Ocean microbes display remarkable genetic diversity

The smallest, most abundant marine microbe, Prochlorococcus, is a photosynthetic bacteria species essential to the marine ecosystem.

An estimated billion billion billion of the single-cell creatures live in the oceans, forming the base of the marine food chain and occupying a range of ecological niches based on temperature, light and chemical preferences, and interactions with other species. But the full extent and characteristics of diversity within this single species remains a puzzle.

To probe this question, scientists in MIT's Department of Civil and Environmental Engineering (CEE) recently performed a cell-by-cell genomic analysis on a wild population of Prochlorococcus living in a milliliter -- less than a quarter teaspoon -- of ocean water, and found hundreds of distinct genetic subpopulations.

Each subpopulation in those few drops of water is characterized by a set of core gene alleles linked to a few flexible genes -- a combination the MIT scientists call the "genomic backbone" -- that endows the subpopulation with a finely tuned suitability for a particular ecological niche. Diversity also exists within the backbone subpopulations; most individual cells in the samples they studied carried at least one set of flexible genes not found in any other cell in its subpopulation.

The researchers estimate that the subpopulations diverged at least a few million years ago. The backbone is an older, more slowly evolving component of the genome, while the flexible genes reside in areas of the genome where gene exchange is relatively frequent, facilitating more rapid evolution.