Ecogenomic approaches to monitor Kakadu estuaries

Current models predict that saltwater intrusion will increasingly impact the coastal regions of Kakadu National Park in Northern Australia. This project used molecular techniques termed ecogenomics to provide fundamental information on how saltwater exposure may alter the microbial ecology of the region’s floodplains and benthos of the estuaries.

The findings provide a comprehensive DNA-based inventory of the region’s unique biota. The research also presented strong evidence that increases to saltwater exposure will alter the composition of floodplain bacterial taxa associated with key biogeochemical processes. Furthermore, estuarine research emphasised how biodiversity is strongly shaped by seasonal changes in oceanic and freshwater inputs, hydrodynamics, such as tidal energy, and floodplain morphology.

Whilst much of Kakadu’s megafauna has been well studied, very little is known about the region’s aquatic macro, meio and microfauna. These groups are crucial for maintaining the productivity of the region’s aquatic ecosystems. In order to understand the biotic integrity of the region, some prior knowledge on sedimentary ecology is required. The data produced through this project could be used to increase our understanding of Kakadu’s estuaries and floodplains, and provide information on how microbiota respond to natural changes.

The team collected soil samples from sites along the East and South Alligator River channels and floodplains. Bacteria and animals living in the sediment leave behind traces of their DNA. Advanced genetic techniques termed ‘ecogenomics’ read the sequence of the DNA to simultaneously identify thousands of bacteria and animals in samples. The team identified patterns of biodiversity within the region’s sediments in relation to soil salinity and other environmental variables.

Prior to this project there was no information available regarding the bacterial communities of Kakadu’s floodplains. This project provided a comprehensive inventory of the microbial communities present on the floodplain. The project identified tens of thousands of bacteria residing in Kakadu’s soil floodplain ecosystem – this is equivalent to over 2,000 species of bacteria in every one gram of floodplain soil. This information can be used as a baseline for future studies, necessary for understanding how future inundation scenarios may affect the park.

Additional outcomes included:

• examination of the soil chemistry emphasised that the positioning along the floodplain and the tidal energy of the site not only altered the salinity of the soils, but also, the concentrations of range of elements;
• ecogenomic survey research provided an unprecedented view of the underpinning benthic ecology of the South and East Alligator estuaries; and
• the ecological research performed on both the floodplain and estuarine systems highlights the capacity for ecogenomics to obtain relatively rapid and cost effective data, which can comprehensively examine ecological communities from the soils.

The project was undertaken in the Alligator Rivers Region, Kakadu National Park, Northern Territory. Specifically, the floodplain work was performed adjacent to the South Alligator River. The estuarine research was performed in both the South and East Alligator Rivers.