Ark in the Park facilitating eDNA research
Ark in the Park (AiP), an eco-restoration project in the Waitakere Ranges, is providing researchers with the perfect laboratory to investigate the role of environmental DNA (eDNA) in species identification and biodiversity monitoring.
AiP, a collaboration between Forest and Bird and Auckland Council, supported by Te Kawerau a Maki and a dedicated group of hard-working volunteers, celebrated its 15th birthday this year. Since work started in 2002 the team has worked tirelessly to control predators and pests in the Cascade Kauri Park in the northern Waitakere Ranges Regional Park.
A grid of bait lines, 203kms long if the lines were placed end-on-end, covers the 2100 hectares that make up the AiP. The bait stations target rats and mice. In addition, traps are set to target stoats, weasels, ferrets and possums. Auckland Council also carry out pig and rabbit control.
Invasive social wasps are targeted during the "wasp season" (February to April).
In addition there is a 600 hectare buffer zone around the Park where owners of neighbouring properties also control predators.
The baiting and trapping in combination with a weeding and replanting programme is helping to restore the ecosystem, letting the native plants and animals thrive. It has also allowed the team to return iconic species to the park. So far whitehead (Mohoua albicilla), North Island robin (Petroica longipes), and kōkako (Callaeas wilsoni) have been released. Hihi (Notiomystis cincta) were released but this translocation was not successful.
Kōkako, North Island robin and whitehead are now establishing territories and breeding successfully across AiP. Bird counts carried out within AiP and at a nearby unmanaged site as a comparison show an average of 30-50% more birds within AiP.
As AiP is an open sanctuary (no predator-proof fence) the team maintain a continuous pest control operation. Maintaining the bait and trap lines is a massive task and AiP estimates that volunteers contribute about 9000 hours a year to the project.
Rat numbers fluctuate throughout the year and also vary between lines in any one monitoring event but numbers are greatly suppressed within AiP. The goal is ultimately to have rat tracking indices below the 5% level.
Monitoring the presence/absence and distribution of targeted species during pest control is an important component of any ecosystem restoration operation and is challenging especially when they are present at low numbers.
As well as monitoring predator numbers, researchers need to identify high density predator hotspots, reinvasion fronts and incursions from new threats (e.g., kauri dieback). Current monitoring methods are hard work and time consuming but due to the advances in DNA technologies, monitoring species presence from DNA left in the environment may offer a better solution.
In recent years, there has been an increase in the use of molecular methods to study not only the diversity of microorganisms present in a range of environments, but also to detect and monitor macro-organisms. eDNA from shed or excreted cells or tissue such as urine, faeces, hairs and skin persists in the environment and can be detected from a range of different environmental samples including soil, leaf litter, freshwater and sediments. As there is a strong link between freshwater and terrestrial environments through hydrological networks, the eDNA present in river and stream water is suspected to incorporate biodiversity information from both these environments within a catchment.
In future biodiversity monitoring may be as simple as collecting water samples.
Dr. Gavin Lear and his team are testing this theory. Initially they are exploring what the eDNA present in stream water can tell us about the terrestrial diversity and distribution of the microbial community throughout a catchment in the AiP. If successful, similar techniques can be implemented to explore the presence of both invasive and priority-indigenous species in forest catchments, with the analysis of DNA in stream water.
Gavin highlights the importance of AiP in carrying out the research. “The expert knowledge and logistical support provided by AiP, and particularly their dedicated team of volunteers remains essential for the success of our research. Their intensive monitoring of pest organisms in particular, is providing essential baseline data to compare the findings of our DNA surveys” he says.
An important component of the study is to develop a standard DNA extraction method to identify the wide range of organisms present in diverse sample types (soil/water/leaf litter). Each of these sample types presents unique challenges for the extraction of DNA, and often different methods are used. However, there is ample evidence that different DNA extraction techniques not only result in different quantities and qualities of DNA, but also impact measures of community richness, diversity and composition.
PhD student Syrie Hermans is testing the ability of multiple DNA extraction kits to obtain high-quality DNA from a variety of different sample types and also from ‘mock communities’ composed of a range of known microbial, plant, fish and invertebrate species, to evaluate each methods ability to extract DNA. Syrie's research will lead to the project adopting a single extraction technique which performs optimally on a wide range of sample types, and obtains DNA from both macro and microorganisms.
Syrie’s says that “so far we’ve sequenced hundreds of samples for the presence of microbial, fish, animal and plant species present. I’m currently working through the data to determine if different kits have biases against certain taxa, to allow us to choose the best methods for further eDNA research. It’s great to be able to complete this work on samples collected from such a well-known, and successful, eco-restoration area, since it is conservation efforts such as the AiP project that we are ultimately trying to provide new tools for”.
Syrie’s work will have wider implications, a standard extraction method would be greatly beneficial to the overall field of eDNA research, and allow better integration of molecular methods into ecological studies for assessing biodiversity, the detection and tracking of invasive species and monitoring endangered species.
This work is funded by the Biological Heritage Challenge and part of a larger study — A national framework for biological heritage assessment across natural and production landscapes — that aims to develop tools to detect incursions, and changes in biodiversity and ecosystem function in order to implement effective mitigation strategies and assess conservation performance. The integration of nationally-consistent eDNA methodologies with existing monitoring programmes will deliver a step change in biodiversity assessment.
The Ark is sustained by both its volunteers and funders. To find out more about Ark in the Park, or how you can contribute, visit their website.