A muddy time capsule: Using environmental DNA and geochronology from sediment cores to reconstruct past coastal vegetation dynamics and inform future ecosystem management.

A project undertaken at The University of Adelaide, and supervised by Alice Jones


Coastal vegetated ecosystems are located at the boundary between land and sea and provide irreplaceable ecosystem services. These ecosystems have undergone rapid and unprecedented degradation due to human impacts, including climate change and sea-level rise. Monitoring change in coastal ecosystems is difficult using traditional methods that generate relatively short-term datasets (~100 years), leading to poor documentation of long-term dynamics. Sediment cores act as `muddy time capsules', providing records of ecosystem change through time in buried sediment layers that are stored for millennia (see figure 1). DNA traces recovered from sediment cores (as environmental, or 'e' DNA) offer a method for studying coastal environmental change over meaningful timescales (1000s of years), and can therefore produce data from prior to large-scale human intervention. Our project combines established sediment dating methods and novel genetic techniques to develop a new evidence base for reconstructing long-term coastal vegetation changes. The results will show how coastal vegetated ecosystems changed in response to past environmental change and human impacts, and will generate insight into the likely responses of these valuable ecosystems to future human activities and climate change. The outcomes will progress coastal change research and inform conservation, restoration and management for coastal vegetated ecosystems.

Monitoring coastal ecosystem change has traditionally been done using direct observations and remote sensing. However, such data have limited temporal coverage and their usefulness depends on the same sites being reliably monitored over time. Other evidence sources, such as fossilised pollen, lipid biomarkers and macrofossils can provide a longer-term evidence base but cannot achieve good taxonomic resolution, which limits them to providing general insights on past climate and vegetation types, rather than determining the responses of specific plant species to environmental change and human impacts. Traces of plant DNA preserved in sediment are evidence of the historical presence of plant species, which can be detected by environmental DNA (eDNA). eDNA thus enables palaeoecological reconstruction of past vegetation communities and detection of vegetation change using sediment from core samples, with the potential for reconstruction over hundreds to thousands of years (see figure 2).

Understanding the past to predict the future:

Our overarching aim is to develop a new evidence base for tracking coastal vegetation dynamics in near-shore coastal environments over millennia, which can be used to monitor the response of coastal systems to human impacts and climate change. By understanding how these systems were affected by historical change, we can better predict the impacts of future change.

We will:

  1. Create a South Australian coastal vegetation reference DNA database for reliable taxonomic identification. A taxonomically verified reference database underpins our study, because extracted DNA sequences have little meaning without the ability to match them to species in a reference database.
  2. Reconstruct SA coastal vegetation change and explore links to human impacts and past environmental change. Plant eDNA will be extracted from sediments at different depths (representing different time periods) along each core. This will enable reconstruction of coastal vegetation dynamics over 100s to 1000s of years, which can be examined for signs of major human impacts and effects of previous environmental changes.


Figure 1: Conceptual model of coastal ecosystem change over hundreds to thousands of years, and how sediment cores taken at different locations can sample 'through time' to capture these dynamics

Figure 2: Schematic showing the process of extracting environmental DNA ('eDNA') from different depths through a sediment cores and extracting plant DNA sequences to track vegetation community change over time

Figure 3: Dr Alice Jones and Nicole Foster (PhD candidate at the University of Adelaide) collecting sediment cores from mangrove and saltmarsh areas (with volunteer support)

Figure 4: Nicole Foster working in the lab processing coastal plant reference library samples for eDNA extraction.