Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters

Abstract

Studies of the ecological effects of global change often focus on one or a few species at a time. Consequently, we know relatively little about the changes underway at real-world scales of biological communities, which typically have hundreds or thousands of interacting species. Here, we use COI mtDNA amplicons from monthly samples of environmental DNA to survey 221 planktonic taxa along a gradient of temperature, salinity, dissolved oxygen and carbonate chemistry in nearshore marine habitat. The result is a high-resolution picture of changes in ecological communities using a technique replicable across a wide variety of ecosystems. We estimate community-level differences associated with time, space and environmental variables, and use these results to forecast near-term community changes due to warming and ocean acidification. We find distinct communities in warmer and more acidified conditions, with overall reduced richness in diatom assemblages and increased richness in dinoflagellates. Individual taxa finding more suitable habitat in near-future waters are more taxonomically varied and include the ubiquitous coccolithophore Emiliania huxleyi and the harmful dinoflagellate Alexandrium sp. These results suggest foundational changes for nearshore food webs under near-future conditions.

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

“…It is critical to assess the impact of these threats on biodiversity (Brito-Morales et al, 2020;Sala et al, 2021;St John et al, 2016;Worm and Lotze, 2021). Metabarcoding analysis of environmental DNA (eDNA) is an important new tool that can efficiently and effectively help to fill this need (Gallego et al, 2020;Gilbey et al, 2021). DNA sequencing of the trace genetic remains of animals found in bulk environmental samples provides detailed information on the taxonomic makeup of marine communities, and leads to important insights on the diversity, distribution, and ecology of community inhabitants (e.g., Sawaya et al, 2018;Jeunen et al, 2019;Closek et al, 2019;Djurhuus et al, 2020;West et al, 2021;Visser et al, 2021).…”

Message in a Bottle: Archived DNA Reveals Marine Heatwave-Associated Shifts in Fish Assemblages

“…All sequence data were processed using the Anacapa Toolkit (Curd et al, 2019). After quality control, sequence-variant (ASV) dereplication, and decontamination processes (Curd et al, 2019;Gallego et al, 2020;Gold et al, 2021), we retained a total of 54.5 million reads (technical replicate range: 36,050-1.2 million reads) (See Supplement 1 Methods). From these data, we classified 130 unique taxa including 103 specieslevel assignments (79%), 15 genus-level assignments (12%), 11 family-level assignments (8.5%), and one class-level assignment.…”

Environmental DNA Reveals Patterns of Biological Invasion in an Inland Sea

“…To characterize eDNA assemblages we used data originally collected for the analysis reported in Gallego et al (2020). Water samples were collected in the intertidal zone of state and county parks along shores of Hood Canal and San Juan Island, Washington, USA (Figure 1).…”