Identification of bacteria in groundwater used for domestic supply in the southeast San Joaquin Valley, California, 2014

Abstract

Groundwater is an important source of drinking water in California. Water-borne diseases caused by microbial contamination are a growing concern. The MI test, a membrane filtration method for the chromogenic/fluorogenic detection of total coliforms and Escherichia coli, was used for samples collected January to April 2014 from 42 domestic wells in the southeastern San Joaquin Valley. The wells were sampled as part of the Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP), a cooperative study between the U.S. Geological Survey and the California State Water Resources Control Board. Polymerase chain reaction analysis and sequencing of deoxyribonucleic acid (DNA) were used for 34 target and nontarget colonies that grew on the MI media from samples collected from 13 of the domestic wells to identify what genera of bacteria could exist in groundwater used by domestic wells. Gene sequences obtained using the Sanger method were entered into the basic local alignment search tool (BLAST) database, and 17 genera of bacteria were identified. Of these, 13 genera contain species that are human pathogens or opportunistic human pathogens. All the genera that include human pathogens are naturally present in soil, plants, or water; one of the pathogens also can be found in fecal matter. Six of the human pathogens were from non-target colony growth on the MI media. Target and non-target microbial growth on MI media are indicators of the possible presence of pathogenic bacteria even if the bacteria naturally are from soil rather than from a fecal source. 1U.S. Geological Survey 2Formerly with the U.S. Geological Survey Introduction Diseases can be spread by waterborne microbial pathogens in groundwater. Most waterborne microbial pathogens are derived from human or animal waste; however, evidence exists that many microorganisms can survive in viable but nonculturable forms in non-fecal conditions (Levin and others, 2002). For the years 2013–14, the Centers for Disease Control and Prevention (CDC) listed 42 reported outbreaks associated with drinking water (Benedict and others, 2017). Of the 42 outbreaks, 9 were caused by pathogens in groundwater. To test for each pathogen is difficult, prohibitively costly, and risks pathogenic exposure to the person doing the test. Fecal indicator bacteria (FIB), such as total coliforms (TCs) and enterococci, are commonly used to indicate the possible presence of waterborne disease-causing organisms of fecal origin. Fecal indicator bacteria were chosen as indicators of potential microbial contamination in the U.S. Environmental Protection Agency’s (EPA) “total coliform rule and ground water rule” because they generally are not pathogenic, are easy to culture, and can be fecal in origin (U.S. Environmental Protection Agency, 2008, 2020b). Coliforms inhabit the intestines of warm-blooded animals and are found in feces. Coliforms also are present in soil, on vegetation, and in water (Foppen and Schijven, 2006; Brennan and others, 2010; Krentz, 2012). Studies show that Escherichia coli (E. coli), one species of coliform always found in feces, and enterococci, another group of bacteria that are mostly of fecal origin, could be better indicators of fecal contamination than TCs (U.S. Environmental Protection Agency, 1986). 2 Identification of Bacteria in Groundwater Used for Domestic Supply in the Southeast San Joaquin Valley, California, 2014 About 60 percent of the water used for public and domestic drinking-water supply in California is groundwater (Dieter and others, 2018). Public-supply wells are routinely tested for TCs and E. coli as part of regulatory compliance monitoring, and corrective actions are taken if the maximum contaminant levels (MCLs) are exceeded (U.S. Environmental Protection Agency, 2008; California State Water Resources Control Board, 2019). In contrast, the State of California and the EPA do not regulate water quality in privately owned domestic wells (California State Water Resources Control Board, 2015; U.S. Environmental Protection Agency, 2020a). In a study by the U.S. Geological Survey (USGS) of domestic wells from 1991 to 2004, 34 percent of wells tested positive for TCs and 8 percent tested positive for E. coli (DeSimone and others, 2009). Testing of domestic wells in six California counties by the California State Water Resources Control Board found 14 to 33 percent of the wells tested positive for TCs, with the highest frequency in Tulare County in the southeast San Joaquin Valley (California State Water Resources Control Board, 2018). No information is available concerning the genera of bacteria causing these TC detections in the California domestic wells, however. Knowledge about the genera gives information about the possible origin of the bacteria, which informs what type of action might be needed to protect the well or the consumers of the water from the well from microbial contamination. In addition, knowledge of the genera could be useful for assessing the selectivity and specificity of commonly used TC tests for indicating the presence of potentially pathogenic bacteria. The EPA has approved several analytical methods for monitoring FIBs including traditional membrane filtration methods and defined substrate technology (Covert and others, 1989; Brenner and others, 1996; U.S. Environmental Protection Agency, 2002, 2006, 2008; Buckalew and others, 2006; Oldstadt and others, 2007; Zhang and others, 2015). Polymerase chain reaction (PCR) analysis is widely used to identify bacteria. In particular, the 16S ribosomal ribonucleic acid (rRNA) gene is a well-studied universal gene in bacteria and is a standard method for the identification of species (Barry and others, 1991; Jensen and others, 1993; Gürtler and Stanisich, 1996; Clermont and others, 2000; Ryu and others, 2013). The membrane filtration methods result in bacterial colonies that can be used for PCR analysis for identification of bacteria in the water samples that the defined substrate methods do not. Two common membrane filtration methods use MI medium (Brenner and others, 1993; U.S. Environmental Protection Agency, 2002) and mEI medium (U.S. Environmental Protection Agency, 2006). The USGS has an ongoing statewide assessment of water quality in groundwater resources used for drinking-water supplies for the California State Water Resources Control Board’s Groundwater Ambient Monitoring and Assessment Program Priority Basin Project (GAMA-PBP). The FIB samples were collected as part of a GAMA-PBP study of domestic wells in the southeastern part of the San Joaquin Valley from January to April 2014 (fig. 1). As the FIB tests used in this study are not generaor species-specific, the objective of this study was to identify the genera of bacteria cultured by these FIB methods from samples collected at domestic wells. The purposes of this report are to (1) identify some of the genera of bacteria that can be present in domestic wells in the San Joaquin Valley, (2) examine potential pathogenicity of bacteria cultured on MI media, and (3) present results of a literature review describing the general sources of bacteria identified by FIB methods.