Genome-resolved metagenomics links microbial dynamics to failure and recovery of a bioreactor removing nitrate and selenate from mine-influenced water

Abstract

A packed-bed bioreactor designed for selenium removal from coal waste leachate experienced reduced hydraulic conductivity and loss of performance soon after forward flow of mine-influenced water containing nitrate and selenate as the main contaminants. A metagenomic study was initiated to help diagnose the causes for the bioreactor’s poor operation. Despite being inoculated with a custom consortium of Pseudomonas strains capable of nitrate and selenate reduction, the microbial community shifted towards dominance by Trichococcus- and Candidatus Saccharibacteria- related species. Metagenomic assembled genomes for these revealed that they did not have the metabolic potential for denitrification or selenate reduction, and displayed an affinity for carbohydrate carbon sources through the PTS pathway. We speculate that the sugar-based carbon sources fed to the bioreactor lead to favourable growth of the filamentous forms of these species under the conditions of the bioreactor, which may have allowed for infiltration of oxygen. Decreasing ORP coincided with decrease in relative abundance of the filamentous species and increase in relative abundance of uncharacterized species in the Burkholderiales and Rhodocyclales orders with the metabolic potential for all steps of the denitrification pathway including nitrate reductases closely related to those with an affinity for selenate as well as nitrate.