Towards a conceptual and operational union of bacterial systematics, ecology, and evolution

Abstract

To completely understand the ecology of a bacterial community, we need to identify its ecologically distinct populations (ecotypes). The greatest promise for enumerating a community's constituent ecotypes is held by molecular approaches that identify bacterial ecotypes as DNA sequence clusters. These approaches succeed when ecotypes correspond with sequence clusters, but some models of bacterial speciation predict a one-to-many and others a many-to-one relationship between ecotypes and sequence clusters. A further challenge is that sequence-based phylogenies often contain a hierarchy of clusters and subclusters within clusters, and there is no widely accepted theory to guide systematists and ecologists to the size of cluster most likely to correspond to ecotypes. While present systematics attempts to use universal thresholds of sequence divergence to help demarcate species, the recently developed 'community phylogeny' approach assumes no universal thresholds, but demarcates ecotypes based on the analysis of a lineage's evolutionary dynamics. Theory-based approaches like this one can give a conceptual framework as well as operational criteria for hypothesizing the identity and membership of ecotypes from sequence data; ecology-based approaches can then confirm that the putative ecotypes are actually ecologically distinct. Bacterial ecotypes that are demonstrated to have a history of coexistence as ecologically distinct lineages (based on sequence analysis) and as a prognosis of future coexistence (based on ecological differences), are the fundamental units of bacterial ecology and evolution, and should be recognized by bacterial systematics.

Phenotypic and genetic diversification of Pseudanabaena spp. (cyanobacteria)

“…Cluster II or the 'PCCA ecotype' occurs as a group with 99% similarity ('microdiversity cluster'), at a variety of different loci (ITS, cpcBA gene and cpcBA-IGS analysis). Previous studies indicate that such microdiversity clusters could represent important units of differentiation as ecotypes in natural populations of bacteria (Palys et al, 1997;Moore et al, 1998;Rocap et al, 2003;Konstantinidis and Tiedje, 2005;Lopez-Lopez et al, 2005;Thompson et al, 2005;Cohan, 2006;Polz et al, 2006;Cohan and Perry, 2007), and are often observed in environmental clone libraries (Field et al, 1997;Acinas et al, 2004;Morris et al, 2005;Johnson et al, 2006;Pommier et al, 2007). The microdiversity clusters identified here are correlated with morphological and ecophysiological traits such as cell length and the capacity to perform CCA (Figures 4 and 5), providing further support for the designation as an ecotype (Ahlgren and Rocap, 2006;Johnson et al, 2006;Polz et al, 2006;Ward et al, 2006).…”

Seasonal dynamics of SAR11 populations in the euphotic and mesopelagic zones of the northwestern Sargasso Sea

“…Evidence for ecotypes: vertical stratification and seasonality Ecotypes are similar phylogenetic subgroups of bacteria that differ in physiological details that determine niche specificity (Cohan, 2006). Patterns of variation in time and space are often used to identify ecotypes.…”

Patterns and mechanisms of genetic and phenotypic differentiation in marine microbes

“…One possible mechanism is that selective sweeps may periodically purge genetic variation from coexisting genomes (Cohan 2002(Cohan , 2006. This assumes that clonally reproducing bacteria will accumulate mutations, which, in rare cases, are adaptive.…”