Delimitation of Some Taxa of Ulnaria and Fragilaria (Bacillariophyceae) Based on Genetic, Morphological Data and Mating Compatibility

Fragilaria and Ulnaria are two closely related diatom genera for which the delimitation and circumscription of several species is unclear. We studied strains isolated from Lake Baikal and compared them with the species from freshwater reservoirs in Europe and Asia using phylogenetic and species delimitation methods, microscopy and interclonal crossing experiments. The results of the phylogenetic analyses of the fragments of rbcL and 18S rRNA genes revealed that baikalian F. radians clade was independent from the representatives of the genus from other localities. Among Ulnaria we found the following 18S rRNA phylogenetic tree groups at species level: U. acus, U. ulna and U. danica. Genetic distance between genera varied between 3.9-10.2% substitutions in rbcL gene and 3.2-11.5% in 18S rRNA. The boundary between intraspecies and interspecies polymorphism for studied species of Ulnaria and Fragilaria in these marker genes was around 0.8% substitutions. Morphometric characters of individual strains showed their variability and division into F. radians, U. acus and U. ulna together with U. danica. Strains of U. acus and U. danica from different localities of Europe and Asia were sexually compatible inside the species. Sexual reproduction has never been observed in monoclonal cultures, either between this species or with strains of the Fragilaria

Genome-Based Taxa Delimitation (GBTD): A New Approach

Proper taxonomic identification is essential for biological research. Unfortunately, there are no clear guidelines for taxonomic assignment above the species level. Here, we present a novel approach—GBTD—to the use of genetic divergence to evaluate the taxonomic position of certain samples with simultaneous estimation of the current systematics correctness. This approach includes measuring the raw and model-adjusted distances between DNA sequences and attributing them to the lowest taxonomic levels that are common in sample pairs to reveal distance distributions matching different taxonomic levels (species, genus, family etc.). GBTD facilitated the reassessment of the taxonomic position of the samples, whose genetic distances relative to other samples in the dataset did not match their taxonomic divergence. A data set of complete mitochondrial genome sequences of segmented worms was chosen to test this approach. As a result, numerous inconsistencies in the systematics of samples from GenBank were pointed out. These inconsistencies included both the oversplitting and overlumping of individuals into taxa of different levels and clear cases of misidentification. Our approach sparks re-evaluation of the current systematics where traditional methods fail to provide sufficient resolution

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

Diversity Variation of Silica-Scaled Chrysophytes Related to Differences in Physicochemical Variables in Estuaries of Rivers in an Arctic Watershed

The present study examined the taxonomic diversity of silica-scaled chrysophytes in the estuaries of the Arctic watershed of Yakutia in the context of global climate change, as these aquatic organisms are highly sensitive to environmental changes. Previously, 41 species of silica-scaled chrysophytes were recorded in the waters of Yakutia. In the present study, we supplemented this list with 55 species. We observed a high species richness (82 taxa) of silica-scaled chrysophytes in the study area. Of these, eight species were recorded in the waters of Russia for the first time. At present, the study area represents the northernmost habitat for most species observed during the study. The diversity of silica-scaled chrysophytes in Arctic rivers is comparable to or even greater than the diversity of chrysophycean flora at the middle latitudes. Most of these chrysophytes are represented by polyzonal and ubiquitous species. During 2008–2010, we noted increased relative numbers of boreal species in northern waters compared with data obtained during the previous 30 years. Overall, the species richness of silica-scaled chrysophytes in the studied rivers increased with increase in water transparency, temperature, and magnesium ion concentration, but decreased with increase in surfactant concentration. The origin of samples from a certain river; distance of the sampling site from the estuary; water temperature, transparency, and colour; and concentration of carbon dioxide, magnesium ions, total iron, surfactants, and oil products affect the species composition of silica-scaled chrysophytes in the study area. Our findings are fundamental to evaluate the current status of Arctic aquatic microflora and its further monitoring in the context of anthropogenic and climatic impacts

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

Diversity Variation of Silica-Scaled Chrysophytes Related to Differences in Physicochemical Variables in Estuaries of Rivers in an Arctic Watershed

The present study examined the taxonomic diversity of silica-scaled chrysophytes in the estuaries of the Arctic watershed of Yakutia in the context of global climate change, as these aquatic organisms are highly sensitive to environmental changes. Previously, 41 species of silica-scaled chrysophytes were recorded in the waters of Yakutia. In the present study, we supplemented this list with 55 species. We observed a high species richness (82 taxa) of silica-scaled chrysophytes in the study area. Of these, eight species were recorded in the waters of Russia for the first time. At present, the study area represents the northernmost habitat for most species observed during the study. The diversity of silica-scaled chrysophytes in Arctic rivers is comparable to or even greater than the diversity of chrysophycean flora at the middle latitudes. Most of these chrysophytes are represented by polyzonal and ubiquitous species. During 2008–2010, we noted increased relative numbers of boreal species in northern waters compared with data obtained during the previous 30 years. Overall, the species richness of silica-scaled chrysophytes in the studied rivers increased with increase in water transparency, temperature, and magnesium ion concentration, but decreased with increase in surfactant concentration. The origin of samples from a certain river; distance of the sampling site from the estuary; water temperature, transparency, and colour; and concentration of carbon dioxide, magnesium ions, total iron, surfactants, and oil products affect the species composition of silica-scaled chrysophytes in the study area. Our findings are fundamental to evaluate the current status of Arctic aquatic microflora and its further monitoring in the context of anthropogenic and climatic impacts

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