Microbial Genome-Resolved Metaproteomic Analyses Frame Intertwined Carbon and Nitrogen Cycles in River Hyporheic Sediments

Abstract

Background:Rivers serve as a nexus for nutrient transfer between terrestrial and marine ecosystems and as such, have a significant impact on global carbon and nitrogen cycles. In river ecosystems, the sediments found within the hyporheic zone are microbial hotspots that can account for a significant portion of ecosystem respiration and have profound impacts on system biogeochemistry. Despite this, studies using genome-resolved analyses linking microbial and viral communities to nitrogen and carbon biogeochemistry are limited.Results:Here, we characterized the microbial and viral communities of Columbia River hyporheic zone sediments to reveal the metabolisms that actively cycle carbon and nitrogen. Using genome-resolved metagenomics, we created the Hyporheic Uncultured Microbial and Viral (HUM-V) database, containing a dereplicated database of 55 microbial Metagenome-Assembled Genomes (MAGs), representing 12 distinct phyla. We also sampled 111 viral Metagenome Assembled Genomes (vMAGs) from 26 distinct and novel genera. The HUM-V recruited metaproteomes from these same samples, providing the first inventory of microbial gene expression in hyporheic zone sediments. Combining this data with metabolite data, we generated a conceptual model where heterotrophic and autotrophic metabolisms co-occur to drive an integrated carbon and nitrogen cycle, revealing microbial sources and sinks for carbon dioxide and ammonium in these sediments. We uncovered the metabolic handoffs underpinning these processes including mutualistic nitrification by Thermoproteota (formerly Thaumarchaeota) and Nitrospirota, as well as identified possible cooperative and cheating behavior impacting nitrogen mineralization. Finally, by linking vMAGs to microbial genome hosts, we reveal possible viral controls on microbial nitrification and organic carbon degradation.Conclusions:Our multi-omics analyses provide new mechanistic insight into coupled carbon-nitrogen cycling in the hyporheic zone. This is a key step in developing predictive hydrobiogeochemical models that account for microbial cross-feeding and viral influences over potential and expressed microbial metabolisms. Furthermore, the publicly available HUM-V genome resource can be queried and expanded by researchers working in other ecosystems to assess the transferability of our results to other parts of the globe.

Dominant nitrogen metabolisms of a warm, seasonally anoxic freshwater ecosystem revealed using genome resolved metatranscriptomics

“…Our study highlights the putative contributions of mineralization and DNRA to the hypolimnetic NH4 + pool of a large tropical lake. Although we acknowledge that multiple other pathways may play an important role in the accumulation of hypolimnetic N (e.g., sediment derived NH4 + flux (22), mineralization of fish waste or interactive effects of Lake Yojoa's virome on N cycling (38,39)), DNRA, because of its competition with inorganic N ecosystem loss pathways, remains a critical pathway for assessing annual N dynamics, particularly in systems, like Lake Yojoa, that experience seasonal N limitation (17). Determining controls on competing NO3 -/NO2reduction pathways the warm anoxic waters in Lake Yojoa and other lowlatitude lakes, are critical steps in broadening our mechanistic understanding of microbially driven biogeochemical processes that influence the trophic state of tropical freshwater ecosystems.…”