Species from feces: Order-wide identification of chiroptera from guano and other non-invasive genetic samples

Faith M. Walker, Charles H.D. Williamson, Daniel E. Sanchez, Colin J. Sobek, Carol L Chambers

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

Bat guano is a relatively untapped reservoir of information, having great utility as a DNA source because it is often available at roosts even when bats are not and is an easy type of sample to collect from a difficult-to-study mammalian order. Recent advances from microbial community studies in primer design, sequencing, and analysis enable fast, accurate, and cost-effective species identification. Here, we borrow from this discipline to develop an order-wide DNA mini-barcode assay (Species from Feces) based on a segment of the mitochondrial gene cytochrome c oxidase I (COI). The assay works effectively with fecal DNA and is conveniently transferable to low-cost, high-throughput Illumina MiSeq technology that also allows simultaneous pairing with other markers. Our PCR primers target a region of COI that is highly discriminatory among Chiroptera (92% species-level identification of barcoded species), and are sufficiently degenerate to allow hybridization across diverse bat taxa. We successfully validated our system with 54 bat species across both suborders. Despite abundant arthropod prey DNA in guano, our primers were highly specific to bats; no arthropod DNA was detected in thousands of feces run on Sangerand Illumina platforms. The assay is extendable to fecal pellets of unknown age as well as individual and pooled guano, to allow for individual (using singular fecal pellets) and community (using combined pellets collected from across long-term roost sites) analyses. We developed a searchable database (http://nau.edu/CEFNS/Forestry/Research/Bats/Search-Tool/) that allows users to determine the discriminatory capability of our markers for bat species of interest. Our assay has applications worldwide for examining disease impacts on vulnerable species, determining species assemblages within roosts, and assessing the presence of bat species that are vulnerable or facing extinction. The development and analytical pathways are rapid, reliable, and inexpensive, and can be applied to ecology and conservation studies of other taxa.

Original languageEnglish (US)
Article numbere0162342
JournalPLoS One
Volume11
Issue number9
DOIs
StatePublished - Sep 1 2016

Fingerprint

Feces
animal manures
Chiroptera
feces
Assays
DNA
sampling
pellets
Arthropods
assays
Forestry
Electron Transport Complex IV
Ecology
arthropods
Costs
Conservation
Oxidoreductases
Genes
Throughput
Costs and Cost Analysis

ASJC Scopus subject areas

  • Medicine(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Agricultural and Biological Sciences(all)

Cite this

Species from feces : Order-wide identification of chiroptera from guano and other non-invasive genetic samples. / Walker, Faith M.; Williamson, Charles H.D.; Sanchez, Daniel E.; Sobek, Colin J.; Chambers, Carol L.

In: PLoS One, Vol. 11, No. 9, e0162342, 01.09.2016.

Research output: Contribution to journalArticle

Walker, Faith M. ; Williamson, Charles H.D. ; Sanchez, Daniel E. ; Sobek, Colin J. ; Chambers, Carol L. / Species from feces : Order-wide identification of chiroptera from guano and other non-invasive genetic samples. In: PLoS One. 2016 ; Vol. 11, No. 9.
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