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.

Figure 1

The effects of adaptive mutations on diversity within and between ecotypes. (a) The effect of a periodic selection event. Here, a mutant (or recombinant) with improved ability to compete for the resources of ecotype 1, indicated by an asterisk, is able to extinguish the diversity within the same ecotype. The diversity within ecotype 2 is not affected by periodic selection occurring within ecotype 1. After the periodic selection, diversity once again accumulates within ecotype 1. (b) The effect of a niche-invasion mutation. Here, a mutant, indicated by a plus sign, obtains the ability to utilize a new set of resources and thereby founds an ecotype. Ecotype 2 begins as a clone, with no diversity, but it eventually accumulates genetic diversity by mutation and recombination (Ward & Cohan 2005). (Used with permission from the Thermal Biology Institute.)

Figure 2

The phylogenetic history of two closely related ecotypes under the stable ecotype model. After each periodic selection event, indicated by an asterisk, only one variant from an ecotype survives. After periodic selection, the descendants of the surviving variant diverge (indicated by dashed lines), but with the next periodic selection event, again only one variant survives. Note that a sequence-based phylogeny of two ecotypes will indicate very limited sequence diversity within an ecotype, with much greater sequence divergence between members of different ecotypes. This model yields a one-to-one correspondence between ecotypes and sequence clusters. (Used with permission from the Thermal Biology Institute.)

Figure 3

Observed and predicted community sequence diversity pattern for gyrA sequences of the strains of B. licheniformis–B. sonorensis clade isolated from ‘Evolution Canyon’ III. Complete linkage clustering was used to bin the sequences into clusters with different levels of minimum pairwise identity ranging from 0.85 to 1.00. The model curves are based on the mean number of bins for each sequence-identity criterion, over 1000 replicate runs of the high-drift and low-drift parameter solutions (Cohan et al. submitted).

Figure 4

The community phylogeny simulation. To begin a simulation with a given quartet of values for the net ecotype formation rate (Ω), the periodic selection rate (σ), the genetic drift rate (d) and the number of ecotypes (n), the υ contemporary organisms are distributed randomly among the n ecotypes. (In the case of this figure, υ=14 and n=3.) Working backwards from the present, the processes of ecotype formation, periodic selection and drift occur stochastically in time according to their respective rates. The backward phase of the simulation ends when only a single lineage remains; this represents the most recent common ancestor of the community. The forward simulation begins when a sequence is assigned to the most recent common ancestor. Substitutions then occur stochastically, going forward in time, between each pair of nodes in the phylogeny, according to the time between the events determining the nodes (Cohan et al. submitted).

Figure 5

Phylogeny of the Bacillus licheniformis subclade of the B. subtilis–B. licheniformis clade based on the neighbour-joining analysis of sequence diversity at rpoB. The putative ecotypes demarcated by community phylogeny are listed as the ‘Groups’ in the figure. The ecotypes were demarcated as the largest clades that were each consistent with being a single ecotype (i.e. such that 95% CI included n=1 ecotype). The phylogeny is rooted by B. halodurans. Microhabitat sources were the south-facing slope (open circles), the north-facing slope (filled circles) and the canyon bottom (V-shaped) within ‘Evolution Canyon’; asterisks indicate reference strains isolated outside of ‘Evolution Canyon’. The phylogeny of the B. subtilis subclade, which was included in the community phylogeny analysis, is not shown here.