Establishing a regional microbial blueprint of metabolic function in sediment collected from pristine tropical estuarine systems

Traditional environmental monitoring techniques are well suited to resolving acute exposure effects, but lack resolution in determining subtle shifts in ecosystem functions resulting from chronic exposure(s) to toxicants. Surveillance with sensitive omics-based technologies could bridge this gap but, to date, these studies have been focused on identifying key metabolic differences resulting from anthropogenic perturbations. Here, we apply omics-based approaches to pristine environments to establish blueprints of microbial functionality within healthy estuarine sediment communities. To do so, we collected surface sediments (n = 50) from four pristine estuaries (Far North Queensland, Australia). Sediment microbiomes were analyzed for 16S rRNA amplicon sequences, central carbon metabolism metabolites, and associated secondary metabolites. Taxa-function relationships were established to predict community metabolism potential. Twenty-four correlated gene-metabolite pathways were identified and used to establish sediment microbial blueprints of essential carbon metabolism and amino acid biosynthesis that were positively correlated with community metabolic function outputs. Our results establish a baseline microbial blueprint for the pristine sediment microbiome of tropical marine environments, one that drives important ecosystem services and to which future ecosurveillance monitoring can be compared.