School of Marine and Environmental Affairs Faculty Papers

Permanent URI for this collectionhttps://digital.lib.washington.edu/handle/1773/25571

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Environmental DNA metabarcoding reveals winners and losers of global change in coastal waters
(2020-12-09) Gallego, Ramón; Jacobs-Palmer, Emily; Cribari, Kelly; Kelly, Ryan P.
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.
The effect of Tides on nearshore environmental DNA
(2018-03-19) Kelly, Ryan P.; Gallego, Ramón; Jacobs-Palmer, Emily
We can recover genetic information from organisms of all kinds using environmental sampling. In recent years, sequencing this environmental DNA (eDNA) has become a tractable means of surveying many species using water, air, or soil samples. The technique is beginning to become a core tool for ecologists, environmental scientists, and biologists of many kinds, but the temporal resolution of eDNA sampling is often unclear, limiting the ecological interpretations of the resulting datasets. Here, in a temporally and spatially replicated field study using ca. 313 bp of eukaryotic COI mtDNA as a marker, we find that nearshore organismal communities are largely consistent across tides. Our findings suggest that nearshore eDNA from both benthic and planktonic taxa tends to be endogenous to the site and water mass sampled, rather than changing with each tidal cycle. However, where physiochemical water mass characteristics change, we find that the relative contributions of a broad range of organisms to eDNA communities shift in concert.
A halo of reduced dinoflagellate abundances in and around eelgrass beds
(2020-04-07) Jacobs-Palmer, Emily; Gallego,Ramón; Ramón-Laca, Ana; Kunselman, Emily; Cribaril, Kelly; Horwith, Micah; Kelly, Ryan P.
Seagrass beds provide a variety of ecosystem services, both within and outside the bounds of the habitat itself. Here we use environmental DNA (eDNA) amplicons to analyze a broad cross-section of taxa from ecological communities in and immediately surrounding eelgrass (Zostera marina). Sampling seawater along transects extending alongshore outward from eelgrass beds, we demonstrate that eDNA provides meter-scale resolution of communities in the field. We evaluate eDNA abundance indices for 13 major phylogenetic groups of marine and estuarine taxa along these transects, finding highly local changes linked with proximity to Z. marina for a diverse group of dinoflagellates, and for no other group of taxa. Eelgrass habitat is consistently associated with dramatic reductions in dinoflagellate abundance both within the contiguous beds and for at least 15 m outside, relative to nearby sites without eelgrass. These results are consistent with the hypothesis that eelgrass-associated communities have allelopathic effects on dinoflagellates, and that these effects can extend in a halo beyond the bounds of the contiguous beds. Because many dinoflagellates are capable of forming harmful algal blooms (HABs) toxic to humans and other animal species, the apparent salutary effect of eelgrass habitat on neighboring waters has important implications for public health as well as shellfish aquaculture and harvesting.
Archived DNA reveals marine heatwave-associated shifts infish assemblages
(2023-02-17) Gold, Zachary; Kelly, Ryan P.; Shelton, Andrew Olaf; Thompson, Andrew R.; Goodwin, Kelly D.; Gallego, Ramón; Parsons, Kim M.; Thompson, Luke R.; Kacev, Dovi; Barber, Paul H.
Marine heatwaves can drive large-scale shifts in marine ecosystems, but studyingtheir impacts on whole species assemblages is difficult. Analysis combining micro-scopic observations with environmental DNA (eDNA) metabarcoding of the ethanolpreservative of an ichthyoplankton biorepository spanning a 23 years time series cap-tures major and sometimes unexpected changes to fish assemblages in the CaliforniaCurrent Large Marine Ecosystem during and after the 2014–2016 Pacific MarineHeatwave. Joint modeling efforts reveal patterns of tropicalization with increasesin southern, mesopelagic species and associated declines in commercially importanttemperate fish species (e.g., North Pacific Hake [Merluccius productus] and PacificSardine [Sardinops sagax]). Data show shifts in fisheries assemblages (e.g., NorthernAnchovy, Engraulis mordax) even after the return to average water temperatures,corroborating ecosystem impacts found through multiple traditional surveys of thisstudy area. Our innovative approach of metabarcoding preservative eDNA coupledwith quantitative modeling leverages the taxonomic breadth and resolution of DNAsequences combined with microscopy-derived ichthyoplankton identification toyield higher-resolution, species-specific quantitative abundance estimates. This workopens the door to economically reconstruct the historical dynamics of assemblagesfrom modern and archived samples worldwide.
Understanding PCR Processes to Draw Meaningful Conclusions from Environmental DNA Studies
(2019-08-20) Kelly, Ryan P.; Shelton, Andrew Olaf; Gallego, Ramón
As environmental DNA (eDNA) studies have grown in popularity for use in ecological applications, it has become clear that their results differ in significant ways from those of traditional, non-PCR-based surveys. In general, eDNA studies that rely on amplicon sequencing may detect hundreds of species present in a sampled environment, but the resulting species composition can be idiosyncratic, reflecting species’ true biomass abundances poorly or not at all. Here, we use a set of simulations to develop a mechanistic understanding of the processes leading to the kinds of results common in mixed-template PCR-based (metabarcoding) studies. In particular, we focus on the effects of PCR cycle number and primer amplification efficiency on the results of diversity metrics in sequencing studies. We then show that proportional indices of amplicon reads capture trends in taxon biomass with high accuracy, particularly where amplification efficiency is high (median correlation up to 0.97). Our results explain much of the observed behavior of PCR-based studies, and lead to recommendations for best practices in the field.

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