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Authors: Jana C. Massing, Ashkaan Fahimipour, Carina Bunse, Jarone Pinhassi, Thilo Gross
Progress in molecular methods has enabled us to monitor bacterial community composition over time. Nevertheless, understanding community dynamics and its impact on ecosystem functioning is challenging due to the tremendous diversity. This highlights the need for conceptual frameworks to make sense of the time-series of diverse bacterial taxa, regarding their strategies and function. A key concept for such synthesis is the niche, the set of capabilities that enables a population to persist and that defines its impacts on the surroundings. Here we use diffusion maps to re-construct the metabolic niche space of a bacterial community from a long-term time-series, the Linnaeus Microbial Observatory (LMO) in the Baltic Sea. Using manifold learning, we propose a framework to organize genomic information into potentially occupied metabolic niches over time. The results reveal a broad spectrum of metabolic strategies of the bacterial community. Their combined niche-space has a tree-like structure comprising clusters of taxa featuring localized traits and continuous branches. Time patterns of potentially occupied niches seem to be strongly driven by seasonality, a key feature in the Baltic Sea. We find some functional strategies clearly dominated by one bacterial group and others that are divided between bacterial groups depending on season. These results illustrate the power of the diffusion map approach to advance our understanding of community dynamics and ecosystem function.
