Environmental DNA (eDNA): a New Tool for Monitoring Status and Trends of Ecosystems and Taxa in Hawaii and Pacific Islands

Science Center Objects

Remote locations, rugged topography, extreme weather conditions, high numbers of threatened and endangered taxa, and widespread degradation of native ecosystems by invasive species makes routine monitoring to determine status and trends of ecosystems and native and invasive taxa difficult and expensive in the Hawaiian Islands. There is a need to supplement existing monitoring protocols with more cost effective methods that can monitor both individual taxa and entire communities of organisms of interest across larger geographic areas. Recent advances in methodologies for detecting environmental DNA (eDNA) from water and soil are promising and may have applications in Hawaii for monitoring native communities, rare taxa, and high impact invasive species.

Overview:

Muddy trail at Hakalau Forest NWR

Difficult terrain like this trail at Hakalau Forest National Wildlife Refuge make eDNA a desirable method of species monitoring. Photo: K. Hooker, USGS 

Remote locations, rugged topography, extreme weather conditions, high numbers of threatened and endangered taxa, and widespread degradation of native ecosystems by invasive species makes routine monitoring to determine status and trends of ecosystems and native and invasive taxa difficult and expensive in the Hawaiian Islands. With the exception of a few high profile native species, e.g. Haleakala Silversword, most rare species and many invasives are monitored infrequently or have distributions that are only partially known. There is a need to supplement existing monitoring protocols with more cost effective methods that can monitor both individual taxa and entire communities of organisms of interest across larger geographic areas. Recent advances in methodologies for detecting environmental DNA (eDNA) from water and soil are promising and have been successfully applied to detecting rare and invasive aquatic species in the continental U.S.  This technology may have applications here in Hawaii for monitoring native communities, rare taxa, and high impact invasive species in remote locations where traditional field sampling methods are expensive and often dangerous or impossible to perform because of extreme topology or difficult access.

Project Objectives:

This project will focus on:

  1. developing and applying technologies for capturing and purifying eDNA from environmental samples
  2. developing techniques for amplifying eDNA to detect and monitor selected native and invasive species and communities of organisms in terrestrial and aquatic ecosystems

Progress: 

Air sampling station in a grassy field with ocean in background

A trap designed for collecting airborne particulates deployed on the Hāmākua Coast of the island of Hawai‘i. The traps appear to be an effective method for monitoring airborne fungal spores as hundreds of fungal taxa were identified from a handful of samples screened by second generation sequencing.(Credit: Carter Atkinson, USGS-PIERC. Public domain.)

We developed sampling protocols for collecting, filtering, and extracting eDNA from stream samples. We collected weekly samples from the streams on the island of Hawai‘i and conducted preliminary screens for presence of Leptospira and Ceratocystis, the fungal pathogen responsible for Rapid ‘Ōhi‘a Death. We have also made progress in developing a recombinase polymerase field assay for Ceratocystis and are working to optimize the assay and evaluate sensitivity and specificity with field collected samples. We are also working on a concurrent assay for avian malaria based on the same technology. Additionally, we are working to develop eDNA sampling methods to monitor the air column for detection of Ceratocystis fungal spores and pollen, and develop sampling methods to detect fungal spores on forest birds to determine their role in spreading the pathogen. We plan to continue monitoring of stream samples for Ceratocystis and are also developing cytochrome oxidae I primers for detection of forest bird eDNA in stream samples by next generation sequencing methods. 

Highlights and Key Findings:

Newly designed traps for collecting airborne particulates appear to be an effective method for monitoring airborne fungal spores. Hundreds of fungal taxa were identified from a handful of samples that were screened by second generation sequencing, suggesting that this approach may be effective for monitoring airborne spread of introduced plant pathogens and other taxa.

Additionally, we are making progress on developing applications and methodology for studying eDNA from a variety of environmental sources in Hawai‘i, including air samples and water samples from streams and intermittent water sources. Preliminary tests using water samples collected from aviaries at Keauhou Bird Conservation Center and recently developed cytochrome oxidase primers suggest that the primers can amplify DNA from a variety of endangered forest birds that drink from and bath in dishes that are provided as water sources.

Research is ongoing.