eDNA captures depth partitioning in a kelp forest ecosystem

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.