Macroalgal-associated bacterial communities: species vs genes

A previous study by Burke et al. (2011a) analysed the species composition of Ulva australis associated bacterial communities (covered in my earlier blog). Surprisingly, it was found that there is very little phylogenetic similarity between bacterial communities on different U. australis samples (15% similarity). To explain this variability in community structure, Burke et al. proposed a competitive lottery hypothesis which states that community composition is determined by the functional roles needed to colonise ecological niches. In terms of bacteria, this means there are ‘pools’ of species which share functional roles and any species from within these pools may colonise an ecological niche, depending on who gets there first. Importantly, members of each pool may be phylogenetically related or unrelated.

To test the competitive lottery model, Burke et al. (2011b) set out to show that algal-associated bacterial communities are functionally distinct from the surrounding seawater, but contain a core of functional genes which are present across all algal samples.

Bacterial DNA was extracted from six individual U. australis samples and eight seawater samples (corresponding to samples from Burke et al. (2011a)). DNA samples were then cut down to a small size (around 2 kb) and large scale shotgun sequencing was then performed (a method of sampling an entire genome by aligning the overlap among small samples of DNA).

Results showed that algal-associated communities were functionally distinct from those in the surrounding seawater. Furthermore, 70% similarity in functional composition was found between U. australis-associated bacterial communities, indicating that despite the large differences in species composition between hosts (found in the previous study) many functions are shared, supporting the competitive lottery model. As a result of these shared functions, authors were able to define a set of ‘core functions’ to U. australis-associated bacterial communities, these were; detection and movement toward host surfaces, attachment and biofilm formation, response to algal host environment, regulation in response to environmental stimuli, lateral gene transfer and defense. Finally, after phylogenetic and taxonomic analysis, it was found that core functions were not restricted to a particular taxonomic group, suggesting functional equivalence between taxa and further supporting the competitive lottery model.

This key study by Burke and colleagues highlights the underestimated importance of genes/gene clusters in understanding community assembly in bacterial systems. Currently, most theory regarding the understanding of microbial diversity comes from the study of eukaryote ecology, where genetic coherence within eukaryotic species can be assumed; therefore the unit of species is relevant. However, results from this study and an earlier publication Burke et al. (2011a) suggest the analysis of species composition may tell us little about bacterial community structure due to the massive amount of genetic exchange between taxonomically distinct bacteria. Finally, the model used in this study could also be applicable to other complex host-associated microbial communities, where species composition is highly variable between hosts, such as the human microbiome.

Burke, C., Thomas, T., Lewis, M., Steinberg, P. and Kjelleberg, S. (2011) Composition, uniqueness and variability of the epiphytic bacterial community of the green alga Ulva asutralis. The International Society for Mircobial Ecology journal  5. 590-600.

Burke, C., Steinberg, P., Rusch, D., Kjelleberg, S. and Thomans, T. (2011) Bacterial community assembly based on functional genes rather than species. Proceedings of the National Academy of Sciences 108. 14288-14293.