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1. Environmental DNA detects Spawning Habitat of an ephemeral migrant fish (Anadromous Rainbow Smelt: Osmerus mordax)

   https://doi.org/10.1186/s12862-022-02073-y  

   Holmes, Vaughn; Aman, Jacob; York, Geneva; Kinnison, Michael T. (December 2022, BMC Ecology and Evolution)

   Abstract Background Anadromous rainbow smelt ( Osmerus mordax ) have experienced a large range reduction in recent decades and the status of remnant spawning populations is poorly known in Maine, where these fish have significant ecological, cultural, and commercial relevance. Defining the remnant range of anadromous smelt is more difficult than for many declining fish species because adults are only ephemerally present while spawning in small coastal streams at night during spring runoff periods when traditional assessments can be unreliable or even hazardous. We hypothesized that eDNA might facilitate improved survey efforts to define smelt spawning habitat, but that detection could also face challenges from adult eDNA quickly flushing out of these small stream systems. We combined daytime eDNA sampling with nighttime fyke netting to ascertain a potential window of eDNA detection before conducting eDNA surveys in four streams of varying abundance. Hierarchical occupancy modeling was in turn employed to estimate eDNA encounter probabilities relative to numbers of sampling events (date), samples within events, and qPCR replicates within samples. Results Results from the combined eDNA and fyke net study indicated eDNA was detectable over an extended period, culminating approximately 8–13 days following peak spawning, suggesting developing smelt larvae might be the primary source of eDNA. Subsequently, smelt eDNA was readily detected in eDNA surveys of four streams, particularly following remediation of PCR inhibitors. Hierarchical occupancy modeling confirmed our surveys had high empirical detection for most sites, and that future surveys employing at least three sampling events, three samples per event, and six qPCR replicates can afford greater than 90% combined detection capability in low abundance systems. Conclusions These results demonstrate that relatively modest eDNA sampling effort has high capacity to detect this ephemerally present species of concern at low to moderate abundances. As such, smelt eDNA detection could improve range mapping by providing longer survey windows, safer sampling conditions, and lower field effort in low density systems, than afforded by existing visual and netting approaches. 

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2. Including environmental covariates clarifies the relationship between endangered Atlantic salmon (Salmo salar) abundance and environmental DNA

   https://doi.org/10.1002/edn3.424  

   Morrison, Melissa K.; Lacoursière‐Roussel, Anaïs; Wood, Zachary T.; Trudel, Marc; Gagné, Nellie; LeBlanc, Francis; Samways, Kurt; Kinnison, Michael T.; Pavey, Scott A. (September 2023, Environmental DNA)

   Abstract Collecting environmental DNA (eDNA) as a nonlethal sampling approach has been valuable in detecting the presence/absence of many imperiled taxa; however, its application to indicate species abundance poses many challenges. A deeper understanding of eDNA dynamics in aquatic systems is required to better interpret the substantial variability often associated with eDNA samples. Our sampling design took advantage of natural variation in juvenile Atlantic salmon (Salmo salar) distribution and abundance along 9 km of a single river in the Province of New Brunswick (Canada), covering different spatial and temporal scales to address the unknown seasonal impacts of environmental variables on the quantitative relationship between eDNA concentration and species abundance. First, we asked whether accounting for environmental variables strengthened the relationship between eDNA and salmon abundance by sampling eDNA during their spring seaward migration. Second, we asked how environmental variables affected eDNA dynamics during the summer as the parr abundance remained relatively constant. Spring eDNA samples were collected over a 6‐week period (12 times) near a rotary screw trap that captured approximately 18.6% of migrating smolts, whereas summer sampling occurred (i) at three distinct salmon habitats (9 times) and (ii) along the full 9 km (3 times). We modeled eDNA concentration as a product of fish abundance and environmental variables, demonstrating that (1) with inclusion of abundance and environmental covariates, eDNA was highly correlated with spring smolt abundance and (2) the relationships among environmental covariates and eDNA were affected by seasonal variation with relatively constant parr abundance in summer. Our findings underscore that with appropriate study design that accounts for seasonal environmental variation and life history phenology, eDNA salmon population assessments may have the potential to evaluate abundance fluctuations in spring and summer. 

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3. Northeast Pacific eelgrass fish communities characterized by environmental DNA represent local diversity and show habitat specificity

   https://doi.org/10.1002/edn3.431  

   Beatty, Deanna S.; Deen, Emma; Gross, Collin; Stachowicz, John J. (July 2023, Environmental DNA)

   Abstract Fish biodiversity is an important indicator of ecosystem health and a priority for the National Park Service in Drakes Estero, a shallow estuary within Point Reyes National Seashore, Marin County, California. However, fish diversity has yet to be described following the removal of oyster aquaculture infrastructure within Drakes Estero from 2016 to 2017. We used environmental DNA (eDNA) to characterize fish biodiversity within Drakes Estero. We amplified fish eDNA with MiFish primers and classified sequences with a 12S rRNA reference database. We identified 110 unique operational taxonomic units (OTUs, at 97% similarity) within the estuary from 40 samples across 4 sites. From these 110 OTUs, we identified 9 species and 13 taxonomic groups at the genus, family, order, or class level within the estuary. Species‐level assignments are limited by a lack of representative sequences targeted by the MiFish primers for 42% of eelgrass fishes in our region that we identified from a literature review in the Northeast Pacific (NEP) from Elkhorn Slough to Humboldt Bay. Despite this limitation, we identified some common Drakes Estero fishes with our eDNA surveys, including the three‐spined stickleback (Gasterosteus aculeatus), Pacific staghorn sculpin (Leptocottus armatus), surfperches (Embiotocidae), gobies (Gobiidae), and a hound shark (Triakidae). We also compared fish biodiversity within the estuary with that from nearby Limantour Beach, a coastal site. Limantour beach differed in community composition from Drakes Estero and was characterized by high relative abundances of anchovy (Engraulissp.) and herring (Clupeasp.). Thus, we can distinguish estuarine and non‐estuarine sites (<10 km away) with eDNA surveys. Further, eDNA surveys accounted for greater fish diversity than seine surveys conducted at one site within the estuary. Environmental DNA surveys will likely be a useful tool to monitor fish biodiversity across eelgrass estuaries in the Northeast Pacific, especially as reference databases become better populated with regional species. 

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4. Lotic‐SIPCO2 : Adaptation of an open‐source CO₂ sensor system and examination of associated emission uncertainties across a range of stream sizes and land uses

   https://doi.org/10.1002/lom3.10600  

   Robison, Andrew L.; Koenig, Lauren E.; Potter, Jody D.; Snyder, Lisle E.; Hunt, Christopher W.; McDowell, William H.; Wollheim, Wilfred M. (February 2024, Limnology and Oceanography: Methods)

   Abstract River networks play a crucial role in the global carbon cycle, as relevant sources of carbon dioxide (CO₂) to the atmosphere. Advancements in high‐frequency monitoring in aquatic environments have enabled measurement of dissolved CO₂concentration at temporal resolutions essential for studying carbon variability and evasion from these dynamic ecosystems. Here, we describe the adaptation, deployment, and validation of an open‐source and relatively low‐cost in situpCO₂sensor system for lotic ecosystems, the lotic‐SIPCO2. We tested the lotic‐SIPCO2 in 10 streams that spanned a range of land cover and basin size. Key system adaptations for lotic environments included prevention of biofouling, configuration for variable stage height, and reduction of headspace equilibration time. We then examined which input parameters contribute the most to uncertainty in estimating CO₂emission rates and found scaling factors related to the gas exchange velocity were the most influential when CO₂concentration was significantly above saturation. Near saturation, sensor measurement ofpCO₂contributed most to uncertainty in estimating CO₂emissions. We also found high‐frequency measurements ofpCO₂were not necessary to accurately estimate median emission rates given the CO₂regimes of our streams, but daily to weekly sampling was sufficient. High‐frequency measurements ofpCO₂remain valuable for exploring in‐stream metabolic variability, source partitioning, and storm event dynamics. Our adaptations to the SIPCO2 offer a relatively affordable and robust means of monitoring dissolved CO₂in lotic ecosystems. Our findings demonstrate priorities and related considerations in the design of monitoring projects of dissolved CO₂and CO₂evasion dynamics more broadly. 

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5. Applications of Environmental DNA Metabarcoding in Stream Biomonitoring

   Davis, B (August 2024, University of Maine Electronic Theses and Dissertations)

   Advancements in genetic technology and processing allows for the presence of loose genetic material in the environment to become a resource, capable of assisting habitat and wildlife management efforts by providing information about organisms in a region without having to disturb or disrupt the organisms and environment. This use of environmental DNA has gained traction across biomes, with researchers continuing to test extraction and processing of DNA from various environmental media. However, the high variability in media quality, characteristics, and taxonomic knowledge means that the tested capabilities of eDNA vary wildly depending on the application and species of interest. In this thesis, I focus on the use of eDNA metabarcoding in freshwater streams in Maine, examining the ability and existing libraries of two genetic loci to identify Maine fish and macroinvertebrate species. eDNA results are compared against a traditional specimen-based surveying method utilized by the Maine Department of Environmental Protection and the Penobscot Nation’s Department of Natural Resources, and over time to monitor the success of stream restoration initiatives. While eDNA samples successfully detected fish and invertebrate species in both datasets, no strong correlation was found between benthic macroinvertebrate abundance counts and detected sequence variants. Furthermore, eDNA detection led to highly different community survey results than the specimen-based survey method, and limitations of available reference sequences indicate a strong need for localized references for future eDNA work. While eDNA was able to identify ASVs at a higher clarity than the specimen-based survey method, only 4 taxonomic families were shared between the survey method categorization and eDNA detection. However, eDNA was successful when applied to a broader range of taxa for presence-absence detection and community composition detection, and found that stream communities did change significantly based on installment of large wood addition projects. 

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