Wildfires disturb the natural skin microbiota of terrestrial salamanders.

Environmental change can disturb natural associations between wildlife and microbial symbionts, in many cases to the detriment of host health. We used a North American terrestrial salamander system to assess how the skin microbiota of amphibians responds to wildfires. In northern California's redwood/oak forests, we assessed how recent wildfires affected the skin microbiota of three different salamander species (Taricha sp., Batrachoseps attenuatus, and Ensatina eschscholtzii) over two different sampling seasons in 2018 and 2021. We found species-specific responses to wildfire disturbance on the alpha diversity of the skin microbiota of terrestrial salamanders, although burning in general altered the composition of the skin microbiota. The effect of burning on alpha diversities and body condition indices varied by sampling season, suggesting an additional effect of annual climatic conditions on body condition and skin microbiota response. We tested all salamanders for Batrachochytrium dendrobatidis and found four infected individuals in 2018 and none in 2021. Our study documents correlations in the skin microbiota response to an increasing source of disturbance in western North American ecosystems. In addition, our results highlight the need to consider the effects of increased wildfire regimes/intensities and longitudinal effects on wildlife-associated microbiota and animal health.

Transcriptomic analysis of cave, surface, and hybrid samples of the isopod Asellus aquaticus and identification of chromosomal location of candidate genes for cave phenotype evolution.

BACKGROUND: Transcriptomic methods can be used to elucidate genes and pathways responsible for phenotypic differences between populations. Asellus aquaticus is a freshwater isopod crustacean with surface- and cave-dwelling ecomorphs that differ greatly in multiple phenotypes including pigmentation and eye size. Multiple genetic resources have been generated for this species, but the genes and pathways responsible for cave-specific characteristics have not yet been identified. Our goal was to generate transcriptomic resources in tandem with taking advantage of the species' ability to interbreed and generate hybrid individuals. RESULTS: We generated transcriptomes of the Rakov Skocjan surface population and the Rak Channel of Planina Cave population that combined Illumina short-read assemblies and PacBio Iso-seq long-read sequences. We investigated differential expression at two different embryonic time points as well as allele-specific expression of F1 hybrids between cave and surface individuals. RNAseq of F2 hybrids, as well as genotyping of a backcross, allowed for positional information of multiple candidate genes from the differential expression and allele-specific analyses. CONCLUSIONS: As expected, genes involved in phototransduction and ommochrome synthesis were under-expressed in the cave samples as compared to the surface samples. Allele-specific expression analysis of F1 hybrids identified genes with cave-biased (cave allele has higher mRNA levels than the surface allele) and surface-biased expression (surface allele has higher mRNA levels than the cave allele). RNAseq of F2 hybrids allowed for multiple genes to be placed to previously mapped genomic regions responsible for eye and pigmentation phenotypes. In the future, these transcriptomic resources will guide prioritization of candidates for functional analysis.

Bacterial communities of the threatened Western Pond Turtle may be impacted by land use.

As semi-aquatic species that use both terrestrial and aquatic habitats, freshwater turtles and their microbial communities are especially sensitive to the impacts of habitat disturbance. In this study, we use 16S rRNA amplicon sequencing to characterize the shell and cloacal bacterial communities of turtles in the San Francisco Bay Area. We captured western pond turtles (Actinemys/Emys marmorata) across eight sites located in urban and rural environments, along with invasive red-eared sliders (Trachemys scripta elegans). We assessed differences in western pond turtle bacterial communities diversity/composition between shell and cloacal samples and evaluated how alpha/beta diversity metrics were influenced by habitat quality. We found phylum-level bacterial taxonomic turnover in the bacterial communities of western pond turtles relative to the host tissue substrate samples. Our findings indicate that location identity elicits a high degree of lower-level (i.e. species/genus) bacterial taxonomic turnover. Further, we found that samples originating from good quality habitat had poorer shell bacterial communities but more diverse cloacal ones. The shell bacterial communities of red-eared sliders overlapped with those western pond turtles suggesting the existence of microbial dispersal between these two species. Our results add to our current understanding of turtle symbiont microbial ecology by establishing patterns of bacterial symbiont variation in an urban to rural gradient.