The phylum Actinobacteria
contains several of the recognized freshwater cosmopolitan bacterial groups. Within this phylum, the acI lineage is one of the most abundant lineages in freshwater and at times accounts for more than 50% of the total 4′,6′-diamidino-2-phenylindole (DAPI)-stained bacterioplankton cells in a lake's epilimnion (1
). It is also known that acI is an active and exclusive component of freshwater systems (36
). This lineage is globally distributed and occurs in a variety of limnetic systems characterized by extremely different physical, chemical, and biological qualities (21
). It has been postulated that the acI lineage's relatively small cell size, which provides protection from protistan grazing, may contribute to its global distribution (19
). However, it seems unlikely that small cell size is the single driving force behind acI's remarkable capacity to inhabit such a broad range of freshwater systems. Although the acI lineage is widely distributed and often very abundant, it remains an uncultured group of bacteria; therefore, identification of coherent but phylogenetically narrow clades and the distribution of these clades among lakes with different environmental characteristics are important for understanding acI's unique prevalence in freshwater ecosystems.
Recently, the acI lineage was divided into three more refined clades (36
), with a small expansion by Allgaier and Grossart (1
); however, the level of 16S rRNA gene identity within these three clades is relatively low (~95%). The broad clade definitions prevent a robust examination of acI community composition in relation to environmental variation. Coherent responses of bacterial groups to environmental conditions have been documented for groups defined by levels of 16S rRNA gene sequence identity near 98% (35
). Thus, finding significant relationships between acI community composition and environmental variation may require finer-scale taxonomic resolution than has been defined previously.
Analyzing communities from a phylogenetic perspective can provide significant insight into the forces that shape community composition at regional and local scales (38
). This linkage between ecology and evolutionary analysis can be termed phylogenetic ecology (39
). Despite the power of a phylogenetic perspective to explain community structure, few studies have employed this approach to study microbes (15
Since closely related taxa tend to have similar traits and have similar ecology (4
), at local spatial scales environmental factors can select for taxa in a regional pool of dispersing taxa (i.e., the taxon pool) that are closely related, which is termed environmental filtering (13a
). Environmental filtering may be an important force that affects the composition of bacterial communities (15
). The implicit assumption in this line of reasoning is that closely related taxa respond similarly, in terms of prevalence or abundance, to a particular environmental factor. However, the radiation of a taxon of bacteria with a competitive advantage in one region can result in bacterial communities dominated by closely related taxa, regardless of the environmental conditions at the local-community scale (15
). In contrast, physical isolation of bacterial communities can result in relatively unrelated communities in a region even though the environmental conditions of systems in the region are very similar (29
). Thus, the phylogeographic patterns of taxa must be taken into account in order to assess whether environmental filtering occurs in a set of communities.
At local spatial scales, a community may instead be composed of more distantly related taxa. In local communities, this pattern is consistent with the hypothesis of competitive exclusion (22
) or environmental filtering for unrelated taxa with convergently evolved tolerances to particular environmental factors (6
). The taxon pool may also be dominated by more distantly related taxa. This pattern is consistent with the hypothesis that the abundant taxa inhabit separate niches (i.e., they are separate ecotypes) and are the survivors of the most recent selective sweep (11
In this study we sought to significantly improve the current acI phylogeny and to use this phylogeny to identify lake environmental factors that are related to acI community composition. We applied a novel phylogenetic ecology approach to our data set and illustrated the usefulness of taking a phylogenetic perspective when forces that influence bacterial community composition are examined.