Abstract
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 (0.2–5.3 Mb each). The mixolimnion (3.0 m) had the most diverse archaeal, bacterial, and viral communities, followed by the monimolimnion (5.5 m) and chemocline (5.0 m). 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.
Highlights
Meromictic lakes have a mixed upper oxic mixolimnion, an interface chemocline, and a lower stagnant anoxic monimolimnion, which does not mix with either of the upper layers (Bowman et al, 2000)
We conducted Non-metric Multidimensional Scaling (NMDS) on the basis of bacterial and archaeal community structures, followed by post-hoc regression of individual environmental variables; the results revealed that parameters including H2S, O2, NH+4, and NO−2, as well as 11 other parameters, significantly explained the variance of both community structures with depth (Figures 3C,D)
Archaeal and Bacterial Diversity Was High in Lake Shunet
Summary
Meromictic lakes have a mixed upper oxic mixolimnion, an interface chemocline, and a lower stagnant anoxic monimolimnion, which does not mix with either of the upper layers (Bowman et al, 2000). Microscopic techniques, pigment analysis, culture, FISH-TSA techniques and PCR-DGGE have been used to disentangle the seasonal changes of anoxygenic photosynthetic bacterial community, sulfate reduction and methanogenesis and ecophysiology of phototrophic sulfur bacteria at the chemocline of Lake Shunet (Kallistova et al, 2006; Lunina et al, 2007; Rogozin et al, 2009, 2010, 2012) These approaches are limited in providing a fine-scale, comprehensive insight into the microbial assemblages and their potential functions. Ace Lake is one of the most investigated lakes in Antarctica, in terms of its physicochemical profile, community structure, and functional dynamics (Laybourn-Parry and Bell, 2014) Both lakes are analogous, exhibiting characteristics such as permanent water stratification into three main zones, high H2S in the monimolimnion, and a gradient of dissolved oxygen (Table 1) (Lauro et al, 2011; Laybourn-Parry and Bell, 2014)
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