Fig. 4

Metagenomics distinguishes the functional repertoire of the fiddler crab gill microbiome from the neighbouring sediment microbiome. a Grouping of gill and sediment microbiome samples (2–3 independent replicates per species/site) based on the Bray-Curtis dissimilarity index calculated using abundance/coverage of a random set of 100,000 genes in the annotated gene catalogue of both microbiomes. Crab species and site samples are colour-coded by location (same as in Fig. 1), and crab names are labelled according to crab species names: T. urvillei (TU), C. inversa (CI), A. albimana (AA), A. occidentalis (AO), and P. chlorophthalmus (PC); see Supplementary Table S1 for more details. b, c The abundance of the fifty most highly represented functions based on random forest predictions in gill (b) and sediment (c) microbiomes (2–3 replicates per sample). The plots represent independent gene sets that may have a few copies with low coverage in the gill or sediment microbiome, explaining the additional x-axis labels despite these being abundant in either the gill or sediment microbiomes. Boxplots show median coverage as the middle horizontal line and interquartile ranges as boxes (whiskers extend no further than 1.5× the interquartile range). Circular symbols reveal the diversity of enriched genes, with colours reflecting the location of the sample. Mean values are shown as white coloured diamonds. Different lowercase letters at the top of each boxplot denote significance differences based on the two-tailed unpaired Wilcoxon test (p<0.05). RPKM, reads per kilobase per million mapped reads. d Bar graphs show the high proportion of genes encoding transposases among the fifty most enriched annotated KOs in the crab gill microbiomes relative to the sediment microbiome