Fig 1.
Scute sampling locations 1–8 for carapace (upper) and plastron (lower) shell surfaces, and pictures of representative sample of T. scripta.
Scute abbreviations: Ab = abdominal; An = anal; G = gular; M = marginal; N = nuchal; S = supracaudal.
Table 1.
Site locations, descriptions and sampling dates for turtle collections.
Fig 2.
Venn diagrams of recovered taxon counts across all 16S and 18S turtle and environmental samples at the Class, Order, Family and Genus level.
Counts of shared and unique taxonomic assignments recovered in environmental and turtle samples are indicated for 16S (left column) and 18S (right column) communities. Data from T. scripta and P. concinna is included, as inclusion of P. concinna samples had negligible impact on counts of recovered taxonomic assignments.
Fig 3.
Taxonomic diversity of turtle scute and environmental microbial communities.
(A) Taxonomic affiliation of 16S communities at the Class level; (B) Taxonomic affiliation of 18S communities at the Order level. Samples are grouped by site, and separated within site by environmental (E) and turtle (T) samples. Vertical arrows indicate scute microbial communities sampled from P. concinna at the NCS site.
Fig 4.
Representative alpha and beta diversity comparisons between environmental, carapace and plastron microbial communities.
A) Alpha diversity (Faith’s Phylogenetic diversity) estimates for 16S (left) and 18S (right) environmental, T. scripta carapace (scute 3) and T. scripta plastron (scute 8) communities. B) Beta diversity (unweighted UniFrac) PCoA plots for all wood and rock/concrete environmental samples, and all T. scripta and P. concinna scute samples. Sample provenance is indicated by color and shape (see legend). C) Beta diversity (unweighted UniFrac) PCoA plots for wood and rock/concrete environmental samples, and T. scripta carapace (scute 3) and plastron (scute 8) samples. Sample provenance is indicated by color (see legend). Corresponding plots for all applied alpha and beta diversity metrics are available in S4 Appendix.
Table 2.
Results of significance testing for alpha and beta diversity metrics in T. scripta scute and environmental sample comparisons.
Alpha and beta diversity test corrected p-values are shown in scientific notation; significant results (corrected p-value ≤ 0.05) are indicated in bold. p-values shown are corrected using either a Satterthwaite approximation (alpha diversity) or Benjamini-Hochberg correction (beta diversity). “Substrate” was included as a fixed effect for linear mixed effect modeling of 18S Shannon diversity, Jaccard, Bray-Curtis and unweighted UniFrac, since we recovered significant differences between wood- and rock/concrete-associated microbial communities for these metrics (see Methods and Materials). env = shallow water environmental samples.
Table 3.
Number of taxa with significantly different abundance in turtle shell- versus environmental sample-associated 16S and 18S communities.
Counts are shown for taxonomic levels Class through Genus. Numbers in parentheses indicate numbers of instances of significantly higher abundance taxonomic assignments in (turtle samples, environmental samples) across sites.