Geology topics

Emily T. Richardson

Publications and source records attributed to Emily T. Richardson.

8 recordsLinked to original sources

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.

California↗

USGS2025

Designs for cyanobacterial harmful algal bloom monitoring in the Sacramento–San Joaquin Delta, California

Cyanobacterial harmful algal blooms (CHABs) are a growing concern in freshwater environments. These blooms can lead to degraded water quality, ecosystem disruptions, and public health threats due to the production of potent cyanotoxins. The Sacramento–San Joaquin Delta (California, USA; the Delta) has experienced CHABs since 1999, including CHABs that produce cyanotoxins at concentrations exceeding recreational advisory threshold levels. In response to the CHAB monitoring needs in the Delta, in 2024 a CHAB monitoring strategy for the Sacramento–San Joaquin Delta was released. The CHAB monitoring strategy recommended implementing a comprehensive monitoring program aligned with regional priorities, and this report responds directly to that recommendation. Building on the CHAB monitoring strategy, it describes three example monitoring designs that draw from past studies to address present needs. To develop designs, the report outlines key components and considerations for implementing a CHAB monitoring program in the Delta. It provides: background on monitoring and modeling approaches, an overview of current monitoring programs in the region, guidance for selecting monitoring locations, indicators, and sampling frequencies, and example designs to guide program planning and budgeting. The overarching goal of the report is to help agencies and stakeholders move from high-level recommendations to practical, actionable designs that are tailored to the Delta’s physical, anthropogenic, and ecological landscape.

ESS Open Archive↗

USGS2025

Identifying conditions associated with outliers produced by three different chlorophyll fluorometers: A comparison of instrumentation and development of correction formulae

Measurements of chlorophyll concentration reported by fluorometers (fChl) are used in environmental research and monitoring, as inputs to models, and in the interpretation of remote sensing data. Researchers and managers benefit from understanding how to interpret and ensure the accuracy of fChl data collected by in situ fluorometers. Although fChl values produced by different manufacturers are often in agreement with discrete laboratory-derived Chlorophyll a (Chl a ) concentration measurements, there are instances in which results significantly differ. Further, when measuring fChl side by side, different fluorometers may report values that differ significantly from each other, despite passing calibration checks prior to deployment. We compared environmental conditions and phytoplankton species composition associated with instances in which fChl measurements from three different fluorometers (EXO2 Total Algae Smart Sensor, YSI Inc./Xylem Inc., Yellow Springs, Ohio; FluoroProbe III, bbe Moldaenke GmbH, Kiel, Germany; WETStar, Sea-Bird Scientific, Bellevue, Washington) were significantly different from laboratory-derived Chl a concentrations. Results indicated that elevated primary productivity, as indicated by high pH, dissolved oxygen, and the ratio of Chl a to phaeophytin, were correlated with underestimated fChl values recorded by each sensor. After removing outliers, we determined unique correction guidance for each of the three sensors and demonstrated that after applying correction formulae, fChl measurements produced by each sensor became directly comparable.

California↗

USGS2024

Assessing spatial variability of nutrients, phytoplankton, and related water-quality constituents in the California Sacramento–San Joaquin Delta at the landscape scale—2018 high resolution mapping surveys

Executive Summary This study examined the abundance and distribution of nutrients and phytoplankton in the tidal aquatic environments of the Sacramento–San Joaquin Delta (Delta) and Suisun Bay, comprising three spatial surveys conducted in May, July, and October of 2018 that used continuous underway high frequency sampling and measurements onboard a high-speed boat to characterize spatial variation across the extent of the Delta. The method used involves simultaneously collecting information about the concentration and spatial distribution of all major nutrient forms with analogous information about the major classes of phytoplankton and associated water-quality conditions. The results showed substantial variation across space and time, providing an unprecedented snapshot of the dynamic environmental processes that shape the ways nutrients interact with and affect aquatic habitats in the Delta. The purposes of this study were to improve our understanding of how hydrodynamics, landscape features, and aquatic primary productivity interact to drive nutrient cycling and transport in the Delta and to provide insights into the underlying processes most directly responsible for the conditions at the time of this study, and thus into the range of conditions that may be expected following the wide array of prospective future changes to the Delta. One major anticipated change at the time of this study was the planned upgrade to the Sacramento Regional Wastewater Treatment Plant, but the study also informs our understanding of potential effects from other changes to the Delta, such as those caused by other nutrient-management actions, flow actions, large-scale wetland restoration, drought, flood, levee failure, and changes to water management. Nutrient loading is the primary driver of nutrient concentrations in the Delta, but several other major drivers interact to shape their distribution and effects: geomorphology, hydrodynamics, landscape features, and aquatic productivity. Hydrodynamics affect timescales of transport and dilution of nutrient loads in the Delta. During transit through the system, channel geometry, tidal mixing, and water exports affect hydrodynamics in diverse ways that influence water-residence and transport times, thereby markedly affecting the range of times during which natural internal cycling can alter nutrient concentrations and forms. Channel geometry and location shape tidal energy and river currents into these observed dynamics. Interactions with Delta aquatic landscapes such as herbaceous tidal marsh, submerged aquatic vegetation, and large expanses of intertidal or subtidal sediments (all highly productive landscapes) exert demand on available nutrient supplies but can also simultaneously transform and generate nutrients. Finally, while phytoplankton require nutrients to sustain production and thus are a potential nutrient sink, the amount and form of nutrients also can influence the occurrence of harmful algal blooms (HABs) that adversely affect aquatic organisms as well as affect the occurrence of beneficial algal blooms that result in production of algae that are favorable for imperiled Delta pelagic aquatic food webs. The surveys revealed a complex mosaic of spatial variation, with nutrient concentrations varying from near zero to well above concentrations considered eutrophic; nutrient concentrations were more often related to the extent of hydrologic transport and mixing than to specific geographic locations or to specific landscape features. Similarly, the surveys identified phytoplankton abundance ranging from near detection to the level of large phytoplankton blooms, with large variation in phytoplankton community composition. Although the study occurred during a period of low bloom activity, phytoplankton productivity appeared to be the strongest potential sink for inorganic nutrients in the Delta, indicating that it is a larger control on nutrient concentrations and distribution than previously understood. Cycling and transformation within the water column only appeared to substantially lower total nutrient concentrations at the longest estimated transport timescales. Contrary to expectations, we did not observe substantial nutrient depletion near landscape-scale features such as open-water habitats, submerged aquatic vegetation beds, extensive wetlands, or exposed sediments, indicating that these habitat types did not act as major sinks for nutrients in the Delta during these surveys. These results indicated that nutrient reduction efforts may have the greatest effect on pelagic phytoplankton productivity in the more productive reaches of the Delta and estuary, but these effects are unlikely to be magnified by changes to nutrient loss within the Delta over conceivable changes in flow conditions, Delta water management actions, or large-scale wetland restoration activities. Nevertheless, local processes were shown to cause substantial loss, and thus integrating of nutrient effects with other indicators of aquatic habitat conditions will help inform planning future actions at specific sites. Finally, we note that the primary contribution of this study was intended to be the survey data themselves. Aside from the results highlighted in this report, the surveys are a benchmark against which future environmental change may be evaluated, including changes to nutrient management or water exports, drought, large-scale wetland restoration, and climate change. Further, although we highlight some of the main findings from the surveys in this report, the necessarily limited scope precludes examination of many topics for which these surveys may be highly informative. To facilitate the utility of these data to stakeholders, managers, and researchers, we have released the data online (Bergamaschi and others, 2020) and created an online data exploration portal ( https://ca.water.usgs.gov/bay-delta/2018-delta-wide-mapping-surveys.html ) where users may query the surveys in a variety of ways to test hypotheses, examine relationships, assess spatial trends, and download data. The data exploration portal is intended to be an immersive experience that allows users to gain greater understanding of the complex interactions that shape Delta aquatic environments. This report is intended as a companion to the portal, allowing the reader to challenge and further explore the highlighted findings. This study was a collaboration between the U.S. Geological Survey and the Delta Regional Monitoring Program, with additional funding provided from U.S. Geological Survey Cooperative Matching Funds Program.

California↗

USGS2024

Evaluation and refinement of chlorophyll-a algorithms for high-biomass blooms in San Francisco Bay (USA)

A massive bloom of the raphidophyte Heterosigma akashiwo occurred in summer 2022 in San Francisco Bay, causing widespread ecological impacts including events of low dissolved oxygen and mass fish kills. The rapidly evolving bloom required equally rapid management response, leading to the use of near-real-time image analysis of chlorophyll from the Ocean and Land Colour Instrument (OLCI) aboard Sentinel-3. Standard algorithms failed to adequately capture the bloom, signifying a need to refine a two-band algorithm developed for coastal and inland waters that relates the red-edge part of the remote sensing reflectance spectrum to chlorophyll. While the bloom was the initial motivation for optimizing this algorithm, an extensive dataset of in-water validation measurements from both bloom and non-bloom periods was used to evaluate performance over a range of concentrations and community composition. The modified red-edge algorithm with a simplified atmospheric correction scheme outperformed existing standard products across diverse conditions, and given the modest computational requirements, was found suitable for operational use and near-real-time product generation. The final version of the algorithm successfully minimizes error for non-bloom periods when chlorophyll a is typically <30 mg m −3 , while also capturing bloom periods of >100 mg m −3 chlorophyll a .

California↗

USGS2023

A simple approach to modeling light attenuation in the Sacramento-San Joaquin Delta using commonly available data

The diffuse attenuation coefficient of photosynthetically active radiation (KdPAR) is commonly used to predict light attenuation in aquatic productivity models, but obtaining measurements of PAR to compute KdPAR is difficult. In situ calculations of KdPAR require multiple measurements of PAR through the water column, and these measurements are infeasible for real-time recording. Instead, predictive models using surface-water measurements may be used. Traditional KdPAR models are based on open-ocean habitats and rely on chlorophyll—as a proxy measurement for phytoplankton abundance—as the main predictive parameter. However, elevated suspended sediments and dissolved organic materials may also affect KdPAR values of inland water bodies and estuaries. In this study, we leverage KdPAR calculations derived from in situ light measurements collected along with surface-water-quality parameters across the Sacramento-San Joaquin River Delta in California, USA (the Delta). Sampling occurred between January of 2013 and May of 2014. We also explored regional and seasonal effects, but these did not clearly affect the model. Ultimately, the best-performing model included surface-level turbidity only (R2 = 0.91). The simplicity of the model facilitates use of KdPAR estimates for a variety of purposes throughout the Delta, including euphotic depth calculations, and as inputs to primary-productivity and habitat-suitability models. We demonstrate the model’s usability with two open-sources data sets (one spatially dense, and one temporally dense), and estimate KdPAR, euphotic depth, and primary productivity within the Delta. We provide calculations for each estimation, allowing users to easily adopt these models and apply them to their own data or with open-sourced data, which are abundant.

California↗

USGS2023

A novel boat-based field application of a high-frequency conductometric ammonium analyzer to characterize spatial variation in aquatic ecosystems

Documenting dissolved inorganic nitrogen (DIN) concentration and form at appropriate temporal and spatial scales is key to understanding aquatic ecosystem health, particularly as DIN fuels primary productivity. In addition to point and non-point source nutrient inputs, factors such as hydrology, geomorphology, temperature, light, and biogeochemical transformations influence nutrient dynamics in surface waters, allowing for the formation of steep spatial gradients and patchiness. Documenting nutrient variability is also necessary to identify sources, quantify transformation rates, and understand drivers. Due to logistical and cost constraints, it is often unfeasible to measure concentrations of nutrients in surface waters using discrete sampling followed by laboratory analysis at a resolution high enough to identify steep spatial gradients and patchiness. Because of these constraints, data generated from discrete sampling are limited in space and time, often missing key variabilities. Recent advancements of in situ nitrate plus nitrite (NO3- and NO2-) sensor technology has enabled highly temporally and spatially resolved NO3- concentration measurements in aquatic ecosystems. However, comparable information about ammonium (NH4+) concentrations remains unavailable. To address this need, U.S. Geological Survey collaborated with Timberline Instruments to modify their commercially available benchtop TL-2800 ammonia analyzer to collect high-frequency continuous (1 unique sample measurement per second) NH4+ concentration measurements at a micromolar (0.5 µM) resolution in flow-through mode while receiving water pumped from a moving boat. Although the utility of this method is described for spatial surveys, we anticipate that it would be adaptable to installation at a fixed station for continuous monitoring of NH4+ concentration.

California↗

USGS2021

Long-term salinity change and growth of the harmful alga, Prymnesium parvum

Prymnesium parvum is a euryhaline, toxin-producing microalga. Although its abundance in inland waters and growth potential in the laboratory is reduced at high salinity (>20), the ability of inland strains to adjust their growth after long-term residence in high salinity is uncertain. An inland strain of P. parvum maintained at salinity of 5 in modified artificial seawater medium (ASM-5) was subjected to the following treatments over five sequential batch culture rounds: ASM-5 (control); modified ASM at salinity of 30, raised with NaCl; modified ASM at salinity incrementally increased to 30 with NaCl; and Instant Ocean ® at salinity of 30 (IO-30). Exponential growth rate ( r ) was reduced when salinity was increased from 5 to 30 in ASM but returned to control values during the second round. When salinity was incrementally increased, a reduction in r still occurred when salinity reached 25-30. Maximum density was reduced at salinity of 30 in ASM upon abrupt transfer or incremental increase, and compensation did not occur. Growth performance in IO-30 was comparable to control values. In conclusion, (i) long-term compensation for acute inhibitory effects of high salinity occurred for r but not maximum density, (ii) incremental increases in salinity did not prevent growth inhibition, suggesting the existence of a salinity threshold of 25–30 for onset of salinity stress, and (iii) the presence of a seawater-like salt mixture prevented growth inhibition by high salinity. These findings provide new insights on P. parvum 's long-term ability to adjust its growth in environments of different salinity and ionic composition.

Journal of Phycology↗