Microbial diversity in formation water and enrichment cultures from the Gangxi bed of the Dagang terrigenous oilfield (PRC)

Microbial diversity and biogeochemical processes of the Gangxi bed with low-mineral water and a temperature gradient from 35 to 54°C were studied. The 16S rRNA gene clone libraries (over 800 clones) were obtained from microbial DNA isolated from formation water and from the primary enrichment cultures for fermenting, sulfate-reducing, methanogenic, and aerobic organotrophic prokaryotes. While both sulfate reduction and methanogenesis were registered in formation water by radioisotope techniques, the genes of sulfate-reducing prokaryotes were not revealed in the 16S rRNA gene clone library from formation water. The 16S rRNA genes of Methanobacterium congolense and Methanococcus vannielii predominated among archaeal sequences retrieved from formation water, while the genes of Methanothermobacter thermoautotrophicus, Methanomethylovorans thermophila, and Methanoculleus sp. predominated in the combined library from enrichment cultures. In the library of Bacteria 16S rRNA genes from formation water, the genes of thermophilic fermentative bacteria of the family Thermoanaerobacteriaceae predominated; the remaining sequences belonged to mesophiles (genera Brevundimonas, Sphingomonas, Oxalicibacterium, and Stenotrophomonas), the phylum Chloroflexi, and unidentified bacteria. The combined library from enrichment cultures, contained, apart from the sequences of the family Thermoanaerobacteriaceae, the genes of fermentative bacteria (genera Anaerobaculum, Coprothermobacter, Thermanaerovibrio, Soehngenia, Bacteroides, and Aminobacterium and the order Thermotogales), of aerobic hydrocarbon-oxidizing bacteria (genera Pannonibacter and Pseudomonas), and of sulfate reducers (genera Desulfomicrobium, Thermodesulfovibrio, and Desulfotomaculum). High coverage was shown for bacterial (97.6%) and archaeal (100%) clone libraries, indicating that a significant portion of the microbial diversity in the studied communities was revealed.     

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).     

Comparative analysis of nucleotide sequences of chromosomal DNA isolated from nuclear envelopes and cores of rosette-like structures of murine interphase chromosomes]

Six DNA fragments of interphase chromosomes isolated from nuclear envelopes of murine hepatocytes were cloned and sequenced. Analysis of their structural-functional organization suggests that these fragments are highly specified protein-nonencoding fractions of a eukaryotic genome. In the evolutionary process, they appear already in archaebacteria and may be "ancestral" for DNA sequences involved in structuring chromosomal domains (rosette-like structures) of tissue-specific genes. In their composition, these fragments have nucleotide sequences homologous to the repeats of the SINE and LINE families and to the satellite DNA of murine centromeres.     

Diminished transmission of drug resistant HIV-1 variants with reduced replication capacity in a human transmission model

Background

Different patterns of drug resistance are observed in treated and therapy naïve HIV-1 infected populations. Especially the NRTI-related M184I/V variants, which are among the most frequently encountered mutations in treated patients, are underrepresented in the antiretroviral naïve population. M184I/V mutations are known to have a profound effect on viral replication and tend to revert over time in the new host. However it is debated whether a diminished transmission efficacy of HIV variants with a reduced replication capacity can also contribute to the observed discrepancy in genotypic patterns.As dendritic cells (DCs) play a pivotal role in HIV-1 transmission, we used a model containing primary human Langerhans cells (LCs) and DCs to compare the transmission efficacy M184 variants (HIV-M184V/I/T) to HIV wild type (HIV-WT). As control, we used HIV harboring the NNRTI mutation K103N (HIV-K103N) which has a minor effect on replication and is found at a similar prevalence in treated and untreated individuals.

Results

In comparison to HIV-WT, the HIV-M184 variants were less efficiently transmitted to CCR5⁺ Jurkat T cells by both LCs and DCs. The transmission rate of HIV-K103N was slightly reduced to HIV-WT in LCs and even higher than HIV-WT in DCs. Replication experiments in CCR5⁺ Jurkat T cells revealed no apparent differences in replication capacity between the mutant viruses and HIV-WT. However, viral replication in LCs and DCs was in concordance with the transmission results; replication by the HIV-M184 variants was lower than replication by HIV-WT, and the level of replication of HIV-K103N was intermediate for LCs and higher than HIV-WT for DCs.

Conclusions

Our data demonstrate that drug resistant M184-variants display a reduced replication capacity in LCs and DCs which directly impairs their transmission efficacy. As such, diminished transmission efficacy may contribute to the lower prevalence of drug resistant variants in therapy naive individuals.

     

Molecular-genetic characteristics of a medieval population from the northern Russian territory

Forty-seven individual mitochondrial DNA (mtDNA) samples isolated from bones samples found in the Nefedyevo, Minino, and Shuygino gravesites have been analyzed to perform molecular genetic study of the medieval (12th to 13th centuries AD) human population from the vicinity of Lake Beloe (Vologda oblast, northern Russia). The mitotypic structure of the population has been determined on the basis of sequencing the mtDNA hypervariable-region segment I (HVSI; positions 15,989-16,410). Three mitotypes characterizing the population studied have been found in the 47 representatives of the medieval population: mitotype 1 corresponding to the Cambridge reference sequence, mitotype 2 (transition G-A at position 16,129), and mitotype 3 (transitions G-A and C-T at loci 16,129 and 16,223, respectively). Mitotypes 1, 2, and 3 have been found in 91.6, 4.2, and 4.2% of the individual samples studied. This high frequency of the Cambridge mitotype is considerably higher than its mean frequencies in European populations. The frequencies of other mitotypes found correspond to their mean European values. The absence of a Mongoloid component has been demonstrated for the female lineage of the population. Comparison of the molecular genetic characteristics of contemporary European ethnic groups and the population studied has demonstrated that it may be assigned to the European population group. The high homogeneity of the mitochondrial pool suggests a strong founder effect, which agrees with the view of archeologists and anthropologists that the first migrant settlers were very few.     

Description of Desulfotomaculum nigrificans subsp. salinus as a new species, Desulfotomaculum salinum sp. nov

This study focused on the physiological, chemotaxonomic, and genotypic characteristics of two thermophilic spore-forming sulfate-reducing bacterial strains, 435T 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 60-65 degrees 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 435T and 781 with each other was 97%, while that with closely related species D. kuznetsovii 17T was 51-52%. Based on the phenotypic and genotypic properties of strains 435T and 781, it is suggested that they be assigned to a new species: Desulfotomaculum salinum sp. nov., comb. nov. (type strain 435T = VKM B 1492T).