Hypothesizing ecological population structure from environmental sequences
Although it was recognized well over two decades ago that in most environments the diversity of genes used as markers for microbial taxa is vast, it was not clear how much of this diversity really matters when we want to estimate the number of ecologically distinct populations. We showed that thousands of 16S rRNA and protein-coding genes, which are used to survey microbial diversity, are retrieved from samples but that sequence diversity is organized into microdiverse clusters. This observation led us to hypothesize that these clusters represent ecologically distinct populations. Using marine bacteria of the genus Vibrio as a model, we tested this hypothesis using a combination of fine-scale environmental sampling and mathematical modeling, and we showed that sequence clusters differentially partition environmental resources. This represented the first step towards defining population structure in natural environments by allowing categorization of co-existing diversity into distinct ecological units and was the starting point for development of our population genomics model.
Selected references:
Acinas, S.G., Klepac-Ceraj, V., Hunt, D.E., Pharino, C., Ceraj, I., Distel, D.L., Polz, M.F. (2004) Fine-scale phylogenetic architecture of a complex bacterial community. Nature. 430:551-554.
Hunt, D. E., Lawrence, A. D., Gevers, D., Preheim, S., Alm, E. J., Polz, M. F. (2008) Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science. 320:1081-1085.