The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems

  title={The Potential of Sedimentary Ancient DNA to Reconstruct Past Ocean Ecosystems},
  author={Linda Armbrecht},
  • L. Armbrecht
  • Published 1 June 2020
  • Environmental Science
  • Oceanography
Sedimentary ancient DNA (sedaDNA) offers a novel approach to investigating past marine ecosystems—from the smallest bacteria to phytoplankton and their predators— over geological timescales. Knowledge about such paleo-food webs can provide broad-scale biological context to paleoceanographic and environmental reconstructions. However, the field of marine sedaDNA research is still in its infancy; community reconstructions are complicated by the minuscule amounts of ancient DNA preserved in the… 

Figures from this paper

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

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

Comparative analysis of zooplankton diversity in freshwaters: What can we gain from metagenomic analysis?

This study presents one of the first diversity assessments of a group of aquatic metazoans using metagenomes and validates the coherence of the community composition derived from genetic and classical species surveys.

Ancient DNA and microfossils reveal dynamics of three harmful dinoflagellate species off Eastern Tasmania, Australia, over the last 9,000 years

New insights are provided into the distribution and abundance of three HAB species in the Tasmanian region, including clues to past bloom phases and the factors driving bloom phases through time and predict plankton community responses under different future climate scenarios.

Benthic Foraminiferal Indices and Environmental Quality Assessment of Transitional Waters: A Review of Current Challenges and Future Research Perspectives

Transitional waters straddle the interface between marine and terrestrial biomes and, among others, include fjords, bays, lagoons, and estuaries. These coastal systems are essential for transport and

Ancient marine sediment DNA reveals diatom transition in Antarctica

Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency.

Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential

Environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail in the near future, it is anticipated.

Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics

Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths, and overamplification of short reads in metabarcode data.

Hybridisation capture allows DNA damage analysis of ancient marine eukaryotes

This study applied a hybridisation capture ‘baits’ technique to target marine eukaryote seda DNA, establishing a new proxy to assess sedaDNA authenticity, the Ancient: Default (A:D) sequences ratio, and generated the first-ever DNA damage profiles of a key phytoplankton, the ubiquitous coccolithophore Emiliania huxleyi.



An optimized method for the extraction of ancient eukaryote DNA from marine sediments

An optimized extraction protocol integrating these steps, with an optional post‐library LMW size‐selection step to retain DNA fragments of ≤500 base pairs is presented, which should improve quantitative paleo‐monitoring of eukaryotes from marine sediments, as well as other studies relying on the detection of highly fragmented and degraded eUKaryote DNA in sediments.

PalaeoChip Arctic1.0: An optimised eDNA targeted enrichment approach to reconstructing past environments

This work presents an optimised eDNA targeted enrichment approach for reconstructing past environments with a more diverse and sensitive dataset with increased sequencing efficiency of ecologically informative sedaDNA, and presents results of plant and animal presence from permafrost samples.

A global ocean atlas of eukaryotic genes

The authors use metatranscriptomics to analyze four organismal size fractions from open-ocean stations, providing the largest reference collection of eukaryotic transcripts from any single biome.

Eukaryotic plankton diversity in the sunlit ocean

Diversity emerged at all taxonomic levels, both within the groups comprising the ~11,200 cataloged morphospecies of eukaryotic plankton and among twice as many other deep-branching lineages of unappreciated importance in plankton ecology studies.

Towards next‐generation biodiversity assessment using DNA metabarcoding

The near‐term future of DNA metabarcoding has an enormous potential to boost data acquisition in biodiversity research as further developments associated with the impressive progress in DNA sequencing will eliminate the currently required DNA amplification step, and comprehensive taxonomic reference libraries can be built based on the well‐curated DNA extract collections maintained by standardized barcoding initiatives.

Ancient DNA

Ancient DNA has benefited in particular from recent advances in high-throughput sequencing technologies and from the development of analytical techniques that take advantage of the evolutionary information gained by sampling genetic data over both space and time.

Late pleistocene Australian marsupial DNA clarifies the affinities of extinct megafaunal kangaroos and wallabies.

Cross-species DNA capture is applied to fossils from relatively high latitude, high altitude caves in Tasmania to retrieve mitochondrial sequences from two extinct megafaunal macropodid species and Protemnodon emerges as a close relative of Macropus (large living kangaroos), a position not supported by recent morphological phylogenetic analyses.

Mapping of picoeucaryotes in marine ecosystems with quantitative PCR of the 18S rRNA gene.

A Method for Studying Protistan Diversity Using Massively Parallel Sequencing of V9 Hypervariable Regions of Small-Subunit Ribosomal RNA Genes

Massively parallel pyrosequencing of eukaryotic V9 hypervariable regions of SSU rRNA genes provides a means of estimating species richness from deeply-sampled populations and for discovering novel species from the environment.