Microorganisms are critical to maintaining stratified biogeochemical characteristics
in meromictic lakes; however, their community composition and potential roles in
nutrient cycling are not thoroughly described. Both metagenomics and metaviromics
were used to determine the composition and capacity of archaea, bacteria, and
viruses along the water column in the landlocked meromictic Lake Shunet in Siberia.
Deep sequencing of 265 Gb and high-quality assembly revealed a near-complete
genome corresponding to Nonlabens sp. sh3vir. in a viral sample and 38 bacterial
bins (0.2–5.3Mb each). The mixolimnion (3.0m) had the most diverse archaeal,
bacterial, and viral communities, followed by the monimolimnion (5.5m) and chemocline
(5.0m). The bacterial and archaeal communities were dominated by Thiocapsa and
Methanococcoides, respectively, whereas the viral community was dominated by
Siphoviridae. The archaeal and bacterial assemblages and the associated energy
metabolism were significantly related to the various depths, in accordance with the
stratification of physicochemical parameters. Reconstructed elemental nutrient cycles
of the three layers were interconnected, including co-occurrence of denitrification
and nitrogen fixation in each layer and involved unique processes due to specific
biogeochemical properties at the respective depths. According to the gene annotation,
several pre-dominant yet unknown and uncultured bacteria also play potentially important
roles in nutrient cycling. Reciprocal BLAST analysis revealed that the viruses were specific
to the host archaea and bacteria in the mixolimnion. This study provides insights into
the bacterial, archaeal, and viral assemblages and the corresponding capacity potentials
in Lake Shunet, one of the three meromictic lakes in central Asia. Lake Shunet was
determined to harbor specific and diverse viral, bacterial, and archaeal communities
that intimately interacted, revealing patterns shaped by indigenous physicochemical
parameters.