Govindarajan, A. F. | bioRxiv Science

bioRxiv2024

Environmental DNA Transport at an Offshore Mesophotic Bank in the Northwestern Gulf of Mexico

Environmental DNA (eDNA) offers a powerful, non-invasive means of assessing biodiversity in marine ecosystems, yet the spatial resolution of eDNA remains poorly understood. We investigated the vertical and horizontal dispersion of eDNA from an isolated mesophotic coral reef (Bright Bank) in the stratified offshore waters of the northern Gulf of Mexicos shelf edge. We conducted comprehensive vertical and horizontal water column eDNA sampling across multiple radial directions and depths. We characterized invertebrate communities using a paired metabarcoding approach targeting broad (18S) and taxon-specific (28S) markers. We found that vertical transport of benthic eDNA was limited by water column stratification, with distinct benthic community signals confined to the near-bottom layers. In contrast, horizontal dispersal of eDNA extended beyond at least 1.5 km, though the prevalence of eDNA from benthic invertebrates declined with increasing distance from the bank. Taxon-specific primers showed greater detection sensitivity and dispersal range, particularly for benthic corals, than primers that are used to broadly assess eukaryotic biodiversity. These findings demonstrate that water column structure and marker selection critically influence the spatial interpretation of marine eDNA data. The study represents a snapshot of late-summer conditions. Seasonal variability should be considered in future studies. Our results provide a realistic framework for integrating eDNA into offshore environmental surveillance, biodiversity monitoring, and spatial management.

ecology↗

bioRxiv2022

Improved biodiversity detection using a large-volume environmental DNA sampler with in situ filtration and implications for marine eDNA sampling strategies

Metabarcoding analysis of environmental DNA samples is a promising new tool for marine biodiversity and conservation. Typically, seawater samples are obtained using Niskin bottles and filtered to collect eDNA. However, standard sample volumes are small relative to the scale of the environment, conventional collection strategies are limited, and the filtration process is time consuming. To overcome these limitations, we developed a new large - volume eDNA sampler with in situ filtration, capable of taking up to 12 samples per deployment. We conducted three deployments of our sampler on the robotic vehicle Mesobot in the Flower Garden Banks National Marine Sanctuary in the northwestern Gulf of Mexico and collected samples from 20 to 400 m depth. We compared the large volume ([~]40 - 60 liters) samples collected by Mesobot with small volume ([~]2 liters) samples collected using the conventional CTD - mounted Niskin bottle approach. We sequenced the V9 region of 18S rRNA, which detects a broad range of invertebrate taxa, and found that while both methods detected biodiversity changes associated with depth, our large volume samples detected approximately 66% more taxa than the CTD small volume samples. We found that the fraction of the eDNA signal originating from metazoans relative to the total eDNA signal decreased with sampling depth, indicating that larger volume samples may be especially important for detecting metazoans in mesopelagic and deep ocean environments. We also noted substantial variability in biological replicates from both the large volume Mesobot and small volume CTD sample sets. Both of the sample sets also identified taxa that the other did not - although the number of unique taxa associated with the Mesobot samples was almost four times larger than those from the CTD samples. Large volume eDNA sampling with in situ filtration, particularly when coupled with robotic platforms, has great potential for marine biodiversity surveys, and we discuss practical methodological and sampling considerations for future applications.

ecology↗