Abstract:

Seaside sparrows were captured in Plaquemines Parish, Louisiana, on oiled, unoiled, and reference sites in June 2016 and 2017. Fecal samples were opportunistically collected from all captured birds and gizzard samples were collected from every dissected bird. Prey DNA was extracted from these samples and sequenced on an Illumina MiSeq to generate amplicon sequences of a portion of the COI gene. This metabarcoding (or amplicon) data will allow us to identify prey species in sparrow diet on oiled, unoiled, and control sites, as well as identify any variation in described diet attributed to the sample type used (gizzard or fecal). Sample collection data is reported and COI metabarcoding data is located at NCBI, BioProject PRJNA629391.

Suggested Citation:

Snider, A., Taylor, S.. 2020. COI metabarcoding sequences of seaside sparrow (Ammospiza maritima) fecal samples and gizzard contents collected from oiled, unoiled, and reference sites in in Plaquemines Parish, Louisiana, 2016-06-08 to 2017-06-29. Distributed by: GRIIDC, Harte Research Institute, Texas A&M University–Corpus Christi. doi:10.7266/n7-c3m2-bs32

Purpose:

COI is considered the universal barcoding marker for animals. As such, we selected a COI primer set to allow for the identification of arthropod prey consumed by sparrows. Since invertebrate communities were affected by oil contamination, we are using this diet data to determine if Seaside Sparrows (a predator of these affected invertebrates) have shown corresponding changes in their diet that reflect altered prey communities caused by the Deepwater Horizon spill. Additionally, this unique paired-sample design allows us to compare the utility of fecal and gizzard samples in describing sparrow diet via metabarcoding. Sample type may be an overlooked (but important) factor in dietary metabarcoding studies, as DNA from different prey items can be digested at different rates and may lead to inaccurate descriptions of the diet. By comparing less digested samples (gizzard) to more digested samples (fecal), we will be able to determine if the description of sparrow diet is influenced by digestion and sample type used.

Data Parameters and Units:

SampleID: User defined identifier for each sample; AccessionNumber: NCBI’s accession number for the BioSample in the Sequence Read Archive; Latitude: Latitude of the sampling site, in decimal degrees; Longitude: Longitude of the sampling site, in decimal degrees; CollectionDate: Date of sample or data collection (DD-Mon-YY); Site: User defined site identifier; NCBIName: The name used to identify each sample in NCBI’s Sequence Read Archive; OriginalName: The original identifier for each sample, created upon collection; a mix of band numbers, bird dissection identifying numbers, and library preparation negatives; SampleType: Type of sample analyzed (Fecal, Gizzard, Negative=PCR blanks included to allow for the detection of any contamination that was generated during library preparation); BirdAge: The age of the bird as determined in the field (A=adult, C=no age-negative control) Sex: The sex of the bird as determined in the field, based on physical characteristics like brood batch and cloacal protuberance (M=male, F=female, C=no sex-negative control); For all variables, NA=not applicable.

Methods:

Seaside sparrows were captured on oiled, unoiled, and control plots in Barataria Bay and Pointe-a-la-Hache, Louisiana, in 2016 and 2017. Birds were captured on each plot in mist nests. During holding and handling, any fecal samples produced were collected opportunistically from clean hands, surfaces, or the cotton bags that the birds were placed in. Fecal samples were kept on ice in the field and then placed in a -20 °C freezer. Birds that were collected were euthanized by isoflurane inhalation and gizzard contents and other tissues were collected and immediately frozen in liquid nitrogen. At Louisiana State University, genomic DNA was extracted from fecal samples and gizzard contents, then arthropod-specific COI primers were used to target the prey DNA. This was sequenced on an Illumina MiSeq using v2 chemistry, 250 bp paired-end sequences.

Instruments:

10m-long, 30mm mesh mist nest: Used to capture Seaside Sparrows, Liquid nitrogen tank: Used to flash freeze collected tissue samples, Cryovials: Tubes to store gizzard content samples in liquid nitrogen, 1.5 ml tubes: Tubes used to store fecal samples in -20 °C freezer, Isoflurane: general inhalation anesthetic used to euthanize sparrows, 50 ml falcon tubes: used to hold isoflurane and sparrows during euthanasia, Dissection scissors: Laboratory scissors used to decapitate and remove tissues from the body cavity of sparrows, Dissection tweezers: Laboratory tweezers used to remove tissues from the body cavity of sparrows, Illumina MiSeq: next-generation sequencing platform.

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