Exploring the Use of Environmental DNA (eDNA) to Detect Animal Taxa in the Mesopelagic Zone

Annette F Govindarajan,Peter H Wiebe,Andone C Lavery,Rene D Francolini,J Michael Jech,Weifeng (Gordon) Zhang,Joel K Llopiz

doi:10.3389/fevo.2021.574877

Abstract

Animal biodiversity in the ocean’s vast mesopelagic zone is relatively poorly studied due to technological and logistical challenges. Environmental DNA (eDNA) analyses show great promise for efficiently characterizing biodiversity and could provide new insight into the presence of mesopelagic species, including those that are missed by traditional net sampling. Here, we explore the utility of eDNA for identifying animal taxa. We describe the results from an August 2018 cruise in Slope Water off the northeast United States. Samples for eDNA analysis were collected using Niskin bottles during five CTD casts. Sampling depths along each cast were selected based on the presence of biomass as indicated by the shipboard Simrad EK60 echosounder. Metabarcoding of the 18S V9 gene region was used to assess taxonomic diversity. eDNA metabarcoding results were compared with those from net-collected (MOCNESS) plankton samples. We found that the MOCNESS sampling recovered more animal taxa, but the number of taxa detected per liter of water sampled was significantly higher in the eDNA samples. eDNA was especially useful for detecting delicate gelatinous animals which are undersampled by nets. We also detected eDNA changes in community composition with depth, but not with sample collection time (day vs. night). We provide recommendations for applying eDNA-based methods in the mesopelagic including the need for studies enabling interpretation of eDNA signals and improvement of barcode reference databases.

Highlights

The ocean’s mesopelagic zone is poorly explored, in large part due to the vastness of the habitat and the technological and logistical challenges in accessing it
In the DADA2 analysis, a total of 12,181,342 sequences remained after the filtering, denoising, merging, and chimera removal steps, with an average of 270,696 ± 20,331 (SE) sequences per sample (Supplementary Table S2). These sequences were classified into 10,543 unique amplicon sequence variants (ASVs)
Four additional ASVs that were discovered to be either misclassified by Silva as metazoans or were unlikely mesopelagic inhabitants were removed from our analyses

Summary

Introduction

The ocean’s mesopelagic zone is poorly explored, in large part due to the vastness of the habitat and the technological and logistical challenges in accessing it. It has been discovered that mesopelagic biomass is significantly greater than previously thought (Irigoien et al, 2014; St. John et al, 2016); there is significant uncertainty about the composition of mesopelagic biomass. Deep pelagic waters, including the mesopelagic, likely contain numerous undescribed species (Robison, 2004, 2009). Traditional sampling nets may miss important taxa such as delicate gelatinous species that fall apart when collected, or fish that avoid capture altogether. A recent genetic study suggested that species diversity is significantly underestimated (Sommer et al, 2017), and genetic analysis has shown that many nominal species may consist of multiple cryptic species, sometimes even belonging to different families (Lindsay et al, 2017)

Objectives

Methods

Results

Discussion

Conclusion