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Supplemental Information

Supplemental 1

Rarefaction-based richness estimate with sampling depths plots.

DOI: 10.7287/peerj.preprints.2493v1/supp-1

Supplemental 2

Associated metadata for the bat microbiome project.

DOI: 10.7287/peerj.preprints.2493v1/supp-2

Supplemental 3

Good's Coverage plotted against total number of sequences per sample.

DOI: 10.7287/peerj.preprints.2493v1/supp-3

Supplemental 4

Relative abundance of top phylum found on bats a) ordered by latitude, b) bat species c) by ecoregion.

DOI: 10.7287/peerj.preprints.2493v1/supp-4

Supplemental 5

DESeq2 plots of differential abundance of bacteria phylum by ecoregion.

DOI: 10.7287/peerj.preprints.2493v1/supp-5

Supplemental 6

Frequency of occurrence of phylum in bats plotted against the mean relative abundance in the sample. Showing the bacteria on bats are mostly infrequently occuring and with low relative abundance.

DOI: 10.7287/peerj.preprints.2493v1/supp-6

Supplemental 7

Bayesian model output and posterior distributions for variables to predict total taxa richness on all bats.

DOI: 10.7287/peerj.preprints.2493v1/supp-7

Supplemental 8

Integrated nested Laplace approximation (INLA) prediction of bat species richness on a 10 kilometer grid. This was done to see if bacteria richness on bats shared predictors for overall bat richness in Arizona and New Mexico.

DOI: 10.7287/peerj.preprints.2493v1/supp-8

Additional Information

Competing Interests

Debbie Buecher is an employee of Buecher Biological Consulting.

Author Contributions

Ara S Winter performed the experiments, analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, reviewed drafts of the paper.

Jason C Kimble performed the experiments, analyzed the data, wrote the paper, reviewed drafts of the paper.

Jesse M Young performed the experiments, analyzed the data.

Debbie C. Buecher conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Ernest W. Valdez performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Jennifer J.M. Hathaway contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Andrea Porras-Alfaro wrote the paper, reviewed drafts of the paper.

Kaitlyn J. H. Read conceived and designed the experiments.

Diana E. Northup conceived and designed the experiments, performed the experiments, contributed reagents/materials/analysis tools, wrote the paper, reviewed drafts of the paper.

Animal Ethics

The following information was supplied relating to ethical approvals (i.e., approving body and any reference numbers):

2014 Arizona and New Mexico Game and Fish Department Scientific Collecting Permit (SP670210, SCI#3423, SCI#3350)

National Park Service Scientific Collecting Permit (CAVE-2014-SCI-0012, ELMA-2013-SCI-0005, ELMA-2014-SCI-0001, PARA-2012-SCI-0003)

Fort Collins Science Center Standard Operating Procedure (SOP) SOP#: 2013-01

Institutional Animal Care and Use Committee (IACUC) Permit from the University of New Mexico (Protocol #15-101307-MC) and from the National Park Service (Protocol #IMR_ELMA.PARA.CAVE.SEAZ_Northup_Bats_2015.A2)

Field Study Permissions

The following information was supplied relating to field study approvals (i.e., approving body and any reference numbers):

2014 Arizona and New Mexico Game and Fish Department Scientific Collecting Permit (SP670210, SCI#3423, SCI#3350)

National Park Service Scientific Collecting Permit (CAVE-2014-SCI-0012, ELMA-2013-SCI-0005, ELMA-2014-SCI-0001, PARA-2012-SCI-0003)

Fort Collins Science Center Standard Operating Procedure (SOP) SOP#: 2013-01

Institutional Animal Care and Use Committee (IACUC) Permit from the University of New Mexico (Protocol #15-101307-MC) and from the National Park Service (Protocol #IMR_ELMA.PARA.CAVE.SEAZ_Northup_Bats_2015.A2)

DNA Deposition

The following information was supplied regarding the deposition of DNA sequences:

DNA sequences are available at:

https://zenodo.org/record/50976

Data Deposition

The following information was supplied regarding data availability:

Biome files, QIIME mapping files, workflow, and R scripts are archived at https://zenodo.org/record/17577#

A Binder (http://mybinder.org/) ipython notebook with the full dataset used in this paper is available at: https://github.com/bioinfonm/bat_microbiome_plots .

Funding

Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU) - Carlsbad Caverns National Park (CAVE) Award #P14AC00793, UNM-101 CAVE personnel assisted in choosing netting sites and with netting and processing of bats. Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU) - El Malpais National Monument (ELMA) Award #P14AC00588, UNM-99 ELMA personnel assisted with netting and processing of bats. Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU) - Grand Canyon Parashant National Monument (PARA) Award #P12AC10812, UNM-80 CAVE personnel assisted in choosing netting sites and with netting and processing of bats. Fort Stanton Cave Study Project (FSCSP) & Bureau of Land Management Agreement No. 13-0484 FSCSP personnel assisted with processing bats. Colorado Plateau Cooperative Ecosystems Studies Unit (CPCESU) - United States Geological Survey Award #G13AC00111 USGS bat biologist chose the bat netting sites, netted the bats, and held them while the PI processed the bats. USGS bat biologist also participated in data analysis and write-up. T&E, Inc. Award #TE-EAA-01222014 The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. New Mexico Game & Fish Department Share with Wildlife Award #12516000000045 The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Western National Parks Association ELMA personnel assisted processing of bats in ELMA caves. National Park Service (El Malpais National Monument)-USGS cyclical funding Natural Resources Preservation Project-2013 USGS-Research Wildlife Biologist captured bats for microbiota sampling, provided expertise on bat ecology needed for interpretation of results, and participated with write-up of the manuscript. National Park Service-NPS Reimbursable funding Agreement P14PG00266 USGS-Research Wildlife Biologist captured bats for microbiota sampling, provided expertise on bat ecology needed for interpretation of results, and participated with write-up of the manuscript. United States Geological Survey Salary funding USGS-Research Wildlife Biologist captured bats for microbiota sampling, provided expertise on bat ecology needed for interpretation of results, and participated with write-up of the manuscript. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.


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