Using eDNA tools to examine the impact of kelp farming on underlying sediments

Area of Science:

• Marine Ecology
• Environmental DNA (eDNA) Analysis
• Aquaculture Science

Background:

• Kelp farming is expanding, necessitating methods to assess its ecological footprint.
• Traditional methods like carbon and nitrogen analysis may not fully capture subtle benthic changes.
• Environmental DNA (eDNA) offers a sensitive tool for detecting species presence and ecological shifts.

Purpose of the Study:

• To evaluate the efficacy of eDNA tools in monitoring sediments under a commercial sugar kelp farm.
• To compare eDNA-based detection with traditional sediment nutrient analysis.
• To investigate changes in microbial communities associated with kelp farming.

Main Methods:

• Collected sediment samples from a sugar kelp farm in the Gulf of Maine over two seasons.
• Employed a S. latissima-specific digital PCR (dPCR) assay for kelp eDNA.
• Utilized 16S and 18S rRNA gene metabarcoding for microbial diversity assessment.
• Analyzed sediment carbon and nitrogen content using isotope ratio mass spectrometry (IRMS).

Main Results:

• S. latissima eDNA (COI gene copies) was significantly higher within the farm footprint (~8% increase).
• Highest kelp eDNA concentrations correlated with observed kelp biomass accumulation.
• No conclusive differences in bulk sediment carbon and nitrogen content were found between sites.
• Metabarcoding revealed subtle shifts in microbial community composition inside versus outside the farm.

Conclusions:

• eDNA tools, particularly dPCR, are sensitive and specific for detecting kelp farming's ecological effects.
• eDNA analysis provides a more nuanced understanding of farm impacts than traditional nutrient analysis.
• This study highlights the potential of eDNA for monitoring marine ecosystems and aquaculture impacts.