Lignite coal burning seam in the remote Altai Mountains harbors a hydrogen-driven thermophilic microbial community

Thermal ecosystems associated with underground coal combustion sites are rare and less studied than geothermal features. Here we analysed microbial communities of near-surface ground layer and bituminous substance in an open quarry heated by subsurface coal fire by metagenomic DNA sequencing. Taxonomic classification revealed dominance of only a few groups of Firmicutes. Near-complete genomes of three most abundant species, ‘Candidatus Carbobacillus altaicus’ AL32, Brockia lithotrophica AL31, and Hydrogenibacillus schlegelii AL33, were assembled. According to the genomic data, Ca. Carbobacillus altaicus AL32 is an aerobic heterotroph, while B. lithotrophica AL31 is a chemolithotrophic anaerobe assimilating CO2 via the Calvin cycle. H. schlegelii AL33 is an aerobe capable of both growth on organic compounds and carrying out CO2 fixation via the Calvin cycle. Phylogenetic analysis of the large subunit of RuBisCO of B. lithotrophica AL31 and H. schlegelii AL33 showed that it belongs to the type 1-E. All three Firmicutes species can gain energy from aerobic or anaerobic oxidation of molecular hydrogen, produced as a result of underground coal combustion along with other coal gases. We propose that thermophilic Firmicutes, whose spores can spread from their original geothermal habitats over long distances, are the first colonizers of this recently formed thermal ecosystem

Genome sequence of the copper resistant and acid-tolerant Desulfosporosinus sp. BG isolated from the tailings of a molybdenum-tungsten mine in the Transbaikal area

Here, we report on the draft genome of a copper-resistant and acidophilic Desulfosporosinus sp. BG, isolated from the tailings of a molybdenum-tungsten mine in Transbaikal area. The draft genome has a size of 4.52 Mb and encodes transporters of heavy metals. The phylogenetic analysis based on concatenated ribosomal proteins revealed that strain BG clusters together with the other acidophilic copper-resistant strains Desulfosporosinus sp. OT and Desulfosporosinus sp. I2. The K+-ATPase, Na+/H+ antiporter and amino acid decarboxylases may participate in enabling growth at low pH. The draft genome sequence and annotation have been deposited at GenBank under the accession number NZ_MASS00000000

Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1

Ravin NV, Eldarov MA, Kadnikov VV, et al. Genome sequence and analysis of methylotrophic yeast Hansenula polymorpha DL1. BMC Genomics. 2013;14(1): 837.Background: Hansenula polymorpha DL1 is a methylotrophic yeast, widely used in fundamental studies of methanol metabolism, peroxisome biogenesis and function, and also as a microbial cell factory for production of recombinant proteins and metabolic engineering towards the goal of high temperature ethanol production. Results: We have sequenced the 9 Mbp H. polymorpha DL1 genome and performed whole genome analysis for the H. polymorpha transcriptome obtained from both methanol- and glucose-grown cells. RNA-seq analysis revealed the complex and dynamic character of the H. polymorpha transcriptome under the two studied conditions, identified abundant and highly unregulated expression of 40% of the genome in methanol grown cells, and revealed alternative splicing events. We have identified subtelomerically biased protein families in H. polymorpha, clusters of LTR elements at G + C-poor chromosomal loci in the middle of each of the seven H. polymorpha chromosomes, and established the evolutionary position of H. polymorpha DL1 within a separate yeast clade together with the methylotrophic yeast Pichia pastoris and the non-methylotrophic yeast Dekkera bruxellensis. Intergenome comparisons uncovered extensive gene order reshuffling between the three yeast genomes. Phylogenetic analyses enabled us to reveal patterns of evolution of methylotrophy in yeasts and filamentous fungi. Conclusions: Our results open new opportunities for in-depth understanding of many aspects of H. polymorpha life cycle, physiology and metabolism as well as genome evolution in methylotrophic yeasts and may lead to novel improvements toward the application of H. polymorpha DL-1 as a microbial cell factory

Immunological efficacy and tolerability of vaccination in patients with noncommunicable diseases

Aim. To study the efficacy and tolerability of Sputnik V vaccination in patients with noncommunicable diseases (NCDs) compared with healthy individuals.Material and methods. The retrospective analysis included data from 800 men and women aged 18 to 90 who were vaccinated from February to May 2021 at the National Medical Research Center for Therapy and Preventive Medicine. Sputnik V (Gam-COVID-Vac, Russia), consisting of two doses, was used as a vaccine. The mean age of the patients was 50,46±13,16 years. Patients were questioned in two stages: before vaccination and after the first dose of vaccination. The following clinical and paraclinical investigations were carried out: saturation assessment, measurement of temperature, blood pressure and heart rate at rest, pharynx examination, auscultation of the heart and respiratory organs. The blood concentration of antibodies (IgM and IgG) was determined after 21 days and 42 days. For analysis, patients were divided into three groups. The first group included healthy individuals (n=238, 29,8%), the second group — patients with one NCD (n=385, 48,1%), and the third group — patients with two or more NCDs (n=177, 22,1%).Results. The sex composition was comparable in all three groups, while the mean age differed. In the first group, the mean age was 43,93±10,80 years, while in the second and third groups — 50,51±12,55 and 59,12±12,37 years, respectively (p<0,001). Statistical analysis was performed with adjustment for age and sex. The median blood concentration of immunoglobulin G of vaccinated individuals of the cohort after 21 days was within 4,60 [2,00; 8,40]. A comparative analysis of the groups did not reveal significant differences. After 42 days, the median concentration of immunoglobulin G increased by 4 times, which is significant (p<0,001) and amounted to 16,20 [15,80; 16,40]. In the group of healthy individuals, the concentration of immunoglobulin G was significantly higher compared to groups of individuals with one, as well as two or more NCDs. Forty-two days after vaccination, the concentration of immunoglobulin M both in the cohort and in individual groups did not change significantly compared to the level after 21 days. In addition, 47%, 38% and 40% of participants from the first, second and third groups, respectively, reported some symptoms. A temperature increase on average was detected in 13% of vaccinated individuals. The largest number of persons with fever was registered in the group of healthy individuals — 19%, in the group of patients with one NCD — 14%, and in the group with two or more diseases, the temperature increase was the lowest and amounted to 3% (p<0,001). After the first dose, 18,6% of patients reported taking additional drugs as follows: first group — 23,9%, second group — 15,1%, third group — 19,2%. These are mainly analgesic, non-steroidal anti-inflammatory and antihistamine drugs.Conclusion. Vaccination with Sputnik V increases the immunoglobulin G level in the blood after 42 days by four times compared to after 21 days. This pattern is observed both in the group of healthy individuals and in patients with one, two or more chronic NCDs. Tolerability of vaccination in all groups was comparable and did not lead to visits to healthcare facilities

Specific features of telomerase RNA from Hansenula polymorpha.

Telomerase, a ribonucleoprotein, is responsible for the maintenance of eukaryotic genome integrity by replicating the ends of chromosomes. The core enzyme comprises the conserved protein TERT and an RNA subunit (TER) that, in contrast, displays large variations in size and structure. Here, we report the identification of the telomerase RNA from thermotolerant yeast Hansenula polymorpha (HpTER) and describe its structural features. We show further that the H. polymorpha telomerase reverse transcribes the template beyond the predicted boundary and adds a nontelomeric dT in vitro. Sequencing of the chromosomal ends revealed that this nucleotide is specifically present as a terminal nucleotide at the 3' end of telomeres. Mutational analysis of HpTER confirmed that the incorporation of dT functions to limit telomere length in this species

Microbial and Geochemical Evidence of Permafrost Formation at Mamontova Gora and Syrdakh, Central Yakutia

Biotracers marking the geologic history and permafrost evolution in Central Yakutia, including Yedoma Ice Complex (IC) deposits, were identified in a multiproxy analysis of water chemistry, isotopic signatures, and microbial datasets. The key study sections were the Mamontova Gora and Syrdakh exposures, well covered in the literature. In the Mamontova Gora section, two distinct IC strata with massive ice wedges were described and sampled, the upper and lower IC strata, while previously published studies focused only on the lower IC horizon. Our results suggest that these two IC horizons differ in water origin of wedge ice and in their cryogenic evolution, evidenced by the differences in their chemistry, water isotopic signatures and the microbial community compositions. Microbial community similarity between ground ice and host deposits is shown to be a proxy for syngenetic deposition and freezing. High community similarity indicates syngenetic formation of ice wedges and host deposits of the lower IC horizon at the Mamontova Gora exposure. The upper IC horizon in this exposure has much lower similarity metrics between ice wedge and host sediments, and we suggest epigenetic ice wedge development in this stratum. We found a certain correspondence between the water origin and the degree of evaporative transformation in ice wedges and the microbial community composition, notably, the presence of Chloroflexia bacteria, represented by Gitt-GS-136 and KD4-96 classes. These bacteria are absent at the ice wedges of lower IC stratum at Mamontova Gora originating from snowmelt, but are abundant in the Syrdakh ice wedges, where the meltwater underwent evaporative isotopical fractionation. Minor evaporative transformation of water in the upper IC horizon of Mamontova Gora, whose ice wedges formed by meltwater that was additionally fractionated corresponds with moderate abundance of these classes in its bacterial community. © Copyright © 2021 Cherbunina, Karaevskaya, Vasil’chuk, Tananaev, Shmelev, Budantseva, Merkel, Rakitin, Mardanov, Brouchkov and Bulat.We thank Samsonova Vera, Karzhavin Vladimir, Pankov Alexander, Andreevskaya Maya and Alexander Osipov for their for their invaluable assistance in field work

The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams

Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm−3 day−1 at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance

A Set of 100 Chloroplast DNA Primer Pairs to Study Population Genetics and Phylogeny in Monocotyledons

Chloroplast DNA sequences are of great interest for population genetics and phylogenetic studies. However, only a small set of markers are commonly used. Most of them have been designed for amplification in a large range of Angiosperms and are located in the Large Single Copy (LSC). Here we developed a new set of 100 primer pairs optimized for amplification in Monocotyledons. Primer pairs amplify coding (exon) and non-coding regions (intron and intergenic spacer). They span the different chloroplast regions: 72 are located in the LSC, 13 in the Small Single Copy (SSC) and 15 in the Inverted Repeat region (IR). Amplification and sequencing were tested in 13 species of Monocotyledons: Dioscorea abyssinica, D. praehensilis, D. rotundata, D. dumetorum, D. bulbifera, Trichopus sempervirens (Dioscoreaceae), Phoenix canariensis, P. dactylifera, Astrocaryum scopatum, A. murumuru, Ceroxylon echinulatum (Arecaceae), Digitaria excilis and Pennisetum glaucum (Poaceae). The diversity found in Dioscorea, Digitaria and Pennisetum mainly corresponded to Single Nucleotide Polymorphism (SNP) while the diversity found in Arecaceae also comprises Variable Number Tandem Repeat (VNTR). We observed that the most variable loci (rps15-ycf1, rpl32-ccsA, ndhF-rpl32, ndhG-ndhI and ccsA) are located in the SSC. Through the analysis of the genetic structure of a wild-cultivated species complex in Dioscorea, we demonstrated that this new set of primers is of great interest for population genetics and we anticipate that it will also be useful for phylogeny and bar-coding studies