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 Sustainable Water Project: Ballona Creek Watershed

University of California, Los Angeles (UCLA) | November 1st, 2015

Implementing integrated water management systems (IWM) that incorporate all components of the urban water cycle, including imported water, local groundwater, captured st

Implementing integrated water management systems (IWM) that incorporate all components of the urban water cycle, including imported water, local groundwater, captured stormwater, greywater, and treated wastewater is crucial to creating a sustainable water supply for the city of Los Angeles (City). The City has researched, written, and initiated implementation of recommendations from many reports critical to creating an IWM plan for the City as well as to defining the current capacity of the system. While work on this issue has been ongoing for many years, the extreme drought currently impacting water supplies throughout California has created a new urgency to increase the City’s ability to provide a secure water supply through local sources. In April 2015, Governor Brown directed the first-ever statewide mandatory cut of 25% in urban water use due to the continuing drought conditions. In addition to statewide efforts, many policies and plans have been created on a local level within the City that address urban water management, integrated resources planning, stormwater capture, and groundwater management. The Los Angeles Mayor’s Office recently set strong goals to increase the sustainability of the City’s water supply over the next several years. The goals included completing a comprehensive sustainability plan containing objectives for water supply and demand in the City, which was released in April 2015 (Sustainable City pLAn). In an emergency drought directive released in October 2014, the Mayor identified additional accelerated water goals including reducing per capita potable water use by 20% by 2017 (from 2014 base-line of 130 gallons per capita per day (GPCD) to 104 GPCD), reducing the City’s reliance on MWD water by 50% by 2025, and converting 85% of public golf course acreage to recycled water by 2017. Through building upon regional research and reports that have been generated on potential components of the local water supply portfolio (e.g., groundwater, recycled water, and stormwater), as well as gathering and analyzing current data on flows of water and wastewater throughout the City systems and environment, this project further identifies and refines opportunities to implement integrated water management throughout the City. As water quality regulation in the Los Angeles area currently drives much of the current water management practices, we examined greater water self-reliance through this lens. Therefore, the City has been divided by watershed to assess Total Maximum Daily Load (TMDL) compliance alongside integrated water management opportunities and challenges that exist and must be addressed in order to meet water quality compliance requirements and maximize local water supply. This first report focuses on the Ballona Creek Watershed and the Hyperion Service Area; following reports will focus on the Dominguez Channel and Los Angeles River watersheds.

Lower Peninsula Watershed Condition Assessment 2016. Technical memorandum prepared for the Santa Clara Valley Water District - Priority D5 Project

San Francisco Estuary Institute (SFEI) | October 2nd, 2017

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates that overall ecological conditions of streams using the C

This report describes baseline information about the amount and distribution of aquatic resources, and evaluates that overall ecological conditions of streams using the California Rapid Assessment Method (CRAM), for the Lower Peninsula watershed in Santa Clara County; consisting of Stevens-Permanente Creek, Adobe Creek, southern extent of San Francisquito Creek, and their tributaries. The Lower Peninsula watershed covers approximately 98 square-miles with creeks flowing from the Santa Cruz Mountains into southwest San Francisco Bay and its tidal wetlands.

Lower Tule River Irrigation District Groundwater Sustainability Agency Groundwater Sustainability Plan

Lower Tule River Irrigation District Groundwater Sustainability Agency | January 21st, 2020

Making the Most of Water for the Environment: A Functional Flows Approach for California’s Rivers

Public Policy Institute of California (PPIC) | August 25th, 2020

In California, water and land management activities have substantially altered river flows and degraded river channels and their floodplains. The result has been a precip

In California, water and land management activities have substantially altered river flows and degraded river channels and their floodplains. The result has been a precipitous decline in native fish populations, including the collapse of valued salmon fisheries, and widespread imperilment of freshwater biodiversity. Environmental flows—flows in rivers and streams necessary to sustain ecosystem health—are essential to reversing these trends. Yet many rivers in California lack environmental flows. And for those rivers with such protections, environmental flows are typically established at static minimum levels, which fail to preserve the natural seasonal and interannual variability of flow that sustains healthy ecosystems. A new approach to managing environmental water is needed. 

Managed Aquifer Recharge in California: Four Examples of Managed Groundwater Replenishment Across the State

American Geosciences Institute (AGI) | September 29th, 2017

In California, surface water from rainfall, snowmelt, and distant rivers rarely meets the state’s urban and agricultural water needs. Groundwater is an essentia

In California, surface water from rainfall, snowmelt, and distant rivers rarely meets the state’s urban and agricultural water needs. Groundwater is an essential water source, providing 35% of the fresh water used in California. However, when groundwater is used more rapidly than it is naturally replenished, groundwater management becomes necessary. One of the tools used by groundwater managers is managed aquifer recharge (MAR). Aquifers, the porous rocks and sediments that hold and transmit groundwater, are naturally replenished by surface water that seeps into the ground. MAR enhances the recharge rate by creating artificial streams and ponds where water trickles into the ground, or by using wells to directly inject water underground. MAR can also be used to improve groundwater quality and prevent some of the negative consequences of groundwater depletion, like ground sinking (subsidence) or the intrusion of salty groundwater from the oceans into coastal freshwater aquifers. Because of its arid climate and large population, California is home to some of the oldest and largest MAR projects in the United States. This case study highlights four of these projects, covering almost a century of MAR and water security in California.

Managing a cyanobacteria harmful algae bloom “hotspot” in the Sacramento – San Joaquin Delta, California

Journal of Environmental Management (Elsevier) | December 10th, 2023

Managing Agricultural Irrigation Drainage Water: A guide for developing Integrated On-Farm Drainage Management systems

California State Water Resources Control Board (SWRCB) | May 6th, 2004

Chronic problems of salt, selenium, boron and other naturally occurring elements in surface and groundwater supplies plague agricultural regions throughout the Westside o

Chronic problems of salt, selenium, boron and other naturally occurring elements in surface and groundwater supplies plague agricultural regions throughout the Westside of the San Joaquin Valley and the western U.S. Compounding the problem is the build-up of salty subsurface groundwater resulting from dense clay layers and inadequate natural drainage. The Integrated On-Farm Drainage Management (IFDM) system was developed to manage these problems. A state-of-the-art, yet practical irrigation management system, the IFDM provides for drainage water reuse to improve water availability for crop production and to minimize salt and selenium risks to water quality and the environment. IFDM manages irrigation water on salt sensitive, high value crops and reuses drainage water to irrigate salt-tolerant crops, trees and halophyte plants. Salt and selenium are removed from the farming system and can be marketed. This system views the subsurface drainage water containing salts and selenium as resources, rather than considering them as wastes and environmental problems.

Managing California’s Freshwater Ecosystems: Lessons from the 2012-16 Drought

Public Policy Institute of California (PPIC) | November 16th, 2017

The 2012–16 drought caused unprecedented stress to California’s ecosystems and pushed many native species to the brink of extinction. It also tested the laws, policie

The 2012–16 drought caused unprecedented stress to California’s ecosystems and pushed many native species to the brink of extinction. It also tested the laws, policies, and institutions charged with protecting the environment. Eight case studies on environmental water management during the drought reveal both strengths and weaknesses in federal, state, and local response that can inform how California addresses future droughts. Three areas of reform hold promise for improving ecosystem conditions and reducing conflict: * Improve water accounting. Drought management requires accurate and timely information about water use and availability and about likely environmental response to changes in water supply. But California’s current tracking systems are neither timely nor transparent. To address these gaps, environmental water accounting and ecosystem monitoring systems need an overhaul. * Prepare for drought. With a few significant exceptions, environmental water managers were unprepared for the environmental consequences of an extended drought, and were forced to make ad hoc decisions during a crisis. Developing watershed-level plans that set ecosystem priorities and identify trade-offs would help managers anticipate drought and drive implementation of habitat investments and water allocation. Annual watering plans that guide management under different types of water years would better engage and inform water users. * Develop ecosystem water budgets. Current methods of allocating water to support ecosystem health rely on minimum flow standards that are unevenly enforced and often insufficient during drought. Ecosystem water budgets, which allocate a portion of water to the ecosystem within watersheds, could enable more flexible and effective water management during dry times. Although state and federal agencies have important

Managing diversions in unregulated streams using a modified percent-of-flow approach

Freshwater Biology (Wiley) | August 22nd, 2017

In Mediterranean-type river systems stream flows are naturally low in summer and autumn. This pattern is often exacerbated by over-exploitation of water resources during

In Mediterranean-type river systems stream flows are naturally low in summer and autumn. This pattern is often exacerbated by over-exploitation of water resources during the dry season, which has implications for managing flows for both environmental and human needs. Mediterranean systems are characterised by strong inter- and intra-annual variability with almost all precipitation occurring in winter months followed by summer droughts with little or no rainfall, and extreme year-to-year variation ranging from intense winter storms to year-round drought (Gasith & Resh, 1999; Power, Kupferberg, Cooper, & Deas, 2015; Power, Parker, & Dietrich, 2008). The seasonal pattern of precipitation in Mediterranean climatic regions results in water availability and demand being out-of-phase; precipitation and runoff occur (almost exclusively) in winter when human demands are lowest, and precipitation is virtually non-existent in summer months when human demand is greatest (Kondolf & Batalla, 2005; Merenlender & Matella, 2013). As a result, rivers in Mediterranean climates tend to have a high degree of alteration with streamsdiverted and dammed to provide scarce water for human use (Kondolf, Podolak, & Grantham, 2013; Marr et al., 2009; Moyle, 2013). While the biophysical responses to alterations of land use, vegetation and hydrology are similar in Mediterranean and other climatic regions, the magnitude of responses tends to be intensified in Mediterranean systems. For example prolonged dry season flows may result in lower dissolved oxygen, higher temperatures and concentration of contaminants among other impacts (Cooper, Lake, Sabater, Melack, & Sabo, 2013). Climate change and increasing frequency and severity of drought promise to increase the conflict between human needs and ecological needs over time (Arthington, 2012).