Beach environmental DNA fills gaps in photographic biomonitoring to track spatiotemporal community turnover across 82 phyla

Abstract

Abstract:Environmental DNA (eDNA) metabarcoding is emerging as a biomonitoring tool available to the citizen science community that promises to augment or replace photographic observation. However, eDNA results and photographic observations have rarely been compared to document their individual or combined power. Here, we use eDNA multilocus metabarcoding, a method deployed by the CALeDNA Program, to inventory and evaluate biodiversity variation along the Pillar Point headland near Half Moon Bay, California. We describe variation in presence of 13,000 taxa spanning 82 phyla, analyzed spatiotemporal patterns of beta diversity, and identified metacommunities. Inventory and measures of turnover across space and time from eDNA analysis were compared to the same measures based on in the Global Biodiversity Information Facility (GBIF), which contains information largely contributed by iNaturalist. We find eDNA depicted local signals with high seasonal turnover, especially in prokaryotes. We find a diverse community dense with pathogens and parasites in the embayment, and a State Marine Conservation Area (SMCA) with lower species richness than the rest of the beach peninsula, but with beta diversity signals showing resemblance to adjacent unprotected tidepools. The SMCA differs in observation density, with higher density of protozoans, and animals in Ascidiacea, Echinoidea, and Polycladida. Local contributions to beta diversity are elevated in a section of East-facing beach. GBIF observations were mostly from outside the SMCA, limiting some spatial comparisons. However, our findings suggest eDNA samples can link the SMCA sites to sites with better GBIF inventory, which may provide hypotheses for whether observations can be imputed for one site given observations from another. Results additionally supported >3800 largely novel biological interactions that no GBIF data had shown. This research, and accompanying interactive website supports eDNA as a gap-filling tool to measure biodiversity that is available to community and citizen scientists.

Environmental DNA metabarcoding differentiates between micro‐habitats within the rocky intertidal

“…But even absent additional field sampling, exploring networks of associations between identified taxa and ASVs (e.g. Djurhuus et al., 2020; Meyer et al., 2019) could enable further ecological analyses. As a first step, we have motivated the utility of this future work by demonstrating that eDNA surveys can indeed resolve small spatiotemporal differences in rocky intertidal ecosystems and that those differences are ecologically meaningful.…”

“…Significant prior research has compared eDNA metabarcoding surveys to visual surveys in marine environments (e.g. Gold, Sprague, et al., 2021; Kelly et al., 2017; Port et al., 2016), including early work in the intertidal in particular (Meyer et al., 2019). Meta‐analyses have shown that generally, eDNA metabarcoding surveys are comparable to visual surveys (Fediajevaite et al., 2021; Keck et al., 2022; McElroy et al., 2020), although the particular complementarity between methods varies by context and research approach.…”