An integrated meta-omics approach for identifying candidate organic micropollutant degraders in complex microbial communities

Abstract

Biotransformation is a significant determinant of the fate of organic micropollutants (OMPs) in natural and engineered environments; yet identifying OMP-transforming microorganisms remains challenging. Integrating metagenomics and metatranscriptomics, we searched for correlations between the biotransformation of ammonia and atenolol and the transcriptional activity of metagenome-assembled genomes (MAGs) across five nitrifier-rich cultures in batch experiments. The biotransformation of ammonia correlated with the activity of ammonia-oxidizing bacterium Nitrosomonas europaea but not with the activity of other bacteria, including several ammonia oxidizers. Additionally, the biotransformation of ammonia correlated with the transcript abundance of the ammonia monooxygenase (AMO) expressed by N. europaea but not with the transcript abundance of AMO at the community level. Atenolol biotransformation correlated with the activity of four MAGs representing three heterotrophic genera: Terrimonas, Flavobacterium, and Zeimonas. It did not correlate with the total transcript abundance of any member of a comprehensive set of amidohydrolases, which are predicted to transform this drug. By contrast, it correlated with the expression of the amidohydrolase asparagine synthase (AsnB) identified in the Terrimonas and Flavobacterium MAGs. In summary, we present a novel association-based method for elucidating biotransformation processes robust to variability in enzyme reaction kinetics with implications for OMP control. SynopsisThe fate of organic micropollutants in natural and engineered systems depends greatly on biotransformation by microbes. This study proposes an approach for identifying these microbes with implications for the study and control of organic micropollutant removal. ABSTRACT GRAPHICS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/639455v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@17c7f1org.highwire.dtl.DTLVardef@147b9eforg.highwire.dtl.DTLVardef@1fffc9eorg.highwire.dtl.DTLVardef@121fd96_HPS_FORMAT_FIGEXP M_FIG C_FIG