The Molecular Ecology of Microcystis sp. Blooms in the San Francisco Estuary Delta

Harmful blooms of the cyanobacterium Microcystis sp. have become increasingly pervasive in the San Francisco Estuary Delta (USA) since the early 2000's and their rise has coincided with substantial decreases in several important fish species. We sought to investigate direct and indirect effects Microcystis blooms may have on the Delta food web. The Microcystis population was tracked for two years at six sites throughout the Delta using quantitative PCR. High-throughput amplicon sequencing and colony PCR sequencing revealed the presence of 10 different strains of Microcystis, including six different microcystin-producing genotypes. Shotgun metagenomic analysis identified a variety of Microcystis secondary metabolite pathways, including those for the biosynthesis of: aeruginosin, cyanopeptolin, microginin, microviridin j and piricyclamide. We observed a sizable reduction in microbial community diversity during a large Microcystis bloom (H'=0.61) relative to periods preceding (H'=2.32) or following (H'=3.71) the bloom. Physicochemical conditions of the water column were stable throughout the bloom period, suggesting a possible role of broad allelopathy influencing microbial food web structure during the bloom. Network analysis was employed to elucidate synergistic and antagonistic relationships between Microcystis and other bacteria and indicated that only very few taxa were positively correlated with Microcystis, providing further support for the allelopathy hypothesis.