Database of Amphibia distribution in West Siberia (Russia)

West Siberia is a large region in North Eurasia, which harbours multiple climatic zones, landscape types and biomes. Its amphibian fauna is characterised by a combination of European and Asian species. For many species, this region is the place where the limits of their global ranges are located (Rana temporaria, R. amurensis, Bufotes sitibundus). West Siberia also has at least two non-native amphibian species (Pelophylax ridibundus, Bufotes viridis). The exact ranges and patterns of distribution of the West Siberian amphibian species are poorly studied. The mapping of species ranges is important for the development of conservation measures and monitoring of invasive species is required to investigate their impacts on the natural ecosystems

Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of whitefish

Introduction: The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. This study has focused on the influence that trophic behavior and resulting parasitism has on the structure of the microbiome. Methods: Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode’s surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the washout procedure from the mucosa to understand the real structure of the fish gut microbiota. Results and discussion: Our results demonstrate that additional microbial community in the intestine are formed by the parasitic helminths that caused the restructuring of the microbiota in infected fish compared to those uninfected. Using the desorption method in Ringer’s solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from “surface” bacteria, and bacteria which are weakly and strongly associated with the tegument, bacteria obtained after treatment of the tegument with detergent, and bacteria obtained after removal of the tegument from the cestodes.info:eu-repo/semantics/publishedVersio

Trophic diversification and parasitic invasion as ecological niche modulators for gut microbiota of whitefish

Introduction: The impact of parasites on gut microbiota of the host is well documented, but the role of the relationship between the parasite and the host in the formation of the microbiota is poorly understood. This study has focused on the influence that trophic behavior and resulting parasitism has on the structure of the microbiome. Methods: Using 16S amplicon sequencing and newly developed methodological approaches, we characterize the gut microbiota of the sympatric pair of whitefish Coregonus lavaretus complex and the associated microbiota of cestodes parasitizing their intestine. The essence of the proposed approaches is, firstly, to use the method of successive washes of the microbiota from the cestode’s surfaces to analyze the degree of bacterial association to the tegument of the parasite. Secondly, to use a method combining the sampling of intestinal content and mucosa with the washout procedure from the mucosa to understand the real structure of the fish gut microbiota. Results and discussion: Our results demonstrate that additional microbial community in the intestine are formed by the parasitic helminths that caused the restructuring of the microbiota in infected fish compared to those uninfected. Using the desorption method in Ringer’s solution, we have demonstrated that Proteocephalus sp. cestodes possess their own microbial community which is put together from “surface” bacteria, and bacteria which are weakly and strongly associated with the tegument, bacteria obtained after treatment of the tegument with detergent, and bacteria obtained after removal of the tegument from the cestodes

Chestnut shell tannins: effects on intestinal inflammation and dysbiosis in zebrafish

The aim of the present study was to test the possible ameliorative efficacy of phytochemicals such as tannins on intestinal inflammation and dysbiosis. The effect of a chestnut shell (Castanea sativa) extract (CSE) rich in polyphenols, mainly represented by tannins, on k-carrageenan-induced intestinal inflammation in adult zebrafish (Danio rerio) was tested in a feeding trial. Intestinal inflammation was induced by 0.1% k-carrageenan added to the diet for 10 days. CSE was administered for10 days after k-carrageenan induced inflammation. The intestinal morphology and histopathology, cytokine expression, and microbiota were analyzed. The k-carrageenan treatment led to gut lumen expansion, reduction of intestinal folds, and increase of the goblet cells number, accompanied by the upregulation of pro-inflammatory factors (TNFα, COX2) and alteration in the number and ratio of taxonomic groups of bacteria. CSE counteracted the inflammatory status enhancing the growth of health helpful bacteria (Enterobacteriaceae and Pseudomonas), decreasing the pro-inflammatory factors, and activating the anti-inflammatory cytokine IL-10. In conclusion, CSE acted as a prebiotic on zebrafish gut microbiota, sustaining the use of tannins as food additives to ameliorate the intestinal inflammation. Our results may be relevant for both aquaculture and medical clinic field

DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio

In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTU's obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures

DNA extraction protocols may influence biodiversity detected in the intestinal microbiome: a case study from wild Prussian carp, Carassius gibelio

In this investigation, we examined the influence of different DNA extraction protocols on results obtained for intestinal microbiota of Prussian carp. We showed that significant differences were observed in numbers of reads, OTUs, Shannon index and taxonomic composition between two different DNA extraction protocols for intestine of Prussian carp (Carassius gibelio), and differences were also evident between microbial communities in the intestinal mucosa and intestinal content. Statistical analyses of 25 published articles also revealed a significant relationship between methods of DNA extraction and bacterial diversity in fish intestine of freshwater species. Microbial diversity, community structure, proportions of read numbers derived from each OTU and the total number of OTU's obtained by different DNA extraction protocols could lead to a bias in results obtained in some cases, and therefore researchers should be conservative in conclusions about community structures

Phylogenetic position of whitefish Coregonus lavaretus (L.) from Teletskoye Lake (Siberia) based on complete mitochondrial DNA

The taxonomy of the European whitefish species complex Coregonus lavaretus (L.) is extremely intricate. Owing to wide distribution from Central Europe to water bodies in Chukotka and high biological plasticity, many forms with different taxonomic status have been described. Teletskoye Lake is inhabited by two endemic whitefishes: Pravdin's whitefish Coregonus lavaretus pravdinellus and Teletskoye whitefish C. smitti. Previously, a total of 106 mitogenomes of whitefishes from the C. lavaretus complex from different populations of the Baltic and North seas were sequenced; however, there are no such data for whitefishes from Siberia. We obtain the mitochondrial genomes of C. smitti and C. l. pravdinellus, 16 738 bp in length, with high coverage. The mitogenomes differ in 46 positions (0.27%). Comparative analysis of C. lavaretus mitogenomes from water bodies of Europe and Teletskoye Lake confirms the common origin of the populations from the eastern part of the Baltic Sea and water bodies of Siberia. In addition, analysis of the complete mitogenomes of C. smitti and C. l. pravdinellus does not confirm their different taxonomic status, at least on the basis of mtDNA

Amphibian diversity and distribution in West Siberia (Russia)

West Siberia is a vast area in North Eurasia lying between the Ural Mountains and the Yenisei River. Its area is more than 2.4 million sq. km. West Siberia extends almost 3,000 km from north to south and has five ecological zones (biomes) following each other in the latitudinal direction: tundra, forest-tundra, forest-steppe, steppe, and the foothills and mountains of Salair, Altai, Kuznetsk Alatau, and Gornaya Shoria. The amphibian fauna of West Siberia is poor due to harsh climatic conditions and includes only 11 species. There is still no complete understanding of distribution patterns of different amphibian species in the region. The aim of this study is to partially fill this gap by summarizing all possible sources of occurrence records for amphibians in West Siberi

Contrasting phylogeographic patterns and demographic history in closely related species of Daphnia longispina group (Crustacea: Cladocera) with focus on North-Eastern Eurasia.

Species with large geographic distributions present a challenge for phylogeographic studies due to the logistic difficulties of obtaining adequate samples. Daphnia O.F. Müller (Anomopoda: Daphniidae) is a model genus for evolutionary biology and ecology, but many regions such as the remote areas of Siberia, remain poorly studied. Here we examined genetic polymorphism in the ribosomal 12S and the protein-coding ND2 mitochondrial genes of three closely related taxa of the Daphnia (Daphnia) longispina complex, namely D. galeata Sars, D. longispina O.F. Müller and D. dentifera Forbes. We estimated the phylogenetic relationships among these taxa based on a concatenated alignment of these two genes. Using sequences from the present study and those available in GenBank, we investigated the geographic distributions of the mitochondrial haplotypes of these species and proposed an evolutionary scenario for each taxon. Network structures, haplotype distribution patterns, and FST values indicated significant differences in the evolutionary history of the examined species. Our analysis of D. galeata populations confirmed its recent and fast expansion, without a previous phase of a strong population disconnection. In contrast, the high haplotype diversity in D. dentifera and D. longispina could be explained by the survival of different phylogroups in several glacial refugia located in different geographic regions. For all studied species, maximum haplotype diversity was recorded in the remote regions of Siberia-lakes of the Yenisei River and Transbaikalia. Our study is an important step in our understanding of the evolutionary history of the Daphnia longispina group and provides further evidence of the biogeographic significance of Siberia for freshwater taxa