eDNA captures depth partitioning in a kelp forest ecosystem

Abstract

Environmental DNA (eDNA) metabarcoding is an increasingly important tool for surveying biodiversity in marine ecosystems. However, the scale of temporal and spatial variability in eDNA signatures, and how this variation may impact eDNA-based marine biodiversity assessments, remains uncertain. To address this question, we systematically examined variation in vertebrate eDNA signatures across depth (0 m to 10 m) and horizontal space (nearshore kelp forest and surf zone) over three successive days in Southern California. Across a broad range of teleost fish and elasmobranchs, results showed significant variation in species richness and community assemblages between surface and depth, reflecting microhabitat depth preferences of common Southern California nearshore rocky reef taxa. Community assemblages between nearshore and surf zone sampling stations at the same depth also differed significantly, consistent with known habitat preferences. Additionally, assemblages also varied across three sampling days, but 69% of habitat preferences remained consistent. Results highlight the sensitivity of eDNA in capturing fine-scale vertical, horizontal, and temporal variation in marine vertebrate communities, demonstrating the ability of eDNA to capture a highly localized snapshot of marine biodiversity in dynamic coastal environments.

Environmental DNA reveals fine‐scale habitat associations for sedentary and resident marine species across a coastal mosaic of soft‐ and hard‐bottom habitats

“…These results add to the growing evidence of localized eDNA signals within coastal marine ecosystems and simultaneously suggest that the ability of eDNA monitoring to document species-habitat associations is to some extent dependent on the mobility and ecology of focal taxa. Notably, this finding is in agreement with a recent study on kelp forest ecosystems, in which the temporal depth variation in eDNA signals from teleost fish and elasmobranchs appeared reflective of species behavioral patterns (Monuki et al, 2021). For highly mobile species and species detected at very low concentrations, our results indicate that monitoring studies might benefit from supplementing eDNA with BRUVS sampling to yield more informative inference through a higher resolution offered by the MaxN metric combined with use of bait attractants to facilitate monitoring of widely dispersed organisms within field sites.…”

“…Still, there is growing evidence that eDNA surveys can differentiate between fine‐scaled patterns in community assemblages (Port et al, 2016; Staehr et al, 2022; Stat et al, 2019; West et al, 2020), even across a wide geographical extent (700 km of coastline; West et al, 2021). While such localized signals may indicate high site fidelity of eDNA to the source community (Harrison et al, 2019), variations in mobility and residency levels across marine species could affect the ability of eDNA sampling to detect species–habitat associations, which has thus far received little attention (but see Monuki et al, 2021).…”

“…While such localized signals may indicate high site fidelity of eDNA to the source community (Harrison et al, 2019), variations in mobility and residency levels across marine species could affect the ability of eDNA sampling to detect species-habitat associations, which has thus far received little attention (but see Monuki et al, 2021).…”

Disentangling the components of coastal fish biodiversity in southern Brittany by applying an environmental DNA approach

“…Furthermore, the use of eDNA should ideally improve (i) the detection of rare species (Balasingham et al, 2018; Wilcox et al, 2013) (ii) the discrimination of morphologically similar species (Holdregger et al, 2020) and (iii) the sampling of difficult‐to‐access areas such as rocky shores (Jeunen et al, 2020; West et al, 2020; but see Antich et al, 2021). Currently, eDNA metabarcoding is already an effective environmental monitoring tool used to detect species in give area (Yates et al, 2019), but whether it can reveal fine‐scale community structure remains to be investigated (Port et al, 2016), especially in open coastal marine systems subject to strong currents (Monuki et al, 2021).…”

Elasmobranchs’ metabarcoding requires a pragmatic approach to reach its promises

“…The metabarcoding approach has been proven to be an efficient tool for marine monitoring and ecosystem health assessment (Thomsen et al, 2012; Leray and Knowlton, 2015). And, recent studies provided a proof-of-concept that sharks, rays, and their relatives can be monitored using eDNA metabarcoding (Fraija-Fernández et al, 2020; Ip et al, 2021; Mariani et al, 2021; Marwayana et al, 2021; Monuki et al, 2021; Liu et al, 2022; Dunn et al, 2022).…”