Combined eDNA and Acoustic Analysis Reflects Diel Vertical Migration of Mixed Consortia in the Gulf of Mexico

Abstract

Oceanic diel vertical migration (DVM) constitutes the daily movement of various mesopelagic organisms migrating vertically from depth to feed in shallower waters and return to deeper water during the day. Accurate classification of taxa that participate in DVM remains non-trivial, and there can be discrepancies between methods. DEEPEND consortium (www.deependconsortium.org) scientists have been characterizing the diversity and trophic structure of pelagic communities in the northern Gulf of Mexico (nGoM). Profiling has included scientific echosounders to provide accurate and quantitative estimates of organismal density and timing as well as quantitative net sampling of micronekton. The use of environmental DNA (eDNA) can detect uncultured microbial taxa and the remnants that larger organisms leave behind in the environment. eDNA offers the potential to increase understanding of the DVM and the organisms that participate. Here we used real-time shipboard echosounder data to direct the sampling of eDNA in seawater at various time-points during the ascending and descending DVM. This approach allowed the observation of shifts in eDNA profiles concurrent with the movement of organisms in the DVM as measured by acoustic sensors. Seawater eDNA was sequenced using a high-throughput metabarcoding approach. Additionally, fine-scale acoustic data using an autonomous multifrequency echosounder was collected simultaneously with the eDNA samples and changes in organism density in the water column were compared with changes in eDNA profiles. Our results show distinct shifts in eukaryotic taxa such as copepods, cnidarians, and tunicates, over short timeframes during the DVM. These shifts in eDNA track changes in the depth of sound scattering layers (SSLs) of organisms and the density of organisms around the CTD during eDNA sampling. Dominant taxa in eDNA samples were mostly smaller organisms that may be below the size limit for acoustic detection, while taxa such as teleost fish were much less abundant in eDNA data compared to acoustic data. Overall, these data suggest that eDNA, may be a powerful new tool for understanding the dynamics and composition of the DVM, yet challenges remain to reconcile differences among sampling methodologies.

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

“…Furthermore, despite a myriad of processes that could potentially blur eDNA signatures in oceanic environments – such as particle sinking, ocean currents, vertical mixing, and biologically-mediated transport such as diel vertical migration, our results and other recent studies indicate that eDNA signatures may remain localized. Our finding that eDNA detected diversity changes on the order of 10s of meters in depth are consistent with modeling results that show midwater eDNA signatures remain within 20 meters of their origin in the vertical direction (Allan et al, 2021), and add to a growing body of field evidence from pelagic systems demonstrating that eDNA can detect biodiversity changes with depth (Canals et al, 2021; Easson et al, 2020; Govindarajan et al, 2021).…”

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep‐sea fishes

“…Probably, the most relevant, unexpected, and promising finding of the present study is the observation that eDNA metabarcoding is not only able to detect shifts at the community level derived by the DVM phenomena as suggested (Easson et al 2020), but to reveal species-specific diel vertical migratory patterns. Here, the most evident cases emerged for B. glaciale and M. muelleri.…”

“…Fish eDNA stratification in the ocean responds to fish vertical distribution Despite the complexity of the vertical structuring of pelagic communities (Sutton 2013) and the call for studies focusing on the deep-sea ecosystem (Mengerink et al 2014;St. John et al 2016;Martin et al 2020), to date just a few studies have used eDNA sampling to explore the deep sea (Thomsen et al 2016;Easson et al 2020;Laroche et al 2020;McClenaghan et al 2020;Govindarajan et al 2021), and none has provided insights on the deep, vertical stratification of eDNA in the ocean. Here, we observed a consistent detection of DNA of the most abundant epipelagic fish species along the water column (e.g., European anchovy is detected down to > 1000 m depth), whereas detection of DNA from deep-sea fish was restricted to the upper depth at which they were assumed to occur and below.…”

Vertical stratification of environmental DNA in the open ocean captures ecological patterns and behavior of deep-sea fishes

“…Probably, the most relevant, unexpected, and promising finding of the present study is the observation that eDNA metabarcoding is not only able to detect shifts at the community level derived by the DVM phenomena as suggested (Easson et al 2020), but to reveal species specific diel vertical migratory patterns. Here, the most evident cases emerged for Benthosema glaciale and Maurolicus muelleri.…”