Lachnospiraceae and Bacteroidales alternative fecal indicators reveal chronic human sewage contamination in an urban harbor

Great Lakes WATER Institute, School of Freshwater Sciences, 600 E. Greenfield Ave., Milwaukee, WI 53204, USA.
Applied and Environmental Microbiology (Impact Factor: 3.95). 07/2011; 77(19):6972-81. DOI: 10.1128/AEM.05480-11
Source: PubMed

ABSTRACT The complexity of fecal microbial communities and overlap among human and other animal sources have made it difficult to identify source-specific fecal indicator bacteria. However, the advent of next-generation sequencing technologies now provides increased sequencing power to resolve microbial community composition within and among environments. These data can be mined for information on source-specific phylotypes and/or assemblages of phylotypes (i.e., microbial signatures). We report the development of a new genetic marker for human fecal contamination identified through microbial pyrotag sequence analysis of the V6 region of the 16S rRNA gene. Sequence analysis of 37 sewage samples and comparison with database sequences revealed a human-associated phylotype within the Lachnospiraceae family, which was closely related to the genus Blautia. This phylotype, termed Lachno2, was on average the second most abundant fecal bacterial phylotype in sewage influent samples from Milwaukee, WI. We developed a quantitative PCR (qPCR) assay for Lachno2 and used it along with the qPCR-based assays for human Bacteroidales (based on the HF183 genetic marker), total Bacteroidales spp., and enterococci and the conventional Escherichia coli and enterococci plate count assays to examine the prevalence of fecal and human fecal pollution in Milwaukee's harbor. Both the conventional fecal indicators and the human-associated indicators revealed chronic fecal pollution in the harbor, with significant increases following heavy rain events and combined sewer overflows. The two human-associated genetic marker abundances were tightly correlated in the harbor, a strong indication they target the same source (i.e., human sewage). Human adenoviruses were routinely detected under all conditions in the harbor, and the probability of their occurrence increased by 154% for every 10-fold increase in the human indicator concentration. Both Lachno2 and human Bacteroidales increased specificity to detect sewage compared to general indicators, and the relationship to a human pathogen group suggests that the use of these alternative indicators will improve assessments for human health risks in urban waters.

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Available from: Ryan J Newton, Aug 27, 2015
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    • "The latter are not well known in conventional testing regimes because they are anaerobes that do not grow in plate culture. Many of the recently proposed indicator bacteria have been identified in the Human Microbiome Project as the dominant bacteria in feces (e. g., Arumugam et al., 2011) and typically belong to the Bacteroidales, Bifidobacterium, Clostridiaceae, Lachnospiraceae or Ruminococcaceae (Mieszkin et al. 2009; Silkie and Nelson 2009; McLellan et al. 2010, 2013; Newton et al. 2011, 2013; McQuaig et al. 2012; Harwood et al. 2013). The use of multiple species and techniques to obtain several lines of evidence is now considered an important component of effective microbial source tracking (Harwood et al. 2013). "
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    • "The mean abundance of each genus was plotted using drop line. The detailed data were displayed using a heat map in Fig. S4 indicator bacteria to monitor sewage pollution and assess water quality (McLellan et al. 2010; McLellan et al. 2013; Newton et al. 2011; Wery et al. 2010). However, it is impossible to find one or several ideal indicator bacteria to represent the actual composition of sewage bacteria. "
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