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The atmospheric environment is formed under the influence of local and distant sources as a result of horizontal and vertical transport. In the present work, microbiological analysis of 604 samples of atmospheric aerosol collected in the period from September 2020 to September 2023 at four sites differing in anthropogenic load, located in Novosibirsk and the region, was carried out. Day and night aerosol samples were collected during 12 h every two weeks by filtration using Sartorius reinforced Teflon membranes, then sown on a set of nutrient media. The taxonomic affiliation of the isolated microbial isolates was determined based on phenotypic characteristics and analysis of 16S rRNA gene nucleotide sequences. Changes in the composition and concentration of culturable microorganisms depending on the season, time of day, and site of aerosol sampling were observed. In winter, lower fungi and bacteria of the genera Bacillus, Staphylococcus, Micrococcus dominated with an average concentration from zero to 12.5 CFU/m3 of aerosol. In the warm period, the concentration and diversity of cocci, spore-forming and non-spore-forming bacteria, actinomycetes, and fungi (up to 1970 CFU/m3), among which pathogenic microorganisms were found, increased sharply in aerosols. The use of 16S metabarcoding techniques has greatly expanded the range of aerosols' microbial diversity detectable. [ABSTRACT FROM AUTHOR]

Composting is an environmentally friendly process, turning animal waste into fertilizer. Chicken litter compost (CLC) improves soil properties, increasing crop yields. However, the CLC effect on the soil microbiome is understudied. This study aimed to compare bacteriobiome diversity in fallow arable Chernozem with and without CLC addition in a field experiment in the Novosibirsk region, Russia, using 16S rRNA gene metabarcoding. Pseudomonadota, Actinomycetota and Acidobacteriota were the most OTU-rich phyla, together accounting for >50% of the total number of sequence reads. CLC-related shifts in the bacteriobiome structure occurred at all taxonomic levels: the Bacillota abundance was 10-fold increased due to increased Bacilli, both being indicator taxa for the CLC-soil. The main Actinomycetota classes were the indicators for the CLC-soil (Actinobacteria) and no-CLC soil (Thermoleophilia, represented Gaiella). Both Bacillota and Actinomycetota phyla were the ultimate constituents of the CLC added, persisting in the soil for five months of fallowing. The no-CLC soil indicator phyla were Acidobacteriota (represented by Acidobacteria_Group3) and Verrucomicrobiota. Future metabarcoding studies of chicken litter application in agricultural soils, including cropped studies, should address the soil microbiome at the species/strain levels in more detail, as well as how it is affected by specific crops, preferably accompanied by a direct methodology revealing the microbiota functions. [ABSTRACT FROM AUTHOR]

Fly ash dumps of thermal power stations have been increasing in area worldwide due to the growing demand for power. One of the cost-effective approaches for restoring such sites is spontaneous revegetation in those areas where adjacent indigenous ecosystems can supply seeds and living organisms. We assessed microbiome taxonomic diversity in a Technosol developed during nine years of spontaneous revegetation of the terminated fly ash pond of a thermal power station in Novosibirsk, Russia, in comparison with microbiome diversity in undisturbed Phaeozem under adjacent birch forest by using 16S (V3-V4) and 1TS2 (ITS3-ITS4) amplicon sequencing with Illumina MiSeq. We identified 577 fungal and 5542 bacterial operational taxonomic units (OTUs); 95-99% of them were minor or rare species. The dominant OTUs were completely different in the studied soils. At the phylum level, the ultimate dominants were Ascomycota (84%) in the Technosol and Basidiomycota (89%) in the Phaeozem. Three phyla (Proteobacteria, Acidobacteria and Actinobacteria), together comprising more than a half of the bacteriobiome, prevailed in both soils; however, at the OTU level, soil-related differences were found for 31% of the OTUs. The Technosol bacteriobiome was less structured and more diverse compared to the mycobiome, displaying the same phylum-level structure and OTU-based a-biodiversity as in the adjacent mature soil. Our finding that few fungal and bacterial OTUs dominated in the soil microbiome, the majority being minor or rare members, implies that key ecosystem processes performed by soil microorganisms rely on a very limited taxonomic diversity, both in young and mature soils. Keywords: ITS DNA diversity, 16S rRNA gene diversity, Technosol, thermoelectric power station., Introduction Despite emerging innovative technologies, the areas occupied by the fly ash dumps of thermal power plants have been increasing worldwide and are projected to increase further due to the [...]

This paper presents the first in-depth research on the biological and genomic properties of lytic rhizobiophage AP-J-162 isolated from the soils of the mountainous region of Dagestan (North Caucasus), which belongs to the centers of origin of cultivated plants, according to Vavilov N.I. The rhizobiophage host strains are nitrogen-fixing bacteria of the genus Sinorhizobium spp., symbionts of leguminous forage grasses. The phage particles have a myovirus virion structure. The genome of rhizobiophage AP-J-162 is double-stranded DNA of 471.5 kb in length; 711 ORFs are annotated and 41 types of tRNAs are detected. The closest phylogenetic relative of phage AP-J-162 is Agrobacterium phage Atu-ph07, but no rhizobiophages are known. The replicative machinery, capsid, and baseplate proteins of phage AP-J-162 are structurally similar to those of Escherichia phage T4, but there is no similarity between their tail protein subunits. Amino acid sequence analysis shows that 339 of the ORFs encode hypothetical or functionally relevant products, while the remaining 304 ORFs are unique. Additionally, 153 ORFs are similar to those of Atu_ph07, with one-third of the ORFs encoding different enzymes. The biological properties and genomic characteristics of phage AP-J-162 distinguish it as a unique model for exploring phage–microbe interactions with nitrogen-fixing symbiotic microorganisms. [ABSTRACT FROM AUTHOR]

The composition and structure of rhizosphere bacteriobiome of the husk tomato (Physalis philadelphica Lam.) plants grown on Phaeozem in the open field in West Siberia, Russia (55°15’ NL, 83°31’ EL) were studied using Illumina MiSeq sequencing of the V3-V4 hypervariable region of 16S rRNA genes. In total 5898 OTUs (Operational Taxonomic Units) were found in the study, representing 20 phyla and 53 identified and 15 non-identified (below the phylum level) classes. The most OTU-rich phyla were Proteobacteria, Acidobacteria and Actinobacteria, their relative abundance in the total number of sequence reads being 26, 22 and 19%, respectively. Bacteroidetes, Gemmatimonadetes and Verrucomicrobia phyla each accounted for 2 ‒ 4%. The rest 14 of the identified phyla were quite negligible, contributing less than 0.5% each. At the OTUs level, the structure was very even and equitable, as only 7 OTUs had relative abundance ranging from 0.5 to 1.1%. The main dominant OTU represented Bradyrhizobiaceae family, implying the importance of nitrogen-fixing bacteria for plant growth and development without any mineral fertilisation. The dominance biodiversity index was very low (0.001), while Shannon index was rather high (7.5). We believe the presented husk tomato rhizosphere bacteriobiome, as the first study using new generation sequencing platform for this species, will help get a better picture of Solanaceae microbiomes in different environments, thus contributing to a more comprehensive understanding of shaping microbial communities by plant roots.

The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest–tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50–80% of bacterial OTUs and 44–60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution. [ABSTRACT FROM AUTHOR]

Managing soil biodiversity using reduced tillage is a popular approach, yet soil bacteriobiomes in the agroecosystems of Siberia has been scarcely studied, especially as they are related to tillage. We studied bacteriobiomes in Chernozem under natural steppe vegetation and cropped for wheat using conventional or no tillage in a long-term field trial in the Novosibirsk region, Russia, by using the sequence diversity of the V3/V4 region of 16S rRNA genes. Actinobacteria, Acidobacteria, and Proteobacteria summarily accounted for 80% of the total number of sequences, with Actinobacteria alone averaging 51%. The vegetation (natural vs. crop) and tillage (ploughed vs. no-till) affected the bacterial relative abundance at all taxonomic levels and many taxa, e.g., hundreds of OTUs. However, such changes did not translate into α-biodiversity changes, i.e., observed and potential OTUs' richness, Shannon, and Simpson, excepting the slightly higher evenness and equitability in the top 0–5 cm of the undisturbed soil. As for the β-biodiversity, substituting conventional ploughing with no tillage and maintaining the latter for 12 years notably shifted the soil bacteriobiome closer to the one in the undisturbed soil. This study, presenting the first inventory of soil bacteriobiomes under different tillage in the south of West Siberia, underscores the need to investigate the seasonality and longevity aspects of tillage, especially as they are related to crop production. [ABSTRACT FROM AUTHOR]