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Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales

  • Environmental Microbiology
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Abstract

Understanding the ecological processes that shape species assemblage patterns is central to community ecology. The effects of ecological processes on assemblage patterns are scale-dependent. We used metabarcoding and shotgun sequencing to determine bacterial taxonomic and functional assemblage patterns among varying defined focal scales (micro-, meso-, and macroscale) within the American alligator (Alligator mississippiensis) nesting microbiome. We correlate bacterial assemblage patterns among eight nesting compartments within and proximal to alligator nests (micro-), across 18 nests (meso-), and between 4 geographic sampling sites (macro-), to determine which ecological processes may drive bacterial assemblage patterns within the nesting environment. Among all focal scales, bacterial taxonomic and functional richness (α-diversity) did not statistically differ. In contrast, bacterial assemblage structure (β-diversity) was unique across all focal scales, whereas functional pathways were redundant within nests and across geographic sites. Considering these observed scale-based patterns, taxonomic bacterial composition may be governed by unique environmental filters and dispersal limitations relative to microbial functional attributes within the alligator nesting environment. These results advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.

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Acknowledgments

We thank C. and D. Kearley for logistical support and A. Grajal for artwork design.

Availability of Data and Materials

All raw sequence data can be found under GenBank SRA accession number(s) PRJNA554418 (amplicon analysis) and PRJNA554694 (metagenomic analysis). Statistical analysis was performed in R version 3.5.1; the corresponding R markdown code file is included in the supplemental material.

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Authors and Affiliations

  1. Department of Biology, Middle Tennessee State University, Murfreesboro, TN, 37132, USA

    Alejandro Grajal-Puche & Donald M. Walker

  2. Department of Biological Sciences, Southeastern Louisiana University, Hammond, LA, 70402, USA

    Christopher M. Murray

  3. Biology Department, Tennessee Technological University, Cookeville, TN, 38505, USA

    Christopher M. Murray

  4. Department of Biological Sciences, Auburn University, Auburn, AL, 36849, USA

    Matthew Kearley

  5. Department of Chemistry, McNeese State University, Lake Charles, LA, 70609, USA

    Mark Merchant

  6. Alabama Wildlife and Freshwater Fisheries Division, Montgomery, AL, 36130, USA

    Christopher Nix

  7. Texas Parks & Wildlife Department, Port Arthur, TX, 77640, USA

    Jonathan K. Warner

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  1. Alejandro Grajal-Puche
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Contributions

AGP, DMW, and CMM conceived the study. All authors contributed to collection of specimens during field work. AGP and DMW completed the high-throughput sequencing, ran the bioinformatics, and statistical analyses. AGP, DMW, and CMM wrote the manuscript and all authors contributed equally to revisions.

Corresponding author

Correspondence to Donald M. Walker.

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Competing Interests

The authors declare that they have no competing interests.

Ethics Approval

Tennessee Technological University research policies and guidelines for the ethical treatment of animals were followed during this study (TTU-IACUC—17-18—007). Research collection permits were obtained from the appropriate governmental organizations (Eufaula National Wildlife Refuge Permit #: 4356020181R1; Alabama Conservation License Permit #: 201807822268680; J.D. Murphree Wildlife Management Area Collection Permit #: TPWD ESCA No. 826). Samples from Cameron Parish, LA were collected from private land under owner consent.

Electronic Supplementary Materials

Supplementary Table I

Taxonomic classification to the rank of order for bacteria indicative of the eggshell microbiome and other within nest assemblages. Indicator value > 0.50, α < 0.01. Highlighted rows are enriched (>3000 reads) bacterial taxa found only on the eggshell surface. (PDF 51 kb)

Supplementary Table II

Functional pathways indicative (indicator value > 0.50, α < 0.01) of the nest chamber (sample E) which is in direct contact with eggshell surfaces. Bolded pathways bordered by “ ** ” designate substrate degredation pathways. (PDF 86 kb)

Supplementary Table III

GPS coordinates of nests sampled in 2018. (PDF 30 kb)

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Grajal-Puche, A., Murray, C.M., Kearley, M. et al. Microbial Assemblage Dynamics Within the American Alligator Nesting Ecosystem: a Comparative Approach Across Ecological Scales. Microb Ecol 80, 603–613 (2020). https://doi.org/10.1007/s00248-020-01522-9

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