Applied Ocean Physics and Engineering (AOP&E)

Permanent URI for this collection

https://hdl.handle.net/1912/10

The Department is a major center for research in fluid mechanics, coastal processes, ocean mixing, acoustics, air-sea interaction, deep submergence, ocean systems and moorings, remote sensing, robotics, certain biological processes, image processing, signal processing and estimation, control theory, and the dynamics of ocean cables.

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Browsing Applied Ocean Physics and Engineering (AOP&E) by Author "Adams, Allan"
  • Article
    Advances 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, Weifeng
    The 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.
  • Article
    Improved 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, Santiago
    Metabarcoding 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.
  • Working Paper
    Pump it Up workshop report
    (Woods Hole Oceanographic Institution, 2017-10-20) Buesseler, Ken O. ; Adams, Allan ; Bellingham, James G. ; Dever, Mathieu ; Edgcomb, Virginia P. ; Estapa, Margaret L. ; Frank, Alex ; Gallager, Scott M. ; Govindarajan, Annette F. ; Horner, Tristan J. ; Hunter, Jon ; Jakuba, Michael V. ; Kapit, Jason ; Katija, Kakani ; Lawson, Gareth L. ; Lu, Yuehan ; Mahadevan, Amala ; Nicholson, David P. ; Omand, Melissa M. ; Palevsky, Hilary I. ; Rauch, Chris ; Sosik, Heidi M. ; Ulmer, Kevin M. ; Wurgaft, Eyal ; Yoerger, Dana R.
    A two-day workshop was conducted to trade ideas and brainstorm about how to advance our understanding of the ocean’s biological pump. The goal was to identify the most important scientific issues that are unresolved but might be addressed with new and future technological advances.