Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

Abstract

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.

Microbial Nitrogen Transformation Potential in Sediments of Two Contrasting Lakes Is Spatially Structured but Seasonally Stable

“…8 ). This is in agreement with metagenomic studies of various ecosystems recovering the genetic potential for most, if not all, N transformation pathways ( 26 , 54 – 57 ). Despite the overall similarities in the N cycling potential, ecosystems harbor unique N transforming microbial communities forming complex networks ( 1 ).…”

Stratification in Microbial Communities with Depth and Redox Status in a Eutrophic Lake Across Two Years

“…The presence of even a small number of Cyanobacteria at the anoxic bottom of the lake is surprising considering their association with aerobic metabolism. However, this has been observed elsewhere (Tran et al 2021). Actinobacteria are known to include the cosmopolitan epilimnetic lineage acI (order Nanopelagicales), and account for much of the abundance in the epilimnion.…”

“…The most coarse taxonomic level, phylum, was a natural starting point to visualize the most general trends in the microbiome. The relative abundance of phyla has been shown to change dramatically with depth in several other depth-discrete sampling studies (Tran et al 2021;Rojas-Jimenez et al 2021;Baatar et al 2016;Garcia et al 2013). These changes in phyla are often attributed to the redox gradients throughout the water column (Jones, Newton, and McMahon 2009;Wu and Hahn 2006;Newton et al 2007;Garcia et al 2013) .…”

“…We also further investigated the taxonomic composition of the Cyanobacteria, particularly to identify the lineages living in the hypolimnion. Despite their reputation as being photoautotrophic, Cyanobacteria have been known to grow in dark and anoxic waters (Callieri et al 2019;Tran et al 2021). In our samples, at the class level, Cyanobacteria were almost exclusively Oxyphotobacteria (~97%).…”

vRhyme enables binning of viral genomes from metagenomes

“…Scaffolds used to benchmark performance were acquired from nine separate publicly available datasets spanning eight unique metagenomes from marine 48,49 , freshwater [50][51][52] , human gut 53 , and soil environments 54,55 . Details on the studies, scaffolds, reads, and accession numbers can be found in Supplemental Table 11 Each dataset was processed separately.…”