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1. Using low volume eDNA methods to sample pelagic marine animal assemblages

   https://doi.org/10.1371/journal.pone.0303263  

   Dan, Michelle E; Portner, Elan J; Bowman, Jeff S; Semmens, Brice X; Owens, Sarah M; Greenwald, Stephanie M; Choy, C Anela (May 2024, PLOS ONE)

   Gorokhova, Elena (Ed.)

   Environmental DNA (eDNA) is an increasingly useful method for detecting pelagic animals in the ocean but typically requires large water volumes to sample diverse assemblages. Ship-based pelagic sampling programs that could implement eDNA methods generally have restrictive water budgets. Studies that quantify how eDNA methods perform on low water volumes in the ocean are limited, especially in deep-sea habitats with low animal biomass and poorly described species assemblages. Using 12S rRNA and COI gene primers, we quantified assemblages comprised of micronekton, coastal forage fishes, and zooplankton from low volume eDNA seawater samples (n = 436, 380–1800 mL) collected at depths of 0–2200 m in the southern California Current. We compared diversity in eDNA samples to concurrently collected pelagic trawl samples (n = 27), detecting a higher diversity of vertebrate and invertebrate groups in the eDNA samples. Differences in assemblage composition could be explained by variability in size-selectivity among methods and DNA primer suitability across taxonomic groups. The number of reads and amplicon sequences variants (ASVs) did not vary substantially among shallow (<200 m) and deep samples (>600 m), but the proportion of invertebrate ASVs that could be assigned a species-level identification decreased with sampling depth. Using hierarchical clustering, we resolved horizontal and vertical variability in marine animal assemblages from samples characterized by a relatively low diversity of ecologically important species. Low volume eDNA samples will quantify greater taxonomic diversity as reference libraries, especially for deep-dwelling invertebrate species, continue to expand. 

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2. Challenges in eDNA detection of the invasive European green crab, Carcinus maenas

   https://doi.org/10.1007/s10530-022-02757-y  

   Danziger, Ariella M.; Frederich, Markus (March 2022, Biological Invasions)

   Abstract The early detection of invasive species is essential to cease the spread of the species before it can cause irreversible damage to the environment. The analysis of environmental DNA (eDNA) has emerged as a non-harmful method to detect the presence of a species before visual detection and is a promising approach to monitor invasive species. Few studies have investigated the use of eDNA for arthropods, as their exoskeleton is expected to limit the release of eDNA into the environment. We tested published primers for the invasive European green crab,Carcinus maenas, in the Gulf of Maine and found them not species-specific enough for reliable use outside of the area for which they were designed for. We then designed new primers, tested them against a broad range of local faunal species, and validated these primers in a field study. We demonstrate that eDNA analyses can be used for crustaceans with an exoskeleton and suggest that primers and probe sequences must be tested on local fauna at each location of use to ensure no positive amplification of these other species. 

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3. Inference from eDNA-based field distributions vs laboratory analysis of isolated strains: physiological performance of non-marine Antarctic biota

   https://doi.org/10.1007/s00300-025-03356-y  

   Novis, Phil M; Monks, Adrian; Hunt, John E; Adams, Byron; Dhami, Manpreet K; Kim, Ji Hee; Mitchell, Caroline; Morgan, Fraser; Hawes, Ian; Aislabie, Jackie; et al (March 2025, Polar Biology)

   Abstract Environmental DNA (eDNA) is frequently used to infer distributions of microorganisms in Antarctica. Their distributions relative to environmental variables are, in turn, sometimes used to infer their physiological range (and a relationship between the two is generally assumed for conservation purposes). We sought to determine whether ecological inferences based on distributions accurately reflect tolerances of the organisms concerned, using 249 legacy non-marine samples from a latitudinal gradient between 72 and 86°S, Antarctica. A cyanobacterium, a heterotrophic bacterium, two eukaryotic algae, two fungi, and a moss were isolated into culture, and their field distributions inferred using eDNA analysis of the samples above. Tolerances of each organism with respect to environmental predictors were then inferred from the eDNA distribution and metadata using Generalised Additive Models. We then measured growth of the cultured isolates in response to a set of these predictors. Laboratory responses were then compared to inferences from the eDNA/metadata. Predictions from eDNA/metadata agreed with the results of physiological laboratory experiments for strains that were detected at high taxonomic resolution in the field samples. However, errors were never completely eliminated, and direct contradictions occurred when strains were represented at lower taxonomic resolution in the field data. We found that accurate ecological inference from eDNA studies would be best achieved via maximising both taxonomic resolution (through marker choice/read length) and ecological signal (through careful sampling design and rigorous metadata collection). 

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4. SDM meets eDNA: optimal sampling of environmental DNA to estimate species–environment relationships in stream networks

   Lambert, Timothy D; Ellner, Stephen P (February 2025, Ecography)

   Rangel, Thiago F (Ed.)

   Species distribution models (SDMs) are frequently data-limited. In aquatic habitats, emerging environmental DNA (eDNA) sampling methods can be quicker and more cost-efficient than traditional count and capture surveys, but their utility for fitting SDMs is complicated by dilution, transport, and loss processes that modulate DNA concentrations and mix eDNA from different locations. Past models for estimating organism densities from measured species-specific eDNA concentrations have accounted for how these processes affect expected concentrations. We built off this previous work to construct a linear hierarchical model that also accounts for how they give rise to spatially correlated concentration errors. We applied our model to 60 simulated stream networks and three types of species niches in order to answer two questions: 1) what is the D-optimal sampling design, i.e. where should eDNA samples be positioned to most precisely estimate species–environment relationships? and 2) How does parameter estimation accuracy depend on the stream network’s topological and hydrologic properties? We found that correcting for eDNA dynamics was necessary to obtain consistent parameter estimates, and that relative to a heuristic benchmark design, optimizing sampling locations improved design efficiency by an average of 41.5%. Samples in the D-optimal design tended to be positioned near downstream ends of stream reaches high in the watershed, where eDNA concentration was high and mostly from homogeneous source areas, and they collectively spanned the full ranges of covariates. When measurement error was large, it was often optimal to collect replicate samples from high-information reaches. eDNA-based estimates of species–environment regression parameters were most precise in stream networks that had many reaches, large geographic size, slow flows, and/or high eDNA loss rates. Our study demonstrates the importance and viability of accounting for eDNA dilution, transport, and loss in order to optimize sampling designs and improve the accuracy of eDNA-based species distribution models. 

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5. 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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