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Here we present a framework for how shotgun metagenomics can be used to definitively identify problematic microorganisms and how these data can guide the development of rapid genetic assays for routine ... and compared with routine monitoring data, including microscopic cell counts, sonde-based physicochemical analyses, and assays of all inorganic and organic nitrogen and phosphorus forms and fractions. ... ACKNOWLEDGMENTS We thank the USGS Wichita field office for collection of routine water quality samples from Cheney Reservoir and Guy Foster, USGS Kansas Water Science Center, for assistance with the design ...doi:10.1128/aem.01334-16 pmid:27342564 pmcid:PMC4988214 fatcat:efvzx2vbtbexrg3ibt3moaddmm