Mycobacterial metabolic characteristics in a water meter biofilm revealed by metagenomics and metatranscriptomics

Mycobacteria represent one of the most persistent bacterial populations in drinking water distribution system (DWDS) biofilm communities; however, mycobacterial in situ metabolic profiles are largely unknown. In this study, the metabolic characteristics of mycobacteria in a household water meter biofilm were unveiled using a coupled metagenomic/metatranscriptomic approach. The water meter biofilm appeared to express nitrogenase genes (nifDKH) and a full complement of genes coding for several carbon-fixation pathways, especially the Calvin cycle, suggesting the CO2 sequestration and dinitrogen fixation potential of the biofilm. These findings indicate that it may be difficult to prevent the formation of DWDS biofilms simply by controlling the availability of organic carbon or nitrogen. The composite genome of mycobacteria (CG-M) was reconstructed based on the obtained omics data. CG-M shared similar genome phylogeny and virulence-factor profiles with Mycobacterium avium complex, suggesting that population CG-M might represent a member of mycobacteria with pathogenicity. According to the gene expression patterns, population CG-M showed the metabolic potential to assimilate CO2 via the Calvin cycle and/or anaplerotic reactions, and even to grow autotrophically with CO as the sole carbon and energy source. This suggests that organic carbon may not be a limiting factor for mycobacterial growth in DWDSs. Moreover, our results suggest that mycobacterial aromatic degradation is primarily achieved through the catechol meta-cleavage pathway, and biofilm mycobacteria could prefer phosphate as the phosphorus source.