Lyudmila V. Lysak

A comprehensive study of prokaryotic communities (microbiomes) of bacterial mats and snottites from the karst cave Sheki-Kh’ekh was carried out for the first time, with comparison to cave soil-like bodies (SLBs) from the Muhammed-Kh’ekh cave and adjacent brown forest soil. The total abundance of bacterial cells in mats and snottites varied within a relatively narrow range, from 0.26 to 0.35 billion cells per mL, reaching maximum values in floating bacterial mats and minimum values in snottites. In soil-like bodies, the total bacterial abundance was 0.28 billion cells per g. Actinomycete mycelium was detected in all cave samples, with the highest values observed in floating bacterial mats and the lowest in shoreline bacterial mats. Metabarcoding analysis (16S rRNA gene sequencing) revealed high taxonomic diversity of prokaryotic communities across the studied substrates. The greatest diversity was recorded in floating bacterial mats (25 phyla and 74 genera). In all cave substrates, the dominant phyla were Pseudomonadota and Bacillota , while Bacteroidota also dominated in floating bacterial mats. Lower relative abundances were observed for Actinomycetota , Verrucomicrobiota , Chlorofl exota , Chlorobiota , and Th ermodesulfobacteriota . Eleven bacterial phyla were shared between soil and floating bacterial mats: Pseudomonadota , Bacillota , Bacteroidota , Verrucomicrobiota , Chlorobiota , Chlorofl exota , Actinomycetota , Acidobacteriota , Cyanobacteriota , Planctomycetota , and Armatimonadota , along with two candidate phyla, Sumerlaeota and Hydrogenedentes . Two archaeal phyla, Woesearchaeota and Nanoarchaeota , were detected in bacterial mats. A total of 191 bacterial genera were identified across all studied substrates. Only 12 genera were common to ba cterial mats and soil: Brevundimonas , Devosia , Flavobacterium , Luteolibacter , Paenibacillus , Paenisporosarcina , Pseudarthrobacter , Pseudomonas , Rhodanobacter , Sphingomonas , Sumerlaea , and Thermomonas . A distinctive feature of floating bacterial mat communities was the high representation of genera involved in sulfur cycling processes. Functional profiling revealed the predominance of sulfur- and iron-cycle-related functions in bacterial mats, whereas nitrogen-cycle-related functions and chemoheterotrophy prevailed in soil communities. This study significantly expands current knowledge of the taxonomic composition of prokaryotic communities inhabiting bacterial mats and snottites of sulfidic caves in the Chechen Republic. The presence of bacterial genera involved in sulfur and iron transformation processes highlights their ecological significance. The results obtained on the diversity of prokaryotic communities in mats, snottites, and soil-like bodies are of interest for understanding ecosystem functioning and for the targeted search of strains with valuable biotechnological properties.

This study presents the findings of an investigation into the abundance and morphological diversity of bacteriophages in samples of urban soils (Urbanozem and Replantozem) and atmospheric dustfall (ADF) collected across Moscow from sites with varying degrees of anthropogenic impact. Using direct epifluorescence microscopy with the SYBR Gold stain, it was demonstrated that bacteriophage abundance (virus-like particles, VLPs) was higher in soils (1.12-2.10∙109 VLP∙g-1) than in ADF (0.42-0.64∙109 VLP∙g-1), correlating with total bacterial counts. Through enrichment culture techniques followed by biological purification, a collection of bacteriophages (coliphages) infecting Escherichia coli strains with different cell surface compositions (different O-antigen types) was obtained. Transmission electron microscopy revealed that some of the isolated coliphages belong to the class Caudoviricetes (tailed phages) and are characterized by Siphoviridae (possessing long, non-contractile tails) and Podoviridae (possessing short tails) morphotypes. The obtained data underscore the significant role of bacteriophages in the functioning of microbial communities within urban ecosystems and their potential for use in the bioremediation of urban soils.

журнал Живые и биокосные системы Обилие и таксономическое разнообразие прокариотных сообществ почвоподобных тел пещер Вьетнама

A comprehensive study of prokaryotic communities of zonal Ferralsols and intrazonal Fluvisols, as well as associated leaf litter and “suspended” soil from epiphytic fern baskets was carried out. The maximum number of bacteria determined by the direct luminescence method (5.59 billion cells) was found in the samples of Fluvisols, while the lengths of fungal (2038 m/g) and actinomycete (1086 m/g) mycelia were the largest in the mountainous Ferralsols. Bacteria of the genus Streptomyces included in the saprotrophic bacterial complex of the studied substrates made a significant contribution to the destruction of plant material. The bacteria of the phyla Firmicutes (80%) and Proteobacteria (15%) predominated in the prokaryotic community of the zonal Ferralsols, while the phyla Proteobacteria (51%) and Actinobacteria (38%) dominated in the sample of the “suspended” soil. The phyla Chloroflexi, Acidobacteria, Bacteroidetes, and Cyanobacteria were significantly less represented. Against the background of significant differences between the studied prokaryotic communities at the level of genera, they were characterized by similar functional groups of microorganisms: xenobiotic decomposers, nitrogen cycle bacteria, extremophiles, as well as bacteria that inhibit the growth of micromycetes. The metabolically active part of the prokaryotic community represented by the phyla Proteobacteria, Actinobacteria, and Acidobacteria, was the highest in the “suspended” soil and the least active in the leaf litter and A horizon of Ferralsols, which correlated with the high abundance of these phyla and the significant taxonomic diversity of bacteria in this locus. Functional genes nifH and alkB encoding nitrogenase and alkane-hydroxylase, respectively, were detected in all studied substrates. The number of copies of functional genes was the highest in the “suspended” soil sample, which makes this locus promising for isolating strains with a high biotechnological potential.

Abundance and Diversity of Microorganisms in Soils and Associated Substrates (Leaf Litter and “Suspended Soil”) in Some Nature Reserves of Vietnam Обилие и разнообразие микроорганизмов в почвах и сопряженных субстратах (опаде и “подвешенной почве”) некоторых заповедников Вьетнама

A comprehensive quantitative and qualitative characterization of prokaryotic communities of solid atmospheric fallout (dust aerosol) and soils in the areas with different anthropogenic loads within the territory of Moscow was obtained. The total number of bacteria in the studied samples of solid atmospheric fallouts (SAF) was lower than the number of bacteria in soil samples; actinomycete mycelium was not found in dust samples, although it was found in soil samples. The number of culturable saprotrophic bacteria in dust samples was an order of magnitude lower than in Urbic Technosols taken at the same plots. Representatives of the genus Micrococcus dominated the culturable bacteria in the dust aerosols, while representatives of the phylum Proteobacteria dominated in soils. Representatives of the Enterobacteriaceae family were found in the dust samples, among which there were species that are potential human pathogens. The maximum biodiversity of bacteria of the Enterobacteriaceae family was recorded in the dust samples taken in areas with increased anthropogenic and transport load. The sanitary-indicative bacterium Escherichia coli was found in all samples of the dust and Urbic Technosols; its content varied from 10 to 100 CFU/g, which corresponds to the moderate degree of epidemic danger. Ecological indices calculated for prokaryotic communities in situ (barcoding of the 16S rRNA gene) indicate a lower taxonomic diversity of SAF prokaryotic communities in comparison with communities of closely spaced Urbic Technosols.

Abundance and Diversity of Prokaryotic Communities of Dust Aerosol and Urban Soils on the Territory of Moscow Обилие и разнообразие прокариотных сообществ пылеаэрозоля и городских почв на территории Москвы

Actinomycetes are an important group of bioactive hydrolytic bacteria in any ecosystem. However, the actinomycete biodiversity in tropical ecosystems, particularly in Vietnam, is still underexplored. The aim of this article is to analyze the abundance, taxonomic structure and ecophysiological features of actinomycete complexes of soils and litter in Vietnam’s protected areas. A total of 41 samples of soils, plant litter and suspended soils were collected from six of Vietnam’s national parks and nature reserves. The direct inoculation technique showed that the total abundance of actinomycetes varied from 2.0 × 10⁴ to 1.0 × 10⁸ CFU/g. According to the luminescent microscopy with acridine orange dye, the length of the actinomycete mycelium was as long as 1000 m/g in the litter of Xuan Son National Park. A total of 80 strains were isolated and tested for antagonistic activity against Bacillus subtilis, Aspergillus niger and Candida albicans. Inoculation on Getchinson’s medium showed high cellulolytic activity. The most active strains were isolated from alluvial brown soil, plant litter and suspended soil of the Pu Hoat Nature Reserve. In these samples, actinomycetes adapted to high temperatures and low pH were found to be predominant. High-throughput sequencing of the V3–V4 region of the 16S rRNA gene and bioinformatic analysis confirmed the high taxonomic diversity and high hydrolytic activity of actinomycete complexes of the Pu Hoat Nature Reserve samples.

The quantitative and qualitative characteristics are given of the soil prokaryotic communities in the Dystric Fluvisol, litter, and “suspended soil” in epiphyte baskets. The number of bacteria (direct luminescence method) varied from 1.1 to 2.6 billion cells/g soil and was the highest in the suspended soil sample and lower in the litter and A and AB horizons of Dystric Fluvisol (brown meadow alluvial soil). Proteobacteria, Actinobacteria, and Acidobacteria predominated in the prokaryotic community (at the phylum level); Chloroflexi, Firmicutes, and Verrucomicrobia were found in smaller amounts; the content of Nitrospirae, Planctomycetes, and Gemmatimonadetes was even lower. Representatives of the Archaea domain were found in the A horizon and in the suspended soil. Their content was significantly lower than that of the Bacteria domain and did not exceed 1%. Archaea were represented by the Thaumarchaeota and Euryarchaeota phyla in the A horizon and by Thaumarchaeota and Woesearchaeota phyla in the suspended soil. Based on the calculated ecological indices (alpha and beta diversity, measures of similarity by Bray-Curtis metrics and weighted UniFrac), it was shown that the microbiome of the suspended soil was closer to the microbiome of A horizon of Dystric Fluvisol than to the microbiome of litter. The metabolically active part of the prokaryotic community represented by the Proteobacteria, Actinobacteria, and Acidobacteria phyla reached its maximum in the suspended soil and was lower in the litter and A horizon of Dystric Fluvisol, and this correlated with the high abundance of these phyla and the significant taxonomic diversity of bacteria in this locus. Functional genes (nifH and alkB) were detected in all studied substrates. The number of copies of functional genes was the highest in the suspended soil sample, which makes this locus promising for isolating the strains with high biotechnological potential.