Andruszkiewicz Allan
Elizabeth
Andruszkiewicz Allan
Elizabeth
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ArticleImproved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies(Elsevier, 2022-09-22) Govindarajan, Annette F. ; McCartin, Luke ; Adams, Allan ; Allan, Elizabeth ; Belani, Abhimanyu ; Francolini, Rene ; Fujii, Justin ; Gomez-Ibañez, Daniel ; Kukulya, Amy ; Marin, Fredrick ; Tradd, Kaitlyn ; Yoerger, Dana R. ; McDermott, Jill M. ; Herrera, SantiagoMetabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large – volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume (∼40–60 L) samples collected by Mesobot with small volume (∼2 L) samples collected using the conventional CTD rosette – mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not – although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.•A large-volume eDNA sampler was developed and deployed on the midwater robot Mesobot.•Compared to conventional small-volume samples, the sampler detected more metazoan taxa.•Both sampling approaches detected community changes with depth on the scale of 10's of meters.•The metazoan eDNA signal declined with depth.•Large volume sampling may be especially important in the mesopelagic and deep sea.
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ArticleModeling characterization of the vertical and temporal variability of environmental DNA in the mesopelagic ocean(Nature Research, 2021-10-28) Andruszkiewicz Allan, Elizabeth ; DiBenedetto, Michelle H. ; Lavery, Andone C. ; Govindarajan, Annette F. ; Zhang, Weifeng G.Increasingly, researchers are using innovative methods to census marine life, including identification of environmental DNA (eDNA) left behind by organisms in the water column. However, little is understood about how eDNA is distributed in the ocean, given that organisms are mobile and that physical and biological processes can transport eDNA after release from a host. Particularly in the vast mesopelagic ocean where many species vertically migrate hundreds of meters diurnally, it is important to link the location at which eDNA was shed by a host organism to the location at which eDNA was collected in a water sample. Here, we present a one-dimensional mechanistic model to simulate the eDNA vertical distribution after its release and to compare the impact of key biological and physical parameters on the eDNA vertical and temporal distribution. The modeled vertical eDNA profiles allow us to quantify spatial and temporal variability in eDNA concentration and to identify the most important parameters to consider when interpreting eDNA signals. We find that the vertical displacement by advection, dispersion, and settling has limited influence on the eDNA distribution, and the depth at which eDNA is found is generally within tens of meters of the depth at which the eDNA was originally shed from the organism. Thus, using information about representative vertical migration patterns, eDNA concentration variability can be used to answer ecological questions about migrating organisms such as what depths species can be found in the daytime and nighttime and what percentage of individuals within a species diurnally migrate. These findings are critical both to advance the understanding of the vertical distribution of eDNA in the water column and to link eDNA detection to organism presence in the mesopelagic ocean as well as other aquatic environments.
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ArticleQuantitative PCR assays to detect whales, rockfish, and common murre environmental DNA in marine water samples of the Northeastern Pacific(Public Library of Science, 2020-12-02) Andruszkiewicz Allan, Elizabeth ; Yamahara, Kevan M. ; Closek, Collin J. ; Boehm, Alexandria B.Monitoring aquatic species by identification of environmental DNA (eDNA) is becoming more common. To obtain quantitative eDNA datasets for individual species, organism-specific quantitative PCR (qPCR) assays are required. Here, we present detailed methodology of qPCR assay design and testing, including in silico, in vitro, and in vivo testing, and comment on the challenges associated with assay design and performance. We use the presented methodology to design assays for three important marine organisms common in the California Current Ecosystem (CCE): humpback whale (Megaptera novaeangliae), shortbelly rockfish (Sebastes jordani), and common murre (Uria aalge). All three assays have excellent sensitivity and high efficiencies ranging from 92% to 99%. However, specificities of the assays varied from species-specific in the case of common murre, genus-specific for the shortbelly rockfish assay, and broadly whale-specific for the humpback whale assay, which cross-amplified with other two other whale species, including one in a different family. All assays detected their associated targets in complex environmental water samples.
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ArticleAdvances in environmental DNA sampling for Observing Ocean Twilight Zone animal diversity(Oceanography Society, 2023-01-19) Govindarajan, Annette F. ; Adams, Allan ; Allan, Elizabeth ; Herrera, Santiago ; Lavery, Andone ; Llopiz, Joel ; McCartin, Luke ; Yoerger, Dana R. ; Zhang, WeifengThe ocean’s vast twilight, or mesopelagic, zone (200–1,000 m depth) harbors immense biomass consisting of myriad poorly known and unique animal species whose quantity and diversity are likely considerably underestimated. As they facilitate the movement of carbon from surface waters to the deep sea through feeding and migratory behaviors, ocean twilight zone (OTZ) animals are vital to regulating Earth’s climate (Ducklow et al., 2001). However, anthropogenic threats, such as climate change, ocean acidification, pollution, and overfishing pose an imminent threat to OTZ animals. Long-term spatially and temporally intensive observations are essential to our understanding of biodiversity in the OTZ, to resolving global carbon cycles, and to monitoring ocean health. Environmental DNA (eDNA) analysis, which involves studying the trace genetic signatures of organisms (Figure 1), is a promising approach to filling this urgent need. eDNA can be sampled and diagnostic genetic markers (“barcodes”) can be sequenced in order to detect the animals inhabiting a given water parcel. Other laboratory protocols (e.g., quantitative PCR, or “qPCR” and “digital droplet PCR”) can be applied to facilitate quantitative assessments of specific target species (Eble et al., 2020). In seagoing oceanographic research, eDNA assessment is transitioning from being considered an experimental approach to becoming an established routine that can be scaled up to match ocean observing needs.