Longitudinal metatranscriptomic sequencing of Southern California wastewater representing 16 million people from August 2020–21 reveals widespread transcription of antibiotic resistance genes

Water Research (Elsevier) | November 22nd, 2022

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater sample

Municipal wastewater provides a representative sample of human fecal waste across a catchment area and contains a wide diversity of microbes. Sequencing wastewater samples provides information about human-associated and medically important microbial populations, and may be useful to assay disease prevalence and antimicrobial resistance (AMR). Here, we present a study in which we used untargeted metatranscriptomic sequencing on RNA extracted from 275 sewage influent samples obtained from eight wastewater treatment plants (WTPs) representing approximately 16 million people in Southern California between August 2020 – August 2021. We characterized bacterial and viral transcripts, assessed metabolic pathway activity, and identified over 2,000 AMR genes/variants across all samples. Because we did not deplete ribosomal RNA, we have a unique window into AMR carried as ribosomal mutants. We show that AMR diversity varied between WTPs (as measured through PERMANOVA, P < 0.001) and that the relative abundance of many individual AMR genes/variants increased over time (as measured with MaAsLin2, Padj < 0.05). Similarly, we detected transcripts mapping to human pathogenic bacteria and viruses suggesting RNA sequencing is a powerful tool for wastewater-based epidemiology and that there are geographical signatures to microbial transcription. We captured the transcription of gene pathways common to bacterial cell processes, including central carbon metabolism, nucleotide synthesis/salvage, and amino acid biosynthesis. We also posit that due to the ubiquity of many viruses and bacteria in wastewater, new biological targets for microbial water quality assessment can be developed. To the best of our knowledge, our study provides the most complete longitudinal metatranscriptomic analysis of a large population's wastewater to date and demonstrates our ability to monitor the presence and activity of microbes in complex samples. By sequencing RNA, we can track the relative abundance of expressed AMR genes/variants and metabolic pathways, increasing our understanding of AMR activity across large human populations and sewer sheds.

Los Angeles County Department of Public Works Hydrology Manual

Los Angeles County Department of Public Works (LACDPW) | January 30th, 2006

This manual establishes the Los Angeles County Department of Public Works' hydrologic design procedures and serves as a reference and training guide. This manual contains

This manual establishes the Los Angeles County Department of Public Works' hydrologic design procedures and serves as a reference and training guide. This manual contains charts, graphs, and tables necessary to conduct a hydrologic study within the County of Los Angeles. Examples provide guidance on using the hydrologic methods.

Mapping saltwater intrusion with an airborne electromagnetic method in the offshore coastal environment, Monterey Bay, California

Journal of Hydrology (Elsevier) | April 1st, 2019

Study Region: The northern coast of the Monterey Bay, California, USA, extending from the coastline to 3.5 km offshore. Study Focus: Three-hundred and twenty line-kil

Study Region: The northern coast of the Monterey Bay, California, USA, extending from the coastline to 3.5 km offshore. Study Focus: Three-hundred and twenty line-kilometers of airborne electromagnetic (AEM) data were acquired offshore. These data spanned 20 km of coastline, extending up to 3.5 km offshore in water up to 18m in depth. Inversion of these data resulted in resistivity models extending to depths between 50 and 200m below sea level. The data were interpreted in conjunction with onshore monitoring well data, hydrologic and geologic reports, and electrical resistivity tomography (ERT) data to locate the freshwater/saltwater interfaces throughout the region. A resistivity-to-water-quality transform was established using well-based water quality and resistivity logging measurements. For resistivity values that could not be converted to water quality with this transform, local auxiliary information was used on a case-by-case basis to interpret the observed features. Some low resistivity anomalies were identified near the shore at depth, which were interpreted to be artifacts of the 1D assumption in the inversion scheme used for these AEM data. New Hydrogeological Insights for this Region: We found that the acquisition of AEM data provided valuable information about water quality in the offshore extents of the aquifers, a region inaccessible to traditional monitoring methods, but one that plays an important role in the modeling, prediction, and management of saltwater intrusion.

Mapping selected trace elements and major ions, 2000-2012, Mojave River and Morongo Groundwater Basins, Southwestern Mojave Desert, San Bernardino County, California

U.S. Geological Survey (USGS) | July 1st, 2015

The population of the Mojave River and Morongo groundwater basins has grown rapidly during the last several decades, increasing from an estimated population of almost 273

The population of the Mojave River and Morongo groundwater basins has grown rapidly during the last several decades, increasing from an estimated population of almost 273,000 in 1990 (Mojave Water Agency, 2004) to more than 453,000 in 2010 (Mojave Water Agency, 2014). Groundwater is the primary source of potable water in both basins (Mojave Water Agency, 2014). Previous studies noted elevated concentrations of several trace elements, nitrate, and total dissolved solids in groundwater in portions of the two basins (Christensen and Fields-Garland, 2001; Ball and Izbicki, 2004; Izbicki and others, 2008; Mathany and Belitz, 2009; Wright and Belitz, 2010; Dawson and Belitz, 2012; and Izbicki and others, 2012). Since 2000, the U.S. Geological Survey (USGS) has collected water-quality data annually from a network of wells and has provided quality-assurance for Mojave Water Agency (MWA) data that are stored in the USGS National Water Information System (NWIS) database. The new data and results from the joint State of California and USGS Groundwater Ambient Monitoring and Assessment (GAMA) program assessments of regional water quality (these data are also stored in NWIS), in combination with ongoing MWA/USGS groundwater-quality monitoring provide a timely opportunity for mapping of groundwater quality in the Mojave River and Morongo groundwater basins. The purpose of this report is to provide maps and time-series plots of concentrations of selected water-quality constituents (arsenic, boron, chromium-6, total chromium, dissolved oxygen, fluoride, iron, manganese, nitriate plus nitrite as nitrogen, total dissolved solids, uranium, and vanadium) in the Mojave River and Morongo groundwater basins using data collected by the USGS and MWA from 2000 to 2012. These maps and plots can be accessed on this website.

Measuring and Interpreting Multilayer Aquifer-System Compactions for a Sustainable Groundwater-System Development

American Geophysical Union (AGU) | March 23rd, 2021

Ever decreasing water resources and climate change have driven the increasing use of groundwater causing land subsidence in many countries. Geodetic sensors such as InSAR

Ever decreasing water resources and climate change have driven the increasing use of groundwater causing land subsidence in many countries. Geodetic sensors such as InSAR, GPS and leveling can detect surface deformation but cannot measure subsurface deformation. A single‐well, single‐depth extensometer can be used to measure subsurface deformation, but it cannot delineate the depths of major compaction and provide insight about the deformation mechanism throughout a complex aquifer system, unless man extensometers at different depths are used. We present a multilayer compaction well (MLCW), installed in a borehole, that uses magnetic rings to detect stratum compaction at 25 depths as deep as 300 m below land surface. Our laboratory and field assessments indicate 1 mm precision and accuracy for one single‐depth magnetic reading. We tested the performance of MLCW by measuring aquifer‐system compaction over the proximal, middle, and distal fans of the Choushui River Alluvial Fan (CRAF) that has long experienced severe land subsidence. The MLCW measurements were used to create time‐depth diagrams of compaction, showing different compaction rates at different layers of aquifers and aquitards to identify the depths of major compactions. The elastic (reversible) and inelastic (irreversible) compactions from MLCW were used in stress‐strain analyses to estimate skeletal specific storages and the safe groundwater levels, below which groundwater extractions have caused irreversible compactions. The hydrogeological parameters derived from MLCW measurements can help governmental agencies to determine effective land‐use and water‐use policies, and ascertain the best strategy for utilizing artificial recharge to prevent land subsidence and achieve sustainable groundwater management.

Mercury and Methylmercury in Fish and Water from the Sacramento-San Joaquin Delta: August 2016 – April 2017

San Francisco Estuary Institute (SFEI) | September 3rd, 2018

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest prior

Monitoring of sport fish and water was conducted by the Delta Regional Monitoring Program (Delta RMP) from August 2016 to April 2017 to begin to address the highest priority information needs related to implementation of the Sacramento–San Joaquin Delta Estuary Total Maximum Daily Load (TMDL) for Methylmercury (Wood et al. 2010). Two species of sport fish, largemouth bass (Micropterus salmoides) and spotted bass (Micropterus punctulatus), were collected at six sampling locations in August and September 2016. The length-adjusted (350 mm) mean methylmercury (measured as total mercury, which is a routinely used proxy for methylmercury in predator fish) concentration in bass ranged from 0.15 mg/kg or parts per million (ppm) wet weight at Little Potato Slough to 0.61 ppm at the Sacramento River at Freeport. Water samples were collected on four occasions from August 2016 through April 2017. Concentrations of methylmercury in unfiltered water ranged from 0.021 to 0.22 ng/L or parts per trillion. Concentrations of total mercury in unfiltered water ranged from 0.91 to 13 ng/L. Over 99% of the lab results for this project met the requirements of the Delta RMP Quality Assurance Program Plan, and all data were reportable. This data report presents the methods and results for the first year of monitoring. Historic data from the same or nearby monitoring stations from 1998 to 2011 are also presented to provide context. Monitoring results for both sport fish and water were generally comparable to historic observations. For the next several years, annual monitoring of sport fish will be conducted to firmly establish baseline concentrations and interannual variation in support of monitoring of long-term trends as an essential performance measure for the TMDL. Monitoring of water will solidify the linkage analysis (the quantitative relationship between methylmercury in water and methylmercury in sport fish) in the TMDL. Water monitoring will also provide data that will be useful in verifying patterns and trends predicted by numerical models of mercury transport and cycling being developed for the Delta and Yolo Bypass by the California Department of Water Resources (DWR).

Mercury Contamination from Historical Gold Mining in California

U.S. Geological Survey (USGS) | October 31st, 2005

Methods of Analysis—Determination of Pesticides in Filtered Water and Suspended Sediment using Liquid Chromatography- and Gas Chromatography-Tandem Mass Spectrometry

U.S. Geological Survey (USGS) | January 31st, 2024

The widespread application of pesticides in agricultural and urban areas leads to their presence in surface waters. Presence of these biologically active chemicals in en

The widespread application of pesticides in agricultural and urban areas leads to their presence in surface waters. Presence of these biologically active chemicals in environmental waters potentially has adverse effects on nontarget organisms. To better understand the environmental fate of these contaminants, a robust method to capture chemicals with wide-ranging physicochemical properties has been developed. The method was developed by the U.S. Geological Survey’s Organic Chemistry Research Laboratory to monitor pesticides, pesticide degradates, and other agrochemicals in environmental surface waters throughout the country. The analysis involves a multiresidue method to determine 183 pesticides and pesticide degradates in filtered water samples and 178 pesticides and pesticide degradates in paired suspended sediment samples. After the filtration of whole water, contaminants are individually measured in the filtered water and the collected suspended sediment. Filtered water is extracted via solid-phase extraction, whereas suspended sediment is extracted using an ultrasonication, solid-liquid extraction. Samples are analyzed by liquid chromatography-tandem mass spectrometry using an electrospray ionization source in positive and negative modes and analyzed by gas chromatography-tandem mass spectrometry using an advanced electron ionization source in positive mode. Instrument parameters were optimized for the highest sensitivity, and at least two transitions (quantifier and qualifier) were monitored for each analyte. Recoveries in test filtered water (n=9; 183 analytes) from the American River, California, and suspended sediment (n=9; 178 analytes) samples fortified at 15 nanograms per liter (ng/L) ranged from 70.1 to 121.0 and 71.1 to 117.0 percent in water and suspended sediment filter samples, respectively.

Microbial Water Quality at Minimally Human-Impacted Reference Beaches in Northern California

San Francisco Estuary Institute (SFEI) | September 3rd, 2018

All of the coastal reference beaches that have been used by the State of California for quantifying “natural loads” of fecal indicator bacteria have been in Southern

All of the coastal reference beaches that have been used by the State of California for quantifying “natural loads” of fecal indicator bacteria have been in Southern California. None has been in the northern and central coastal regions of the State. To fill this information gap, this study assessed bacteria concentrations at coastal reference beaches in Northern California, investigated possible factors influencing the bacteria concentrations, and evaluated how these concentrations compare to results from the Southern California reference beaches. Reference beaches were defined as open beaches with breaking waves that receive runoff from undeveloped watersheds. The study beaches were selected to represent a variety of geographical conditions and watershed sizes in Northern California. Five reference beaches were sampled between January 2016 and September 2017 for a total of 25‐30 sampling events, including 10 wet weather events, 10 winter dry events, and 10 summer dry events. The number of samples collected was admittedly small for characterizing variable bacteria concentrations but was deemed sufficient for providing initial information relevant to management questions. At each beach, samples were collected from an ocean site in the surf zone and from a freshwater site in the watershed draining to the beach. Samples were analyzed for total coliform, fecal coliform, Escherichia coli (E. coli), enterococci (ocean sites only), as well as a human‐specific genetic marker (human Bacteroides HF183).

Microparticles, Microplastics, and PAHs in Bivalves in San Francisco Bay

San Francisco Estuary Institute (SFEI) | November 15th, 2019