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Individual animals, bulk animal collections, and environmental DNA can all be genetically barcoded. Image credit: Govindarajan and Renier, WHOI

Biodiversity in the Ocean's Twilight Zone

The vast mesopelagic zone, or twilight zone, is a poorly explored ocean region ranging from 200 to 1000 meters below the ocean surface. I am leading the Biodiversity portion of WHOI's Ocean Twilight Zone project. My work emphasizes the use of molecular approaches such as DNA barcoding and metabarocoding of individuals, plankton tow contents, and eDNA (described below). The animals I am studying include a variety of fish and invertebrates such as jellyfish and crustaceans.

Analyzing traces of genetic material in seawater to detect biodiversity. Photo by Tom Kleindist, WHOI

Using Environmental DNA (eDNA) for biodiversity assessments

Environmental DNA (eDNA) refers to any DNA in the environment, and includes DNA shed by animals through a variety of mechanisms (e.g., spawning, defecation, etc). We can collect eDNA, instead of the animals themselves, to discover what species were present in the area. This approach is powerful, because we can detect animals that traditional sampling methods miss. My laboratory is using eDNA analyses to study the ocean's twilight zone and other marine habitats. For more information, see this primer on eDNA and this Oceanus article.

A conceptual image of eDNA sampling on Mesobot. Image credit: Govindarajan and Renier, WHOI

Scaling up and diversifying midwater eDNA sampling strategies using autonomous environmental DNA sampling with in situ filtration

I am co-developing autonomous environmental DNA samplers specifically targeting eDNA from the Ocean's Twilight Zone. I incorporated an eDNA sampler developed in my laboratory on the towed broadband acoustics and imaging instrument, Deep See. You can read more about it here. In 2019 deployed a new, large-volume eDNA multisampler that I co-developed on the robotic vehicle Mesobot in the Gulf of Mexico. The samplers filter water in situ, which is a great advantage over traditional eDNA sampling. We now have a new version of our eDNA samplers (co-developed by Oceanic-Labs and WHOI; Adams, Govindarajan, and Yoerger, in prep.), that we have deployed on both Mesobot and Deep-See. We are expanding to include eDNA samplers on other platforms, including ROVs and a benthic lander. We are also expanding our sampling strategies to include adaptive sampling in response to real-time acoustic backscatter data from the platform itself, the ship, or even another autonomous vehicle.


Images of mesopelagic animals. Reference barcodes for these and other species will enable DNA barcoding analyses, including eDNA analyses. Images by Paul Caiger and Larry Madin.

Reference libraries for DNA barcoding analysis

A major obstacle to DNA barcoding and metabarcoding analysis of samples and eDNA is the lack of reference sequences for taxonomic assignment. As part of the OTZ project, my laboratory is barcoding fish and invertebrate specimens obtained from midwater trawls and MOCNESS sampling. It is critical that the animals used to provide DNA for reference barcodes are accurately identified.

Research Assistants Erin Frates and Fred Marin with an eDNA sampling pole that we designed in our lab. Photo by Annette Govindarajan

Assessing the impacts of aquaculture with environmental DNA

We are using eDNA analysis to assess the impacts of regenerative ocean farming on local biodiversity. We are collaborating with Cottage City Oysters on the island of Martha's Vineyard and researchers from Southern Connecticut State University to collect and analyze a time series of eDNA samples in the vicinity of the farm.

The clinging jellyfish Gonionemus.
Photo credit: Annette Govindarajan

Biogeography of the clinging jellyfish Gonionemus spp.

Clinging jellyfish are hydrozoan medusae that cling to eelgrass and seaweeds. Despite their small size (adults range from 1 to 3 cm), some clinging jellyfish are known for their powerful stings. The occurrence of severe jellyfish stings since 1990 in Cape Cod and nearby regions suggests a recent invasion from a toxic population. I am using population genomics methods to better understand the origin and spread of Northwest Atlantic clinging jellyfish, and their ecology.