IntroductionSoil microbiome is a major source of physiologically active microorganisms, which can be potentially mobilized by adding various nutrients. To study this process, a long-term experiment was conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum.MethodsCombined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing were applied to study taxonomic, carbohydrate-active enzyme (CAZy), and polysaccharide utilization loci (PULs) composition of microbial communities at different stages of decomposition between substrates.ResultsIn straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified nine metagenome-assembled genomes (MAGs) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of substrate degradation. MAGs from Bacteroidota (Chitinophaga and Ohtaekwangia) and Actinomycetota (Streptomyces) were found in both composts, while those from Bacillota (Pristimantibacillus) were specific for leaf litter. The most frequently identified PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be underrepresented in clusters for complex substrates.DiscussionOur study explores microbial communities from natural ecosystems, such as soil and lignocellulosic waste, which are capable of decomposing lignocellulosic substrates. Using a comprehensive approach with chemical analyses of the substrates, amplicon, and full metagenome sequencing data, we have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

Amoebozoa is a poorly studied component of the soil microbiota.Data on amoebozoan diversity in different types of soil remains drastically limited.In this paper, we present results of our study of species composition and abundance of naked amoebae in tall-herbaceous rainforest ecosystem unique to Siberia -the Chernevaya taiga, located in the low mountains of Western Siberia (Russia).The soils of this ecosystem have high fertility, which causes plant gigantism.The abundance of naked amoebae in sampled soil, recovered by culture-based MPN method, varied from 194 to 265 g -1 and was higher than in usual oligotrophic taiga soil from the nearby sampling site (130 g -1 ).Fifteen amoebae species were recovered from the samples.Amoebae of the order Leptomyxida were highly abundant in all samples.Since we worked with soil transported for a long distance, we believe that the list of recovered species is a "minimal" one and could be expanded in the future.Relatively high abundance of naked amoebae suggests their significant influence on the microbiota of the soil of Chernevaya taiga.

A whole genome sequence of a new strain of the nitrogen-fixing bacterium Azospirillum doebereinerae, known for its diverse plant growth-promoting bacteria (PGPB), was obtained for the first time. The strain, designated Azospirillum doebereinerae AT, was isolated during a soil analysis in the Chernevaya taiga of Western Siberia, a unique and fertile forest ecosystem known for its diverse plant growth-promoting bacteria (PGPB). The A. doebereinerae genome under study is fully assembled into seven circular molecules, none of which are unequivocally plasmids, with a total length of 6.94 Mb and a G + C content of 68.66%. A detailed phylogenomic analysis confirmed its placement within the genus Azospirillum, specifically closely related to A. doebereinerae GSF71T. Functional annotation revealed genes involved in nitrogen metabolism, highlighting the potential of strain TA as a biofertilizer and plant growth-promoting agent. The findings contribute to our understanding of the genomic diversity and metabolic potential of the Azospirillum genus, and they are of interest for further study in the field of comparative bacterial genomics, given the strain’s multi-chromosomal genome structure.

For the targeted selection of microbial communities that provide cellulose degradation, soil samples containing cellulolytic microorganisms and specific plant residues as a substrate can be used. The details of this process have not been studied: in particular, whether the use of different soils determines the varying efficiency of communities; whether these established cellulolytic communities will have substrate specificity, and other factors. To answer these questions, four soil microbial communities with different cellulolytic activity (Podzol and the soil of Chernevaya taiga) and substrates (oat straw and hemp shives) with different levels of cellulose availability were used, followed by trained communities that were tested on botrooth substrates (in all possible combinations). Based on the analysis of the taxonomic structure of all communities and their efficiency across all substrates (decomposition level, carbon, and nitrogen content), it was shown that the most important taxa of all trained microbial cellulolytic communities are recruited from secondary soil taxa. The original soil does not affect the efficiency of cellulose decomposition: both soils produce equally active communities. Unexpectedly, the resulting communities trained on oats were more effective on hemp than the communities trained on hemp. In general, the usage of pre-trained microbial communities increases the efficiency of decomposition.

The objects of this study are microbial communities formed on two types of contrasting lignocellulosic biomass. To study them, a long-term experiment was set up and conducted on the decomposition of oat straw and leaf litter using soil as a microbial inoculum. Combined analyses of enzymatic activity and NGS data for 16S rRNA gene amplicon and full metagenome sequencing was applied to study taxonomic, CAZy (Carbohydrate-Active enzymes), and PULs (Polysaccharide Utilization Loci) composition of microbial communities at different stages of decomposition between substrates. using a combination of 16S rRNA gene amplicon and long-read nanopore sequencing. In straw degradation, the microbial community demonstrated higher amylase, protease, catalase, and cellulase activities, while peroxidase, invertase, and polyphenol oxidase were more active in leaf litter. Consistent with this, the metagenome analysis showed that the microbiome of straw compost was enriched in genes for metabolic pathways of simpler compounds. At the same time, there were more genes for aromatic compound degradation pathways in leaf litter compost. We identified 9 MAGs (Metagenome-assembled genomes) as the most promising prokaryotic decomposers due to their abnormally high quantity of PULs for their genome sizes, which were confirmed by 16S rRNA gene amplicon sequencing to constitute the bulk of the community at all stages of degradation. MAGs classified as Bacteroidota ( Chitinophaga , Ohtaekwangia ), and Actinomycetota ( Streptomyces ) were found in both substrates, while those from Bacillota ( Pristimantibacillus ) were specific for leaf litter. The most frequent PULs were specialized on xylans and pectins, but not cellulose, suggesting that PUL databases may be lacking PULs for complex substrates. Importance Our study explores the microbial communities from natural ecosystems, like soil and lignocellulosic waste, capable of decomposing lignocellulosic substrates. We used a comprehensive approach with chemical analyses of the substrates, amplicon and full-metagenome sequencing data. We have shown that such communities may be a source of identifying the highly effective decomposing species with novel PULs.

Chernevaya taiga of Western Siberia, Russia, is a unique ecosystem characterized by fertile soil, exceptionally large herbaceous plant sizes, and extraordinarily rapid rates of plant residue degradation. We expected that growing crops on soil collected from Chernevaya taiga, which has never been used for agricultural purposes before, would result in a distinct rhizospheric fungal community. This community could potentially yield novel, potent biostimulators and biocontrol fungi for modern agriculture. To check this idea, we used high-throughput ITS sequencing to examine the microbial communities in the rhizosphere of spring wheat and radish grown in greenhouse experiments on Chernevaya and control soils. Additionally, representative fungal strains were isolated and assessed for their ability to promote growth in wheat seedlings. The study revealed that the most abundant phyla in the rhizospheric fungal community were Mortierellomycota, primarily consisting of Mortierella species, and Ascomycota. Mucor and Umbelopsis comprised the majority of Mucoromycota in the control soils. Fusarium and Oidiodendron, two potentially plant-pathogenic fungi, were only found in the rhizosphere of crops grown in the control soil. Conversely, Chernevaya soil contained a diverse range of potential biocontrol fungi for plants. Tested novel fungal isolates showed a stimulating effect on the development of wheat seedlings and positively affected their rate of biomass accumulation. The results of the study demonstrate that the soil of Chernevaya taiga do indeed contain fungi with prominent potential to stimulate agricultural plants growth.

The Chernevaya taiga is a unique ecosystem formed under the influence of a complex of geogenic and bioclimatic factors located in the foothill border of the southeastern part of Western Siberia. The combination of local climatic conditions and the composition of parent material led to the formation of specific soil conditions on the territory of these habitats. The soils of the Chernevaya taiga have unique morphogenesis. They have a thick podzolized horizon and are fertile, unlike the typical soils of the oligotrophic pine forests of Siberia; however, the microstructure of these soils is poorly studied. The purpose of the research is to analyze the micromorphological organization and microstructure of three types of soils in Western Siberia (two typical soils from the Chernevaya taiga (Greyzemic Phaeozem (Albic) and Albic Stagnic Luvisol (Ochric)) and one from oligotrophic pine stand (Eutric Protoargic Arenosol)). It was found that the soils of the Chernevaya taiga differ greatly from the background (zonal) soils of the region on both the macro- and microlevels. In the Phaeozems and Luvisols of the Chernevaya taiga, there are actively formed organomineral aggregates and the quantity of porous media is more than 50%. At the bottom of the podzolized part of the soil profiles, we noted illuvial processes and a sharp change in the type of microstructure. The presence of pyrogenic materials (charcoal) and coprolitic (vermicular) materials in the humus-accumulative horizon indicates a high rate of material transformation and high biological activity and bioturbation in the soil. The skeleton part of the Chernevaya taiga soils is represented by a quartz–feldspar base with an admixture of sericite; augite; biotite; and a minimal admixture of tourmaline, zircon, and glauconite.

The analysis of metagenomic data obtained via high-throughput DNA sequencing is primarily carried out by a dedicated binning process involving clustering contigs, presumably belonging to the same species. Here, we present a protocol for improving the quality of binning using BinSPreader. We describe steps for typical metagenome assembly and binning workflow. We then detail binning refining, its variants, output, and possible caveats. This protocol optimizes the process of reconstructing more complete genomes of microorganisms that make up the metagenome.For complete details on the use and execution of this protocol, please refer to Tolstoganov et al.1

Annotating newly sequenced genomes and determining alternative isoforms from long-read RNA data are complex and incompletely solved problems. Here we present IsoQuant—a computational tool using intron graphs that accurately reconstructs transcripts both with and without reference genome annotation. For novel transcript discovery, IsoQuant reduces the false-positive rate fivefold and 2.5-fold for Oxford Nanopore reference-based or reference-free mode, respectively. IsoQuant also improves performance for Pacific Biosciences data.

Pusa sibirica, the Baikal seal, is the only extant, exclusively freshwater, pinniped species. The pending issue is, how and when they reached their current habitat—the rift lake Baikal, more than three thousand kilometers away from the Arctic Ocean. To explore the demographic history and genetic diversity of this species, we generated a de novo chromosome-length assembly, and compared it with three closely related marine pinniped species. Multiple whole genome alignment of the four species compared with their karyotypes showed high conservation of chromosomal features, except for three large inversions on chromosome VI. We found the mean heterozygosity of the studied Baikal seal individuals was relatively low (0.61 SNPs/kbp), but comparable to other analyzed pinniped samples. Demographic reconstruction of seals revealed differing trajectories, yet remarkable variations in Ne occurred during approximately the same time periods. The Baikal seal showed a significantly more severe decline relative to other species. This could be due to the difference in environmental conditions encountered by the earlier populations of Baikal seals, as ice sheets changed during glacial–interglacial cycles. We connect this period to the time of migration to Lake Baikal, which occurred ~3–0.3 Mya, after which the population stabilized, indicating balanced habitat conditions.

EDITORIAL article Front. Microbiol., 16 December 2022Sec. Evolutionary and Genomic Microbiology Volume 13 - 2022 | https://doi.org/10.3389/fmicb.2022.1098065

Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored whether agricultural plants can recruit specific microorganisms from within virgin Chernevaya Umbrisol and thus increase their productivity. Radish and wheat plants were grown on the Umbrisol (T1) and control Retisol of Scotch pine forest stand (T3) soils in the phytotron, and then a bacterial community analysis of the rhizosphere was performed using high-throughput sequencing of the 16S rRNA genes. In laboratory experiments, the plant physiological parameters were significantly higher when growing on the Umbrisol as compared to the Retisol. Bacterial diversity in T1 soil was considerably higher than in the control sample, and the principal coordinate analysis demonstrated apparent differences in the bacterial communities associated with the plants. Agricultural plants growing in the T1 soil form specific prokaryotic communities, with dominant genera Chthoniobacter, Pseudomonas, Burkholderia, and Massilia. These communities also include less abundant but essential for plant growth nitrifiers Cand. Nitrosocosmius and Nitrospira, and representatives of Proteobacteria, Bacilli, and Actinobacteria, known to be gibberellin-producers.

Two multinucleate amoebae species, nowadays belonging to the genus Thecochaos, were never seen alive since 1913. Stained preparations deposited with the British Museum of Natural History (London) by E. Penard remain the only material proof of the existence of these organisms. We recently found an amoeba, identified as Thecochaos fibrillosum, in the soil sample originating from Chernevaya taiga soil in South Siberia (Russia). In total, we have got 15 cells of this species; however, using this amount of cells, we performed light- and electron-microscopic study, made permanent stained preparations, obtained SSU rRNA gene sequence using single-cell DNA isolation technique, and performed NGS sequencing to obtain genomic data for multigene analysis. Its SSU gene is unusually short (1586 bp), has significant losses in many laps, and, to the moment, is the shortest one known among Amoebozoa. The SSU sequence of this species robustly groups within the family Thecamoebidae as a sister to Thecamoeba/Sappinia clade. Multigene analysis either supported this position of Thecochaos or suggested its grouping with Sappinia. This study demonstrates that modern single-cell techniques allow correct and complete study and description of rare and almost non-cultivable amoebae species.

The identification of new SARS-CoV-2 and human protein and gene targets, which may be markers of the severity and outcome of the disease, are extremely important during the COVID-19 pandemic. The goal of this study was to carry out genetic analysis of SARS-CoV-2 RNA samples to elucidate correlations of genetic parameters (SNPs) with clinical data and severity of COVID-19 infection.Material and Methods. The study included viral RNA samples isolated from 56 patients with COVID-19 infection who received treatment at the City Hospital No. 40 of St. Petersburg from 04/18/2020 to 04/18/2021. Patients underwent physical examination with the assessments of hemodynamic and respiratory parameters, clinical risk according to National Early Warning Score (NEWS), computed tomography (CT) of the chest, and laboratory studies including clinical blood analysis, assessment of ferritin, C-reactive protein (CRP), interleukin-6 (IL-6), lactate dehydrogenase (LDH), D-dimer, creatinine, and glucose levels. All patients tested positive for SARS-CoV-2 RNA by polymerase chain reaction (PCR). Single nucleotide polymorphisms (SNPs) in viral RNA were identified through the creation of cDNA libraries by targeted sequencing (MiSeq Illumina). Bioinformatic analysis of viral samples was performed using the viralrecon v2 pipeline with the further annotation via Pangolin and Nextlade. Sampled genomes were visualized using the Integrative Genomics Viewer (IGV) software. Statistical data processing (descriptive statistics and graphical analysis of data relationships from diff erent tables) was performed using a GraphPad device on the Prism 8.01 platform.Results. A comparative analysis of SNP frequencies in the virus genome in samples from deceased and discharged patients was carried out. The SNPs associated with risk of death (OR > 1), neutral SNPs (OR = 1), and protective SNPs (OR < 1) were identifi ed. Patient samples were infected with 14 lines of SARS-CoV-2, fi ve of which (B.1.1.129, B.1.1.407, B.1.1.373, B.1.1.397, and B.1.1.152) were of Russian origin. The SNPs in the samples infected with the strains of non-Russian origin were associated with an increased risk of mortality (OR = 2.267, 95% confi dence interval 0.1594-8.653) compared to the SNPs in the samples obtained from the group of patients infected with the strains of Russian origin. Positive correlations were identifi ed between the average SNP number, nonsynonymous SNPs, and S-protein SNPs with the degree of respiratory failure, total NEWS score, CT-based form of disease, duration of treatment with mechanical ventilation, disease outcome, levels of LDH, glucose, D-dimer, and ferritin, and RNA amount in the PCR test. S-protein SNPs negatively correlated with the leukocyte and neutrophil counts.

The isolation of soil bacteria from various environments with exceptionally high fertility rates represents an opportunity to identify promising agents to promote agriculture production. The paper aims to study the densities of cultivable bacteria and isolate bacteria from the radish and spring wheat rhizosphere. Plants were grown in the pot experiment with virgin Chernevaya soil, which possessed extraordinary productivity, and zonal forest soil that did not demonstrate similar features. Fifty-nine bacterial isolates were purified and evaluated for their beneficial effects on the early growth of wheat. Isolates belonged to Proteobacteria, Actinobacteria, and Firmicutes phyla, and the most represented genera were Pseudomonas, Streptomyces, Paenibacillus, and Methylobacterium. These dominant bacteria were used in plant inoculation studies. Strains promoted a significant increase in shoot and root length and biomass, thus they may be considered plant growth-promoting rhizobacteria [PGPR]. Regarding biotest assays, strains that displayed high plant growth-promoting capabilities [PGP] were selected for further investigation. This study contributed to bacteria isolates from a unique natural environment with biotechnological potentials in improving plant growth and showed potency to be exploited as bioinoculants.

The boreal forests of Russia are one of the largest forest areas on the planet. As a result of climate change, the rate of carbon sequestration and stabilization of organic matter are important indicators of environmental conservation. To understand mechanisms of stabilization and the structure of soil organic carbon, the molecular-weight (MW) distribution of humic acids (HAs) in soils of the central deciduous-forest zone of boreal forests (Chernevaya taiga, transitional ecotone forest, coniferous forest) was studied. Analysis of the MW distribution of HAs was conducted using size-exclusion chromatography. This approach allowed us to obtain the distribution of high-, medium-, and low-molecular fractions of HAs. It has been revealed that the content of the low-MW fraction prevails over the content of the medium- and high-MW fractions of HAs, which indicates the process of stabilization in soil organic matter. The accumulation of low-molecular-weight fraction occurs with the aromaticity increase in HAs, which indicates that HAs with a relatively high proportion of aromatic fragments have smaller hydrodynamic radius and a lower MW. It has been statistically substantiated that the low-molecular-weight fraction correlates with the content of aromatic compounds and carboxyl structural fragments of HAs, which indicates the resistance of the soil organic matter of Chernevaya taiga to biodegradation.

Here, we present the draft genome sequence of Bordetella sp. strain FB-8, a mixotrophic iron-oxidizing bacterium isolated from creek sediment in the former uranium-mining district of Ronneburg, Germany. To date, iron oxidation has not been reported in Bordetella species, indicating that FB-8 may be an environmentally important Bordetella sp.

The soils of Chernevaya taiga (tallgrass fir-aspen hemiboreal rainforest) have high fertility in comparison with oligotrophic analogs formed in boreal taiga. We have studied humic acids isolated from the soils of Chernevaya and oligotrophic taiga in the Novosibirsk, Tomsk, Kemerovo and the Altai regions of Russia and for the first time the structural and molecular composition of humic acids was determined using 13C CP/MAS and 1H-13C HETCOR NMR spectroscopy. According to data obtained in this study, up to 48% of aromatic compounds accumulate in the soils of Chernevaya taiga, which is higher than in the oligotrophic taiga and comparable with this rate of steppe Chernozems. In the course of active processes of transformation of organic matter, a significant number of aromatic fragments accumulates in the middle horizons of soil profiles. Using 13C CP/MAS spectroscopy, it was possible to identify the main structural fragments (aliphatic and aromatic) that formed in humic acids of the Chernevaya taiga. The HETCOR experiment made it possible to accurately determine the boundaries of chemical shifts of the main groups of structural fragments of humic acids. Our results demonstrate that the stabilization of organic compounds occurs in the soil of the Chernevaya taiga, which leads to the resistance of organic matter to biodegradation that is not typical for benchmark soils of boreal environments.

During the studies of amoebae from the rare and highly productive soil of Chernevaya taiga (West Siberia, Russia) we have found an isolate of a leptomyxid amoeba showing 18s rDNA sequence significantly different from those of other known species of the order Leptomyxida. Here we describe this isolate as a new species, Leptomyxa silvatica n.sp. This species has both morphological and sequence differences from related ones. This finding confirms that reliable morphological differentiation and identification of leptomyxid amoebae is possible only for several remarkable species, while others require molecular data to be correctly labeled or described.