Geology topics

David Senn

Publications and source records attributed to David Senn.

5 recordsLinked to original sources

USGS2026

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

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.

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USGS2025

Assessing environmental drivers and protist community dynamics that shaped the historic August 2022 Heterosigma akashiwo bloom in San Francisco Bay, California

San Francisco Bay, California, typically has chlorophyll a (chl- a ) concentrations below 10 µg L −1 , despite nutrient loadings exceeding those in many estuaries with recurring harmful algal blooms (HABs). However, in August 2022 there was a Heterosigma akashiwo (raphidophyte) bloom with chl- a concentrations exceeding 450 µg L −1 , resulting in widespread hypoxia and fish die-off. We used protist community (18S ribosomal ribonucleic acid gene metabarcoding) and environmental data collected 2–3 times per month from 2015–2023 to assess differences between 2022 and other years, and capture dynamics pre-, during, and post-bloom. The 2022 protist community clustered separately from other years in non-metric multidimensional scaling and hierarchical cluster analyses. A diatom bloom in June generated the highest median June chl- a concentration (15 µg L −1 ) recorded between 1977–2023 and drew down nutrients (nitrogen, silicate), leading to the establishment of a heterotrophic community in July with low dinoflagellate abundance (0.9% of protists versus 5.9% average in other years). The absence of dinoflagellates, potentially including H. akashiwo predators , plus suitable habitat (13–14 daylight hours, temperatures 17–21˚C, nitrate concentrations 17–24 µmol L −1 , neap tides) likely provided opportunity for H. akashiwo to proliferate from 0.03% to 48% of protists between July 20 and August 25. As the bloom collapsed, the genus Gyrodinium (dinoflagellate predator of H. akashiwo ) increased from 3.0% to 52% of protists between August 25 and August 31, likely exerting grazing pressure. Results show that antecedent protist community dynamics play important roles in shaping HABs, and interactions between biotic and abiotic factors govern the development of blooms.

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USGS2024

Estimating biogeochemical rates using a computationally efficient Lagrangian approach

Nutrient concentrations in many estuaries have increased over the past century due to increases in wastewater discharge and increased agricultural intensity, contributing to multiple environmental problems. Numerous biogeochemical and physical processes in estuaries influence nutrient concentrations during transport, resulting in complex spatial and temporal variability and challenges identifying predominant processes and their rates. Mechanistic models which require these rates to quantify biogeochemical processes become complex and difficult to calibrate as the number of processes and parameters grows, owing to the high dimensionality of the parameter space and the computational cost of simultaneously modeling the transport and transformations of constituents. We developed a modeling approach that decouples transport from transformations, enabling fast, data-driven exploration of the parameter space. The approach extracted information including water age, cumulative exposure to specific habitats, and mean water depth exposure from a hydrodynamic model. Using this information, a biogeochemical model was implemented to predict ammonium and nitrate concentrations in a Lagrangian frame. The model performed each simulation in milliseconds on a laptop computer, allowing the fitting of rate parameters for key transformations by optimization. The optimization used fixed station nitrate observations and the model was then validated against high-resolution mapping observations of ammonium and nitrate. The results suggest that the observed spatial and temporal variation can be largely represented with five transformation processes and their associated rates. Dissolved inorganic nitrogen (DIN) losses occurred only in shallow vegetated areas in the model, highlighting that biogeochemical processes in these areas should be included in DIN models.

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USGS2020

Changing nitrogen inputs to the northern San Francisco Estuary: Potential ecosystem responses and opportunities for investigation

Anthropogenic activities have resulted in elevated ambient nitrogen (N) and phosphorus (P) concentrations in many regions of the Sacramento-San Joaquin Delta and Suisun Bay (northern San Francisco Estuary, (nSFE). The Sacramento Regional wastewater treatment plant (SRWTP WWTP) currently acts as the largest N point source to the system, discharging 13,000-15,000 kg/d of ammonium-N (NH4) near the nSFE’s northeastern boundary. By end of 2021, SRWTP will complete major upgrades that will reduce its effluent dissolved inorganic nitrogen (DIN) loads by >65% and release the remaining DIN as predominantly nitrate (NO3). This major change in nitrogen inputs provides a unique opportunity to study ecosystem-scale responses to an altered nutrient regime. While, in general, the nSFE has not experienced some classic symptoms of nutrient over-enrichment typical in other estuaries—e.g., large phytoplankton blooms and hypoxia—other concerning nutrient- related impacts have been hypothesized, including: occurrence of harmful algal blooms (HABs) and the production of cyanotoxins; excessive growth of invasive aquatic vegetation; and declines in the abundance and nutritional quality of phytoplankton. These impacts have repercussions for the system’s food web, habitat quality, and the way we manage for transportation, recreation, water conveyance, and drinking water quality. This report develops and applies a framework for i) identifying and examining ecosystem response scenarios to the forthcoming decreased N loads; and ii) identifying opportunities, and constraints or considerations, for investigating those responses, including key data needs or knowledge gaps. Through applying this framework, we identify a set of plausible response scenarios, and evaluate the feasibility of studying or observing those responses along with key study considerations and data and knowledge gaps.

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USGS2017

Novel analyses of long-term data provide a scientific basis for chlorophyll-a thresholds in San Francisco Bay

San Francisco Bay (SFB), USA, is highly enriched in nitrogen and phosphorus, but has been resistant to the classic symptoms of eutrophication associated with over-production of phytoplankton . Observations in recent years suggest that this resistance may be weakening, shown by: significant increases of chlorophyll- a ( chl-a ) and decreases of dissolved oxygen (DO), common occurrences of phytoplankton taxa that can form Harmful Algal Blooms (HAB), and algal toxins in water and mussels reaching levels of concern. As a result, managers now ask: what levels of chl-a in SFB constitute tipping points of phytoplankton biomass beyond which water quality will become degraded, requiring significant nutrient reductions to avoid impairments? We analyzed data for DO, phytoplankton species composition, chl-a, and algal toxins to derive quantitative relationships between three indicators (HAB abundance, toxin concentrations, DO) and chl-a . Quantile regressions relating HAB abundance and DO to chl-a were significant, indicating SFB is at increased risk of adverse HAB and low DO levels if chl-a continues to increase. Conditional probability analysis (CPA) showed chl-a of 13 mg m −3 as a “protective” threshold below which probabilities for exceeding alert levels for HAB abundance and toxins were reduced. This threshold was similar to chl-a of 13–16 mg m −3 that would meet a SFB-wide 80% saturation Water Quality Criterion (WQC) for DO. Higher “at risk” chl-a thresholds from 25 to 40 mg m −3 corresponded to 0.5 probability of exceeding alert levels for HAB abundance, and for DO below a WQC of 5.0 mg L −1 designated for lower South Bay (LSB) and South Bay (SB). We submit these thresholds as a basis to assess eutrophication status of SFB and to inform nutrient management actions. This approach is transferrable to other estuaries to derive chl-a thresholds protective against eutrophication.

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