Fig. 2

Relative abundance and diversity of key metabolic and biogeochemical cycling genes in Bundera Sinkhole. a, b Non-linear multidimensional scaling (NMDS) based on Bray–Curtis distances of the relative abundance for (a) whole metagenomes (with genes dereplicated at 98% nucleotide identity) and (b) key metabolic genes displayed in panel c. In a, NMDS points that represent replicate samples lie on top of each other, as do those representing all samples from 17, 18, 22, and 28 m depths. The NMDS groupings (circles, triangles, and squares) represent samples with similar levels of dissolved oxygen (DO) and salinity (Supplementary Table S2). In both NMDS plots, the grouping of samples from 17, 18, 22, and 28 m depths (squares) is supported by PERMANOVA (p = 0.04; Supplementary Table S3). c Relative abundance of key metabolic marker genes within each sample. Colour scale displays the relative abundance as log₁₀(TPM + 1) to account for TPM values of zero. Gene names are displayed to the left of the heatmap, and the reactions that they facilitate are on the right. d Visualisation of microbial nitrogen and sulphur cycling pathways present in Bundera Sinkhole. Chemical compounds that represent either the substrate or product of a reaction are boxed, with oxidation states shown in parentheses