Environmental DNA successfully captures marine biodiversity

Measuring marine biodiversity with "environmental DNA" – an application of genetic sequencing in environmental biology – should make it possible to rapidly assess changes in
marine life.
This makes environmental DNA (eDNA) a key tool
in managing our fight against climate change.
But according to a new study on the Los Angeles and Long Beach areas published in the journal PeerJ, eDNA works well only if key implementation steps are
followed.

"What do we need to know to use eDNA in coastal oceans, and can we make it work well in important urban environments?" These questions prompted us to undertake this study," said
Regina Wetzer, curator and director of the Center for Marine Biodiversity at the Los Angeles County Museum of Natural History (NHM).

Answering these questions requires contributions from natural history museums, several academic institutions, environmental advisors and government agencies, highlighting the challenges of using eDNA, but also reflecting a broad interest in
its use.

eDNA uses genetic sequencing from environmental samples (in this case, seawater) to inventory biodiversity
.
"There are enough genes that differ between species that they can be used as identification markers
.
Every organism sheds DNA by dropping skin cells or something else, so we can take a glass of seawater, sequence the DNA in it, and use it to investigate organisms in the area," said
Zach Gold, lead author of the study.

The neighboring ports of Los Angeles and Long Beach, which form one of the largest port complexes in the world, are a location
of strong environmental interest.
This makes it an interesting website
for testing eDNA's ability to serve as an effective tool for biodiversity assessment.

In this study, eDNA sampling and conventional vessel trawl sampling were paired
at 7 sites at the port complex.
At each site, the researchers collected multiple eDNA samples, each about a liter of seawater, just before
the trawl passed through the same area.
This allows eDNA to be compared to traditional biodiversity assessment techniques: eDNA detected almost all 17 species of fish found in trawls, but also detected another 55 native species
.
Detecting these additional species through routine sampling requires more sampling times and very high costs
.

"We're excited to see eDNA validated alongside 'traditional' sampling, but we're really excited to see additional information from eDNA," said
Dean Pentcheff, researcher and project manager at NHM's Southern California Marine Diversity Initiative (DISCO).
But to get this additional information, you must have a complete genetic reference library of all fish in the region — the genetic sequence of a species can only be parsed
if there is a reference sequence of a species in the eDNA sample.
In this study, the fish in all eDNA samples were resolved only after the researchers added references to the last few fish to the sequence library
.

EDNA samples from different locations in the port yielded statistically significant lists of different species
.
This answers an important question: Can eDNA measure changes in a small area like a port complex, or is the sea water mixed so thoroughly that it completely obscures local differences? The study shows that in this marine environment, eDNA can expose differences
between places that are hundreds of meters away.

Based on this pilot project, the authors collected a set of recommendations
for managers considering eDNA as a biodiversity assessment tool.
These recommendations include specific recommendations
for careful selection of identifying genes and how to clean sequence data from eDNA samples before searching for sequence matches.
Since species elucidation has been successfully achieved by establishing a complete sequence reference library, a key recommendation is the establishment of regional reference databases
.

"These environmental samples are like time capsules that we can use in the future," said
Adam Wall, crustacean collection manager at the National Maritime Museum.
This sentiment led the group to make another recommendation: to archive eDNA samples and sequence data for long-term use
.
As sequencing technology improves, more information may come from the sample
.
With improvements in genetic data analysis techniques and expansion of genetic reference libraries, sequence data can be re-analyzed to obtain additional results
beyond the fish lists published in this study.

Co-authors of the study include researchers from multiple institutions: Zachary Gold (now with the National Oceanic and Atmospheric Administration), Rachel S.
Meyer (now at UC Santa Cruz), Paul H.
Barber, and Robert Wayne from UCLA; Teia M.
Schweizer of Colorado State University; Emily E.
Curd of Landmark College in Vermont; Regina Wetzer, Adam R.
Wall and N.
of the Los Angeles County Museum of Natural History Dean Pentcheff; Kevin Stolzenbach of Wood Environment and Infrastructure; Kat Prickett of the Port of Los Angeles, Justin Luedy
of the Port of Long Beach.
The project is funded
by the Ports of Los Angeles and Long Beach.

Journal Reference:

1. Zachary Gold, Adam R.
   Wall, Teia M.
   Schweizer, N.
   Dean Pentcheff, Emily E.
   Curd, Paul H.
   Barber, Rachel S.
   Meyer, Robert Wayne, Kevin Stolzenbach, Kat Prickett, Justin Luedy, Regina Wetzer.
   A manager’ s guide to using eDNA metabarcoding in marine ecosystems.
   PeerJ, 2022; 10: e14071 DOI: 10.
   7717/peerj.
   14071