Revisiting chlorophyll a thresholds for San Francisco Bay: Insights from observations of phytoplankton molecular abundance

Elsevier | February 14th, 2026

Harmful Algal Blooms (HABs) are a hazard for coastal environments worldwide; identifying screening thresholds of chlorophyll-a (chl-a) associated with inc

Harmful Algal Blooms (HABs) are a hazard for coastal environments worldwide; identifying screening thresholds of chlorophyll-a (chl-a) associated with increased risk of HABs is a management priority. Molecular surveillance of coastal phytoplankton and bivalve biotoxins could be used to link chl-a with HAB risk, but requires an understanding of whether the HAB risks increase uniformly as chl-a rises, or whether some taxa are disproportionately favored, and if these relationships vary by season. In this study, we present a novel use of molecular abundance data to investigate the scientific bases for estuarine chl-a thresholds protective against HABs. In San Francisco Bay (SFB), California, the relationship between molecular relative abundance (as measured by 18S metabarcoding) of nine different HAB taxa, absolute quantitative polymerase chain reaction (qPCR) abundance, and mussel toxin concentrations of a subset of the taxa were investigated for thresholds as a function of increasing chl-a. Our results show most HAB taxa did not increase in absolute or relative abundance during SFB’s spring bloom interval, when chl-a levels were highest (>10 µg/L) but the assemblage was dominated by non-harmful diatoms. However, several flagellated, mixotrophic taxa did increase above their molecular baseline in fall, and the combined probability of any HAB occurring above baseline was elevated when chl-a reached ∼4.6 µg/L in the fall. This work demonstrates the promise of molecular approaches in disentangling the seasonally complex interplay between stressors and phytoplankton/HAB community responses and has the potential to provide clearer, more cost-effective monitoring and mitigation strategies for managers.

Risks of ocean acidification in the California Current food web and fisheries: ecosystem model projections

Wiley | January 12th, 2017

The benefits and ecosystem services that humans derive from the oceans are threatened by numerous global change stressors, one of which is ocean acidification. Here, we d

The benefits and ecosystem services that humans derive from the oceans are threatened by numerous global change stressors, one of which is ocean acidification. Here, we describe the effects of ocean acidification on an upwelling system that already experiences inherently low pH conditions, the California Current. We used an end‐to‐end ecosystem model (Atlantis), forced by downscaled global climate models and informed by a meta‐analysis of the pH sensitivities of local taxa, to investigate the direct and indirect effects of future pH on biomass and fisheries revenues. Our model projects a 0.2‐unit drop in pH during the summer upwelling season from 2013 to 2063, which results in wide‐ranging magnitudes of effects across guilds and functional groups. The most dramatic direct effects of future pH may be expected on epibenthic invertebrates (crabs, shrimps, benthic grazers, benthic detritivores, bivalves), and strong indirect effects expected on some demersal fish, sharks, and epibenthic invertebrates (Dungeness crab) because they consume species known to be sensitive to changing pH. The model's pelagic community, including marine mammals and seabirds, was much less influenced by future pH. Some functional groups were less affected to changing pH in the model than might be expected from experimental studies in the empirical literature due to high population productivity (e.g., copepods, pteropods). Model results suggest strong effects of reduced pH on nearshore state‐managed invertebrate fisheries, but modest effects on the groundfish fishery because individual groundfish species exhibited diverse responses to changing pH. Our results provide a set of projections that generally support and build upon previous findings and set the stage for hypotheses to guide future modeling and experimental analysis on the effects of OA on marine ecosystems and fisheries.

Role of Science and Engineering in Decision-Making Within the State and Regional Water Boards

California State Water Resources Control Board (SWRCB) | December 16th, 2005

The primary purpose of State Water Resources Control Board and the nine Regional Water Quality Control Boards is to preserve and protect the beneficial uses of all waters

The primary purpose of State Water Resources Control Board and the nine Regional Water Quality Control Boards is to preserve and protect the beneficial uses of all waters of the State. This includes all ground water, more than 1.6 million acres of lakes, 211,000 miles of rivers and streams, more than 1.3 million acres of bays and estuaries, 1,609 miles of coastline, and the first three miles of ocean off of our coastline. The California legislature found that “activities and factors which may affect the quality of the waters of the State shall be regulated to attain the highest water quality that is reasonable . . . (and) that the state must protect the quality of waters in the state from degradation inside or outside the boundaries of the state.” How we use water, or expect to use water in the future determines its beneficial uses. A designated beneficial use determines the quality of water that must be maintained for that use. Protecting water quality and preventing degradation in order to preserve beneficial uses of water relies heavily on science and engineering. Protecting water quality also depends on an equitable system for allocating water resources, which is carried out by the State Water Resources Control Board’s water rights program. This report discusses the role of science and engineering (technology) in decision-making at the water boards in implementing federal and state laws along with their implementing regulations, and water board plans and policies.

Root Creek Water District Groundwater Sustainability Agency Groundwater Sustainability Plan

Root Creek Water District | November 11th, 2019

SacPAS Fish Model: A model for emergence, migration and survival of Sacramento River salmon

Delta Stewardship Council (Delta Council) | November 1st, 2017

Sacramento River Temperature Task Group Annual Report of Activities October 1, 2013 through September 30, 2014

Delta Stewardship Council (Delta Council) | October 6th, 2014

Sacramento River Temperature Task Group Annual Report of Activities October 1, 2017 through September 30, 2018

Delta Stewardship Council (Delta Council) | November 21st, 2018

Sacramento River Temperature Task Group Annual Report of Activities, October 1, 2015 through September 30, 2016

Delta Stewardship Council (Delta Council) | October 31st, 2016

Safe Clean Water Water for Los Angeles County Residents

Los Angeles County Department of Public Works (LACDPW) | November 7th, 2017

We live in a water-scarce area, and forces outside of our control can threaten our local water resources, including lakes, rivers and beaches. LA Count

We live in a water-scarce area, and forces outside of our control can threaten our local water resources, including lakes, rivers and beaches. LA County residents rely heavily on imported water from the Sierra Mountains, the Central Valley and even from states as far away as Colorado. Climate change is causing more and more extreme weather conditions, making these remote sources more unreliable . The impacts of the recent five-year drought were widely felt here. Rainfall is an essential, local source of LA’s water . Rain runs through local rivers, creeks and streams and can be absorbed underground, replenishing groundwater, which is a local source of drinking water. However, because so much of our region is paved over, when we do experience heavy rain, too much of that precious water is lost to the ocean before we can capture it for use. Our local water resources are also threatened by toxins and pollution as stormwater runs through streets and over-paved areas into our rivers, creeks and streams. Pollution flows onto our beaches and into the ocean, posing a public health risk and harming marine life.

Sailing the Salt Line

Bay Nature | July 2nd, 2024

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. T

A strait is a place of motion. Change is a constant in our universe, a fact we humans often struggle with, but certain places are especially good at reminding us of it. The Carquinez Strait itself was only just born, some 560,000 years ago—explosively, according to one theory—when a giant inland lake forced a path to the ocean. This created the unusual inverted river delta (with the fan pointing inland, instead of spreading out onto the coast) that is the San Francisco Bay.