Virophages Found in Viromes from Lake Baikal.

In this study, a previously little-studied group of viruses-virophages-was searched for and identified in the viromes of the ancient oligotrophic Lake Baikal. Virophages are small dsDNA viruses that parasitize giant viruses (e.g.

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.

Water Quality, Toxicity and Diversity of Planktonic and Benthic Cyanobacteria in Pristine Ancient Lake Khubsugul (Hövsgöl), Mongolia.

For the first time, microcystin-producing cyanobacteria have been detected in Khubsugul, which is ancient, pristine and one of the world's largest lakes. The microcystin synthetase genes belonged to the genera , and possibly spp. No microcystins were found in the water of the lake.

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.

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.

Elucidating the picocyanobacteria salinity divide through ecogenomics of new freshwater isolates.

Background: Cyanobacteria are the major prokaryotic primary producers occupying a range of aquatic habitats worldwide that differ in levels of salinity, making them a group of interest to study one of the major unresolved conundrums in aquatic microbiology which is what distinguishes a marine microbe from a freshwater one? We address this question using ecogenomics of a group of picocyanobacteria (cluster 5) that have recently evolved to inhabit geographically disparate salinity niches. Our analysis is made possible by the sequencing of 58 new genomes from freshwater representatives of this group that are presented here, representing a 6-fold increase in the available genomic data.

Results: Overall, freshwater strains had larger genomes (≈2.

α-cyanobacteria possessing form IA RuBisCO globally dominate aquatic habitats.

RuBisCO (ribulose 1,5-bisphosphate carboxylase/oxygenase) is one the most abundant enzymes on Earth. Virtually all food webs depend on its activity to supply fixed carbon. In aerobic environments, RuBisCO struggles to distinguish efficiently between CO and O.

Diversity of Aerobic Anoxygenic Phototrophs and Rhodopsin-Containing Bacteria in the Surface Microlayer, Water Column and Epilithic Biofilms of Lake Baikal.

The diversity of aerobic anoxygenic phototrophs (AAPs) and rhodopsin-containing bacteria in the surface microlayer, water column, and epilithic biofilms of Lake Baikal was studied for the first time, employing and rhodopsin genes, and compared to 16S rRNA diversity. We detected -containing Alphaproteobacteria (orders Rhodobacterales, Rhizobiales, Rhodospirillales, and Sphingomonadales), Betaproteobacteria (order Burkholderiales), Gemmatimonadetes, and Planctomycetes. Rhodobacterales dominated all the studied biotopes.

Metagenomic Analysis of Virioplankton from the Pelagic Zone of Lake Baikal.

This study describes two viral communities from the world's oldest lake, Lake Baikal. For the analysis, we chose under-ice and late spring periods of the year as the most productive for Lake Baikal. These periods show the maximum seasonal biomass of phytoplankton and bacterioplankton, which are targets for viruses, including bacteriophages.

Estimate of the diversity of viral and bacterial assemblage in the coastal water of Lake Baikal.

In this study, we analysed the diversity and composition of double-stranded DNA viral and bacterial communities within the sample of surface coastal water of Southern Baikal through metagenomics and deep sequencing of the 16S ribosomal RNA gene, respectively. The 16S rRNA gene analysis has revealed 14 phyla and dominance of the 'Actinobacteria' (43.6%), 'Proteobacteria' (25.

Bacterioneuston in Lake Baikal: Abundance, Spatial and Temporal Distribution.

An aquatic surface microlayer covers more than 70% of the world's surface. Our knowledge about the biology of the surface microlayer of Lake Baikal, the most ancient lake on Earth with a surface area of 31,500 km², is still scarce. The total bacterial abundance, the number of cultured heterotrophic temporal bacteria, and the spatial distribution of bacteria in the surface microlayer and underlying waters of Lake Baikal were studied.

First detection of benthic cyanobacteria in Lake Baikal producing paralytic shellfish toxins.

Cyanobacteria were screened from the surface of diseased sponges, stone and bedrock in Lake Baikal for the presence of saxitoxin using enzyme-linked immunosorbent assay. In sequel, eight paralytic shellfish toxin (PST) variants were identified using a MALDI mass spectrometry. Microscopic examination found that Tolypothrix distorta dominated in the biofouling samples.

Application of a new cultivation technology, I-tip, for studying microbial diversity in freshwater sponges of Lake Baikal, Russia.

One of the fundamental methods for cultivating bacterial strains is conventional plating on solid media, but this method does not reveal the true diversity of the bacterial community. In this study, we develop a new technique and introduce a new device we term, I-tip. The I-tip was developed as an in situ cultivation device that allows microorganisms to enter and natural chemical compounds to diffuse, thereby permitting the microorganisms to grow utilizing chemical compounds in their natural environment.

Diversity of cyanobacterial species and phylotypes in biofilms from the littoral zone of Lake Baikal.

The majority of naturally occurring biofilms contain numerous microorganisms that have not yet been cultured. Additionally, there is little information available regarding the genetic structure and species diversity of these communities. Therefore, we characterised the species diversity, structure and metagenome of biofilms grown on stones and steel plates in the littoral zone of Lake Baikal (East Siberia, Russia) by applying three different approaches.

Diversity of the major capsid genes (g23) of T4-like bacteriophages in the eutrophic Lake Kotokel in East Siberia, Russia.

Numerous studies revealed high diversity of T4-like bacteriophages in various environments, but so far, little is known about T4-like virus diversity in freshwater bodies, particularly in eutrophic lakes. The present study was aimed at elucidating molecular diversity of T4-like bacteriophages in eutrophic Lake Kotokel located near Lake Baikal by partial sequencing of the major capsid genes (g23) of T4-like bacteriophages. The majority of g23 fragments from Lake Kotokel were most similar to those from freshwater lakes and paddy fields.

Stratified distribution of nutrients and extremophile biota within freshwater ice covering the surface of Lake Baikal.

Biological entities and gradients of selected chemicals within the seemingly barren ice layers covering Lake Baikal were investigated. Ice cores 40-68 cm long were obtained from in shore and offshore sites of Southern Lake Baikal during the cold period of a year (March-April) in 2007 and 2008. In microscopic observations of the melted ice, both algae and bacteria were found in considerable numbers (>10(3) cells/L and >10(4) cells/ml, respectively).

Ecological development and genetic diversity of Microcystis aeruginosa from artificial reservoir in Russia.

Microcystis aeruginosa is a well-known Cyanobacterium responsible for the formation of toxic water blooms around the world. Shallow, warm, and eutrophic reservoirs provide the most favourable conditions for M. aeruginosa development.

Phylogenetic diversity of T4-like bacteriophages in Lake Baikal, East Siberia.

Among the tailed phages, the myoviruses, those with contractile tails, are widespread and diverse. An important component of the Myoviridae family is the genus 'T4-like viruses'. The present study was aimed at elucidating the molecular diversity of T4-type bacteriophages in Lake Baikal by partial sequencing of g23 genes of T4-type bacteriophages.