Endemic sponge Lubomirskia baikalensis as a bioindicator of chemical elements pollution in Lake Baikal.

To evaluate the prospects of using Baikal endemic sponges as bioindicators of chemical elements pollution, the elemental composition of sponges, water and substrate samples, collected in two areas with different levels of anthropogenic loading of the Baikal Lake, was determined using two analytical techniques. The content of Cl, Ca, V, Zn, As, Se, Ba, Cd, and Cu in the sponges collected in Listvennichny Bay was significantly higher than in Bolshye Koty Bay. The values of the pollution indices point at the slight to moderate pollution of the substrates. According to the bioaccumulation factor values, sponges accumulate mainly Cd, Cu and Br from the substrate, and the main part of the elements from water. The distribution of elements longwise the sponges and their intraspecific variation were evaluated. It was shown that Lubomirskia baikalensis sponges were suitable bioindicators to assess the pollution of Lake Baikal.

Metavirome datasets from two endemic Baikal sponges Baikalospongia bacillifera.

Sponges are ecologically important components of marine and freshwater benthic environments; these holobionts contain a variety of microorganisms and viruses. For the metagenomic characterization of potential taxonomic and functional diversity of sponge-associated dsDNA viruses, we surveyed two samples of Baikal endemic sponge Baikalospongia bacillifera (diseased and visually healthy). In total, after quality processing, we have obtained 3 375 063 and 4 063 311 reads; of these 97 557 and 88 517 sequences, accounting for ca. 2.9 and 2.2% of datasets, have been identified as viral. We have revealed approximately 28 viral families, among which the bacteriophages of the Myoviridae, Siphoviridae and Podoviridae families, as well as the viruses of the Phycodnaviridae and Poxviridae families, dominated in the samples. Analysis of viral sequences using the COG database has indicated 22 functional categories of proteins. Viral communities of visually healthy and diseased Baikal sponges were significantly different. The metagenome sequence data were deposited to NCBI SRA as BioProject PRJNA577390.

A new species of Baikal endemic sponges (Porifera, Demospongiae, Spongillida, Lubomirskiidae).

This paper reports on a new species of the Baikal endemic sponge (fam. Lubomirskiidae) Swartschewskia khanaevi sp. nov. The description of this species is based on morphological and molecular data (ITS and mitochondrial IGRs). Morphologically, S. khanaevi sp. nov. differs from S. papyracea by loose tracts arranged in an irregular network as well as the presence on strongyles of compound spines looking like tubercles densely ornamented with simple spines. Moreover, specimens of S. khanaevi sp. nov. show a peculiar structure of the aquiferous system at the body surface that may be an adaptive trait for environmental conditions. Phylogenetic analysis has revealed that S. khanaevi sp. nov. forms a well-supported (0.99) monophyletic clade with S. papyracea and is allocated as its sister taxa.

Diversity and shifts of the bacterial community associated with Baikal sponge mass mortalities.

The disease of freshwater sponges was first discovered in 2011, when pink samples were found in the Central Basin of Lake Baikal. Subsequently, the visible signs of the disease have changed, and now sponges appear with various symptoms of damage to the body, such as discoloration, tissue necrosis, the formation of brown patches and dirty-purple biofilms on some branches. These signs of the disease are accompanied by the mass death of sponges. We identified differences in microbiomes by sequencing 16S rRNA genes and found changes in the consortium of microorganisms of freshwater Baikal sponges. We found that the observed imbalance in the studied microbial communities of diseased sponges is caused by several different conditionally pathogenic microorganisms that increase their negative effect by acting together and in concert, which leads to the death of photosynthetic microalgae and sponges. Sponges are an important component of coastal communities, and the massive loss of sponges can obviously affect the structure of benthic communities and the purity of water.

Genetic diversity of Diplomonadida in fish of the genus Coregonus from Southeastern Siberia.

Diplomonadida are primitive flagellate protozoa, among which both commensals and pathogens have been recorded. To date, members of the genera Hexamita and Spironucleus have been reported in the digestive system of fish in the Baikal region. We determined the genetic diversity of Diplomonadida in fish of the genus Coregonus from south-eastern Siberia using molecular-genetic methods. Fish for analysis were caught in Lake Baikal and in the Barguzin, Nepa, Chechuy, and Kirenga rivers from 2010 to 2013. Gall bladders, hindguts and foreguts of 120 specimens of Coregonus migratorius representing three morpho-ecological groups, 25 specimens of Coregonus lavaretus baicalensis, 25 specimens of Coregonus tugun and 30 specimens of Coregonus lavaretus pidschian were analysed via amplification with primers specifically designed for eukaryotes. Amplicons positive for Diplomonadida were sequenced. A phylogenetic analysis revealed that diplomonad flagellates of whitefish from Southeastern Siberia belong to Spironucleus barkhanus. Positive Diplomonadida DNA samples were analysed with primers designed in the present study for the amplification of small subunits of ribosomal DNA fragments of S. barkhanus (about 1,430 bp) and sequenced. Phylogenetic analysis revealed inside the clade of S. barkhanus besides the cosmopolitan genotype from European salmon that was detected earlier in Baikalian grayling, a new genotype unique to the fish of the genus Coregonus from Lake Baikal.

The complete mitochondrial genome of Baikalospongia intermedia (Lubomirskiidae): description and phylogenetic analysis.

The complete mitochondrial genome of the Lake Baikal sponge Baikalospongia intermedia was sequenced. The circular mitochondrial genome is 28,327 bp in length and includes 14 protein-coding genes, 2 ribosomal RNA genes and 25 transfer RNA genes. Bayesian comparative analysis of molecular evolution rates was found no acceleration of the mtDNA evolution of B. intermedia. This species clustered with other species of the genus Baikalospongia on the Bayesian tree.

Small inverted repeats drive mitochondrial genome evolution in Lake Baikal sponges.

Demosponges, the largest and most diverse class in the phylum Porifera, possess mitochondrial DNA (mtDNA) markedly different from that in other animals. Although several studies investigated evolution of demosponge mtDNA among major lineages of the group, the changes within these groups remain largely unexplored. Recently we determined mitochondrial genomic sequence of the Lake Baikal sponge Lubomirskia baicalensis and described proliferation of small inverted repeats (hairpins) that occurred in it since the divergence between L. baicalensis and the most closely related cosmopolitan freshwater sponge Ephydatia muelleri. Here we report mitochondrial genomes of three additional species of Lake Baikal sponges: Swartschewskia papyracea, Rezinkovia echinata and Baikalospongia intermedia morpha profundalis (Demospongiae, Haplosclerida, Lubomirskiidae) and from a more distantly related freshwater sponge Corvomeyenia sp. (Demospongiae, Haplosclerida, Metaniidae). We use these additional sequences to explore mtDNA evolution in Baikalian sponges, paying particular attention to the variation in the rates of nucleotide substitutions and the distribution of hairpins, abundant in these genomes. We show that most of the changes in Lubomirskiidae mitochondrial genomes are due to insertion/deletion/duplication of these elements rather than single nucleotide substitutions. Thus inverted repeats can act as an important force in evolution of mitochondrial genome architecture and be a valuable marker for population- and species-level studies in this group. In addition, we infer (((Rezinkovia+Lubomirskia)+Swartschewskia)+Baikalospongia) phylogeny for the family Lubomirskiidae based on the analysis of mitochondrial coding sequences from freshwater sponges.