Table_4_Comprehensive Insights Into Composition, Metabolic Potentials, and Interactions Among Archaeal, Bacterial, and Viral Assemblages in Meromictic Lake Shunet in Siberia.DOCX

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.

微生物对于维持分层湖（meromictic lake）的生物地球化学特征至关重要；然而，其群落组成及其在养分循环中的潜在功能尚未得到充分阐明。本研究采用宏基因组学（metagenomics）与宏病毒组学（metaviromics）相结合的策略，对西伯利亚内陆分层湖舒内特湖（Lake Shunet）水柱中古菌、细菌与病毒的组成及功能潜能进行解析。通过对265 Gb测序数据进行深度测序与高质量组装，在病毒样本中获得了与Nonlabens sp. sh3vir.对应的近乎完整基因组，以及38个细菌基因组箱（每个大小为0.2–5.3 Mb）。变温层（3.0 m处）的古菌、细菌与病毒群落多样性最高，其次为滞水层（5.5 m处）与化学跃层（5.0 m处）。细菌与古菌群落分别以荚硫菌属（Thiocapsa）和甲基球菌属（Methanococcoides）为优势类群，而病毒群落则以长尾病毒科（Siphoviridae）为主导。古菌与细菌群落及其相关能量代谢过程与不同水深显著相关，这与物理化学参数的分层分布特征相一致。重构的三层元素养分循环网络相互关联，包括各层均存在反硝化作用与固氮作用的共现现象，且由于各深度处独特的生物地球化学属性，该循环涉及特有代谢过程。基因注释结果显示，多种优势未培养且尚未被表征的细菌在养分循环中也发挥着潜在的重要作用。双向BLAST（reciprocal BLAST）分析表明，本研究中的病毒与变温层中的宿主古菌和细菌具有严格的宿主特异性。本研究为舒内特湖——中亚三大分层湖之一——中的细菌、古菌与病毒群落组成及其对应功能潜力提供了全新的认知。舒内特湖拥有独特且多样的病毒、细菌与古菌群落，这些群落间存在密切的相互作用，其分布模式由当地的物理化学参数所塑造。