Measuring marine biodiversity with ‘environmental DNA’ – an application of gene sequencing to environmental biology – should enable rapid assessment of changes in marine life. This makes environmental DNA (eDNA) an essential tool for managing our response to climate change. But eDNA only works well if the main implementation steps are followed, according to a new study of the Los Angeles and Long Beach area published in the magazine PeerJ.
“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).
Answering these questions involved contributions from a natural history museum, several academic institutions, environmental consultants and government agencies – highlighting the challenges of using eDNA, but also the widespread interest in its use.
eDNA uses genetic sequencing of samples from the environment (in this case, seawater) to inventory biodiversity. “There are genes that differ enough between species to be used as identification 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,” said Zack Gold, lead author of the study.
The nearby Port of Los Angeles and the Port of Long Beach form one of the largest port complexes in the world and are a site of intense environmental interest. This made it an interesting site to test the ability of eDNA to act as an effective tool for biodiversity assessment.
This study combined eDNA sampling with conventional shipboard trawl sampling at seven sites in the port complex. At each site, the researchers collected several eDNA samples, each from around a liter of seawater, just before the trawl was towed into the same area. This allowed a comparison between eDNA and traditional biodiversity assessment techniques: eDNA detected almost all of the 17 fish species found in the trawls, but also detected an additional 55 native fish species. Detection of these additional species through conventional sampling requires many additional sampling trips and a very high expense.
“We were happy to see eDNA validated alongside ‘conventional’ sampling, but we were really excited to see the additional information that came from eDNA,” said Dean Pentcheff, researcher and program manager of the Diversity Initiative for the Southern California Ocean (DISCO) at NHM. But obtaining this additional information required a comprehensive genetic reference library for all the fish in the region. A genetic sequence in an eDNA sample can only be resolved to a species if there is a reference sequence registered for that species. All of the fish in the eDNA samples from this study were resolved only after the researchers added the latest fish references to the sequence library.
The eDNA samples from different locations in the ports produced different species inventories at a statistically significant level. This answered an important question: can eDNA measure variability over an area as small as the port complex, or does seawater mix so well that local differences are completely blurred? This study demonstrated that eDNA in this ocean environment can exhibit differences between locations as close as a few hundred meters apart.
Based on this pilot project, the authors have put together a set of recommendations for managers considering eDNA as a biodiversity assessment tool. Recommendations cover careful selection of identification genes and specific guidance on how to clean sequence data from eDNA samples before searching for sequence matches. Due to the successful species resolution that has resulted from building a comprehensive sequence reference library, a key recommendation is to create regional reference databases.
“These environmental samples are like time capsules that we can mine in the future,” said Adam Wall, head of crustacean collections at NHM. This sentiment prompted another of the group’s recommendations: archive eDNA samples and sequence data for long-term use. As sequencing technology improves, additional information may come from samples. As techniques for analyzing genetic data improve and genetic reference libraries are expanded, sequence data can be re-analyzed to obtain additional results beyond the fish inventories published in this study.
Reference: Gold Z, Wall AR, Schweizer TM, et al. Manager’s Guide to Using eDNA Metabarcoding in Marine Ecosystems. Bowers H, ed. PeerJ. 2022;10:e14071. two: 10.7717/peerj.14071.
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