Comparing the microbial communities of natural and supplemental nests of an endangered ecosystem engineer

Supplemental nests are often used to restore habitats for a variety of rare and endangered taxa. However, though supplemental nests mimic the function of natural nests, they vary in design and building material. We know from previous research on human homes and other buildings that these differences in architecture can alter the types of microbes to which inhabitants are exposed, and these shifts in microbial interactions can be detrimental for health and well-being. Yet, no one has tested whether microbial communities in supplemental structures are distinct from those found in natural nests. Here we sampled the bacteria from inside supplemental nests of the endangered Key Largo woodrat (Neotoma floridana smalli). We then compared the diversity and composition of those bacteria to those collected from natural stick-nests and the forest floor in Key Largo, Florida. In addition, we sampled woodrat bodies to assess the microbiota of nest inhabitants. We observed distinct bacterial communities in Key Largo woodrat nests, relative to the forest environment; however, we could not differentiate between the microbial communities collected from supplemental and natural nests. Furthermore, when we considered genera known to contain bacterial pathogens of wild rodents, supplemental and natural nests exhibited similarly low relative abundances of these taxa. Where we expected to see an accumulation of pathogens, we instead observed high relative abundances of bacteria from antimicrobial-producing groups (i.e., Pseudonocardiaceae and Streptomycetaceae). The microbial biota of Key Largo woodrat individuals resembled those of their nests, with low relative abundances of potentially pathogenic bacteria and high abundances of antimicrobial-producing groups. Our results suggest that, although there is some microbial interaction between nests and nest inhabitants, there are no detectable differences in the types of bacteria to which Key Largo woodrats are exposed in supplemental and natural nest structures.