Geology topics

Susanna Theroux

Publications and source records attributed to Susanna Theroux.

8 recordsLinked to original sources

USGS2026

Environmental DNA pilot monitoring program for invasive species and biodiversity assessments on Santa Cruz Island: Interim report, September 2025

The U.S. Geological Survey (USGS) and Southern California Coastal Water Research Project supported Channel Islands National Park, The Nature Conservancy’s (TNC) Santa Cruz Island Preserve, and University of California San Diego (UCSD) researchers in using environmental DNA sampling to monitor for invasive Argentine ant ( Linepithema humile ) and to describe spatial biodiversity patterns in a freshwater stream on Santa Cruz Island that is colloquially known as Cañada del Puerto Creek (hydrologic unit code 12 number 180600140201). An eDNA autosampler was deployed May 27–June 02, 2025, which filtered and preserved four 2-L water samples every 12 hours (n = 48 samples). These samples were extracted by USGS and shipped to UCSD for targeted eDNA analyses of Argentine ant. Environmental DNA sampling kits were used to filter and preserve water samples at four sites along the creek spanning ~ 5 km of stream distance. Six 1-L samples were collected at each site May 27–28 and samples were analyzed for eDNA metabarcoding using a comprehensive panel, which encompasses species across the tree of life. In these samples, eDNA from 2,134 unique taxa spanning 30 taxonomic groups (e.g., amoebas, insects, plants) were found. These sampling efforts demonstrated how eDNA autonomous and manual sampling approaches can be applied by National Park Service, TNC, and partners at scale to provide otherwise difficult and expensive to acquire information about biological threats and biodiversity.

California↗

USGS2026

Best practice guidelines for targeted environmental DNA-based proficiency testing in non-regulatory contexts

The effective use of environmental DNA (eDNA) tools is contingent on strict adherence to established and validated methods. Differences in eDNA methods and quality assurance protocols may contribute to variability in results. However, quality assurance measures such as proficiency testing can provide independent evaluation of laboratory performance against pre-established test criteria. With this commentary, we discuss how broad implementation of recurring proficiency testing in eDNA laboratories can build decision-maker confidence in eDNA results. It can also create a culture of continuous evaluation and improvement that minimizes error and meets performance requirements to inform the sustainable use or monitoring of natural resources. We provide an overview of proficiency testing across molecular disciplines, review the state of proficiency testing in eDNA applications, and draft a roadmap for the expanded application of proficiency testing informed by best practices for targeted eDNA detection. We suggest that best practice proficiency testing can be conducted by an independent, third-party sample provider. By demonstrating that laboratories are competent and capable of producing reliable results, implementation of proficiency testing best practices should foster confidence in eDNA measurements and its use in decision-making processes. Increased confidence in eDNA methods and a clear expectation of what is considered satisfactory performance are also likely to create more favorable conditions for investments in eDNA-based monitoring.

Environmental DNA↗

USGS2025

What is eDNA method standardization and why do we need it?

The rapid advancement of environmental DNA ( eDNA ) science in the past two decades has inspired a concomitant growth in the development of eDNA sampling and analytical methods. However, these methods are often developed by individual laboratories or institutions, which can isolate protocols within programmes, agencies or regions and prevent the beneficial exchange of data and ideas. Recent efforts to advance national and international coordination have resulted in a groundswell of standardisation efforts, but there is still considerable confusion around the role of formal standards for regulatory or research applications. With this commentary, we hope to provide clarity on the terminology used in standardisation discussions, including the differences between formal standards and best practice guidelines. Additionally, we discuss how eDNA method choice may be informed by environmental management scenarios and review examples of formal eDNA method standards being used to inform management action. The eDNA community now has an opportunity to develop a roadmap for method development to help close standardisation gaps, advance eDNA method adoption and accelerate our ability to monitor biological life at the scales our current environmental challenges demand.

Metabarcoding and Metagenomics↗

USGS2024

The MIEM guidelines: Minimum information for reporting of environmental metabarcoding data

Environmental DNA ( eDNA ) and RNA ( eRNA ) metabarcoding has become a popular tool for assessing biodiversity from environmental samples, but inconsistent documentation of methods, data and metadata makes results difficult to reproduce and synthesise. A working group of scientists have collaborated to produce a set of minimum reporting guidelines for the constituent steps of metabarcoding workflows, from the physical layout of laboratories through to data archiving. We emphasise how reporting the suite of data and metadata should adhere to findable, accessible, interoperable and reproducible ( FAIR ) data standards, thereby providing context for evaluating and understanding study results. An overview of the documentation considerations for each workflow step is presented and then summarised in a checklist that can accompany a published study or report. Ensuring workflows are transparent and documented is critical to reproducible research and should allow for more efficient uptake of metabarcoding data into management decision-making.

Metabarcoding and Metagenomics↗

USGS2023

Toward a national eDNA strategy for the United States

Environmental DNA (eDNA) data make it possible to measure and monitor biodiversity at unprecedented resolution and scale. As use-cases multiply and scientific consensus grows regarding the value of eDNA analysis, public agencies have an opportunity to decide how and where eDNA data fit into their mandates. Within the United States, many federal and state agencies are individually using eDNA data in various applications and developing relevant scientific expertise. A national strategy for eDNA implementation would capitalize on recent scientific developments, providing a common set of next-generation tools for natural resource management and public health protection. Such a strategy would avoid patchwork and possibly inconsistent guidelines in different agencies, smoothing the way for efficient uptake of eDNA data in management. Because eDNA analysis is already in widespread use in both ocean and freshwater settings, we focus here on applications in these environments. However, we foresee the broad adoption of eDNA analysis to meet many resource management issues across the nation because the same tools have immediate terrestrial and aerial applications.

Environmental DNA↗

USGS2022

Integrative monitoring strategy for marine and freshwater harmful algal blooms and toxins across the freshwater-to-marine continuum

Many coastal states throughout the USA have observed negative effects in marine and estuarine environments caused by cyanotoxins produced in inland waterbodies that were transported downstream or produced in the estuaries. Estuaries and other downstream receiving waters now face the dual risk of impacts from harmful algal blooms (HABs) that occur in the coastal ocean as well as those originating in inland watersheds. Despite this risk, most HAB monitoring efforts do not account for hydrological connections in their monitoring strategies and designs. Monitoring efforts in California have revealed the persistent detection of cyanotoxins across the freshwater-to-marine continuum. These studies underscore the importance of inland waters as conduits for the transfer of cyanotoxins to the marine environment and highlight the importance of approaches that can monitor across hydrologically connected waterbodies. A HAB monitoring strategy is presented for the freshwater-to-marine continuum to inform HAB management and mitigation efforts and address the physical and hydrologic challenges encountered when monitoring in these systems. Three main recommendations are presented based on published studies, new datasets, and existing monitoring programs. First, HAB monitoring would benefit from coordinated and cohesive efforts across hydrologically interconnected waterbodies and across organizational and political boundaries and jurisdictions. Second, a combination of sampling modalities would provide the most effective monitoring for HAB toxin dynamics and transport across hydrologically connected waterbodies, from headwater sources to downstream receiving waterbodies. Third, routine monitoring is needed for toxin mixtures at the land–sea interface including algal toxins of marine origins as well as cyanotoxins that are sourced from inland freshwater or produced in estuaries. Case studies from California are presented to illustrate the implementation of these recommendations, but these recommendations can also be applied to inland states or regions where the downstream receiving waterbody is a freshwater lake, reservoir, or river.

California, Oregon↗

USGS2021

Multiple co-occurring and persistently detected cyanotoxins and associated cyanobacteria in adjacent California lakes

The global proliferation of toxin producing cyanobacterial blooms has been attributed to a wide variety of environmental factors with nutrient pollution, increased temperatures, and drought being three of the most significant. The current study is the first formal assessment of cyanotoxins in two impaired lakes, Canyon Lake and Lake Elsinore, in southern California that have a history of cyanobacterial blooms producing high biomass as measured by chl-a. Cyanotoxins in Lake Elsinore were detected at concentrations that persistently exceeded California recreational health thresholds, whereas Canyon Lake experienced persistent concentrations that only occasionally exceeded health thresholds. The study results are the highest recorded concentrations of microcystins, anatoxin-a, and cylindrospermopsin detected in southern California lakes. Concentrations exceeded health thresholds that caused both lakes to be closed for recreational activities. Cyanobacterial identifications indicated a high risk for the presence of potentially toxic genera and agreed with the cyanotoxin results that indicated frequent detection of multiple cyanotoxins simultaneously. A statistically significant correlation was observed between chlorophyll-a (chl-a) and microcystin concentrations for Lake Elsinore but not Canyon Lake, and chl-a was not a good indicator of cylindrospermopsin, anatoxin-a, or nodularin. Therefore, chl-a was not a viable screening indicator of cyanotoxin risk in these lakes. The study results indicate potential acute and chronic risk of exposure to cyanotoxins in these lakes and supports the need for future monitoring efforts to help minimize human and domestic pet exposure and to better understand potential effects to wildlife. The frequent co-occurrence of complex cyanotoxin mixtures further complicates the risk assessment process for these lakes given uncertainty in the toxicology of mixtures.

California↗

USGS2020

Characterizing benthic macroinvertebrate and algal biological condition gradient models for California wadeable Streams, USA

The Biological Condition Gradient (BCG) is a conceptual model that describes changes in aquatic communities under increasing levels of anthropogenic stress. The BCG helps decision-makers connect narrative water quality goals (e.g., maintenance of natural structure and function) to quantitative measures of ecological condition by linking index thresholds based on statistical distributions (e.g., percentiles of reference distributions) to expert descriptions of changes in biological condition along disturbance gradients. As a result, the BCG may be more meaningful to managers and the public than indices alone. To develop a BCG model, biological response to stress is divided into 6 levels of condition, represented as changes in biological structure (abundance and diversity of pollution sensitive versus tolerant taxa) and function. We developed benthic macroinvertebrate (BMI) and algal BCG models for California perennial wadeable streams to support interpretation of percentiles of reference-based thresholds for bioassessment indices (i.e., the California Stream Condition Index [CSCI] for BMI and the Algal Stream Condition Index [ASCI] for diatoms and soft-bodied algae). Two panels (one of BMI ecologists and the other of algal ecologists) each calibrated a general BCG model to California wadeable streams by first assigning taxa to specific tolerance and sensitivity attributes, and then independently assigning test samples (264 BMI and 248 algae samples) to BCG Levels 1–6. Consensus on the assignments was developed within each assemblage panel using a modified Delphi method. Panels then developed detailed narratives of changes in BMI and algal taxa that correspond to the 6 BCG levels. Consensus among experts was high, with 81% and 82% expert agreement within 0.5 units of assigned BCG level for BMIs and algae, respectively. According to both BCG models, the 10th percentiles index scores at reference sites corresponded to a BCG Level 3, suggesting that this type of threshold would protect against moderate changes in structure and function while allowing loss of some sensitive taxa. The BCG provides a framework to interpret changes in aquatic biological condition along a gradient of stress. The resulting relationship between index scores and BCG levels and narratives can help decision-makers select thresholds and communicate how these values protect aquatic life use goals.

California↗