Patterns of phylogenetic and functional diversity in a salt marsh microbial mat

Background/Question/Methods

Coastal microbial mats are comprised of distinctly-colored millimeter-thick layers whose bacterial and archaeal communities organize in response to environmental gradients such as light availability, oxygen/sulfur concentrations, and redox potential. Here, slight changes in depth correspond to sharp niche boundaries. We explore the patterns of biodiversity along this depth gradient as it relates to functional groups of bacteria, as well as trait-encoding genes. We investigated how the mat's layers differed from one another with respect to taxonomic, phylogenetic, and trait diversity, and used these metrics to assess potential drivers of community assembly. We used 454 pyrosequencing to generate SSU-rRNA amplicon libraries and a shotgun metagenome for three mat cores, each of which was sectioned into its constituent layers prior to DNA extraction. For each layer, we calculated rarefied taxonomic, phylogenetic, and trait richness measures, as well as phylogenetic diversity profiles. We then compared these values within and among our mat cores and across other types of mat habitats. We used a range of null models to compute the degree of phylogenetic and functional dispersion for each layer, which can elucidate the effects of niche-driven habitat filtering within a community.

Results/Conclusions

Our reads were dominated by Cyanobacteria and purple sulfur bacteria (Chromatiales), but contained a wide range of taxa (total richness = 3,357 OTUs). The taxonomic composition of our communities was significantly different for mat age, year, and layer. UniFrac analysis revealed that mats of a given age and year were most similar, with the exception of the top (green) layers, which all clustered together. Phylogenetic richness and evenness positively covaried with depth, and trait richness tended to decrease with depth. We found evidence for significant phylogenetic clustering for all bacteria in the oldest mat layers, supporting the role of habitat filtering in the assembly of mat layers. However, this signal disappeared when the phylogenetic dispersion of particular functional groups, such as sulfate-reducing bacteria, was measured. Overall, trait diversity measured by orthologous gene annotations was also lower than would be expected by chance, except for genes related to photosynthesis in the topmost layer. Additionally, we show how the choice of taxa pools, null models, spatial scale, and phylogenies can convolute hypotheses about the community's assembly. Our results demonstrate that given the appropriate abiotic conditions, strong phylogenetic and trait turnover, as well as habitat filtering, can occur at the millimeter scale