A non-phylogenetic alpha diversity approach on prokaryotic community structure in aquatic systems

Comparative analyses of accumulating phylotype-abundance data of prokaryotic communities are relatively scarce and mainly approached with phylogenetic methodologies. However, when a great fraction of phylotypes is captured within a sample, application of alpha diversity measures is also possible, enabling the exploration of structural changes in prokaryotic communities. In the present study, phylotype-abundance data of Archaea and Bacteria were compiled from previous works on freshwater, thermal springs, and submarine mud volcanoes in Eastern Mediterranean region. Samples within each environment were used as pseudo-replicates to enable comparisons between the two assemblages (Archaea and Bacteria) and among different environments whereas sampling effort was found similar among samples using rarefaction curves. Phylotypes were defined as 16S rRNA sequences with 98% similarity. The most common diversity indices were calculated and relative abundance distributions (RADs) were employed to provide a more detailed interpretation of observed diversity patterns. The freshwater and mud volcanoes environments were the most diverse with respect to Bacteria but the least diverse considering Archaea, whereas thermal springs yielded very similar diversity for both assemblages. Overall, bacterial diversity was higher than archaeal with respect to richness and evenness since Archaea were characterized by high dominance and phylotype-poor distributions. The present comparative analysis of alpha diversity may offer useful insights into ecological processes shaping prokaryotic community structure, however equal sampling effort among different environments must be verified prior to analysis.