Diversity and Structure of Denitrifying Bacterial Communities in Different Biotopes of the Littoral Zone of Lake Baikal

Abstract— The composition and diversity of denitrifying bacteria inhabiting biofilms on rocky substrates (epilithic biofilms), the surface microlayer, the water column, and the near-bottom water layer in Southern Lake Baikal were studied using high-throughput amplicon sequencing of the functional genes (nirK and nirS) that encode nitrite reductases. It was revealed that denitrifying bacteria in the lake’s littoral zone are represented by the phyla Pseudomonadota and Gemmatimonadota. Denitrifiers of the nirS-type represented the classes Betaproteobacteria (64.9%), Alphaproteobacteria (28.6%), and Gammaproteobacteria (6.5%), while those of the nirK-type included Alphaproteobacteria (99.96%) and Gemmatimonadia (0.04%). Both similarities and differences were detected among biotopes in terms of the taxonomic composition of their denitrifier communities at the level of families and genera. Among nirS-containing bacteria, representatives of the family Rhodocyclaceae (25%) dominated epilithic biofilms. In the surface microlayer, water column, and bottom water layer, bacteria of the family Azonexaceae (23.6–36.6%) prevailed. A distinctive feature of the surface microlayer was the presence of the family Zoogloeaceae (9.3%). On the genus level, Geminicoccus (19.6%) was the most abundant genus of nirS-containing bacteria in epilithic biofilms, Rhizobacter (28.2%) in the water column, and Azonexus in the surface microlayer and bottom water layer (22.8 and 20.5%, respectively). Among the detected nirK-containing denitrifiers, bacteria of the family Paracoccaceae (66.3–84.4%) were the most abundant in all studied biotopes, represented predominantly by the genus Tabrizicola (59.4–76.7%). In epilithic biofilms, a substantial proportion of the bacteria belonged to the family Aestuariivirgaceae represented by the genus Aestuarivirga (25%) and in the surface microlayer, to the family Brucellaceae represented by the genus Ochrobactrum (10.2%). In addition, the surface microlayer was characterized by the presence of the family Gemmatimonadaceae (0.3%). The highest diversity of nirS-containing bacteria was observed in epilithic biofilms, while nirK-containing bacteria were most diverse in the near-bottom water layer. Using distance-based redundancy analysis (db-RDA), it was shown that the community structure of nirK-containing denitrifiers was largely determined by the concentration of nitrate nitrogen, but no significant correlations with the tested factors were found for nirS-containing bacteria.