Phylogenetic analysis of a microbial community involved in anaerobic oxidation of ammonium nitrogen

The phylogenetic diversity of a microbial community involved in anaerobic oxidation of ammonium nitrogen in the DEAMOX process was studied. Analysis of clone libraries containing 16S rRNA gene inserts of Bacteria, (including Planctomycetes) and Archaea revealed the presence of nucleotide sequences of the microorganisms involved in the main reactions of the carbon, nitrogen, and sulfur cycles, including nitrifying, denitrifying, and ANAMMOX bacteria. In the bacterial clone library, 16S rRNA gene sequences of representatives of the phyla Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Verrucomicrobia, Lentisphaerae, Spirochaetales, and Planctomycetes, as well as of some new groups, were detected. In the archaeal clone library, nucleotide sequences of methanogens belonging to the orders Methanomicrobiales, Methanobacteriales, and Methanosarcinales were found. It is possible that both ANAMMOX bacteria and bacteria of the genus Nitrosomonas are involved in anaerobic ammonium oxidation in the DEAMOX reactor. Many sequences were similar to those from the clone libraries obtained previously from the ANAMMOX community of marine sediments. It is also probable that the DEAMOX reactions occur in natural ecosystems (in marine and freshwater sediments and the oceanic water column), thereby providing for the coupling of the nitrogen and sulfur cycles.     

Identification of the dominant bacterium of two-stage biooxidation of gold-arsenic concentrate

In the process of biooxidation at 39°C in a continuous mode of the gold-arsenic concentrate from the Olympiadinskoe deposit, which was pretreated by chemical leaching with ferric ions, by a microbial association from the BIO department reactors of the Polyus gold mining company, a bacterial culture designated as strain HT-4 was isolated. The bacterium was a spore-forming rod 0.5–0.6 × 1.4–2.0 μm with a flagellum. The optimal temperature for growth and Fe²⁺ oxidation was 55°C. The strain grew in the pH range from 1.21 to 2.10 with the optimum at pH 1.6. The organism was incapable of lithotrophic and organotrophic growth. It grew mixotrophically by Fe²⁺ oxidation in the presence of 0.02% yeast extract. The DNA G+C base content was 48.6 mol %. Based on comparative phylogenetic analysis of 1472-bp nucleotide sequences of 16S rRNA genes, strain HT-4 was classified as Sulfobacillus thermosulfidooxidans. Analysis by pulse-field gel electrophoresis revealed a unique profile of the NotI fragments of the chromosomal DNA. These results demonstrate the strain and species diversity of sulfobacilli in microbial associations involved in biooxidation of concentrates in different technological conditions. The strain “S. olympiadicus S-5” dominated in the process of biooxidation of original concentrate not treated with ferric iron, while S. thermosulfidooxidans HT-4 was predominant in biooxidation of the chemically leached concentrate.     

<Emphasis Type="Italic">Natronoflexus pectinivorans</Emphasis> gen. nov. sp. nov., an obligately anaerobic and alkaliphilic fermentative member of <Emphasis Type="Italic">Bacteroidetes</Emphasis> from soda lakes

Anaerobic enrichment with pectin at pH 10 and moderate salinity inoculated with sediments from soda lakes of the Kulunda Steppe (Altai, Russia) resulted in the isolation of a novel member of the Bacteroidetes, strain AP1^T. The cells are long, flexible, Gram-negative rods forming pink carotenoids. The isolate is an obligate anaerobe, fermenting various carbohydrates to acetate and succinate. It can hydrolyze and utilize pectin, xylan, starch, laminarin and pullulan as growth substrates. Growth is possible in a pH range from 8 to 10.5, with an optimum at pH 9.5, and at a salinity range from 0.1 to 2 M Na⁺. Phylogenetic analysis based on 16S rRNA sequences placed the isolate into the phylum Bacteroidetes as a separate lineage within the family Marinilabilaceae. On the basis of distinct phenotype and phylogeny, the soda lake isolate AP1^T is proposed to be assigned in a new genus and species Natronoflexus pectinivorans (=DSM24179^T = UNIQEM U807^T).     

Description of “<Emphasis Type="Italic">Desulfotomaculum nigrificans</Emphasis> subsp. <Emphasis Type="Italic">salinus</Emphasis>” as a New Species, <Emphasis Type="Italic">Desulfotomaculum salinum</Emphasis> sp. nov.

This study focused on the physiological, chemotaxonomic, and genotypic characteristics of two thermophilic spore-forming sulfate-reducing bacterial strains, 435^T and 781, of which the former has previously been assigned to the subspecies “Desulfotomaculum nigrificans subsp. salinus”. Both strains reduced sulfate with the resulting production of H₂S on media supplemented with H₂ + CO₂, formate, lactate, pyruvate, malate, fumarate, succinate, methanol, ethanol, propanol, butanol, butyrate, valerate, or palmitate. Lactate oxidation resulted in acetate accumulation; butyrate was oxidized completely, with acetate as an intermediate product. Growth on acetate was slow and weak. Sulfate, sulfite, thiosulfate, and elemental sulfur, but not nitrate, served as electron acceptors for growth with lactate. The bacteria performed dismutation of thiosulfate to sulfate and hydrogen sulfide. In the absence of sulfate, pyruvate but not lactate was fermented. Cytochromes of b and c types were present. The temperature and pH optima for both strains were 60–6°C and pH 7.0. Bacteria grew at 0 to 4.5–6.0% NaCl in the medium, with the optimum being at 0.5–1.0%. Phylogenetic analysis based on a comparison of incomplete 16S rRNA sequences revealed that both strains belonged to the C cluster of the genus Desulfotomaculum, exhibiting 95.5–98.3% homology with the previously described species. The level of DNA–DNA hybridization of strains 435^T and 781 with each other was 97%, while that with closely related species D. kuznetsovii 17^T was 51–52%. Based on the phenotypic and genotypic properties of strains 435^T and 781, it is suggested that they be assigned to a new species: Desulfotomaculum salinum sp. nov., comb. nov. (type strain 435^T = VKM B 1492^T).     

Molecular phylogeny and taxonomy of colorless, filamentous sulfur bacteria of the genus Thiothrix

Comprehensive investigation combining molecular genetic techniques and comparative studies of morphological and physiological properties made it possible to resolve the disputed issue of the taxonomic status of the groups ??T. nivea?? and ??Eikelboom type 021N?? of the genus Thiothrix. The phylogenetic trees constructed on the basis of 16S rRNA and gyrB gene sequences demonstrated that members of the genus Thiothrix formed a cluster within the order Thiotrichales. According to the ??ribosomal?? tree, the cluster of the genus Thiothrix was divided into two main groups, I and II, corresponding to the groups ??T. nivea?? and ??Eikelboom type 021N??. The levels of similarity between the 16S rRNA gene sequences of Thiothrix species reached 88.9?C100%. On the contrary, in the ??gyrase?? tree, these species were not divided into ??T. nivea?? and ??Eikelboom type 021N?? groups. The levels of similarity between the amino acid sequences of the gyrB gene fragments of Thiothrix species varied from 74.5 to 99.2%. Importantly, members of the groups ??T. nivea?? and ??Eikelboom type 021N?? formed very similar 16S rRNA secondary structures in the variable region V3, where a 30-nucleotide deletion characteristic of all Thiothrix species was detected. Phenotypic analysis of the studied bacteria revealed some morphological and physiological properties shared by the groups ??T. nivea?? and ??Eikelboom type 021N??. The data obtained indicate that members of the groups ??T. nivea?? and ??Eikelboom type 021N?? are phenotypically and genetically heterogeneous species within the single monophyletic genus Thiothrix..     

Copy Number of Ribosomal Operons in Prokaryotes and Its Effect on Phylogenetic Analyses

Different aspects of the presence of multiple copies of ribosomal operons in prokaryotic genomes are reviewed. The structure of prokaryotic ribosomal operons is briefly described. The available data are summarized regarding the copy number of ribosomal genes in various prokaryotic genomes, the degree of polymorphism of their individual copies, and physiological and evolutional aspects of the presence of the multiple copies of ribosomal genes. The review also considers the influence of the presence of multiple copies of ribosomal genes on the results of identification of prokaryotic isolates and of the studies of prokaryotic diversity in environmental samples based on phylogenetic analysis of 16S rRNA gene sequences.     

The Phylogenetic Diversity of Aerobic Organotrophic Bacteria from the Dagang High-Temperature Oil Field

The distribution and species diversity of aerobic organotrophic bacteria in the Dagang high-temperature oil field (China), which is exploited with water-flooding, have been studied. Twenty-two strains of the most characteristic thermophilic and mesophilic aerobic organotrophic bacteria have been isolated from the oil stratum. It has been found that, in a laboratory, the mesophilic and thermophilic isolates grow in the temperature, pH, and salinity ranges characteristic of the injection well near-bottom zones or of the oil stratum, respectively, and assimilate a wide range of hydrocarbons, fatty acids, lower alcohols, and crude oil, thus exhibiting adaptation to the environment. Using comparative phylogenetic 16S rRNA analysis, the taxonomic affiliation of the isolates has been established. The aerobic microbial community includes gram-positive bacteria with a high and low G+C content of DNA, and γ and β subclasses of Proteobacteria. The thermophilic bacteria belong to the genera Geobacillus and Thermoactinomyces, and the mesophilic strains belong to the genera Bacillus, Micrococcus, Cellulomonas, Pseudomonas, and Acinetobacter. The microbial community of the oil stratum is dominated by known species of the genus Geobacillus (G. subterraneus, G. stearothermophilus, and G. thermoglucosidasius) and a novel species “Geobacillus jurassicus.” A number of novel thermophilic oil-oxidizing bacilli have been isolated.__________Translated from Mikrobiologiya, Vol. 74, No. 3, 2005, pp. 401–409.Original Russian Text Copyright © 2005 by Nazina, Sokolova, Shestakova, Grigoryan, Mikhailova, Babich, Lysenko, Tourova, Poltaraus, Qingxian Feng, Fangtian Ni, Belyaev.     

Phylogenetic characterization of the purple sulfur bacterium Thiocapsa sp. BBS by analysis of the 16S rRNA, cbbL, and nifH genes and its description as Thiocapsa bogorovii sp. nov., a new species

Strain BBS, the purple sulfur bacterium assigned initially to the species Thiocapsa roseopersicina, is the best studied representative of this species. However, no molecular phylogenetic analysis has been performed to confirm its systematic position. Based on the results of analysis of the sequences of 16S rRNA, cbbL, and nifH genes, DNA-DNA hybridization with the T. roseopersicina type strain, and comparative analysis of the phenotypic characteristics of various species belonging to the genus Thiocapsa, we suggest that strain BBS should be assigned to a new species of the genus Thiocapsa, Thiocapsa bogorovii sp. nov. Original Russian Text ? T.P. Tourova, O.I. Keppen, O.L. Kovaleva, N.V. Slobodova, I.A. Berg, R.N. Ivanovsky, 2009, published in Mikrobiologiya, 2009, Vol. 78, No. 3, pp. 381–392.     

Phylogeny of anoxygenic filamentous phototrophic bacteria of the family Oscillochloridaceae as inferred from comparative analyses of the rrs, cbbL, and nifH genes

Phylogeny of anoxygenic filamentous phototrophic bacteria (AFPB) of the family Oscillochloridaceae (Oscillochloris trichoides DG6^T and the recently isolated strains Oscillochloris sp. R and C6) was studied based on comparative analyses of the genes coding for 16S rRNA (rrs), ribulose-1,5-bisphosphate carboxylase/oxygenase (cbbL), and nitrogenase (nifH). The sequences of the genes studied proved to be identical in the three strains, which is in agreement with data obtained earlier that showed a lack of differentiating phenotypic distinctions between these strains; therefore, it is proposed that the new strains should be identified as representatives of the species O. trichoides. Using an earlier designed system of oligonucleotide primers and a specially designed additional primer, fragments of the cbbL genes of the “red-like” form I RuBisCO were amplified and sequenced for all of the O. trichoides strains. Analysis of the cbbL genes suggested a separate position of the bacteria studied in the phylogenetic tree, where O. trichoides strains formed an independent branch, which, apart from this species, also included the only studied species of gram-positive facultatively chemoautotrophic bacteria, Sulfobacillus acidophilus. In the phylogenetic tree inferred from the analysis of nifH genes, the bacteria under study also formed a new separate branch, deviating near the root, which indicated a lack of relatedness between them and other phototrophic bacteria. The data obtained support the conclusion that AFPB has an ancient origin and their allocation as one of the main evolutionary lineages of eubacteria, which was made based on the analysis of ribosomal genes.