New environmental DNA tools can accurately and inexpensively quantify kelp-derived biomass in sediments below commercial kelp farms, according to research recently published in PLOS One .
The new study, led by researchers at Bigelow Laboratory, demonstrates the value of ecosystem-wide and kelp-specific eDNA tools and confirms that kelp aquaculture has little impact on the bottom communities living below the farm. The findings also showcase how eDNA tools could inform "blue carbon" accounting effort by helping quantify the deposition rates of kelp-derived carbon into marine sediments.
"If you look on the seafloor below a kelp farm, there's a lot of organic matter, but we haven't had very specific ways of detecting what is in these sediments and where it comes from," said Senior Research Scientist David Emerson, the senior author on the paper. "The eventual goal is to find evidence for kelp biomass being buried into sediments for long-term removal of CO2, and we've shown that eDNA may be an effective way to examine that."
Maine is the largest kelp-producing state in the country with a rapidly growing industry focused largely on Saccharina latissima, or sugar kelp. Researchers have been working to understand whether carbon-rich biomass shed from commercial farms — both naturally throughout the growing season and from excess material lost during harvesting — accumulates in underlying sediments. If so, passive transfer of kelp to the seabed could potentially be a tool for carbon dioxide sequestration and generate added revenue for a farmer. Assessing how valuable kelp is as a blue carbon strategy, though, requires quantitative methods for precisely measuring that accumulation of kelp-derived carbon in sediments over time.
Bulk stable isotope methods can be used to estimate the overall amount of organic carbon and nitrogen in sediments. However, scientists can't precisely say how much of that carbon comes from any one algal species, and the method remains expensive and time consuming.
That's where new molecular tools come in. In the study, the team tested two tools, sampling for eDNA in the sediments underlying a long-running commercial kelp farm in the Gulf of Maine over two farming seasons.
Metabarcoding involves extracting all the available DNA in the sediment to fingerprint all of the marine organisms in a sample. It provides a relative measure of how abundant different organisms are and a sense of the overall biological diversity.
The team applied this approach to examine what's living in sediments both directly underneath and nearby the farm. It revealed subtle but minor differences inside versus outside, providing some of the first quantitative evidence in New England that the farms have little effect on the makeup of the seafloor community.
The metabarcoding approaches, though, were not sensitive enough to detect much kelp eDNA. To that end, the team also developed a digital polymerase chain reaction (dPCR) probe designed specifically to detect sugar kelp. Similar to a COVID test, this PCR approach allows researchers to precisely measure the number of gene copies, down to single digits, of kelp DNA in each sample.
"With DNA, unlike the stable isotope methods we used for comparison, there's little question that what you're measuring is biomass directly from kelp — in fact the specific species of kelp being grown on that farm," Emerson said. "The metabarcoding approach is valuable for teasing apart subtle differences in the community as a whole, but this species-specific tool is proving to be extremely sensitive and pretty cost effective for detecting kelp alone."
With the quantitative PCR method, the team confirmed that the amount of kelp biomass in sediment was more variable, and on the whole slightly higher, in sampling sites directly below the farm compared to those nearby.
The study's lead author, Samuel Tan, points out that kelp DNA appears to break down faster than other parts of the plant. That means it's not a perfect 1:1 relationship between the number of gene copies they measure and total kelp biomass, and the method is likely a conservative estimate of the amount of kelp being deposited in sediment.
"The study shows that eDNA can be a powerful tool for providing information about even fairly subtle changes, providing sensitivity and specificity that few methods can match," said Tan, a University of Maine doctoral candidate advised by Emerson and Jeremy Rich, a professor at the Darling Marine Center and co-author on the paper. "There are still unknowns of course, so we're working to expand and intensify our sampling efforts and better understand the relationship between the amount of DNA we measure and kelp biomass."
To that end, the researchers have been sampling systematically at more sites below this farm and others, which has confirmed these initial results and allowed them to start teasing apart the variability in deposition beneath each farm.
Emerson stressed that this initial work showed that there is relatively little kelp naturally deposited beneath these kelp farms on the whole. But the next round of sampling is ongoing, and related research suggests that the amount of organic carbon in sediments tends to be higher in larger, older kelp farms found in other parts of the world.
"Back to our overarching question of carbon sequestration, we're starting to think about how we could actually help farmers to improve — and capitalize on — the process to ensure more kelp is deposited, strategically and for longer," Emerson said. "That's a question that was previously near impossible to answer, but is increasingly straightforward with these novel eDNA methods we're developing."
This study was supported by the NSF Established Program to Stimulate Competitive Research (Grant #OIA-1849227) and the Builders Initiative Foundation. The study also features researchers from the Darling Marine Center and the University of British Columbia. From Bigelow Laboratory, co-authors include Shane Farrell and Nichole Price.
