Application of Phylogenetic Microarray Analysis to Discriminate Sources of Fecal Pollution

Conventional methods for fecal source tracking typically use single biomarkers to systematically identify or exclude sources. High-throughput DNA sequence analysis can potentially identify all sources of microbial contaminants in a single test by measuring the total diversity of fecal microbial communities. In this study, we used phylogenetic microarray analysis to determine the comprehensive suite of bacteria that define major sources of fecal contamination in coastal California. Fecal wastes were collected from 42 different populations of humans, birds, cows, horses, elk, and pinnipeds. We characterized bacterial community composition using a DNA microarray that probes for 16S rRNA genes of 59 316 different bacterial taxa. Cluster analysis revealed strong differences in community composition among fecal wastes from human, birds, pinnipeds, and grazers. Actinobacteria, Bacilli, and many Gammaproteobacteria taxa discriminated birds from mammalian sources. Diverse families within the Clostridia and Bacteroidetes taxa discriminated human wastes, grazers, and pinnipeds from each other. We found 1058 different bacterial taxa that were unique to either human, grazing mammal, or bird fecal wastes. These OTUs can serve as specific identifier taxa for these sources in environmental waters. Two field tests in marine waters demonstrate the capacity of phylogenetic microarray analysis to track multiple sources with one test

Decay of Coliphages in Sewage-Contaminated Freshwater: Uncertainty and Seasonal Effects

Understanding the fate of enteric viruses in water is vital for protection of water quality. However, the decay of enteric viruses is not well characterized, and its uncertainty has not been examined yet. In this study, the decay of coliphages, an indicator for enteric viruses, was investigated in situ under both sunlit and shaded conditions as well as in summer and winter. The decay rates of coliphages and their uncertainties were analyzed using a Bayesian approach. The results from the summer experiments revealed that the decay rates of somatic coliphages were significantly higher in sunlight (1.29 ± 0.06 day^–1) than in shade (0.96 ± 0.04 day^–1), but the decay rates of male-specific (F+) coliphages were not significantly different between sunlight (1.09 ± 0.09 day^–1) and shaded treatments (1.11 ± 0.08 day^–1). The decay rates of both F+ coliphages (0.25 ± 0.02 day^–1) and somatic coliphages (0.12 ± 0.01 day^–1) in winter were considerably lower than those in summer. Temperature and chlorophyll a (chla) concentration varied significantly (<i>p</i> < 0.001) between the two seasons, suggesting that these parameters might be important contributors to the seasonal variation of coliphage decay. Additionally, the Bayesian approach provided full distributions of decay rates and reduced the uncertainty, offering useful information for comparing decay rates under different conditions

Solar Inactivation of Enterococci and <i>Escherichia coli</i> in Natural Waters: Effects of Water Absorbance and Depth

The decay of sewage-sourced <i>Escherichia coli</i> and enterococci was measured at multiple depths in a freshwater marsh, a brackish water lagoon, and a marine site, all located in California. The marine site had very clear water, while the waters from the marsh and lagoon contained colored dissolved organic matter that not only blocked light but also produced reactive oxygen species. First order decay rate constants of both enterococci and <i>E. coli</i> were between 1 and 2 d^–1 under low light conditions and as high as 6 d^–1 under high light conditions. First order decay rate constants were well correlated to the daily average UVB light intensity corrected for light screening incorporating water absorbance and depth, suggesting endogenous photoinactivation is a major pathway for bacterial decay. Additional laboratory experiments demonstrated the presence of colored dissolved organic matter in marsh water enhanced photoinactivation of a laboratory strain of <i>Enterococcus faecalis</i>, but depressed photoinactivation of sewage-sourced enterococci and <i>E. coli</i> after correcting for UVB light screening, suggesting that although the exogenous indirect photoinactivation mechanism may be active against <i>Ent. faecalis,</i> it is not for the sewage-source organisms. A simple linear regression model based on UVB light intensity appears to be a useful tool for predicting inactivation rate constants in natural waters of any depth and absorbance