Biodiversity discovery, host and diet identification, and pathogen detection
Bat Species from Feces
In 2014 the Bat Ecology and Genetics Lab was newly-minted, co-directed by Carol Chambers, and had two outstanding lab genetics technicians on board - Dan Sanchez and Colin Sobek. First on our research agenda was to determine if we could develop a robust genetic assay to identify bat species from their feces, and do so globally for a suite of applications for bat conservation and management. This effort was successful, and is described in our 2016 paper and a 2019 follow-up paper. We also put together a searchable database for users to determine the utility of the assay for their species of interest. We have now completed >200 projects for state and federal agencies, NGOs, environmental consultants, and university groups interested in better understanding the bat species that use key roosts. More information is at nau.edu/sff and on our FAQ page.
Diet Species from Feces
Our Species from Feces metabarcoding approach has evolved, so that we now use feces from many different taxa to genetically identify their diet. We like to say we work with anything that poops. We regularly identify diet items to the genus level, and for a high proportion are able to identify to the species level. Our ability to identify taxa to finer levels depends on the match between the DNA in the feces and the barcode data available. Sometimes we generate DNA barcodes for potential diet items as part of the project. We also commonly develop qPCR assays to detect a particular species of interest.
Pathogen Species from Feces
We test bat feces for Pd, the fungus that causes white-nose syndrome in bats, and any feces for SARS-coV-2, the virus that causes COVID19. We have also screened feces of the endangered New Mexico jumping mouse for pathogenic forms of E. coli, and are testing other fecal matters including guano for rabies virus thanks to a new highly-sensitive assay.
Biodiversity discovery - Species from Feces
Sometimes we want to know about all the DNA within a fecal sample, so we apply metagenomics as a first pass, with targeted metabarcoding assays later. We've done this for jumping mice, wombats, mammoths, and ground sloths.
Species from Feces Mobile
Our latest effort has been to use miniaturized DNA sequencers that plug into a laptop for answers in the field. As proof of concept we put together a field kit that fits into a carry-on sized backpack, and took it to the field in Zambia to learn about large carnivore diets and to understand the practicalities of this approach. A paper describing this work is in review.
