The prospects for application of metagenomic technologies in environmental studies are discussed. The advantages in investigating the taxonomic composition of aquatic and terrestrial ecosystems, as well as examples of trophic and phoric relationships found in ecosystems using the metagenomic approach, are described. The capabilities of metagenomics to study prokaryotic communities in complicated environments such as soils or animal intestines are shown. The role of relic DNA in the metagenome and the possibilities to study ancient organisms are highlighted. Particular attention is paid to the criticism of metagenomic technologies related to the low reproducibility of the sequencing data. Common methodological mistakes in bioinformatics processing of metagenomic data leading to misleading results are considered.

Nitrogenase activity, the abundance of diazotrophic bacteria, the structure and functional characteristics of the complex of microorganisms, and the content of nitrogen and carbon were determined in the contents of the gastrointestinal tract of the European beaver. A high nitrogen-fixing activity in the large intestine correlated with an increase in nitrogen content in the chyme upon its transfer over the gastrointestinal tract. It is assumed that microbial nitrogen fixation plays a major role in nitrogen nutrition of the European beaver.

The intensity of urea recycling in the wild herbivorous European hare has been investigated. The intensity of urease activity in the gastrointestinal tract has been selected as a convenient quantitative measure of nitrogen recycling. High urease activity was detected in the large intestine; it was higher than the previously detected activity in other mammals with postgastric fermentation: pigs, rats, and rabbits. The strong seasonal dynamics of urease activity has been noted: it increases during winter diet consumption, which is poor in available nitrogen.

Climate changes cause a dramatical increase in the ice-free season in the Arctic, forcing polar bears ashore, closer to human settlements associated with new and non-natural food objects. Such a diet may crucially transform the intestinal microbiome and metabolism of polar bears. The aim of this study was to characterize changes in the gut bacterial and fungal communities resulting from the transition to anthropogenic food objects by the means of 16S and ITS metabarcoding. Thus, rectal samples from 16 wild polar bears from the Kara–Barents subpopulation were studied. Human waste consuming resulted in a significant increase in the relative abundance of fermentative bacteria (Lactobacillaceae, Leuconostocaceae, and Streptococcaceae) and a decrease in proteolytic Enterobacteriaceae. However, the alpha-diversity parameters remained similar. Also, for the first time, the composition of the fungal community of the polar bear intestine was determined. Diet change is associated with the displacement of eurybiontic fungi (Thelebolus, Dipodascus, Candida (sake), and Geotrichum) by opportunistic Candida (tropicalis), Kazachstania, and Trichosporon. Feeding on human waste does not cause any signs of dysbiosis and probably leads to adaptive changes in the bacterial microbiome. However, the emergence of fungal facultative pathogens increases the risk of infections.

Nitrogenase activity, abundance of diazotrophic bacteria, and structural and functional parameters have been determined in microbial complexes of three populations of the termite Reticulitermes lucifugus and their nest materials. These data have been used for comparative analysis of nitrogen-fixing microorganism communities in termite guts and in nest materials from different termite populations. Similarities in the structure and other parameters of these communities have been revealed. The taxonomic composition of microbial communities differs among the populations, but the functional properties of these communities are almost identical. It is concluded that no symbiotic (mutualistic) relationship exists between nitrogen-fixing intestinal bacteria and their host termites.

In order to assess the role of the microbiocenosis of the digestive tract of herbivorous birds in transforming poor forage, the activity of cellulolytic enzymes in all departments of the gastrointestinal tract of the black grouse (Lyrurus tetrix) and Western capercaillie (Tetrao urogallus) was studied. The functional diversity of microbial communities of different departments was also investigated. In both species of birds, nitrogenase and cellobiohydrolase activities were discovered in the digestive tract, with the maximum observed in the cecum.