The effects of nutrient limitation and cyanophage on heterotrophic microbial diversity

Marine viruses are critically important in the regulation of biogeochemical cycles and host microbial communities. In this study, we tested whether the indirect effects of virus predation on a phototroph (i.e., Synechococcus) affected the composition of co-occurring heterotrophic bacteria under nitrogen and phosphorus limitation in long-term chemostat experiments. Using 454 Titanium barcoded pyrosequencing of the 16S rRNA gene, microbial diversity and technical (i.e., sequencing) reproducibility were assessed for nine individual chemostats across five different time points. A total of 325,142 reads were obtained; 194,778 high-quality, non-cyanobacterial sequences were assigned to 110 OTUs. Our results show high reproducibility with most communities clustering closest with their technical replicate, and a similar distribution of taxonomic assignments across replicates. The most abundant phylum was Proteobacteria, with Cyanobacteria representing only 20% of the sequences. OTU-based analyses revealed similar trends across chemostats; Sulfitobacter was the dominant genus while Pseudomonas was unique to the phosphorus-limited chemostats. A statistical examination of biological replicates revealed significant differences between the nitrogen- and phosphorus-limited treatments (p = 0.0001) and time (p = 0.0001), as well as a significant interaction between nutrient limitation and time (p = 0.0091). These results demonstrate the relative importance of nutrient-limitation as a potential primary driver of non-target heterotrophic community change as opposed to the indirect effects of viruses on a marine food web.