Uncovering the Prokaryotic Diversity of the Bathyal Waters above the Kuril–Kamchatka Trench

The Kuril–Kamchatka Trench (North-West Pacific Ocean) is included in the deepest trenches (>9000 m). This study is the first that aims at uncovering the bathyal prokaryotic diversity (1000–2000 m) of this fascinating extreme environment. The analysis of α-diversity revealed that bacterial communities showed greater diversity than archaeal communities and that both communities were characterized by poor evenness (indicative of the presence of few dominant OTUs). The metabarcoding analysis showed that Proteobacteria (65.5–90.7%), Bacteroidetes (2.4–10.7%), and Actinobacteria (2.5–9.6%) were the highly represented phyla of bacteria, with Acinetobacter (21.5–62.5%) as the most abundant genus. Moreover, the recently described Pseudofrancisella genus, which has been isolated from estuarine environments, has been found among the major bacterial taxa. This work represents the first report stating the presence of this genus in bathyal waters. The archaeal communities were dominated by the phylum Thaumarchaeota (53.6–94.0%), with Nitrosopumilus (53.6–94%) as its representative genus. The functional diversity analysis revealed that overall, the bacterial communities had a higher involvement in the carbon and nitrogen biogeochemical cycles, with chemoheterotrophy (mostly aerobic), aromatic compound degradation, and nitrate reduction as the most represented functions. In the archaeal communities, the most represented ecological function was the aerobic oxidation of ammonia (first stage of nitrification), a functional feature characteristic of Nitrosopumilus.