Recovering sedimentary ancient DNA of harmful dinoflagellates off Eastern Tasmania, Australia, over the last 9 000 years

Abstract

Harmful algal blooms (HABs) have significantly impacted the seafood industry along the Tasmanian east coast over the past three decades, and are expected to change in frequency and magnitude due to climate change induced changing oceanographic conditions. To investigate the long-term history of regional HABs, a combination of palynological and sedimentary ancient DNA (sedaDNA) analyses was applied to marine sediment cores from inshore (up to 145 years old) and offshore (up to ~9,000 years) sites at Maria Island, southeast Tasmania. Analyses focused Paralytic Shellfish Toxin (PST) producing dinoflagellates Alexandrium catenella and Gymnodinium catenatum, and the red-tide dinoflagellate Noctiluca scintillans, which were specifically targeted using a hybridization capture sedaDNA technique. Identification of primulin-stained A. catenella cysts throughout the inshore sediment core, together with sedaDNA evidence of a bloom-phase of Alexandrium ~15 years ago, indicates recent stimulation of a cryptic endemic population. Morphologically similar but unstained Alexandrium cysts were observed throughout the offshore core, with sedaDNA confirming the presence of A. catenella from ~8,300 years ago to present. Gymnodinium catenatum cysts were detected only in inshore surface sediments from 30 years ago to present, supporting previous evidence of a 1970s introduction via shipping ballast water. sedaDNA confirmed the presence of G. catenatum-related sequences in the inshore and offshore cores, however, unambiguous species identification could not be achieved due to limited reference sequence coverage of Gymnodinium. Our hybridization capture sedaDNA data also confirmed the historically recent dispersal of the non-fossilizing dinoflagellate Noctiluca scintillans, detected inshore from ~30 years ago, matching first observations of this species in Tasmanian waters in 1994. At the offshore site, N. scintillans sedaDNA was detected only in surface sediments, confirming a recent climate-driven range expansion this species. This study provides new insights into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases. Further research into paleo-environmental conditions and paleo-community structure are required to identify the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios.

Millennia‐old coral holobiont DNA provides insight into future adaptive trajectories

“…The ability to detect genetic diversity declines associated with population bottlenecks and instances of genetic turnover (i.e., replacement of earlier populations with new, genetically distinct, ones) of key coral taxa in response to past stressors will enable better prediction of extant corals' responses to continued environmental disturbances in the future. As the field of coral aDNA is further being developed, particularly with the adoption of hybridization capture technology (e.g., Armbrecht, Paine, et al, 2021), it will be possible to investigate these past changes directly. Through coral aDNA we can gain a "window into the past" to evaluate the evolutionary history of the coral holobiont.…”

“…In aDNA research applied to other organisms, target capture techniques have been used to increase target organism read retention or to restrict analysis to known polymorphisms (Armbrecht, Hallegraeff, et al, 2021; Fu et al, 2015; Haak et al, 2015) or enrich for damaged DNA molecules (Gansauge & Meyer, 2014). Specifically, Armbrecht, Paine, et al (2021) successfully applied hybridization‐capture methodology to marine eukaryotes to greatly increase eukaryote and archaea DNA capture with respect to bacteria, while retaining patterns of aDNA damage. In the future, applications of capture technology to coral aDNA may similarly increase both the feasibility and the efficiency of this method.…”

“…Long‐term variation in marine microbes and eukaryotes using aDNA has previously yielded exciting results about marine community composition at distant timescales. For example, Armbrecht, Paine, et al (2021) revealed the dynamics of harmful algal blooms using marine sediment cores up to 9000 years in the past. In a similar vein, del Cabrera et al (2019) explored variability of coral‐associated macroalgae in the sediment record over the past 750 years through paleoecological DNA, correlating it with the coral fossil record.…”