DNA-metabarcoding of cyanobacteria and microalgae in chernozem soils of temperate continental climate of the forest-steppe zone of Eurasia under different degrees of agrotechnology intensification.

Chernozem soil is a valuable resource and contains a great diversity of microorganisms that play a global role in the process of soil formation, the species diversity of which has changed over the last five years under the influence of different agrotechnologies. For the first time, under the conditions of the Central Chernozem region, grain and fallow crop rotation, studies using the DNA-metabarcoding method were carried out to study the taxonomic structure of bacteria, fungi, cyanobacteria, and microalgae communities in the arable horizon of typical medium loamy chernozem under winter wheat cultivation. A comparative analysis of the composition of the genotypes showed significant differences in the presented level of mineral nutrition of the soil NPK (60) and NPK (100) compared with the control variant.

The genus Coelastrella (Chlorophyceae, Chlorophyta): molecular species delimitation, biotechnological potential, and description of a new species Coelastrella affinis sp. nov., based on an integrative taxonomic approach.

Despite the long research history on the genus Coelastrella, its species diversity and biotechnological potential have not been fully explored. For the first time, cluster analysis of morphological characteristics was done in the representatives of the said genus. The results obtained have shown that morphological similarity does not necessarily indicate a molecular genetic relationship.

Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).

A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25 g/L) and hydrogen sulfide (up to 1 mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria.

Viral Diversity in Samples of Freshwater Gastropods (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing.

Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, , and ). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses.

Case Study of Diesters of o-Phthalic Acid in Surface Waters with Background Levels of Pollution.

Lake Baikal was studied as a model for elucidating the general pattern of -phthalic acid diester (PAE) distributions in surface waters with background pollution levels. The influence of factors including congeners, concentrations, sampling points, seasons, years, and potential sources was considered and the environmental risk for various hydrobionts was established. Priority PAEs in Baikal waters are represented by dimethyl phthalate (DMP), diethyl phthalates (DEP), di--butyl phthalate (DBP) and di-(2-ethylhexyl)phthalate (DEHP).

Inferring Evolutionary Timescale of Omsk Hemorrhagic Fever Virus.

Until 2020, there were only three original complete genome (CG) nucleotide sequences of Omsk hemorrhagic fever virus (OHFV) in GenBank. For this reason, the evolutionary rate and divergence time assessments reported in the literature were based on the E gene sequences, but notably without temporal signal evaluation, such that their reliability is unclear. As of July 2022, 47 OHFV CG sequences have been published, which enables testing of temporal signal in the data and inferring unbiased and reliable substitution rate and divergence time values.

Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia).

We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic , , and , as well as aerobic and anaerobic participants of the methane cycle ( and , respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the and members and a substantial increase in the sequences of the phylum Firmicutes.

The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton.

Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy.

Dates and Rates of Tick-Borne Encephalitis Virus-The Slowest Changing Tick-Borne Flavivirus.

We evaluated the temporal signal and substitution rate of tick-borne encephalitis virus (TBEV) using 276 complete open reading frame (ORF) sequences with known collection dates. According to a permutation test, the TBEV Siberian subtype (TBEV-S) data set has no temporal structure and cannot be applied for substitution rate estimation without other TBEV subtypes. The substitution rate obtained suggests that the common clade of TBEV (TBEV-common), including all TBEV subtypes and louping-ill virus (LIV), is characterized by the lowest rate (1.

Description and Genomic Analysis of the First Facultatively Lithoautotrophic, Thermophilic Bacteria of the Genus Thermaerobacter Isolated from Low-temperature Sediments of Lake Baikal.

Members of the genus Thermaerobacter belong to the phylum Firmicutes and all isolates characterised to date are strictly aerobic and thermophilic. They were isolated from a mud sample of the Challenger Deep in the Mariana Trench, hydrothermal vents, and silt compost. A novel thermophilic, facultatively lithoautotrophic bacteria of the genus Thermaerobacter, strain PB12/4term (=VKM B-3151), with a metabolism that is uncharacteristic of the type species, was isolated from low-temperature surface sediments near the Posolsk Bank methane seep, Lake Baikal, Russia.

Genomic Determinants Potentially Associated with Clinical Manifestations of Human-Pathogenic Tick-Borne Flaviviruses.

The tick-borne flavivirus group contains at least five species that are pathogenic to humans, three of which induce encephalitis (tick-borne encephalitis virus, louping-ill virus, Powassan virus) and another two species induce hemorrhagic fever (Omsk hemorrhagic fever virus, Kyasanur Forest disease virus). To date, the molecular mechanisms responsible for these strikingly different clinical forms are not completely understood. Using a bioinformatic approach, we performed the analysis of each amino acid (aa) position in the alignment of 323 polyprotein sequences to calculate the fixation index () per site and find the regions (determinants) where sequences belonging to two designated groups were most different.

Species delimitation and microalgal cryptic diversity analysis of the genus Micractinium (Chlorophyta).

In this article, the system of the green microalgal genus Micractinium, based on morphological, physiological, ecological and molecular data, is considered. The main diagnostic species characteristics and the taxonomic placement of some taxa are also discussed. Phylogenetic analysis showed that the genus Micractinium is characterized by high cryptic diversity.

DNA metabarcoding of benthic algae and associated eukaryotes from Lake Baikal in the face of rapid environmental changes.

Here we report new data describing the biodiversity of phytobenthic communities based on DNA-metabarcoding using the 18S rDNA marker and the Illumina MiSeq system. The study was initiated due to the blooming of f ilamentous algae (mainly of the genus Spirogyra) and cyanobacteria in the coastal zone of Lake Baikal under climate change and anthropogenic impact. The composition and taxonomic diversity of algae and other organisms associated with them on different sites of Lake Baikal (near Bolshoi Ushkaniy Island, in Listvennichny Bay) and in the Kaya (within the city of Irkutsk, located in the same drainage basin as Lake Baikal) were determined using DNAmetabarcoding.

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, .

Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, , using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample).

Lacustrine, wastewater, interstitial and fluvial water quality in the Southern Lake Baikal region.

The coastal area of the southern Lake Baikal with the population over 35,000 people remains an attractive spot for both tourists and local residents. Despite high anthropogenic impact, a detailed assessment of water quality in this area has not been performed so far. Here, we performed a comprehensive evaluation of the quality of the surface, bottom and interstitial water in rivers, lacustrine water and wastewater in the southern Lake Baikal region.

Delimitation of the tick-borne flaviviruses. Resolving the tick-borne encephalitis virus and louping-ill virus paraphyletic taxa.

The tick-borne flavivirus (TBFV) group contains at least 12 members where five of them are important pathogens of humans inducing diseases with varying severity (from mild fever forms to acute encephalitis). The taxonomy structure of TBFV is not fully clarified at present. In particular, there is a number of paraphyletic issues of tick-borne encephalitis virus (TBEV) and louping-ill virus (LIV).

The Mitochondrial Genome of a Freshwater Pelagic Amphipod Is among the Longest in Metazoa.

There are more than 350 species of amphipods (Crustacea) in Lake Baikal, which have emerged predominantly through the course of endemic radiation. This group represents a remarkable model for studying various aspects of evolution, one of which is the evolution of mitochondrial (mt) genome architectures. We sequenced and assembled the mt genome of a pelagic Baikalian amphipod species The mt genome is revealed to have an extraordinary length (42,256 bp), deviating significantly from the genomes of other amphipod species and the majority of animals.

Phylogeography and Re-Evaluation of Evolutionary Rate of Powassan Virus Using Complete Genome Data.

In this paper, we revealed the genetic structure and migration history of the Powassan virus (POWV) reconstructed based on 25 complete genomes available in NCBI and ViPR databases (accessed in June 2021). The usage of this data set allowed us to perform a more precise assessment of the evolutionary rate of this virus. In addition, we proposed a simple Bayesian technique for the evaluation and visualization of 'temporal signal dynamics' along the phylogenetic tree.

Seasonal Succession and Coherence Among Bacteria and Microeukaryotes in Lake Baikal.

Microorganisms exhibit seasonal succession governed by physicochemical factors and interspecies interactions, yet drivers of this process in different environments remain to be determined. We used high-throughput sequencing of 16S rRNA and 18S rRNA genes to study seasonal dynamics of bacterial and microeukaryotic communities at pelagic site of Lake Baikal from spring (under-ice, mixing) to autumn (direct stratification). The microbial community was subdivided into distinctive coherent clusters of operational taxonomic units (OTUs).

Phylogenetic reconstruction of the initial stages of the spread of the SARS-CoV-2 virus in the Eurasian and American continents by analyzing genomic data.

Samples from complete genomes of SARS-CoV-2 isolated during the first wave (December 2019-July 2020) of the global COVID-19 pandemic from 21 countries (Asia, Europe, Middle East and America) around the world, were analyzed using the phylogenetic method with molecular clock dating. Results showed that the first cases of COVID-19 in the human population appeared in the period between July and November 2019 in China. The spread of the virus into other countries of the world began in the autumn of 2019.

Extended Evaluation of Viral Diversity in Lake Baikal through Metagenomics.

Lake Baikal is a unique oligotrophic freshwater lake with unusually cold conditions and amazing biological diversity. Studies of the lake's viral communities have begun recently, and their full diversity is not elucidated yet. Here, we performed DNA viral metagenomic analysis on integral samples from four different deep-water and shallow stations of the southern and central basins of the lake.

Virome Analysis of Near-Bottom Coastal Water of Lake Baikal.

In recent years, Lake Baikal has undergone significant changes in the composition of coastal communities associated with the increasing anthropogenic influence and global climate changes. In this context, we carried out metagenomic sequencing of the DNA viral community of an integral near-bottom water sample from the littoral zone of the lake.

Interconnection of bacterial and phytoplanktonic communities with hydrochemical parameters from ice and under-ice water in coastal zone of Lake Baikal.

We analysed the relationship between the chemical complex (concentration of dissolved ions, nutrients, pH) and biological parameters (primary production, biomass of phytoplankton, abundance and activity of bacterial communities) at estuaries of rivers and coastal waters of Southern Baikal during the under-ice period. Correlation network analysis revealed CO to be the main limiting factor for the development of algae and microbial communities in the coastal zone of Lake Baikal. This study indicates that primarily reverse synthesis of bicarbonate and carbonate ions associated with the development of phytoplankton and accumulation of dissolved CO during photosynthesis regulates pH in the Baikal water.

Bioinformatic tools for tRNA gene analyses in mitochondrial DNA sequence data.

The data presented here are related to the research article entitled "Hidden cases of tRNA genes duplication and remolding in mitochondrial genomes of amphipods" (Romanova et al., 2020) [1]. Correct tRNA gene sequence annotation in mitochondrial (mt) and nuclear genomes sometimes can be a challenging task because of the differential performances of tRNA annotation/prediction programmes.