Lake Tanganyika (LT) is the largest tropical freshwater lake, and the largest body of anoxic freshwater on Earth’s surface. LT’s mixed oxygenated surface waters float atop a permanently anoxic layer and host rich animal biodiversity. However, little is known about microorganisms inhabiting LT’s 1470 meter deep water column and their contributions to nutrient cycling, which affect ecosystem-level function and productivity. Here, we applied genome-resolved metagenomics and environmental analyses to link specific taxa to key biogeochemical processes across a vertical depth gradient in LT. We reconstructed 523 unique metagenome-assembled genomes (MAGs) from 34 bacterial and archaeal phyla, including many rarely observed in freshwater lakes. We identified sharp contrasts in community composition and metabolic potential with an abundance of typical freshwater taxa in oxygenated mixed upper layers, and Archaea and uncultured Candidate Phyla in deep anoxic waters. Genomic capacity for nitrogen and sulfur cycling was abundant in MAGs recovered from anoxic waters, highlighting microbial contributions to the productive surface layers via recycling of upwelled nutrients, and greenhouse gases such as nitrous oxide. Overall, our study provides a blueprint for incorporation of aquatic microbial genomics in the representation of tropical freshwater lakes, especially in the context of ongoing climate change, which is predicted to bring increased stratification and anoxia to freshwater lakes.

坦噶尼喀湖（LT）是最大的热带淡水湖，也是地球表面最大的缺氧淡水湖。LT 的混合含氧地表水漂浮在永久缺氧层之上，拥有丰富的动物生物多样性。然而，人们对居住在 LT 1470 米深水柱中的微生物及其对养分循环的贡献知之甚少，而养分循环会影响生态系统层面的功能和生产力。在这里，我们应用基因组解析的宏基因组学和环境分析将特定类群与 LT 垂直深度梯度上的关键生物地球化学过程联系起来。我们从 34 个细菌和古细菌门中重建了 523 个独特的宏基因组组装基因组 (MAG)，其中包括许多在淡水湖泊中很少观察到的基因组。我们发现，在含氧混合上层中存在丰富的典型淡水类群，在深层缺氧水域中存在古细菌和未培养的候选门，这在群落组成和代谢潜力方面存在鲜明对比。从缺氧水中回收的 MAG 具有丰富的氮和硫循环的基因组能力，这突显了微生物通过回收上涌的营养物和一氧化二氮等温室气体对生产性表层的贡献。总的来说，我们的研究为将水生微生物基因组学纳入热带淡水湖泊的代表性提供了蓝图，特别是在持续气候变化的背景下，预计这将给淡水湖泊带来分层和缺氧的加剧。