Assessment of PCBs in Surface Waters at Ultratrace Levels: Traditional Approaches and Biomonitoring (Lake Baikal, Russia)

This article presents the results of the assessment of PCB concentrations in surface waters at ultratrace level of concentrations. The assessment of PCB concentrations is based on data from monitoring PCBs in Baikal water within the conventional approach as well as from biomonitoring of PCBs using Baikal omul, Coregonus migratorius, Georgi, 1775 (C. migratorius), as a bioindicator. The time cycle of the monitoring covered the period from 2014 to 2021. The concentrations of PCBs in the water were estimated from the concentrations of seven indicator congeners: 28, 52, 101, 118, 138, 153, and 180, and from congeners of dioxin-like (dl) PCBs in the tissues of C. migratorius. The average value and the statistically significant range of the detected total concentrations (Ʃ7PCBs) in Baikal water were 0.30 and 0.26–0.34 ng/L, respectively. In the tissues of C. migratorius, the average value and the range of Ʃ7PCB concentrations were 5.6 and 4.9–6.3 ng/g (ww), respectively, and for dl-PCBs, 1.5 and 1.3–1.7 ng/g (ww), respectively. The total toxicity equivalent of the detected dl-PCBs was in the WHO-TEQ (2005) range from 0.03 to 0.06 pg/g (ww). The concentrations of Ʃ7PCBs in Baikal water and dl-PCBs in the tissues of C. migratorius corresponded to the concentration levels in the European alpine lakes and the tissues of S. trutta fish inhabiting these lakes

Assessment of PCBs in Surface Waters at Ultratrace Levels: Traditional Approaches and Biomonitoring (Lake Baikal, Russia)

This article presents the results of the assessment of PCB concentrations in surface waters at ultratrace level of concentrations. The assessment of PCB concentrations is based on data from monitoring PCBs in Baikal water within the conventional approach as well as from biomonitoring of PCBs using Baikal omul, Coregonus migratorius, Georgi, 1775 (C. migratorius), as a bioindicator. The time cycle of the monitoring covered the period from 2014 to 2021. The concentrations of PCBs in the water were estimated from the concentrations of seven indicator congeners: 28, 52, 101, 118, 138, 153, and 180, and from congeners of dioxin-like (dl) PCBs in the tissues of C. migratorius. The average value and the statistically significant range of the detected total concentrations (Ʃ7PCBs) in Baikal water were 0.30 and 0.26–0.34 ng/L, respectively. In the tissues of C. migratorius, the average value and the range of Ʃ7PCB concentrations were 5.6 and 4.9–6.3 ng/g (ww), respectively, and for dl-PCBs, 1.5 and 1.3–1.7 ng/g (ww), respectively. The total toxicity equivalent of the detected dl-PCBs was in the WHO-TEQ (2005) range from 0.03 to 0.06 pg/g (ww). The concentrations of Ʃ7PCBs in Baikal water and dl-PCBs in the tissues of C. migratorius corresponded to the concentration levels in the European alpine lakes and the tissues of S. trutta fish inhabiting these lakes

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

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, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges

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 (1.87 × 10−5 substitutions per site per year (s/s/y) or 1 nucleotide substitution per ORF per 4.9 years; 95% highest posterior density (HPD) interval, 1.3–2.4 × 10−5 s/s/y) among all tick-borne flaviviruses previously assessed. Within TBEV-common, the TBEV European subtype (TBEV-E) has the lowest substitution rate (1.3 × 10−5 s/s/y or 1 nucleotide substitution per ORF per 7.5 years; 95% HPD, 1.0–1.8 × 10−5 s/s/y) as compared with TBEV Far-Eastern subtype (3.0 × 10−5 s/s/y or 1 nucleotide substitution per ORF per 3.2 years; 95% HPD, 1.6–4.5 × 10−5 s/s/y). TBEV-common representing the species tick-borne encephalitis virus diverged 9623 years ago (95% HPD interval, 6373–13,208 years). The TBEV Baikalian subtype is the youngest one (489 years; 95% HPD, 291–697 years) which differs significantly by age from TBEV-E (848 years; 95% HPD, 596–1112 years), LIV (2424 years; 95% HPD, 1572–3400 years), TBEV-FE (1936 years, 95% HPD, 1344–2598 years), and the joint clade of TBEV-S (2505 years, 95% HPD, 1700–3421 years) comprising Vasilchenko, Zausaev, and Baltic lineages

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 (Fst) per site and find the regions (determinants) where sequences belonging to two designated groups were most different. Our algorithm revealed 36 potential determinants (Fst ranges from 0.91 to 1.0) located in all viral proteins except a capsid protein. In an envelope (E) protein, most of the determinants were located on the virion surface regions (domains II and III) and one (absolutely specific site 457) was located in the transmembrane region. Another 100% specific determinant site (E63D) with Fst = 1.0 was located in the central hydrophilic domain of the NS2b, which mediates NS3 protease activity. The NS5 protein contains the largest number of determinants (14) and two of them are absolutely specific (T226S, E290D) and are located near the RNA binding site 219 (methyltransferase domain) and the extension structure. We assume that even if not absolutely, highly specific sites, together with absolutely specific ones (Fst = 1.0) can play a supporting role in cell and tissue tropism determination

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. We showed that the evolutionary rate value of POWV is 3.3 × 10−5 nucleotide substitution per site per year (95% HPD, 2.0 × 10−5–4.7 × 10−5), which is lower than values reported in the previous studies. Divergence of the most recent common ancestor (MRCA) of POWV into two independent genetic lineages most likely occurred in the period between 2600 and 6030 years ago. We assume that the divergence of the virus lineages happened due to the melting of glaciers about 12,000 years ago, which led to the disappearance of the Bering Land Bridge between Eurasia and North America (the modern Alaskan territory) and spatial division of the viral areal into two parts. Genomic data provide evidence of the virus migrations between two continents. The mean migration rate detected from the Far East of Russia to North America was one event per 1750 years. The migration to the opposite direction occurred approximately once per 475 years

The Mitochondrial Genome of a Freshwater Pelagic Amphipod Macrohectopus branickii 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 Macrohectopus branickii. 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. The mt genome of M. branickii has a unique gene order within amphipods, duplications of the four tRNA genes and Cox2, and a long non-coding region, that makes up about two thirds of the genome’s size. The extension of the mt genome was most likely caused by multiple duplications and inversions of regions harboring ribosomal RNA genes. In this study, we analyzed the patterns of mt genome length changes in amphipods and other animal phyla. Through a statistical analysis, we demonstrated that the variability in the mt genome length may be a characteristic of certain phyla and is primarily conferred by expansions of non-coding regions