Identification of Bacteria in Groundwater Used for Domestic Supply in the Southeast San Joaquin Valley, California, 2014

Scientific Investigations Report 2021-5030
Prepared in cooperation with California State Water Resources Control Board
A product of the California Groundwater Ambient Monitoring and Assessment Program
By:  and 


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  • Data Release: Data Release - Detections of fecal indicator bacteria and DNA sequencing of selected bacterial growths in samples from the Madera/Chowchilla-Kings domestic aquifer study unit, 2014: Results from the California GAMA priority basin project
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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.

Suggested Citation

Burton, C.A., and Lawrence, C.J., 2021, Identification of bacteria in groundwater used for domestic supply in the southeast San Joaquin Valley, California, 2014: U.S. Geological Survey Scientific Investigations Report 2021-5030, 20 p.,

ISSN: 2328-0328 (online)

Study Area

Table of Contents

  • Acknowledgments  
  • Abstract  
  • Introduction  
  • Methods  
  • Results  
  • Discussion  
  • Conclusions  
  • References Cited 
Publication type Report
Publication Subtype USGS Numbered Series
Title Identification of bacteria in groundwater used for domestic supply in the southeast San Joaquin Valley, California, 2014
Series title Scientific Investigations Report
Series number 2021-5030
DOI 10.3133/sir20215030
Year Published 2021
Language English
Publisher U.S. Geological Survey
Publisher location Reston, VA
Contributing office(s) California Water Science Center
Description Report: vii, 20 p.; Data Release
Country United States
State California
Other Geospatial Southeast San Joaquin Valley
Online Only (Y/N) Y
Google Analytic Metrics Metrics page
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