Wildlife disease ecologist launches Project t

Jeff Foster, NAU Wildlife Disease Ecologist

Image: Associate Professor Jeff Foster (right) from Northern Arizona University’s Department of Biological Sciences and the Pathogen and Microbiome Institute (PMI) recently received a grant from the DoD for a new study titled “Demonstration of Metabarcoding for Monitoring Bird Species Habitat Quality on DoD installations.”
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Photo credit: Northern Arizona University

The US Department of Defense (DoD) owns military installations on nearly 27 million acres across the country — roughly the size of the state of Virginia — and oversees that land through a network of natural resource stewards. According to the DoD, the program “supports the military’s testing and training mission by protecting its biological resources … and working to ensure the long-term sustainability of our nation’s priceless natural heritage.” One of the program’s top priorities is the monitoring and conservation of populations of threatened species and Endangered Bird Species (TES) – particularly those feeding on insects and other arthropods such as spiders, which are particularly hard hit.

Monitoring the quality of the birds’ habitats, including their typical insect diet, is one of the main ways scientists study declining bird populations. The tools that military land managers use to assess diet and habitats are critical, but current methods of measuring habitat quality related to birds’ food resources are time-consuming, expensive and require specific biological expertise.

Associate Professor for this purpose Jeff Foster from Northern Arizona University’s Department of Biological Sciences and the Pathogen and Microbiome Institute (PMI) recently received a grant from the DoD for a new study titled “Demonstration of Metabarcoding for Monitoring Bird Species Habitat Quality on DoD Installations.” This three-year, $900,000 project will focus on five insectivorous species at four military sites:

  • Gold-cheeked Warbler (Setophaga Chrysoparia) and Schwarzkopf Vireo (Vireo atricapilla) at Fort Hood, Texas
  • Vireo of the smallest bell (Vireo bellii pusillus) at Camp Pendleton, California
  • gold-winged singer (Vermivora Chrysoptera) at Fort McCoy, Wisconsin
  • Oahu Elepaio (Chasiempis ibidis) at Schofield Barracks, Hawaii

Advanced approach focuses on bioinformatics, metabarcoding

Metabarcoding is a technique that allows scientists to identify multiple species of plants or animals on a large scale based on rapid, high-throughput DNA sequencing from the environment, representing a major technological advance.

“We will assess habitat quality by using advanced genetic approaches to measure arthropod food resources in bird diets and the vegetation these birds forage on,” Foster said. “Our three main goals are to demonstrate the effectiveness of metabarcoding birdseed and food resources; to compare this genetic approach to conventional approaches using visual identification of arthropods using microscopes; and provide user-friendly guidance for military land managers to understand the process and use this approach for future surveillance.”

“Bioinformatics can be challenging and daunting when you first start with DNA metabarcoding, so we will provide an established workflow that we can share with land managers,” he said. The team will collect droppings samples from the birds (bird droppings) as well as arthropod samples, perform bioinformatic and chemical compositional analysis, validate the technology by comparing it to conventional methods, develop guides, and conduct hands-on technical workshops for military country managers. “We will conduct the most comprehensive nutritional analysis of birds at military installations to date.”

Foster brings his expertise and that of PMI to the project. “There’s a lot more to metabarcoding work than just sequencing a gene. And this is where our team excels. We use tools developed over the last 13 years to analyze the human microbiome. Many of these tools were developed by NAU professors Gregory Caporaso and his team at PMI, so we have significant technical expertise in analysis, including understanding reference libraries of sequences and developing the analysis software.”

Staff include military scientists and undergraduate researchers

Foster will work closely with co-principal investigators Jinelle Sperry and Aron Katz of the Civil Engineer Research Laboratory at the US Army Corps of Engineers’ Engineering Research and Development Center, as well as staff at each of the facilities.

NAU Student Researcher Hanna Brosius is working on the project with Foster and a PMI researcher Alexandra Gibson. Brosius, who will assist with the lab work and analyses, said: “I’m excited about this project because analyzing bird diets from droppings will help us understand why these vulnerable birds may be at risk. It’s fun to be able to take a fecal sample of a species; you can learn a lot by using DNA to understand how an animal lives.”

She is looking forward to her future as a veterinarian. “I am interested in lab work that allows me to focus on a project and get results quickly. This research experience will be important for veterinary studies and will increase my understanding of biology.”

Project to support TES surveillance at DoD locations

The project’s findings will have several benefits that will help Department of Defense land managers monitor threatened and endangered species. “This is an effective and cost-effective way to measure habitat quality,” Foster said, “particularly in relation to a key factor regulating insectivorous bird abundance — arthropod food resources.” The technology can be deployed at any DoD site where understanding of diet or habitat quality is required for TES monitoring of vertebrate taxa. Population surveys can assess the current frequency and distribution of TES, but determining the specific factors limiting their populations adds complexity. This method will not only enable DoD natural resource managers to distinguish low-grade from high-grade habitats, but will also provide important information on restoration, habitat recovery from disturbance, and a baseline for prey availability should the arthropod populations should regionally decline in the future.”

In addition, “numerous other bird species are on the Department of Defense’s list of priority species that could benefit from this technology, as well as other taxa such as amphibians, reptiles and small mammals,” he said.

About Northern Arizona University

Founded in 1899, Northern Arizona University is a community-focused, research-driven university that offers an exceptional student-centric experience to nearly 28,000 students in Flagstaff at 22 campuses statewide and online. Building on a 123-year history of distinctive excellence, NAU aims to be the nation’s pre-eminent engine of opportunity, a vehicle for economic mobility, and an engine for social impact by providing equitable post-secondary value in Arizona and beyond. NAU is committed to meeting talent with access and excellence through its impactful academic programs and enriching experiences, paving the way to a brighter future for the diverse students it serves and the communities they represent.

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