Sergey I. Belikov

Tropodithietic acid (TDA) is a sulfur-containing secondary metabolite with pronounced antimicrobial activity that has been primarily described in marine Alphaproteobacteria of the Roseobacter clade. Despite extensive studies of these bacteria, the occurrence and genetic organization of the TDA biosynthetic pathway in other bacterial groups remain poorly understood. In this study, we report the production of TDA by the freshwater bacterium Janthinobacterium sp. PLB04 isolated from diseased cell cultures of the primmorphs from the Baikal sponge Lubomirskia baikalensis. The presence of a TDA biosynthetic gene cluster homologous to the canonical tda operon previously described in the marine Roseobacter clade was found in Janthinobacterium sp. PLB04 by genome mining with bioinformatic analysis. However, comparative analysis of the cluster architecture demonstrated the absence of the gene tdaC in the Janthinobacterium sp. PLB04 genome. Despite this difference, the strain retained the ability to synthesize TDA. TDA was extracted from the culture medium and identified using chromatographic and MALDI-TOF mass spectrometric analysis. These results suggest that tdaC may not be strictly required for TDA biosynthesis in this strain and may be functionally replaced with alternative enzymatic steps or functional redundancy within the pathway. The discovery of TDA production in a freshwater Janthinobacterium strain expands the known phylogenetic and ecological diversity of TDA-producing bacteria and provides new insights into the plasticity of the TDA biosynthetic gene cluster.

We report here the complete chloroplast genome sequence of the strain BAC9706 of green microalga Chlorella vulgaris isolated from Lake Baikal. The chloroplast genome is a circular DNA molecule of 161,721 bp and contains 78 protein-coding genes, 33 tRNA genes, and 3 rRNA genes. Comparative analysis revealed a high level of conservation of gene content and gene order among other C. vulgaris strains with minor differences mainly associated with introns and non-coding regions. Phylogenetic analysis based on concatenated chloroplast protein-coding genes showed that strain BAC9706 clusters within the C. vulgaris clade with high bootstrap support. These results indicate that strain BAC9706 represents a Baikal ecotype of C. vulgaris rather than a new species.

The identification of a new virus Kiparis-144 (KiparisV) in a half-fed tick I persulcatus, removed from a person in the south of the Russian Far East, determined the goal of further research - to study its role in human pathology and the characteristics of its behavior in the tick microbiome. An ELISA study of 439 blood samples from people affected by tick bites indicated a fairly frequent (up to 16.4±1.7%) encounter of people with the KiparisV virus in the territory of natural foci of the Primorsky Territory. It has been shown that this virus, when mono-infected, can cause clinical symptoms characteristic of acute respiratory diseases. During co-infection under the influence of the KiparisV, there was an increase in the activity of Borrelia spp. with the constant production of antibodies to them only of the IgM class and clinical symptoms of Lyme disease for one year (observation period). Electron microscopy of the KiparisV found in a tick removed from a patient showed a picture of the relationship of the KiparisV (up to 100 nm in size) with unknown representatives of the tick microbiome - pathogens of a viral or bacterial nature. In a comparative aspect, a similar electron microscopic picture of the interaction of the KiparisV virus with a known pathogen of viral nature, the ectromelia virus (ECTV), is presented. The importance of the electron microscopy method in describing the tick microbiome is shown. Thus, it has been established that when co-cultivated in the system the helper-virus KiparisV probably tends to use another pathogen of the tick microbiome for its reproduction, influencing its pathogenicity.

We report here the mitochondrial genome sequence of Lake Baikal green alga extracted from complete genome of Chlorella sp. strain BAC9706. Sequenced mitochondrial genome of strain BAC9706 has 90.8-kbp containing including 34 protein-coding genes. Phylogenetic analysis using the mitochondrial genomes of algae of Chlorellales order indicated that the strain BAC9706 belongs C. vulgaris clade and is Baikal ecotype of C. vulgaris.

Sponges (phylum Porifera) are ancient, marine and inland water, filter feeding metazoans. In recent years, diseased sponges have been increasingly occurring in marine and freshwater environments. Endemic freshwater sponges of the Lubomirskiidae family are widely distributed in the coastal zone of Lake Baikal. The strain Janthinobacterium sp. SLB01 was isolated previously from the diseased sponge Lubomirskia baikalensis (Pallas, 1776), although its pathogenicity is still unknown. The aim of this study was to confirm whether the Janthinobacterium sp. strain SLB01 is the pathogen found in Baikal sponge. To address this aim, we infected the cell culture of primmorphs of the sponge L. baikalensis with strain SLB01 and subsequently reisolated and sequenced the strain Janthinobacterium sp. PLB02. The results showed that the isolated strain has more than 99% homology with strain SLB01. The genomes of both strains contain genes vioABCDE of violacein biosynthesis and floc formation, for strong biofilm, in addition to the type VI secretion system (T6SS) as the main virulence factor. Based on a comparison of complete genomes, we showed the similarity of the studied bacterial strains of Janthinobacterium spp. with the described strain of Janthinobacterium lividum MTR. This study will help expand our understanding of microbial interactions and determine one of the causes in the development of diseases and death in Baikal sponges.

Bacteria of the genus Janthinobacterium are widespread in soils and freshwater ecosystems and belong to the phylum Proteobacteria. The Janthinobacterium sp. SLB01 strain was isolated from diseased freshwater Lubomirskia baicalensis (Pallas, 1776) sponge, and the draft genome was published previously. However, the properties of the SLB01 strain are not known. The aim of the study is to describe some properties of the Janthinobacterium sp. SLB01 strain, isolated from L. baicalensis sponge. The identification of the SLB01 strain was established as Gram-negative, motile, rod-shaped, and psychrotolerant, with growth at 3 and 22 °C. We found that the SLB01 strain has proteolytic, lipolytic, and saccharolytic activity and can use citrates and reduce nitrates. The bacteria Janthinobacterium sp. SLB01 strain can grow, form biofilms, and produce the violet pigment violacein. We identified the pigments violacein and deoxyviolacein by chromatography and mass spectrometry. These metabolites may be of interest to biotechnology in the future. The studied characteristics of the Janthinobacterium sp. SLB01 strain are an important addition to previous studies of the genome of this strain. This study will help us to understand the relationship between the microbial communities of Lake Baikal and sponges.

Our study was devoted to investigating the mass disease and mortality of freshwater sponges (Lubomirskiidae) in Lake Baikal. The first sights of the disease were discovered in 2011 and were associated with a shift in sponge microbial diversity. To study the microbiome, we performed sequencing of the 16S rRNA amplicon DNA extracted from the freshwater sponges.

Sponges (phylum Porifera) are ancient, filtering, multicellular metazoans. Freshwater sponges (Demosponges, Lubomirskiidae) dominate the fauna of the littoral zone of Lake Baikal. Over the last years, there have been mass diseases and death of endemic sponges. Previously, the strain Janthinobacterium sp. SLB01 was isolated from the diseased sponge Lubomirskia baicalensis . The studies of the pathogenicity of the strain Janthinobacterium sp. SLB01 for Baikal sponges has not been carried out. Therefore we infected experimentally in vitro to determine its pathogenicity by the cell culture of the primmorphs with subsequent isolation, sequencing, and analysis of the genomes. The purpose of the study is to show that the strain Janthinobacterium sp. SLB01 isolated from the diseased sponge L. baicalensis is a pathogen for the cell culture of primmorphs. The bacteria from the infected samples of the primmorphs were isolated and identified as strain Janthinobacterium sp. PLB02. A comparative analysis of the genomes of the strains Janthinobacterium sp. SLB01 and Janthinobacterium sp. PLB02 showed that they are practically identical. The genomes of both strains contain genes vioABCDE violacein, flok formation, and strong biofilm, and the type VI secretion system (T6SS), as the primary virulence factor. The bacterial strains Janthinobacterium sp. based on a comparison of complete genomes showed similarity with strain Janthinobacterium lividum MTR. Isolated our strains of Janthinobacterium sp. are pathogens for cell cultures of primmorphs and L. baicalensis sponges. The results of the study will help to expand the understanding of microbial relationships in the development of disease and the death of Baikal sponges.

The strain Janthinobacterium sp. SLB01 was isolated from the diseased freshwater sponge Lubomirskia baicalensis (Pallas, 1776) and the draft genome was published previously. The aim of this work is to analyze the genome of the Janthinobacterium sp. SLB01 to search for pathogenicity factors for Baikal sponges. We performed genomic analysis to determine virulence factors, comparing the genome of the strain SLB01 with genomes of other related J. lividum strains from the environment. The strain Janthinobacterium sp. SLB01 contained genes encoding violacein, alpha-amylases, phospholipases, chitinases, collagenases, hemolysin, and a type VI secretion system. In addition, the presence of conservative clusters of genes for the biosynthesis of secondary metabolites of tropodithietic acid and marinocine was found. We present genes for antibiotic resistance, including five genes encoding various lactamases and eight genes for penicillin-binding proteins, which are conserved in all analyzed strains. Major differences were found between the Janthinobacterium sp. SLB01 and J. lividum strains in the spectra of genes for glycosyltransferases and glycoside hydrolases, serine hydrolases, and trypsin-like peptidase, as well as some TonB-dependent siderophore receptors. Thus, the study of the analysis of the genome of the strain SLB01 allows us to conclude that the strain may be one of the pathogens of freshwater sponges.

Background: The discovery of a new viral disease called tick-borne encephalitis (TBE) in the Far East in 1937 triggered the thematic virology research on the Eurasian continent. The purpose of our study was to conduct a virological and epidemiological monitoring of tick-borne viral infections in the Primorsky Krai over an 80-year period. Materials and methods: Several hundreds of strains belonging to the viruses of the TBE complex (Flaviviridae family) and other families have been isolated; their biological, antigenic and molecular genetic characteristics have been studied. Results: The most complete picture of the Far Eastern population of the TBE virus was obtained in the 1990s based on whole genome sequencing of 50 TBEV strains isolated from patients with different clinical manifestations of the disease and from ixodid ticks. It was established that all the strains belong to the same Far Eastern subtype of TBEV with three clusters (Oshima-, Sofjin-, and Senzhang-). In 1972, the Powassan virus was first isolated from Haemaphisalis longicornis ticks on the Eurasian continent. Phylogenetic analysis based on the whole genome characteristics of the Spassk-9, Nadezdinsk-1991 and Partizansk-2006 strains, as well as the characteristics of five fragments of other Powassan virus strains, indicated that they all belong to the Powassan virus lineage I. The first comparative description of three strains Primorye-155-77, Primorye-20-79 and Primorye-185-91 of the Louping ill virus was given. A comprehensive study of the isolated Ozernoe strain of a deceased female patient enabled identification of the first clinical case of the lyssavirus disease in the Asian part of Russia. This strain is genetically close and has a common ancestor with the Irkut strain and is attributed to pathogens of the genus Lyssavirus, family Rhabdoviridae. Conclusion: Isolation of a highly pathogenic lyssavirus and several viruses of the TBE complex indicates the importance of such virology surveillance and proves the necessity of its continuation.