Metabolic Interactomes Unveil Functional Seasonality in a Time Series Analysis

Abstract

Ecological network analysis has become a particularly useful tool for studying microbial associations in marine environments. Using taxonomic information (typically using the small subunit ribosomal gene as a marker), ecological network analysis has resolved the co-occurrence between different taxonomic units (or species), disclosing potential biotic (microbe-microbe) interactions. However, the study of taxonomical associations alone cannot reveal the metabolic and functional rationale of such interactions. In the current work, we combine metagenomic data of a Mediterranean time-series dataset for picoeukaryotic and prokaryotic cells and ecological network analysis to analyze the associations between key genes involved in different metabolic pathways. We observe abundant potential interactions at the gene level, suggesting widespread metabolic associations between marine microbes. Metabolism of vitamins (including de novo synthesis of cobalamin) shows the highest degree of correlations with other metabolic functions, highlighting vitamins as a key component shaping microbial community structure. Other genes related to nitrogen metabolisms, such as amoA and nitrite reductase (nirK) genes, and genes involved in urea production through purine degradation, also show a strong correlation between them in winter, indicating that during this season microbes may interact between them through nitrogen metabolism. Our preliminary results reveal that gene-based networks are an especially powerful tool to analyze possible metabolic interactions and may facilitate the proposition and future testing of such interaction hypotheses