Couples in the deep: dissolved organic and microbial communities in the oxygenated hypolimnion of a deep freshwater lake

The interaction between dissolved organic matter (DOM) and microbial communities is a critical yet understudied driver of biogeochemical cycling in aquatic ecosystems. Understanding these interactions is essential for elucidating the chemical and microbial dynamics that sustain ecosystem functionings. Here, we combined non-target ultra high-resolution mass spectrometry-based environmental metabolome analysis with microbiome analysis to conduct the first comprehensive investigation of DOM-microbe linkages in both the epilimnion and oxygenated hypolimnion of a deep freshwater lake throughout the stratification period, with Lake Biwa (Japan) as a model system. To facilitate interpretation of DOM-microbe networks, we developed an integrated compound category classification (IC3) framework for assigning molecular formulae (MFs) to specific compound categories. Using a compositional data analysis framework, we identified specific MFs and bacterial taxa that covaried in the hypolimnion, which exhibited substantially more complex networks than the epilimnion. These networks encompassed 1705 out of the 1755 common MFs, representing the majority of total peak intensities, underscoring stronger DOM-microbe coupling in deep waters. Hypolimnion specialist bacteria were associated with specific MFs and co-ocuuring taxa, providing environmental metabolomic evidence for substrate preference and potential symbiotic relations. Notably, more than three-fourths of these MFs in relative abundance were classified as recalcitrant, including lipid-, lignin-, tannin-like, and carboxyl-rich alicyclic molecules, suggesting the capability of hypolimnion specialists to use or produce these compounds. Our study offers the first high-resolution insights into DOM-microbe associations in a deep freshwater lake and establishes a framework for more efficient and robust analyses of such interactions.