DNA in Seawater Can Reveal Fish Diversity in Deep Ocean

The process of sampling seawater from deep in the ocean is akin to swabbing a conference table for skin cells to analyze who’s been there recently.

Deep sea coral and fish [photo credit: Papahanaumokuakea National Monument]

(CN) — A novel technique called eDNA metabarcoding allows scientists to effectively determine which species of fish inhabit a given region of the deep sea by analyzing local water samples for errant genetic material.

Environmental DNA, or eDNA, is a type of genetic material that animals shed as they move through their environment. Sampling deep sea water for eDNA is much akin to taking a swab of a conference table for skin cell-rich dust, then analyzing it to see who has been there recently.

A team of scientists from a private company called eDNAtec Inc. along with their colleagues from Fisheries and Oceans Canada and Memorial University investigated this method of identifying deep sea-dwelling marine life in a new study released Wednesday in the journal PLOS ONE.

The researchers sought to develop an eDNA-sampling protocol specifically tailored for the deep sea to detect which fish species are present and compare the results with those from traditional surveys. They collected seawater samples over the course of two years and refined their methods in the second year. Through their analysis they were able to identify 21 distinct fish families, comprised of 15 individual species, a few of which are listed as being critically endangered.

The team found this new method to be comparable in accuracy with traditional survey methods, which include trawling, long-lining, acoustic monitoring and filtration systems, while exceling over these in its ease of use. These traditional methods all have their own drawbacks as far as where they can be deployed and what they’re able to study, necessitating the use of multiple strategies which increases both complexity and room for error.

“Each of these methods have limitations in their ability to capture a community based on morphological and behavioral selectivity as well as taxonomic resolution. Additionally, not all of these methods can be employed equally well in all areas of the ocean,” the authors wrote in the study.

Understanding these creatures of the deep — who lives where, in what numbers and during which time of year — is critical for conservation and sustainable management efforts as well as understanding the impacts of commercial fishing operations and climate change. The deep sea is the largest biome on Earth so it’s best that we know if these mounting pressures are taking a toll on its residents.

“Environmental DNA (eDNA) metabarcoding has great potential to improve our understanding of this region and to facilitate monitoring across a broad range of taxa. Here we evaluate two eDNA sampling protocols and seven primer sets for elucidating fish diversity from deep sea samples,” the study authors wrote.

The researchers found larger sample volumes than normal to be necessary, 50 ounces versus the typical eight, because samples taken at depths approaching one mile contained significantly lower concentrations of DNA than those taken at the surface or at mid-depths. Larger samples contain more unique DNA sequences, leading to more accurate and robust results, but also requires more cold storage capacity which poses a logistical constraint.

To date, most eDNA oceanic sampling efforts have concentrated on surface waters and the relatively shallow regions along coastlines. The few deep-sea sampling efforts, those sampling waters deeper than 3,200 feet, have focused on sediment sampling to study benthic communities rather than studying fish and pelagic communities.

Despite the improvement in efficiency over traditional methods, certain challenges still exist with deep sea eDNA sampling, such as differing characteristics of the water, light and the organisms themselves leading to varying levels of eDNA being available for analysis. Because of this, optimal protocols for eDNA sampling in the deep ocean need to be tailored specifically for that environment and should be optimized for the particular groups of organisms being studied — a one-size-fits-all approach won’t cut it.

“Using eDNA from deep sea water samples to characterize biodiversity has the potential to provide critical insight into deep ocean biodiversity, however, eDNA sampling protocols need to be optimized for this environment. Abiotic factors, such as the reduced light levels and comparatively low variability in temperature and salinity in deep ocean water, affect the persistence of eDNA while biotic factors, such as the predominant life histories and/or metabolism of the organisms living in the deep ocean may affect the amount of eDNA released into the water,” the authors wrote.

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