MICROBIAL ASSEMBLAGE DYNAMICS WITHIN THE AMERICAN ALLIGATOR NESTING ECOSYSTEM: A COMPARATIVE APPROACH ACROSS ECOLOGICAL SCALES

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. Research that addresses community patterns at different focal scales may discern distinct conclusions about ecological processes that structure communities. Ideally, studies conducted across focal scales may reflect relevant process-shaping assemblage patterns. Here, I use metabarcoding and shotgun sequencing to determine bacterial assemblage patterns among defined focal scales (micro-, meso-, macro-) within the American alligator (Alligator mississippiensis) nesting microbiome. I correlate bacterial assemblage patterns among eight defined compartments within and proximal to alligator nests (microscale), among 27 nests (mesoscale), and across three geographic sampling sites (macroscale), to discern among four main ecological processes (i.e. drift, speciation, selection/filtering, dispersal) that drive bacterial pattern-process dynamics. I hypothesized variation in taxonomic diversity but functional redundancy among defined compartments within alligator nests and between geographic sites. Among all focal scales, bacterial richness (α-diversity) did not statistically differ. In contrast, bacterial composition was unique (β-diversity), with whole nests predicting the largest degree of assemblage variation. Interestingly, functional pathways were redundant within nests. Considering these observed scale-based patterns, alligator nest bacterial assemblages are likely sourced from site-specific reservoirs whose dispersal limitations drive taxonomic differences but are under redundant selection. Critically, the alligator eggshell microbiome is comparably distinct from within-nest assemblages. Bacteria that are found only on the alligator eggshell, are not likely sourced from surrounding environmental reservoirs and are possibly transferred from the mother’s cloaca. I speculate that bacteria found only on the alligator eggshell, with the functional potential to degrade the eggshell surface, are an integrated part of hatching ecology. These findings advance pattern-process dynamics within the field of microbial community ecology and describe processes influencing the American alligator nest microbiome.