NERTO Participants

The morphometric data and sagittal otoliths of 1,955 Red grouper (Epinephelus morio) collected from the FL/AL commercial landings 2021-2022 were used in analyses for a NERTO intern project. The objectives of this project were to demonstrate the efficacies of traditional and new aging methods, analyze historical and current growth trends in Red grouper, and become attuned and familiar with multiple aspects of Red grouper management and life history traits. Specimens subsampled ranged from 392 to 877 mm TL and 3 to 21 years old. New reader (intern) Average Percent Error (APE) was calculated based on SEDAR ages for 1,946 out of the 1,955 specimens 2 aged by expert readers. Specimens were mostly whole-aged; some were sectioned. New reader APE was 3.813 with a coefficient of variation of 5.392%, acceptable based on established APE precision (5% ³). 86 % of new reader ages were within 1 year of expert ages, and 94 % were within 2 years. Distribution metrics point to ages classes 5, 6, 7, and 8, comprising the majority of the sample distribution (71%). Standard 2 parameter and 3-parameter von Bertalanffy growth models were fit to Red grouper fractional ages and observed total lengths (2021-2022) to produce population growth parameters (2 parameter: L¥ = 641 mm, k = .27 mm year -1), (3 parameter: L¥ = 1204 mm, k = .03 mm year -1). Additional samples were included for missing young ages to produce more accurate growth parameters and improve model fit (2 parameter L¥ = 634 mm, k = .28 mm year -1), (3 parameter: L¥ = 671 mm, k = .21 mm year -1). Results from traditional ageing were precise, new ageing methods have promising indications, and growth models while effective can be improved upon.

Black mangroves (Avicennia germinans) are expanding into the northern Gulf of Mexico (GOM) from more southern tropical regions. Due to warming temperatures and climate change, A. germinans thrives as an invasive species. Freeze events in the winter months have become less frequent and less severe, limiting natural control of the expansion of A. germinans. In some areas of the northern GOM A. germinans is outcompeting native marsh grasses like smooth cordgrass (Sporobolus alterniflorus). Researchers suggest both A. germinans and S. alterniflorus could co-exist and provide more habitat structural complexity; however, the long-term impacts on habitats and ecosystems, including impacts on the brown shrimp (Farfantepenaeus aztecus) and white shrimp (Litopenaeus setiferus) fisheries, are unknown. Understanding the habitat preference of penaeid shrimp species in response to the expansion of A. germinans is a knowledge gap. Here, we outline a study of habitat selection and predator-prey interactions for both F. aztecus and L. setiferus to gain insight into the responses of penaeid shrimp to the invasive black mangrove.

Ecosystem based fisheries management (EBFM) involves the incorporation of ecosystem wide research to inform management plans of fisheries, protected species, and marine resources. This holistic fisheries management approach requires a wealth of data to inform ecosystem models. This calls for the review and expanded hypothesis testing of existing management plans for fisheries, protected species and more specifically our marine resource environment inhabitants.

The Gulf of Mexico (GOM) is a complex and diverse ecosystem with dynamic trophic structures that support numerous commercially important and protected species. This study seeks to supply lesser-known dietary data of forage fish species that can improve ecosystem models in the GOM by comparing the diets of Atlantic croaker (Micropogonias undulatus) caught in the east and west regions of the northern GOM. The fish in this study were collected during the 2023 SEAMAP Summer Groundfish Survey. Traditional visual identification of gut content was used to inspect the diets of 108 fish and calculate the proportion by number (Ni) and frequency of occurrence (Oi) for the prey items found. The top prey found in the east region were shrimp (Oi = 48.3%), amphipods (Oi = 27.6%), and fish (Oi = 20.7%). The top prey in the west region were fish (Oi = 27.3%), plant matter (Oi = 24.2%), and shrimp (Oi = 21.2%). Both regions showed notable amounts of unknown prey matter in their guts (east Oi = 37.9%, west Oi = 30.3%). This large unknown portion of the Atlantic croaker diet along with the general taxonomic identifications of known prey items highlight the importance of additional dietary analysis methods to provide the data necessary for models used in EBFM. Future work in this study will seek to add fatty acid, stable isotope, energy density, and DNA barcoding analysis to this data providing a more complete understanding of the diet of Atlantic croaker in the Gulf of Mexico.

The Eastern oyster, Crassostrea virginica, plays a pivotal role in commercial and recreational fisheries, delivering essential ecosystem services such as water filtration and shoreline stabilization. This species also serves as a habitat and food source for other estuarine organisms. However, Eastern oyster populations encounter numerous threats, with microplastic pollution emerging as a significant concern. Oysters are particularly vulnerable to microplastic ingestion due to their filter-feeding behavior, which can physically harm their gills and tissues, potentially impairing feeding efficiency and reproductive capabilities. In line with NOAA’s mission to understand and protect our oceans and coastal resources, the ecotoxicology lab at the Hollings Marine Laboratory has been conducting studies to document the presence of microplastic pollution in this critical ecosystem. My NOAA Experiential Research and Training Opportunities (NERTO) assessed microplastic quantities and types within various components of the oyster reef, including sea surface water, oyster reef sediment, and oyster tissue. Furthermore, I examined variations in microplastic distribution across sites, focusing on areas influenced by varying levels of urban inflow. By addressing these objectives and hypotheses, this research yielded valuable laboratory techniques learned to identify the extent of microplastic pollution in the Eastern oyster population within Charleston Harbor. These findings underscore the significance of safeguarding and preserving these ecologically vital organisms in alignment with NOAA’s mission and commitment to protecting our coastal environments.

In the past 20 years, thousands of salmon habitat restoration projects have occurred in the Pacific Northwest, with a focus on the ecological goal of protecting and recovering threatened and endangered salmon species. However, studies in other regions of the United States have found that in addition to the ecological drivers of restoration projects, there are also social factors that potentially influence restoration. To better understand these dynamics, our project investigated the ecological and social influences on the distribution of salmon habitat restoration efforts in the Puget Sound region of Washington state. We aimed to answer the following research question: How does the regional distribution of completed salmon restoration projects correlate with biological, physical, and human community characteristics? Using salmon habitat restoration projects data obtained from the NOAA managed Pacific Northwest Salmon Habitat Project Database as dependent variables, this project explored whether salmon habitat restoration efforts in the Puget Sound tend to flow towards certain types of ecological and social communities, and the potential equity and environmental justice implications. Preliminary statistical count model results suggest that, depending on the project type, restoration effort was highest in lower elevations catchments with higher ESU counts, water quality impairment and high percentages of non-Hispanics white populations.

The Research for this NERTO internship was completed with the Human Dimension team at the NWFSC, which focuses on addressing social, economic, and cultural issues associated with resource management. The main objective of the internship’s research project was to investigate whether the regional distribution of completed salmon habitat restoration project sites in the Puget Sound correlate with biological, physical, and human community characteristics? Understanding whether salmon restoration efforts tends to flow towards certain types of communities, could inform future effort allocations in the Pacific Northwest and raise awareness about potential equity and environmental justice issues. Previous literature on environmental
justice highlights that environmental hazards may disproportionately affect communities with greater susceptibility to unequal environmental protection, however, social and environmental impact assessments are commonly conducted separately (Sanchez et al 2013). Our project was inspired by a similar research that explored correlations between ecological and social variables and restoration sites along the California coast (Stanford et al. 2018), which found that restoration effort was “highest in catchments with water quality impairment, high population density, high pro-environmental voting, and highly educated, wealthy, non-Hispanic white populations (Stanford et al. 2018). Using similar methods, we were interested in exploring whether or not similar ecological and social trends exist within the Pacific Northwest. To complete our research, we utilized NOAA NWFSC’s managed Pacific Northwest Salmon Habitat Project (PNSHP) database which contains data on over 26,000 restoration actions undertaken at over 42,000 locations At the Puget Sound level, PNSHP contains data on over
1500 restoration actions undertaken at over 2100 locations from 2000- 2015. The number of restoration project sites in each catchment unit (12-digit Hydrological Unit Code) within the Puget Sound region were used as dependent variables. Ecological and social variables were collected for each catchment unit to use as independent variables. We the fit statistical count
models to assess the correlations between dependent and independent variables.

The Pacific lamprey species are a group of anadromous, eel-like, vertebrates that are endemic to the North Pacific. They are an ecologically, culturally and economically important species in the Pacific Northwest region of the United States. Despite their intrinsic value, their populations have declined by approximately 90% in some regions. Currently there is a paucity of information pertaining to their ocean residence phase. Consequently, the goal of this study was to gain insight into the prey species of Pacific lamprey and to determine if lamprey prey are connected to their recent population declines. Lamprey were collected from the Pacific hake (Merluccius productus) fishery and the Pacific pink shrimp fishery (Pandalus jordani) vessels.
The 313 bp COI region of prey mtDNA were extracted according to the Qiagen DNeasy Blood & Tissue Kit protocol; and amplified using Polymer Chain Reactions (PCR). After external sequencing, samples were identified as Pacific lamprey. This highlighted the need for Pacific lamprey DNA blockers in order to identify prey DNA. Currently, I am in the process of creating a protocol to block lamprey DNA based on previous studies and will implement these techniques into my future research. I also wrote a review paper entitled, “eDNA Methodologies for Assessing Genetic Diversity among Marine Populations,” which will be submitted to the Current Molecular Biology Reports Journal.

It is the role of a fisheries manager to make informed management decisions using the best data available. To provide managers with this data the Southeast Fisheries Science Center (SEFSC) conducts the Southeast Fishery Independent Survey (SEFIS). This survey was created to collect data on reef fish from hard bottom habitats in the southeast US using a variety of different sampling methods. The present study focused on a five-year subset of presence/absence data collected via video recorded on baited chevron traps. The purpose of this study was to determine which biotic and abiotic factors determine the community composition of fishes in the southeast US Atlantic Ocean from 2015-2019. We utilized permutational multivariate analysis of variance (PERMANOVA). The major finding of the study was that depth, latitude, and relief appear to be the most influential at determining the community composition of fishes. We also examined the dataset and classified a species as tropical if the center of its geographic distribution fell equal to or less than 10 degrees (north or south) latitude. Those species whose center of geographic distribution was greater than 10 degrees latitude were classified as non-tropical. Over the time period of the study, we determined that the percent change in mean abundance of tropical species was significantly greater than non-tropical species overall (across North Carolina, South Carolina, Georgia, and Florida) in the southeast US Atlantic Ocean. The results of this study may prove useful for fisheries managers to help predict the possible expansion of tropical fishes and potential changes in fisheries management.

The southern distinct population segment (sDPS) of green sturgeon (Acipenser medirostris) that spawn in the Sacramento River is currently listed as “Threatened” under the Endanger Species Act (ESA). The greatest threats to this population are habitat impediments (dams), habitat degradation, and habitat loss which have occurred consistently since the 1950s due to water diversion efforts. Since the sDPS of green sturgeon was listed as “Threatened” in 2006, a substantial amount of research and conservation has been conducted to understand this population’s habitat use and monitor population abundance. The objective of this study was to identify annual fluctuations in spawning run size and how such fluctuations correlate with
environmental variables (i.e. temperature and flow). Additionally, this study attempted to delineate patterns in habitat use for spawning run individuals. Dual-frequency Identification Sonar (DIDSON), a type of acoustic camera, was used to detect the presence of green sturgeon in the Sacramento River during mobile surveys conducted in May/June from 2010 to 2020. The
video collected from these surveys was used to count individual sturgeon at sampled units which were then used to calculate annual estimates of abundance for spawning run sturgeon in the Sacramento River. Annual estimates of abundance were used to investigate correlations with temperature and flow, identify annual fluctuations in spawning run size, and assess patterns in
habitat use. The results from this study found that April flow was the environmental variable with the strongest correlation to annual spawning run size. Four “hot spots” that consistently supported above average abundances of green sturgeon were also identified.

The sagittal otoliths for 499 Lane Snapper (Lutjanus synagris) were collected, processed and aged. Samples were collected from the Gulf of Mexico, ranging from the southwest tip of Florida to the eastern portion of Texas from January 2015 to October 2017. Otoliths were sectioned, mounted to a microscope slide and aged using a compound microscope. One reader counted annuli and sub-samples were read by a second reader to ensure consistent and accurate ageing. Fork length measurements ranged from 202mm to 495mm. The oldest fish aged was 13 years. There was a significant difference in the growth parameter estimates between males and females so they were analyzed separately. The von Bertalanffy growth parameters were for males: growth coefficient, K = 0.462, asymptotic length, L₀₀ =378.17, and t₀ = -0.868; and for females: growth coefficient, K =0.271, asymptotic length, L₀₀ =383.42, and t₀ = -2.08). 

Dinophysis acuminata is an obligate mixotrophic dinoflagellate that is found in coastal marine water of the Atlantic and Pacific Ocean, brackish water tributaries, and bays.  Dinophysis acuminata is known in many cases to produce toxins of okadaic acid, Dinophysis toxins, and pectenotoxins.  These toxins are associated with Diarrhetic Shellfish poisoning in humans. Dinophysis acuminata is emerging as a potential threat to the developing oyster aquaculture industry in the Delaware Inland Bays.  There are sites within the Delaware Inland Bays that D. acuminata has been present in high concentrations, but how close spring blooms of D. acuminata come to shellfish aquaculture sites is not known.  Little is known of the bloom dynamics of this harmful algae bloom species within the Delaware Inland Bays. The results of this study will aid in determining how long chloroplasts acquired by D. acuminata through kleptoplasty remain functional under prey starved conditions.  Nutrients, light, and prey availability are drivers of spring blooms.  Understanding how long chloroplasts remain capable of photosynthesis in D. acuminata can inform questions on bloom dynamics and overwintering strategies. Culture of Dinophysis acuminata was fed prey, Mesodinium rubrum and then starved.  Results from a Fluorescence Induction and Relaxation System show a decline in the variable fluorescence (Fv/Fm) over time, indicating that the maximum quantum yield of photochemical quenching in PSII is decreasing with time. Results at 25 days indicate a decrease from Fv/Fm of 0.56 to 0.48.  Results of a linear regression analysis of the data show little variability between mean data points and relation between Fv/Fm and time.  Sampling and data analysis are still being performed.

Diuretic shellfish poisoning (DSP) is a worldwide problem for bivalve aquaculture. Due to the presence of DSP toxins in oysters at concentrations that exceed set regulatory limits, there have been many closures to shellfish harvesting. This can lead to significant economic loses in both commercial and recreational shellfish industries. The eastern oyster, Crassostrea virginica, can accumulate diuretic shellfish toxins (DST) when exposed to marine dinoflagellates that produce DSTs. Dinophysis and Prorocentrum are two dinoflagellate genera commonly found in Mid-Atlantic waters that are known to produce DSTs.  Studies have shown that dinoflagellate toxins producers, such as Alexandrium catenella can increase oysters’ susceptibility to bacterial infections. However studies on how okadaic acid affects oysters susceptibility is scarce.  Our goal is to provide insight on the stress response of C. virginica after laboratory exposure to OA and the bacterial pathogen Vibrio parahaemolyticus, through the analysis of the expression of HSP70 (Heat shock protein 70) and CP450 (Cytochrome p450) stress genes.

Plastic fragments, pellets, fibers and cosmetic beads less than 5 mm in size are termed as microplastics. These are emerging contaminants that in recent years have been found in tap water samples all over the world and a in a vast array of aquatic organisms with the possibility of toxic effects in them. Multiple studies have implied that, polybrominated diphenyl ethers (PBDEs), persistent bioaccumulative fire-retardant pollutants, in fish tissues display positive correlations with geographic plastic debris densities. Examination of this linear relationship with respect to the benthic environment using sea scallops as model organism is the research main focus. Scallop and bottom water column samples were collected from multiple regions across Georges Bank and Mid-Atlantic Bight. The optimum extraction method to yield the optimum quantification of hydrophobic bioaccumulative compounds in the Atlantic Sea Scallop, Placopecten magellanicus, using modern solid phase extraction “quick, easy, cheap, effective, rugged, and safe” (QUECHERS) has been obtained. Sea scallops are important commercial organisms with fisheries dredging over 50 million pounds annually for seafood consumption; our research directly contributes to NOAA’s goal to conserve and manage coastal and marine ecosystems and resources by providing the scientific foundation for understanding many future studies of the dangers microplastics can have on important ecological commercial species.

Mytilus edulis, commonly known as the blue mussel, relies on circulating hemocytes to eliminate invading pathogens. However, there is a lack of knowledge about other functions hemocytes may carry, as well as their life-cycle and ontogeny. Currently, hemocyte subpopulations are classified by morphological differences observed through light microscopy. Here we report the elucidation of two hemocyte subpopulations based on density step-gradient centrifugation combined with the differential binding of Fluorescein (FITC)-conjugated Aleuria aurantia lectin (AAL) and FITC-conjugated wheat germ agglutinin (WGA) to cell surface glycoproteins.  Earlier lectin blot studies demonstrated that soluble hemocyte extracts from M. edulis hemocytes express glycoconjugates with terminal fucose and N-acetylglucosamine carbohydrate moieties. Flow cytometry analysis of FITC-conjugated AAL and FITC-conjugated WGA stained hemocytes demonstrate the presence of terminal fucose and N-acetylglucosamine carbohydrate moieties on M. edulis cell surface glycoconjugates. Additional studies reveal that the majority of these terminal carbohydrates are found on protein backbones that are susceptible to cleavage with trypsin, a protease known to cleave the carboxyl side of peptides containing lysine or arginine. The expression of these terminal carbohydrate moieties is not evenly distributed among hemocytes. Here we report that approximately 30% of hemocytes express glycoproteins with terminal N-acetylglucosamine, while 70% of hemocytes express glycoproteins with terminal fucose and N-acetylglucosamine. The expression of terminal fucose and N- acetylglucosamine increases as hemocytes increase in size and level of granularity. Interestingly, smaller agranular hemocytes do not express terminal fucose. These results show the presence of two distinct M. edulis hemocyte subpopulations based on the differential expression of cell surface glycoproteins with terminal N-acetylglucosamine only, or terminal fucose and N-acetylglucosamine.

During the NERTO experience from September to December 2018, I developed skills in random effects modeling to understand spatial processes in fish population dynamics, here-in referred to as geostatistical modeling. These models were tested using larval count data from the Southeast Area Monitoring and Assessment Program (SEAMAP) Fall Plankton Survey. Originally, a non-geostatistical model was fit to the data to derive an index of abundance for spawning stock biomass; however, the original index did not explicitly account for the uncertainty in spatial variation on population density or catchability. Failing to account for this source of uncertainty in a model, underestimates the overall uncertainty of an index of abundance. During the NERTO I began to explore the effect of spatial and spatiotemporal variability using a geostatistical model on King mackerel ichthyoplankton abundance indices and density distribution. I began with the use of delta-log normal models for zero inflated data. As expected, considering spatial variability creates a better model according to the Akaike Information Criterion. Additionally, adding spatial and temporal variability to the original model only slightly increases the standard deviation (uncertainty) of the index of abundance. Future research will include using Poisson-link models to better describe the error structure and variability in the data. I will also further investigate the individual contribution of the original covariates when considering spatial structure as well as environmental covariates such as temperature and chlorophyll.

Spatiotemporal variation in demographic parameters can strongly influence a species’ population dynamics but is generally not included in sea turtle population models due in part to lack of sufficient data. For example, Kemp’s ridley sea turtles that inhabit the U.S. Atlantic Coast grow slower than conspecifics that inhabit the U.S. Gulf of Mexico (GoM) Coast, which may lead to differences in age at maturation for individuals or whole cohorts. To evaluate the influence of this variation on Kemp’s ridley population dynamics, this NERTO experience focused on developing an improved age-structured population model for Kemp’s ridley sea turtles that incorporates habitat-specific vital rate estimates (growth, survival). Using a ~30 year dataset of somatic growth rates obtained through skeletochronology, we developed habitat-specific (Atlantic, GoM) maturation schedules for this species. In addition, ongoing analyses are using 20 years of stranding length frequency data collected through the Sea Turtle Stranding and Salvage Network to estimate habitat-specific survival rates that will be included in the model. Ongoing analyses will examine model sensitivity to changes in stage-and habitat-specific model parameters. This project will help answer critical question about the contribution of somatic growth variation, habitat use, and Atlantic turtles, which have been excluded from all existing population models, to Kemp’s ridley population dynamics.

The systematic search strategy currently used for photo evaluation of large image databases does not work well for species with clumped distributions. Therefore, we planned to develop an adaptive search strategy to better define the habitat of and relationship between black sea bass (Centropristis striata) and sea whip coral (Leptogorgia virgulata), which could then be extrapolated to evaluating other species with a clumped distribution. Unprecedented delays and setbacks prevented this study from being completed to the original extent desired. However, we were able to locate 92 images where at least one black sea bass was present, and 57 where at least one sea whip coral was present. The close proximity and overlap of these images further supports the notion that there is a relationship between these two species.

Changes in environmental conditions due to climate change, including increases in sea water temperature, may be linked to increasing rates of pathogen infection in marine animals. One of the pathogens in which host selectivity and prevalence could be influenced by factors like increasing water temperature is Hematodinium sp., an endoparasitic dinoflagellate that can cause significant mortality and economic loss in crustacean fisheries. Hematodinium sp. causes bitter crab disease/syndrome in the economically important snow and Tanner crabs, a fatal infection characterized by lethargy and discoloration of host tissues and carapace due to massive numbers of parasites in host hemolymph and tissues. Work completed during this internship will contribute to future research to better understand the influence of Hematodinium sp. infection on Tanner crab immunity and physiology. My work during this internship consisted of three major parts: 16s sequencing mini project, Tanner crab (Chionoecetes bairdi) sample collection, and Tanner crab RNA extractions.

Direct setting is an alternative technique to remote setting that utilizes pediveliger stage oyster larvae to directly seed oyster reefs. This study investigated the impact of varying concentrations of Adult-Oyster-Conditioned-Water (OCW) on Crassostrea virginica larval setting in the laboratory and field. In the laboratory, oyster larvae were introduced to setting chambers with varying concentrations of OCW and allowed 7 days to settle. Field experiments were conducted in which oyster larvae were exposed to either a low or high OCW treatment for 30 minutes and then directly set on artificial oyster reefs. In the laboratory and field, setting efficiencies varied among treatments. This research suggest that OCW may enhance setting efficiencies in the field.

Weakfish (Cynoscion regalis) is a species that inhabits regions ranging from Nova Scotia, Canada all the way southward to Florida. They are currently regionally regulated, but they feed on important species that are federally regulated and of commercial interest. There are limited studies on weakfish diet variability among these essential prey. Therefore, our objectives were to determine 1) the most dominant prey in weakfish diet 2) if area, size class and year factors explain variation in diet, and 3) quantify how much prey biomass is removed by weakfish over time. We used diet data from The Chesapeake Bay Multispecies Monitoring and Assessment Program (CHESMMAP), the Northeast Area Monitoring and Assessment Program (NEAMAP) and the National Marine Fisheries Service (NMFS) bottom trawl surveys. We used trophic diversity (Shannon H index) curves to determine the adequacy of diet sampling for 3 factors: 1) area (Chesapeake Bay (CHESMMAP), inshore Mid-Atlantic Bight (NEAMAP), and offshore MAB (NMFS), 2) size category (small (1-25 cm) and medium (26-50 cm), and 3) temporal blocks (block 1: 2007-2013, block 2: 2014-2019). For objective 1 We weighted diet composition by mass following a 2-stage cluster sampling estimator based on the survey design. For objective 2, a Canonical Correspondence Analysis (CCA) was performed to examine how much variation these factors explain for the diet of weakfish. For objective 1 and 2 rare prey that constituted less than 1% were excluded. For objective 3, we estimated per capita consumption for each area with the gastric evacuation rate method. In general, the diet composition was mostly dominated by Engraulidae and Osteichthyes (unidentified bony fish) per area and size. The CCA showed that year was not significant, however the amount of variance explained by the 3 factors together was approximately 40%. We also found that prey biomass removed by weakfish occurred mostly at inshore areas. These results show that area and size are significant factors in weakfish diet variation, this highlights their opportunistic nature, and that cannibalism is an essential part of the weakfish diet.

In 2014, the NOAA Office of Education initiated an experiential Research and Training Opportunities (NERTO) for Cooperative Science Center students to engage in a 12-week immersion in NOAA mission aligned priorities.  Students work collaboratively with a NOAA mentor and their academic advisor to foster networking and strengthen graduate education and workforce pipeline.   Due to COVID-19, the program expanded its engagement to include a virtual component and I offer a case example with a stock assessment working group (WG) in the Northeast to highlight some of the best practices to support a successful internship experience.  Due to some of the biological uncertainty in previous stock assessment of American plaice, estimates of maturity of American plaice on Georges Bank (GB) and in the Gulf of Maine (GOM) region were reevaluated during my internship for consideration in the research track assessment in 2022.  I led the working group to analyze biological data collected by the Northeast Fisheries Science Center on the bottom trawl survey in the spring and fall seasons. Analysis and comparison of American plaice maturity parameters in the GB and GOM regions were done to meet the project’s objectives. To obtain the collective objective of the stock assessment working group, a variety of communication platforms were used on a routine basis.  Technology played a vital role to facilitate communication but more importantly, the weekly check-ins by NOAA advisor to discuss technical details of the research and troubleshoot code remotely was crucial.  The NERTO experience was a success due to the intentional and concerted effort to maintain communication.  From the study, the WG concluded that American plaice males tend to mature faster than females and there are no regional differences in maturation rates between GB and the GOM. We recommend that the 2022 research track use an age-specific, time invariant single observed maturity ogive for American plaice on GB and in the GOM.

Monkfish (Lophius americanus) supports high value fisheries in the Mid-Atlantic and Southern New England. Conservative fishing quotas were imposed owing to refutation of traditional ageing methods that resulted in uncertainties in stock status. Without accurate age interpretation or validation, serious errors in the assessment and management of fish stocks can occur. This internship at the NMFS Northeast Fisheries Science Center (NEFSC) examined the current assessment processes including fishery-independent methods, biological sampling, age determination methods for monkfish and other species (black sea bass, haddock, yellowtail flounder, red hake and silver hake) and age-dependent stock assessment models. I participated in a 2-week leg of the Northeast Fall Bottom Trawl Survey. I trained with the NEFSC Age & Growth group reviewing ageing methods for these species. I met with the assessment leads for each species, reviewing how age-dependent assessments are used in establishing biological reference points and evaluating stock status. My thesis research will continue to involve my NEFSC mentors as I develop novel approaches to age monkfish using trace element microconstituent analysis of hardparts.

Exploring the food web based on the abundance of certain forage fish is an important goal in establishing how the ecosystem changes. Forage fish not only support fisheries but are also important prey for many predators in the California Current. A recent development in food web analysis is the California Current Trophic Database (CCTD), containing thousands of predator diets. This database can be used to update stomach-based food web dynamics in the California Current. Here, we developed two Ecopath food web models to compare temporal changes of the predators most dependent on these forage fish, and which predators exert the strongest top-down mortality on forage stocks during certain temporal regimes. These two models estimate the variation of predator diet composition and mortality rates over two temporal regimes of sardine and anchovy abundance, one regime based on 5 years of high biomass and the other regime based on 5 years of low biomass. We used the R implementation of Ecopath and Ecosim called Rpath to build the models and calculated an index to determine which forage species have key ecological roles (Supportive Role to Fishery ecosystem, SURF). Our diet analyses found that most predators consumed higher levels of sardine and anchovy in the regime where forage fish biomass was high, and the proportion of forage fish in the predator diets decreased in the regime of low forage fish biomass. During the high biomass regime, the SURF index identified Anchovy as the only key species. These food web models can be used not only to determine which predators should be considered in monitoring forage fish mortality but also the outputs could supplement the future modeling experience with the outputs/lessons learned from our Ecopath food web modeling efforts.

Marine microbes, which include single-celled Bacteria, Archaea, and Eukarya (i.e. diatoms, foraminifera), play critical roles in global nutrient and carbon cycling and can be considered bottom-up controls of the marine food web. Human induced change is directly affecting the coastal ocean through the increase of carbon dioxide in ocean waters, leading to ocean acidification, as well as excess nutrient runoff from fertilizers/waste resulting in algal blooms and hypoxic zones associated with large die offs. The Salish Sea (Puget Sound, WA) is commercially relevant and hosts many species susceptible to these changes, like oysters and other shellfish. It is important for us to monitor microbial communities through time and space in order to get a better understanding of the normal seasonal dynamics of these populations, to better be able to detect and predict the effects of large scale physical and chemical environmental changes caused by climate change. This project focused on a temporal (Spring/Summer) analysis of the microbial community of the Salish Sea at three stations. It included a five-day research cruise where summer samples were obtained. Samples underwent: DNA extraction, PCR amplification, 16S rRNA gene sequencing with a Nanopore sequencer, and bioinformatic analysis as part of a longer-term monitoring program that will test the hypotheses that changes in microbial and zooplankton community composition are due to changes in pH, eutrophication, and increased hypoxia, controlling for normal seasonal change. Key findings of this smaller work were: 1) the microbial community shifted between Spring and Summer partially due to changes in stratification, 2)  potential HAB (Harmful Algal Bloom) species of algae were identified in many of our samples and at station P28,  Pseudo-nitzschia sp., a potential domoic acid producing diatom, represented almost half the summer surface community near Golden Gardens, a popular Seattle beach, 3) oxygen, salinity, density, and temperature all significantly affected the microbial composition at our sites, and 4) Nanopore sequencing is a valuable tool with a rapid turnaround that can be used to quickly assess risk for recreation and shellfish farming in coastal waters.

Warming oceans and more frequent marine heatwave events can lead to increases in fishes’ metabolic rate, resulting in changes to their foraging, growth, and survival in warm conditions. In recent years, the Gulf of Alaska Pacific Cod (Gadus macrocephalus) population declined dramatically in response to two marine heatwave events in the region. Pacific Cod metabolic demand was likely elevated during the heatwaves; however, there is currently no well-established methodology for quantifying the metabolic rate of fish in the field as they encounter thermal stress. It is hypothesized that metabolic rate can be estimated from the isotopic composition of carbon (𝛿13 ) in fish otoliths or from magnesium and phosphorous trace elements in otoliths (Limburg and Casini 2018; Chung et al. 2019; Martino et al. 2020). None of these potential proxies have been explored for Pacific Cod, and our objectives for this study are to 1) assess the validity of otolith carbon isotopes and Mg:Ca and P:Ca microchemistry as metabolic proxies for age-1 Pacific Cod, and 2) examine how Pacific Cod metabolic rate varies under different temperature conditions. This is the second of two experiments for my dissertation that focus on understanding potential otolith proxies for metabolic rate. The first experiment focused on metabolic rate in response to moderate temperatures that Pacific Cod might experience in a normal year, while this second experiment is focused on temperatures that would be more common in a marine heatwave event. We exposed Pacific Cod to 3 temperature treatments (6, 10, and 14°C) for twelve months and determined their Standard Metabolic Rate (SMR) using swim tunnel respirometry. We will next analyze the otoliths for carbon stable isotope chemistry and Mg:Ca and P:Ca microchemistry analysis and compare these values to the known SMR for each fish. An otolith-derived metabolic proxy for Pacific Cod would be helpful for evaluating changes in field metabolic rate under stressful temperature conditions and allow for more informed management and conservation of the species.

Climate change can cause an increase in the prevalence of Vibrios, alter microbial communities in aquatic species and their surrounding environment, and increase the emergence of antimicrobial resistant and genetically diverse bacteria. Fluctuations in physicochemical parameters can impair water quality and the productivity of blue crabs (Callinectes sapidus). The increase of naturally contaminated crustaceans and water columns can ultimately increase the risk of human exposure to various Vibrio related illnesses. Thus, this study aims to determine the prevalence of total Vibrio parahaemolyticus (Vp) (tlh) and Vibrio vulnificus (Vv) (vvhA) along with pathogenic markers of Vp (tdh and trh) and Vv (vcgC) in blue crabs and seawater from the Maryland Coastal Bays (MCBs) and the correlation between Vibrio levels and physicochemical parameters by developing predictive linear models. Three to five crabs and one liter of seawater will be collected from six sites within the MCBs for three years. Crabs will be collected from April to October and seawater will be collected from January to December. Hemolymph and crab tissue will be extracted and pooled for each site. Extracted hemolymph, crab tissue, and seawater will be analyzed for Vp and VV using Most Probable Number (MPN) and real time PCR. The outcomes of this study will provide valuable information regarding the spatial and temporal distributions of Vibrio spp. and their effect on microbial communities in blue crabs and their surrounding environments. Furthermore, this study provides insight on species diversity, phylogenetic compositions, genetic properties, and genomic distribution profiles of Vp and Vv in blue crabs and seawater in the MCBs. All approaches will help in risk assessments that are essential in the overall advancement of the quality and safety of public health.

Toxoplasmosis is a disease caused by the protozoan parasite Toxoplasma gondii and is one of the most common parasitic infections in warm-blooded animals. Contamination in the environment is widespread due to the shedding of oocysts (i.e., a hardy, thick-walled stage in the life cycle of coccidian parasites) by domestic cats and other Felids. For the critically endangered Hawaiian monk seal (Neomonachus schauinslandi), Toxoplasmosis is the leading cause of death for female adult seals, with adult females accounting for 10 out of the 14 monk seals known to have died from Toxoplasmosis. My NERTO aims to assess the transport and connectivity of the parasite Toxoplasma gondii in waters near the Hawaiian Archipelago and investigate coastal regions where the parasite may be accumulating concerning the location of Hawaiian monk seals.Due to contracting Covid-19 after arriving in Honolulu, HI, my NERTO was impacted, and I could not do all of the objectives I stated in my 12-week plan. However, I was still able to conduct research that is related to the described project. In addition, to conduct the connectivity analyses, I gave presentations about T. gondii and Toxoplasmosis to build a relationship with cat-related networks interested in managing T. gondii spread in Hawai‘i. I was also introduced to researchers who work closely with the HMSRP, Drs. Karen Shapiro and Kim Falinski. In the particle tracking model, I conducted parameterization of the ocean transport model and preliminary analyses of oocyst transport in the ocean. I formulated connectivity matrices to establish the likely pathways of oocysts once they enter the ocean. These steps are essential to get this project moving forward and make connections with those in the Toxoplasmosis community on the island. These steps are also essential to increase my professional network and workforce training that pertains to NOAA missions.

Atlantic reef fishes off the southeastern United States support a multispecies fishery that is important commercially and ecologically. Several snappers and groupers in this fishery have experienced low recruitment in the most recent decades due to unknown causes. Recruitment is important in understanding the stock status and overall health of an organism. An analysis of the autocorrelation and partial autocorrelation within the most recent stock assessments for ten species showed that nine of them experienced a significant autocorrelation of lag one. Three species (gag grouper, snowy grouper, and scamp grouper) also showed decadal cyclic patterns. Correlations and PCA analyses showed that these fish form two groups. These groups are based on fish that are experiencing low recruitment and those that are not. This work also specifically evaluates the hypothesis that overfishing is a main driver causing low recruitment in some of these species. After analyzing different metrics to evaluate recruitment overfishing with simulation data and applying adequate metrics to the most recent fishing and recruitment estimates for each fishes’ stock assessment, it was found that fishing is an unlikely driver causing low recruitment in all species. Other hypotheses that are potentially influencing these species include environmental conditions, changes in predation, or competition from other organisms.

Persistent organic pollutants (POPs) are a group of lipophilic and hydrophobic anthropogenic compounds that are resistant to environmental degradation. The purpose of this study was to determine the POP concentration in the blubber of common bottlenose dolphins (Tursiops truncatus) in the Skidaway River estuary near Savannah, GA. Biopsy samples were collected in Feb and Mar 2017 and 2019 from 81 individuals and analyzed for POPs in Summer 2019. Biopsy samples were analyzed for a suite of POPs using gas chromatography/mass spectrometry (GC/MS). The mean ΣPOPs in male common bottlenose dolphins was 39 μg/g lipid weight compared to 8.8 μg/g lipid weight for females. The class with the highest measured levels in both sexes was ΣPCBs, with 28 μg/g and 6.9 μg/g lipid weight in males and females, respectively. In females, the highest concentrations for all classes of POPs were in individuals that had never been observed with a calf.

Red Snapper, a federally managed, fishery, and sport fish species will be analyzed to determine if there is a correlation between fish size class and ledge height within Gray’s Reef National Marine Sanctuary. An analysis of similarities test will be preformed to determine the aforementioned scientific question. A long-term data set of approximately 12 years was provided by Dr. Roldan Munoz from the NCCOS Beaufort, NC Laboratory that contains all fishes sighting history during annual summer dive surveys. The current hypothesis is that larger (50 – >90 cm) Red Snapper will be sighted significantly more near taller ledges, and smaller Red Snapper (10 – 50 cm) will be sighted significantly more near shorter ledges. The results of this study will better inform management of Gray’s Reef and aid in determining if there are certain areas of the Marine Sanctuary that need additional restrictions and management emphasis. Lastly, the product of this analysis will be able to be used by Gray’s Reef National Marine Sanctuary to determine any organism size class correlation to ledge height with respect to time.