Microbial assembly and co-occurrence network in an aquifer under press perturbation

Abstract

Purpose: Thousands of aquifers worldwide have been polluted by leachate from landfills and many more remained threatened. Microbial communities from these environments play a crucial role in mediating biodegradation and maintaining the biogeochemical cycles, but their co-occurrence and assembly mechanism have not been investigated. Method: Here, we coupled network analysis with multivariate statistics to assess the relative importance of deterministic versus stochastic microbial assembly in an aquifer undergoing intrinsic remediation, using 16S metabarcoding data generated through Illumina MiSeq sequencing of the archaeal/bacterial V3–V4 hypervariable region. Results: Results show that both the aquifer-wide and localised community co-occurrences deviate from expectations under null models, indicating the predominance of deterministic processes in shaping the microbial communities. Further, the amount of variation in the microbial community explained by the measured environmental variables was 55.3%, which illustrates the importance of causal factors in forming the structure of microbial communities in the aquifer. Based on the network topology, several putative keystone taxa were identified which varied remarkably among the wells in terms of their number and composition. They included Nitrospira, Nitrosomonadaceae, Patulibacter, Legionella, uncharacterised Chloroflexi, Vicinamibacteriales, Neisseriaceae, Gemmatimonadaceae, and Steroidobacteraceae. The putative keystone taxa may be providing crucial functions in the aquifer ranging from nitrogen cycling by Nitrospira, Nitrosomonadaceae, and Steroidobacteraceae, to phosphorous bioaccumulation by Gemmatimonadaceae. Conclusion: Collectively, the findings provide answers to fundamental ecological questions which improve our understanding of the microbial ecology of landfill leachate plumes, an ecosystem that remains understudied.