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Barcoding image credit: Govindarajan and Renier, WHOI
Anglerfish image credit: Larry Madin, WHOI

The Audacious Project:

The Ocean 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. Our interdisciplinary team which includes scientists, engineers, and policy experts addresses the following theme areas:

  1. The distribution of biomass and biodiversity
  2. Food web linkages within the twilight zone and among the twilight zone and other ocean realms
  3. The life histories and behaviors of twilight zone animals
  4. The role of the twilight zone and its inhabitants in the global carbon cycle
  5. Technology for studying the mesopelagic zone

I am leading the OTZ Biodiversity theme area, which emphasizes the use of molecular approaches such as DNA barcoding and metabarocoding of individuals, plankton tow contents, and eDNA. See more about some specific projects below.

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. My laboratory is using eDNA analyses to study the ocean's twilight zone. Towards that end, we are adapting protocols designed in shallow water systems to deep midwater habitats and conducting experiments to interpret the signals that we detect. We are also developing new sampling approaches (described below) and conducting adaptive sampling based on acoustics. For more information, see this Oceanus article. This work is part of the Audacious Ocean Twilight Zone Project.

The Mesobot: a new vehicle for tracking and sampling midwater animals and environmental DNA

Mesobot - The Mesobot is a new NSF-funded AUV that is under development. Mesobot will be able to both track targets and take samples. We are using Mesobot to study the ocean's mesopelagic zone, also called the "twilight zone".

Here is an article for more information about the Mesobot.

Mesobot collaborators: Dana Yoerger (lead PI, WHOI), Joel Llopiz(WHOI), Peter H Wiebe (WHOI), Jonathan C Howland (WHOI), Christopher R German (WHOI), Bruce H Robison (MBARI), Kakani Katija (MBARI), Stephen Rock (Stanford), John A Breier (University of Texas Rio Grande Valley)

A conceptual image of eDNA sampling on Mesobot

Autonomous environmental DNA sampling

I am developing autonomous environmental DNA samplers specifically targeting eDNA from the Ocean's Twilight Zone. We are currently deploying a new, large-volume eDNA multisampler on the Mesobot but hope to eventually utilize a variety of platforms.  The sampler filters the water in situ. My co-principal investigators are Dana Yoerger (WHOI) and Allan  Adams (MIT). Additionally I incorporated an eDNA sampler on the new towed broadband acoustics instrument, Deep See. You can read more about it here. Deep See is lead by Andone Lavery (WHOI). Our long term goal is to conduct adaptive sampling, based on acoustics or other sensed information.


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.

The clinging jellyfish Gonionemus.
Photo credit: Annette Govindarajan

Ecology and population genetic structure of the clinging jellyfish Gonionemus

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.