or mixotrophic conditions displayed activity of the key enzyme of the Calvin cycle--ribulose bisphosphate carboxylase--and several other enzymes involved in heterotrophic fixation of carbonic acid. Activities of carboxylases depended on the composition of cultivation media.     

Rapid specific detection and quantification of bacteria and archaea involved in mineral sulfide bioleaching using real-time PCR

A SybrGreen real-time PCR assay was developed to detect and quantify both total and selected 16S rDNA species of bacteria and archaea involved in the bioleaching of metals from sulfide ores. A set of specific and universal primers based on 16S rDNA sequences was designed and validated for specific detection and quantification of DNA isolated from representative strains of Acidianus brierleyi, Sulfolobus sp., Sulfobacillus thermosulfidooxidans, Sulfobacillus acidophilus, Acidithiobacillus caldus, and Leptospirillum ferrooxidans. An artificial sequence based on 16S rDNA was constructed to quantify total 16S rDNA in mixed DNA samples. The real-time PCR assay was further validated using a mixture of 16S rDNA amplicons derived from the six different species, each added at a known amount. Finally, the real-time PCR assay was used to monitor the change of 16S rDNA copies of four bioleaching strains inoculated into chalcopyrite airlift column reactors operated at different temperatures. The growth dynamics of these strains correlated well with the expected effects of temperature in the chalcopyrite-leaching environment. The suitability of this method for monitoring microbial populations in industrial bioleaching environments is discussed.     

不同能源条件下中度嗜热嗜酸细菌多样性分析

采用黄铁矿、黄铜矿、硫酸亚铁和硫粉混合物作为主要能源物质在50°C条件下分别培养中度嗜热细菌混合物,研究其细菌多样性。提取细菌基因组总DNA,采用PCR结合限制性酶切片段多态性分析(RFLP)方法进行细菌16SrRNA基因的系统发育分析,比较不同能源条件下富集培养的混合细菌群落构成的差异。从3个培养物中共获得阳性克隆303个并进行RFLP分析,对29种不同酶切谱型的克隆插入序列进行测定和系统发育分析。大部分序列与已报道的浸矿微生物16SrRNA序列相似性较高(89.1%~99.7%),归属于硫化叶菌属的耐温氧化硫化杆菌(Sulfobacillus thermotolerans)和热氧化硫化杆菌(Sulfobacillus thermosulfidooxidans),嗜酸硫杆菌属的喜温硫杆菌(Acidithiobacillus caldus),钩端螺旋菌属的嗜铁钩端螺旋菌(Leptospirillumferriphilum)以及unculturedforest soil bacterium、uncultured proteobacterium。其中Acidithiobacillus caldus,Sulfobacillus thermotolerans,Leptospirillumferriphilum3种细菌为三类能源物质培养物中的优势细菌类群。L.ferriphilum在黄铁矿培养体系(53.8%)和硫酸亚铁和硫粉为能源的培养体系中(45.9%)中丰度最高;在以黄铜矿为能源物质的培养体系中,S.thermotolerans的比例大幅上升(70.1%)。关键词:中度嗜热细菌;生物多样性;生物浸矿;喜温硫杆菌(Acidithiobacillus caldus);耐温氧化硫化杆菌(Sulfobacillus thermotolerans);嗜铁钩端螺旋菌(Leptospirillumferriphilum)     

Genotypic and phenotypic polymorphism of environmental strains of the moderately thermophilic bacterium Sulfobacillus sibiricus

Five cultures of moderately thermophilic spore-forming acidophilic chemolithotrophic bacteria were isolated from the zones of spontaneous heating of pyrrhotine-containing pyrite-arsenopyrite gold-arsenic sulfide ores in an operating open pit (strains B1, B2, B3, OFO, and SSO). Analysis of the chromosomal DNA structure revealed differences between these cultures at the strain level (apart from B3 and SSO, which had identical restriction profiles). All the strains had a similar G + C DNA molar content (47.4-48.3%). The level of DNA reassociation was 85 to 95%. The similarity between the DNA of the type strain Sulfobacillus sibiricus N1 isolated from arsenopyrite ore concentrate and that of these strains (83-93%) indicates that they belong to the same species. The strains had similar values of pH and temperature optimal for growth on ferrous iron (1.6-2.0 and 45-55 degrees C, respectively). They were mixotrophs; Fe(II), S0, and sulfide minerals along with organic compounds were used as energy sources and electron donors. However, the kinetic parameters of growth and substrate oxidation varied from strain to strain. Genetic variety of the strains from diverse ecosystems and environments is possibly the result of the different rates of microevolution processes.     

Assignment of<Emphasis Type="Italic"> Pseudomonas</Emphasis> sp. strain E-3 to<Emphasis Type="Italic"> Pseudomonas psychrophila</Emphasis> sp. nov., a new facultatively psychrophilic bacterium

A facultatively psychrophilic bacterium, previously described as Pseudomonas sp. strain E-3, has been reassigned by phenotypic characterization, chemotaxonomic analysis, DNA-DNA hybridization, and 16S rRNA gene phylogenetic analysis. The organism was a gram-negative, aerobic. straight rod with polar flagella. It was catalase positive and oxidase positive, able to grow at -1 degree C but not at 40 degree C, and produced acid from D-glucose under aerobic conditions. The major isoprenoid quinone was ubiquinone-9, and the DNA G + C content was 57.2 mol%. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the bacterium is a member of the genus Pseudomonas and was closest to Pseudomonas fragi. Determination of the DNA-DNA relatedness between strain E-3 and P. fragi revealed too low a level of homology (47.9%-51.3%) to identify them as the same species. On the basis of phenotypic characteristics, phylogenetic analysis, and DNA-DNA relatedness data, it is concluded that strain E-3 represents an individual species. Accordingly, the name Pseudomonas psychrophila is proposed. The type strain is E-3T (= JCM 10889).     

Phenotypic characterization ofPhotobacterium logei (sp. nov.), a species related toP. fischeri

Ten luminous marine bacteria having the diagnostic traits ofPhotobacterium fischeri but differing from this species in their ability to grow at 4°C have been subjected to a more extensive phenotypic characterization. The results indicated a high phenotypic similarity toP. fischeri; the major additional diagnostic trait was their inability to grow at 30°C. In these properties the isolates resembled a previously characterized nonluminous strain, ATCC 15382, which had a DNA homology of about 40% toP. fischeri. Immunological comparisons of the glutamine synthetases and Fe-superoxide dismutases of these strains as well as additional properties that are discussed indicated that the ten luminous isolates and strain ATCC 15382 constituted a new species, which we have designatedPhotobacterium logei sp. nov. (type strain 584, ATCC 29985).     

Divergence in the level of DNA hybridization and formation of sibling species in the lactic acid bacteria Streptococcus thermophilus

Previously, five distinct groups with 80-90% intragroup DNA homology values were revealed among 19 lactic acid-producing bacterial strains. The study of 39 new strains of thermophilic streptococci in the present work allowed us to reveal the sixth DNA homology group. The nine strains of this group are similar, at 55-70% DNA homology levels, to the type strain S. thermophilus ATCC 19258. Group VI showed a low level of DNA-DNA reassociation (20-30%) with the DNA homology groups I, II, III, and V. The intergroup DNA-DNA reassociation values determined from DNA renaturation rates varied from 20 to 50%. These data were interpreted as indicative of the existence of at least four sibling species among the thermophilic streptococci studied.     

Helicobacter nemestrinae sp. nov., a spiral bacterium found in the stomach of a pigtailed macaque (Macaca nemestrina)

A new microaerophilic, spirally curved, rod-shaped bacterium was isolated from the gastric mucosa of a pigtailed macaque (Macaca nemestrina). The gram-negative cells of this bacterium are oxidase, catalase, and urease positive and strongly resemble Helicobacter pylori (Campylobacter pylori) cells. Like H. pylori, this organism does not metabolize glucose, does not reduce nitrate or produce indole, does not produce H2S from triple sugar iron agar, does not hydrolyze hippurate or esculin, and does not grow in the presence of 1% glycine, 1.5% salt, or 1% bile. Also like H. pylori, it is resistant to nalidixic acid and susceptible to cephalothin. However, unlike H. pylori, the colorless colonies are flat and have irregular edges. This organism has a unique cellular fatty acid composition, forming a new gas-liquid chromatography group, group K, and a distinctive DNA content (24 mol% guanine plus cytosine). It exhibits less than 10% DNA-DNA homology (as determined by the nylon filter blot method at 65 degrees C) with other members of the genus Helicobacter. Although the levels of DNA relatedness between previously described Helicobacter species and the new organism are low (less than 10%) and the difference in guanine-plus-cytosine content is large (24 versus 36 to 41 mol%), the genus Helicobacter is the only genus in which it is logical to include the organism at this time. We propose that our single strain represents a new species, Helicobacter nemestrinae, and we designate strain T81213-NTB (= ATCC 49396) as the type strain.     

Effects of exogenous factors on the activity of enzymes involved in carbon metabolism in thermoacidophilic bacteria of the genus Sulfobacillus

Aerobic thermoacidophilic chemolithotrophic bacteria Sulfobacillus thermosulfidooxidans 1269T and Sulfobacillus thermosulfidooxidans subsp. asporogenes 41 were shown to be resistant to stress factors, including high concentrations of Zn2+ (0.8 M) and H+ (pH 1.2) that exceeded the optimum values. The growth and biomass gain rates decreased, but bacteria retained their functions. The activity of nearly all enzymes involved in carbon metabolism decreased. Glucose was primarily metabolized via the Entner--Doudoroff pathway. The activity tricarboxylic acid cycle enzymes decreased compared to that in cells grown under normal conditions. After saturation of the growth medium with 5 vol % CO2, sulfobacteria utilized glucose by the Embden-Meyerhof and pentose phosphate pathways under mixotrophic conditions.     

一株茶碱降解菌的分离和鉴定

从制药废水生物处理系统的活性污泥中经富集分离到一株能以茶碱作为唯一碳、氮源生长的茶碱降解菌Tcn3,该菌株可以利用茶碱的最高浓度为3 000 mg/L。当茶碱浓度为1000 mg/L时被彻底降解的时间仅需48 h。Tcn3菌株降解茶碱的最适pH为80。K＋是该菌株降解茶碱的必需元素。采用16S rDNA序列分析法及传统的生理生化特征鉴定法对该菌株进行鉴定,结果表明,Tcn3的16S rDNA的核苷酸序列与善变副球菌(Paracoccus versutus) ATCC 25364的同源性为997%,在细菌系统发育分类学上属于变形菌α亚类,Rhodobacter组：副球菌属,善变副球菌。     

Species composition of the association of acidophilic chemolithotrophic microorganisms participating in the oxidation of gold-arsenic ore concentrate

The species composition of the microbial association involved in industrial tank biooxidation of the concentrate of refractory pyrrhotite-containing pyrite-arsenopyrite gold-arsenic ore of the Olympiadinskoe deposit at 39°C was studied by cultural and molecular biological techniques. Pure microbial cultures were isolated, their physiological characteristics were investigated, and their taxonomic position was determined by 16S rRNA gene sequencing. The library of 16S rRNA gene clones obtained from the total DNA isolated from the biomass of the pulp of industrial reactors was analyzed. The diversity of microorganisms revealed by cultural techniques in the association of acidophilic chemolithotrophs (Acidithiobacillus ferrooxidans, Leptospirillum ferriphilum, Sulfobacillus thermosulfidooxidans, Ferroplasma acidiphilum, Alicyclobacillus tolerans, and Acidiphilium cryptum) was higher than the diversity of the 16S rDNA clone library (At. ferrooxidans, L. ferriphilum, and F. acidiphilum). The combination of microbiological and molecular biological techniques for the investigation of the biodiversity in natural and anthropogenic microbial communities promotes detection of new phylogenetic microbial groups in these communities.     

A novel Acidimicrobium species in continuous cultures of moderately thermophilic, mineral-sulfide-oxidizing acidophiles

A novel species of Acidimicrobium appeared to be the predominant ferrous iron oxidizer in a mixed culture that effected the continuous, efficient extraction of nickel from a mineral concentrate at 49 degrees C, but it was not isolated in pure culture. It outcompeted Acidimicrobium ferrooxidans, which was expected to have a major role in iron oxidation in reactors gassed with air, and was outnumbered at 49 degrees C only by the sulfur-oxidizing Acidithiobacillus caldus. Sulfobacillus species were expected to compete with Acidimicrobium species when culture aeration was enriched with carbon dioxide, but they were a minor component of the populations with and without this enrichment. Sulfobacillus thermosulfidooxidans replaced the Acidimicrobium species and Acidithiobacillus caldus when the temperature was increased to 55 degrees C.     

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).     

极端嗜酸热古菌S5菌株的重新分类研究

对已经鉴定的嗜酸热硫球菌 (Sulfosphaerellusthermoacidophilumgen.nov .sp .nov)S5菌株的进一步研究发现 ,它既能在好氧条件也能在厌氧条件下代谢元素硫进行化能自养生长 ,结合其 1 6SrRNA基因的分子系统学分析 ,S5菌株应归于Acidianus属。另外 ,S5菌株与Acidianus属中三个已知种基因组DNA的同源性分别仅有 44%、2 2 %和 2 3% ,DNA中G +Cmol%为 38,与已知种 31 0和 32 7有较大差异 ;而且 ,在代谢特性上S5菌株为专性化能无机营养型 ,与Acidianusbrierleyi有明显不同。因此S5菌株应是Acidianus属中一个新种 ,建议定名为 :腾冲嗜酸两面菌 (Acidianustengchongensessp .nov .)。     

Genotypic and phenotypic polymorphism of environmental strains of the moderately thermophilic bacterium <Emphasis Type="Italic">Sulfobacillus sibiricus</Emphasis>

Five cultures of moderately thermophilic spore-forming acidophilic chemolithotrophic bacteria were isolated from the zones of spontaneous heating of pyrrhotite-containing pyrite-arsenopyrite gold-arsenic sulfide ores in an operating open pit (strains B1, B2, B3, OFO, and SSO). Analysis of the chromosomal DNA structure revealed the differences between these cultures at the strain level (apart from B3 and SSO, which had identical restriction profiles). All the strains had a similar G+C DNA molar content (47.4–48.3%). The level of DNA reassociation was 85 to 95%. The similarity between the DNA of the type strain Sulfobacillus sibiricus N1 isolated from arsenopyrite ore concentrate and that of these strains (83–93%) indicates that they belong to the same species. The strains had similar values of pH and temperature optimal for growth on ferrous iron (1.6–2.0 and 45–55°C, respectively). They were mixotrophs; Fe(II), S^o, and sulfide minerals along with organic compounds were used as energy sources and electron donors. However, the kinetic parameters of growth and substrate oxidation varied from strain to strain. Genetic variety of the strains from diverse ecosystems and environments is possibly the result of the different rates of microevolution processes.     

Characterization and species recognition of Lactobacillus plantarum strains by restriction fragment length polymorphism (RFLP) of the 16S rRNA gene

Twenty-one strains, labelled Lactobacillus plantarum or Lact. plantarum -like, and isolated from different natural sources, were characterized by restriction fragment length polymorphism (RFLP) of the 16S rRNA gene using Hin dIII and Eco RI cleaved chromosomal DNA, together with Lact. plantarum ATCC 14917^T, Lact. pentosus ATCC 8041^T, Lact. plantarum ATCC 10776 and Lact. plantarum ATCC 8014. The fermentation patterns on API 50CH were recorded at 30°C and 37°C for all strains. The phenotypes were heterogeneous, and the ability to ferment 17 of the 49 carbohydrates varied. The fermentation of some carbohydrates, for example D-raffinose and D-arabitol, was temperature-dependent. Strains having identical API profiles were separated by the plasmid profile. All strains but one (affiliated to Lact. casei ) had identical 16S ribosomal DNA sequences ( Lact. plantarum/Lact. pentosus ). The RFLP study resulted in identical ribopatterns for 17 of the strains, including the type strain of Lact. plantarum (pattern A1). Four strains had related fragment patterns to that of Lact. plantarum sensu stricto; three of these strains had more than 60% DNA: DNA homology to the type strain of Lact. plantarum , and one had less than 50% DNA: DNA homology to Lact. plantarum ATCC 14917^T. Two strains had fragment patterns similar to the type strain of Lact. pentosus , and they had more than 80% DNA: DNA homology to Lact. pentosus ATCC 8041^T. One of the Lact. pentosus strains shared one band with the A1 pattern. The ribopatterns of Lact. plantarum were homogeneous (identical for 85% of the strains), irrespective of phenotype and source of isolation. RFLP of the 16S rRNA genes using Eco RI and Hin dIII might be used for species recognition of Lact. plantarum , but seems less suitable for strain typing.