Fig. 5

Abundance and taxonomic origin of key enzymes encoded by the gill microbiome with relevance to host physiology. a, c, d Boxplots show the normalised abundance of seven different metabolic genes in reads per kilobase per million mapped reads (RPKM) in the microbiome associated with sediment and gills of different crab species. The circular symbols show the mean RPKM value (log-scaled) for each predicted unique gene copy (per enzyme; n = 2–3 replicates) and are coloured according to the sampling location. The mean RPKM value of all genes is shown as a horizontal bar. Different lowercase letters on the x-axis indicate microbiomes with significantly different mean (RPKM) abundances as determined by a two-tailed, unpaired Wilcoxon test (p < 0.05). In all cases, gene family diversity is higher in the sediment microbiome than in the gill microbiome of all crab species. b, e, f Bar graphs show the predicted taxonomic origin (at the phylum level) of genes encoding enzymes in the nitrogen (b), sulphur (e), and carbon (f) cycles in the gill microbiome relative to the sediment microbiome. The percentages in the bar graphs show the relative abundance of each phylum based on the aggregated RPKM of all genes shown in the individual boxplots. Gene abbreviations (and corresponding KO identifiers): AMT, ammonia transporter (K03320); GDH, glutamate dehydrogenase (K15371); GS, glutamine synthetase (K01915); soxC, sulfite oxidase (K00387); SQR, sulphide:quinone oxidoreductase (K17218); psrA, polysulfide reductase subunit A (K08352); and cutL, aerobic carbon monoxide dehydrogenase, large subunit (K03520). Abbreviations of crab species: AA, A. albimana; CI, C. inversa; TU, T. urvillei; AO, A. occidentalis; and PC, P. chlorophthalmus. RPKM, reads per kilobase per million mapped reads