Ancient environmental DNA offers glimpse of a former Great Barrier Reef

By Maria del Carmen (K-le) Gomez Cabrera

In a world-first, scientists have uncovered a way of using ancient environmental DNA to start exploring the past lives of coral reefs.

Studying the past biodiversity of marine ecosystems is difficult because of a lack of precise records.

Traditional palaeoecological studies rely on species that leave behind a fossil record, such as corals and foraminifera, to infer patterns in biodiversity.

Although the fossil record paints an incomplete picture of the past, it is the standard when studying past environments.

But, for the first time ever, a team of researchers—from the ARC Centre of Excellence for Coral Reef Studies at The University of Queensland (UQ) Australian Centre for Ancient DNA—have extracted ancient environmental DNA (aeDNA) from coral reef sediments.

Dr Gomez Cabrera from UQ explains that although aeDNA has been extracted from sediments before, the focus was always on environments with ideal conditions for the survival of aeDNA. This includes permafrost, deep-sea sediments or anoxic lake sediments.

DNA starts to break down as soon as it is shed from the organism, so these studies focused on pushing the limits of the recovery of workable aeDNA as far back in time as possible under non-ideal environmental conditions for preservation.

“Our goal in this study was to probe whether we could extract DNA from sediments collected from the Great Barrier Reef,” Dr Gomez Cabrera said.

“These tropical environments are far from the ideal of low temperature and low oxygen environments typical of aeDNA studies.”

“We were looking for relatively ‘young’ aeDNA spanning only hundreds of years but that could help us complete our understanding of the community ecology of GBR reefs before and after European colonisation.”

Through DNA metabarcoding and high‐throughput sequencing of the 18S rDNA gene in aeDNA derived from sediment cores collected from two sites on Pandora Reef (inshore GBR), the researchers recovered DNA from 12 eukaryotic reef dweller groups as old as 750 years.

Macroalgae was one of the organisms whose DNA was recovered. This spans key groups such as crustose coralline algae (that promotes healthy reefs by binding the reef matrix and providing settlement substrate for corals) and brown algae (a major competitor with corals for space).

While the study found an inverse relationship between corals and brown algae, and a positive one between corals and coralline algae, these results are preliminary. More research covering a larger suite of samples is needed to draw any meaningful conclusion from these findings.

What is clear is that reef sediment can be a valuable source of aeDNA—an important source of information for understanding past distributions of soft-bodied reef organisms.

The UQ team, led by Prof John Pandolfi, is expanding the original study through a more detailed sampling regime using a well curated archived sediment library that includes hundreds of sediment cores obtained along the inner shelf of the GBR over 14 degrees of latitude along the Queensland coast.

This future work also incorporates a number of genes to target specific reef taxa with the goal of utilising this information to detect temporal trends in biodiversity turnover over decadal to millennial time scales.

This study is already attracting some interest from the broader community; it was the focus of the Perspectives section of the most recent issue of Molecular Ecology by Dr Laura Epp and was also highlighted in a popular science article in the online magazine Quanta.

PAPER: Gomez Cabrera M, Young J, Roff G, Staples T, Ortiz J, Pandolfi J, Cooper A (2019).  Molecular Ecology. ‘Broadening the taxonomic scope of coral reef palaeoecological studies using ancient DNA’. DOI: 10.1111/mec.15038