The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems

Hallegraeff

Bolch

et al. 2021

Sci Rep

Marine sedimentary ancient DNA (sedaDNA) is increasingly used to study past ocean ecosystems, however, studies have been severely limited by the very low amounts of DNA preserved in the subseafloor, and the lack of bioinformatic tools to authenticate sedaDNA in metagenomic data. We applied a hybridisation capture ‘baits’ technique to target marine eukaryote sedaDNA (specifically, phyto- and zooplankton, ‘Planktonbaits1’; and harmful algal bloom taxa, ‘HABbaits1’), which resulted in up to 4- and 9-fold increases, respectively, in the relative abundance of eukaryotes compared to shotgun sequencing. We further used the bioinformatic tool ‘HOPS’ to authenticate the sedaDNA component, establishing a new proxy to assess sedaDNA authenticity, “% eukaryote sedaDNA damage”, that is positively correlated with subseafloor depth. We used this proxy to report the first-ever DNA damage profiles from a marine phytoplankton species, the ubiquitous coccolithophore Emiliania huxleyi. Our approach opens new avenues for the detailed investigation of long-term change and evolution of marine eukaryotes over geological timescales.

mentioning

confidence: 99%

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

Hallegraeff

Bolch

et al. 2021

Sci Rep

“…Complete code for data processing can be found preserved at Armbrecht et al., 2020, https://doi.org/10.1111/1755-0998.13162 and Armbrecht et al., 2021, https://doi.org/10.1038/s41598-021-82578-6. Eukaryotic data and R scripts used for the correlation analysis and heatmap figure can be found at https://doi.org/10.5281/zenodo.6342810 on the Zenodo database.…”

Section: Data Availability Statementmentioning

confidence: 99%

“…This scarcity and degraded nature of sed aDNA requires sampling, extraction, laboratory and bioinformatic techniques to be optimized (Armbrecht et al., 2019; Briggs, 2020). Paying utmost attention to avoid contamination throughout all sampling and experimental steps is crucial, as even small amounts of modern environmental DNA contamination can override the weak sed aDNA signal (Armbrecht, 2020).…”

Section: Introductionmentioning

confidence: 99%

“…Additionally, the sed aDNA of important environmental indicator organisms, such as many eukaryotes (phytoplankton, zooplankton, and higher organisms) only occur in trace amounts within marine sediments. For example, sed aDNA fragments from Tasmanian coastal and Antarctic deep ocean sediments have been shown to be only ∼69 and ∼40–50 base pairs (bp) long, respectively (Armbrecht, 2020; Armbrecht et al., 2020), compared to much larger DNA fragments (hundreds to thousands of bp long) that are used to characterize living organisms in the modern ocean (Carradec et al., 2018; Obiol et al., 2020). This scarcity and degraded nature of sed aDNA requires sampling, extraction, laboratory and bioinformatic techniques to be optimized (Armbrecht et al., 2019; Briggs, 2020).…”

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

An Outlook for the Acquisition of Marine Sedimentary Ancient DNA (sedaDNA) From North Atlantic Ocean Archive Material

Selway

Paleoceanog and Paleoclimatol

Thornalley

2022

Self Cite

Studies incorporating sedimentary ancient DNA (sedaDNA) analyses to investigate paleo‐environments have increased considerably over the last few years, and the possibility of utilizing archived sediment cores from previous field campaigns could unlock an immense resource of sampling material for such paleo‐investigations. However, sedaDNA research is at a high risk of contamination by modern environmental DNA, as sub‐optimal sediment storage conditions may allow for contaminants (e.g., fungi) to grow and become dominant over preserved sedaDNA in the sample. Here, we test the feasibility of sedaDNA analysis applied to archive sediment material from five sites in the North Atlantic, collected between 1994 and 2013. We analyzed two samples (one younger and one older) per site using a metagenomic shotgun approach and were able to recover eukaryotic sedaDNA from all samples. We characterized the authenticity of each sample through sedaDNA fragment size and damage analyses, which allowed us to disentangle sedaDNA and contaminant DNA. Although we determined that contaminant sequences originated mainly from Ascomycota (fungi), most samples were dominated by Emiliania huxleyi, a haptophyte species that commonly blooms in the study region. We attribute the presence of contaminants to non‐ideal sampling and sample storage conditions of the investigated samples. Therefore, while we demonstrate that sedaDNA analysis of archival North Atlantic seafloor sediment samples are generally achievable, we stress the importance of best‐practice ship‐board sampling techniques and storage conditions to minimize contamination. We highly recommend the application of robust bioinformatic tools that help distinguish ancient genetic signals from modern contaminants, especially when working with archive material.

“…Recently, sedimentary ancient DNA ( sed aDNA) analyses have been increasingly used as a tool to characterise past marine ecosystems from seafloor sediments over geological timescales. These novel sed aDNA analyses offer great potential to overcome the hurdle of accessing information on less-well preserved species, and gain insights into paleo-communities across all domains of life, including, phyto- and zooplankton (Armbrecht, 2020). Indeed, preliminary DNA analyses on seafloor surface sediments collected near Maria Island (Spring Bay), Tasmania, first pointed to the possibility of retrieving ancient DNA preserved from all three HAB species in this region (Shaw et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

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

Paine

Bolch

et al. 2021

Preprint

Self Cite

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.