Bacterial ecology and evolution converge on seasonal and decadal scales

Ecology and evolution are distinct theories, but both processes unfold on contemporary time scales in microbiomes. To observe this, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. Using 2,855 representative genomes, we observed recurring annual patterns in species abundance and strain composition for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that strain dynamics similar to both ecological differentiation and competition were common. Overlayed upon seasonal patterns, we observed long-term change in strain composition in one in five species, including gradual changes, step changes, and disturbances followed by resilience. Seven members of the most globally abundant freshwater family, Nanopelagicaceae, experienced abrupt change in an unusually hot and dry year following a species invasion. This shift in strain composition coincided with positive selection of genes involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds are central to freshwater responses to global change. Across all taxa, we observed the same seasonal and decadal dynamics in both interspecific ecological and intraspecific evolutionary processes, with no clear delineation between ecology and evolution. We propose that rather than focusing on feedbacks between separate theories of ecology and evolution, we should adopt a new unified approach that views ecology and evolution as a single continuum.

Primary Presenter: Robin Rohwer, The University of Texas at Austin (robin.rohwer@gmail.com)

Authors:

Robin Rohwer, The University of Texas at Austin  (robin.rohwer@gmail.com)

Mark Kirkpatrick, The University of Texas at Austin  (kirkp@austin.utexas.edu)

Sarahi Garcia, 3Stockholm University  (sarahi.garcia@su.se)

Matthew Kellom, DOE Joint Genome Institute  (mkellom@lbl.gov)

Katherine McMahon, University of Wisconsin-Madison  (trina.mcmahon@wisc.edu)

Brett Baker, The University of Texas at Austin  (brett_baker@utexas.edu)