Measuring marine biodiversity using ‘environmental DNA’ – an application of gene sequencing in environmental biology – should allow rapid assessment of changes in marine life. This makes environmental DNA (eDNA) a critical tool for managing our response to climate change. But eDNA only works well if key implementation steps are followed, according to a new Los Angeles and Long Beach area study published in the journal. Berg.
said Regina Wetzer, curator and director of the Center for Marine Biodiversity at the Natural History Museum of Los Angeles County (NHM).
Answering these questions included contributions from the Natural History Museum, multiple academic institutions, environmental consultants, and government agencies—highlighting the challenges involved in the use of eDNA, but also the widespread interest in its use.
eDNA uses genetic sequencing of samples from the environment (in this case, ocean water) to tally biodiversity. “There are genes that vary enough between species that they can be used as identification markers. Every organism secretes DNA by shedding skin cells or other substances, so we can take a cup of seawater, sequence the DNA in it, and use that for inventory,” Zack Gold said. Lead author of the study “Biota of the region.”
The adjacent Port of Los Angeles and the Port of Long Beach make up one of the world’s largest port complexes and are sites of intense environmental interest. This made it an interesting site to test the ability of eDNA to serve as an effective tool for assessing biodiversity.
This study coupled eDNA sampling and conventional vessel trawl sampling at seven locations in the port complex. At each site, the researchers collected multiple RNA samples, each from about one liter of seawater, before hauling a trawl in the same area. This allowed comparison of eDNA with traditional biodiversity assessment techniques: eDNA detected approximately 17 species of trawled fish, but also detected an additional 55 native fish species. Detecting these additional species through conventional sampling requires many sampling trips and very high expenses.
“We were thrilled to see eDNA being validated alongside ‘traditional’ sampling, but we were really excited to see the additional information that came from eDNA,” said Dean Bentchev, researcher and program director at the Diversity Initiative for the Southern California Ocean (DISCO). ) in NHM. But obtaining this additional information depends on having a complete genetic reference library for all the fish in the area—the genetic sequence in an eDNA sample can only be resolved for a species if there is a reference sequence on file for that species. All fish in the eDNA samples in this study were resolved only after the researchers added the last few fish references to the sequence library.
eDNA samples from different port locations yielded inventories of different species at a statistically significant level. That answered an important question: Can eDNA measure variation across a small area such as a port complex, or does seawater mix so thoroughly that local variations become completely blurred? This study showed that eDNA in this ocean environment can detect differences between nearby places that are only a few hundred meters apart.
Building on this pilot project, the authors have compiled a set of recommendations for managers who consider eDNA as a tool for assessing biodiversity. The recommendations cover careful selection of specific genes and specific advice on how to clean sequence data from eDNA samples before searching for sequence matches. Because of the successful species resolution that resulted from the construction of a fully sequenced reference library, the main recommendation is to establish regional reference databases.
“These samples of the environment are like time capsules that we will be able to exploit in the future,” said Adam Wall, Crustacea collections manager at NHM. This sentiment prompted other recommendations of the group: archiving eDNA samples and sequencing data for long-term use. As sequencing technology improves, additional information can come from the samples. As genomic data analysis techniques improve and libraries of genomic references expand, sequence data can be analyzed again for additional results beyond the fish inventories published in this study.
Co-authors on this study include researchers from a wide range of institutions: Zachary Gold (now at the National Oceanic and Atmospheric Administration), Rachel S.Meyer (now at the University of California, Santa Cruz), and Paul H. Robert Wayne of the University of California, Los Angeles. Los Angeles ; T. M. Schweitzer of Colorado State University; Emily E. Cord from Landmark College, Vermont; Regina Weitzer, Adam R. Wall, and N. Dean Benchev at the Los Angeles County Museum of Natural History; Kevin Stolzenbach at Wood Environment and Infrastructure, Inc. Kat Brickett in Los Angeles Harbor and Justin Lloyd in Long Beach Harbor. The project was supported by funding from the Port of Los Angeles and the Port of Long Beach.