Unconventional Methods Open New Doors

(Image credit: OceanX)

Over 3.5 billion of the world’s population depend on fish as a primary source of protein. Additionally, NOAA reports that over 200 million people rely on the fishing industry as a source of income and that the industry makes up 1.5% of the world’s gross domestic product (GDP). With such a heavy reliance on fishing, it’s no wonder there’s a need for fisheries scientists and studies to help guide the conservation and regulation of the industry.

Reporting from a mission in Indonesia onboard OceanXplorer, the world’s most advanced research vessel leveraged by OceanX, Mattie Rodrigue, OceanX Science Program Director, shares that fisheries management is essential to the ability to feed and sustain a population that is critically dependent on fish protein, but it is by no means an easy feat. In a perfect world, fisheries management is built upon the “gold standard” of fisheries surveys, which are made up of fisheries independent data (standardized scientific surveys) and fisheries dependent data (reporting from fishermen within the fishery).

“From an overarching approach, scientists are trying to take independent and dependent fisheries survey data and layer in this bigger picture of what the environment looks like, how that species lives its life, how long it takes to grow up, how long it takes to become sexually reproductive, and then how it will eat and interact with other species and fisheries,” Rodrigue explains.

Mapping 1 1

(Image credit: OceanX)

Fisheries scientists and regulators should be (and sometimes are legally mandated to be) based on the best available science, but with an incomplete understanding of ocean ecosystems and the interactivity of fish stocks within them, sometimes the best available science can be quite limited.

Overcoming Data Limitations

To bridge the data gap, the OceanX team uses a series of technologies and methods to resolve questions without answers. Providing a window into the sampling and survey methods used by the scientific team, Rodrigue offers a unique perspective on the current OceanX campaign: “So what we’re doing in Indonesia is a great case study. To create a baseline understanding of the fish populations that live here independently of what is being caught and analyzed in the market, we’re collaborating with partners on land who are working with local fishermen to sub-sample their catch to genetically identify what those species are. But then offshore, we’re also combining a whole bunch of different methods to understand the fish that live here.”

Wet lab 1

(Image credit: OceanX)

Unlike traditional invasive survey methods—such as line, net, or trawl fishing—OceanX and project collaborators used noninvasive methods to study the regional fishery. Using a combination of observation methods, including baited remote underwater video surveys (BRUVS), a remotely operated vehicle (ROV) standardized visual census method, aerial surveys, scuba diving surveys along standardized transects, and using acoustics to quantify biomass in the water column, all designed using the gold standard for fisheries-independent survey—stratified random sampling design. Combining these methods with environmental DNA (eDNA), they’re creating a spatial distribution of the presence and absence of fish species that live in these waters and using both visual methods and genetic tools to characterize the species and habitats within the sampling area.

eDNA as a Tool

Making its headway as a mainstay applied marine science tool, eDNA is changing the fisheries survey landscape. OceanX has zeroed in on standard operating procedures for eDNA analysis. In summary, the following steps are taken:

  • Scientists collect water and sediment samples from the
  • The collected sample is filtered to capture tiny particles, including cells, mucus, skin, and other materials containing DNA from organisms living in that environment.
  • DNA is extracted from filtered This involves breaking down cells to release the DNA they contain.
  • Specific regions of the extracted DNA are copied multiple times using a technique called PCR (Polymerase Chain Reaction), which produces enough DNA to be detected and
  • The amplified DNA is sequenced, meaning the exact order of the DNA’s building blocks (nucleotides) is This helps identify which species the DNA came from.
  • The DNA sequences are compared to a database of known sequences to identify the species present in the This can reveal which organisms are in the environment without needing to see or capture them directly.

When asked about the progress of eDNA methods and standardization, Rodrigue stresses the need for establishing protocols: “Just like other international organizations and governments—like the World Meteorological Organization, the IOC, and Seabed 2030, to name a few—we (along with other public and private partners leading eDNA tool development) are starting to create a set of standards and best practices for eDNA. Best practices are being developed for different scenarios: best practices for sequencing at sea, best practices for collecting samples, filtering them, bring back to the lab, and best practices for extracting the samples. At the moment, there are all kinds of eDNA kits and tools out there. It will be imperative for a centralized international body to create standardized methods by which we can then derive science-based policy.”

While eDNA is one of today’s most promising tools for marine scientific research, the availability of sequenced DNA genomes, or lack of them, poses a major constraint to the application of eDNA methodology in the field. Since only a small percentage of ocean life has been characterized and sequenced, eDNA survey results are limited to species whose genomes have been sequenced and available in already established databases. For this reason, OceanX takes pride in supplying any genome sequences developed on board to the public and open-access repositories to be used for eDNA surveys in the future.

To keep up with OceanX, visit:https://oceanx.org

This feature appeared in Environment, Coastal & Offshore (ECO) Magazine’s 2024 Autumn edition Sampling & Survey, to read more access the magazine here.

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