According to a new study from the Los Angeles and Long Beach area, environmental DNA succeeds in assessing marine biodiversity when key implementation steps are followed.
The researchers found that marine biodiversity can be measured with environmental DNA (eDNA) – an application of gene sequencing to environmental biology. This method should enable the rapid assessment of changes in marine life, making environmental DNA an essential tool for managing responses to climate change.
However, according to a new study from the Los Angeles and Long Beach area, environmental DNA only works well if key implementation steps are followed.
The study, titled ‘Manager’s Guide to Using eDNA Metabarcoding in Marine Ecosystems,’ is published in the journal PeerJ.
Why was the eDNA study conducted?
“What do we need to know to use eDNA in the coastal ocean, and can we make it work well in a large urban environment? These are the questions that motivated us to initiate this study,” said Regina Wetzer, curator and director of the Marine Biodiversity Center at the Natural History Museum of Los Angeles County (NHM).
To answer these questions, several organizations, such as the Natural History Museum, various academic institutions, environmental consultants and government agencies, participated in the research and highlighted the challenges of using the environmental DNA, but also the widespread interest in its use.
Environmental DNA uses genetic sequencing samples from the environment to inventory biodiversity. In this case, seawater samples were taken.
Zack Gold, lead author of the study, said: “There are genes that differ enough between species to be used as identifying markers. Every organism releases DNA by dropping skin cells or other materials, so we can take a cup of seawater, sequence the DNA in it, and use it to inventory organisms from the region.
Testing the ability of environmental DNA as a biodiversity assessment tool
The team tested eDNA’s ability to act as an effective tool for biodiversity assessment in the nearby Port of Los Angeles and Port of Long Beach, a site of intense environmental concern.
Environmental DNA sampling and conventional shipboard trawl sampling were paired at seven sites in the port complex. At each of these sites, several eDNA samples were collected by the researchers just before the trawl was towed into the same area. These samples contained approximately one liter of seawater each. From this test, the team found that the eDNA detected almost all of the 17 fish species found in the trawls, but also detected an additional 55 native fish species. To detect additional species through conventional sampling, more sampling trips at very high cost are required.
“We were happy to see eDNA validated alongside ‘conventional’ sampling, but we were really excited to see the additional information coming from eDNA,” said Dean Pentcheff, researcher and program manager of the Diversity Initiative for the Southern California Ocean (DISCO) at NHM.
However, a genetic sequence in an eDNA sample can only be resolved to a species if there is a reference sequence recorded for that species, so finding additional information depends on having a complete genetic reference library. for all fish in the area. In this study, all of the fish in the environmental DNA samples were only resolved after the researchers added the last fish references to the sequence library.
eDNA samples from different locations in ports yielded very different species inventories. This showed that environmental DNA in this ocean environment can measure variability over a small area, exposing differences between locations as close as a few hundred meters apart.
Recommend the tool for future uses
Today, the authors of the study have put together a set of recommendations for managers considering environmental DNA as a tool for assessing biodiversity, based on this pilot project. Recommendations cover careful selection of identification genes and specific guidance on how to clean sequence data from eDNA samples before searching for sequence matches. The creation of a regional reference database will be part of the recommendations due to the successful species resolution resulting from the creation of a complete sequence reference library.
“These environmental samples are like time capsules that we can mine in the future,” said Adam Wall, head of crustacean collections at NHM. Another of the group’s recommendations was driven by this sentiment, archiving eDNA samples and sequence data for long-term use.
More information may come from the samples as sequencing technology improves. Sequence data can be re-analyzed once genetic data analysis techniques improve and genetic reference libraries are expanded, to obtain additional results beyond the fish inventories published in this study.
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