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Blooms of the toxin-producing cyanobacterium Microcystis aeruginosa have recently appeared in the Klamath River (KR) and San Francisco Bay delta (SFBD), California, USA. We investigated Microcystis diversity in these systems by targeting cpcBA (phycocyanin gene intergenic spacer and flanking regions) and mcyA gene (encodes part of a peptide synthetase cluster for production of the toxin microcystin). Distinct differences in Microcystis populations in the KR reservoirs (Copco and Iron Gate reservoirs) and SFBD were found in both gene loci, and diversity in the mcyA gene discriminated the populations in the 2 ecosystems entirely. The cpcBA sequences from KR fell into 2 main clusters, and were closely similar to sequences from North and South America, Europe, Asia, and Africa. The majority of the cpcBA sequences in populations from SFBD formed a unique group, while the remaining sequences were closely similar to those from KR. Salinity, soluble reactive phosphorus concentration, pH, water transparency, and NH 4 + and NO 3 - + NO 2 - concentrations were significantly different in the 2 systems. The consistent differences in the 2 genetic markers between KR and SFBD populations suggest that Microcystis populations in the 2 watersheds have had limited connectivity or a different initial source population, or that environmental selection is creating distinct Microcystis populations in the eutrophic KR freshwater reservoirs and the saltwater influenced SFBD. Although Microcystis is globally distributed in temporal and subtropical climates, this study suggests local microdiversity exists and may be linked with environmental regulation.

Diversity of Microcystis aeruginosa in the Klamath River and San Francisco Bay delta, California, USA