Department Environmental Chemistry

Enzyme-Transformation Linkage

Rates and products of microbial biotransformation vary between different activated sludge treatment systems. This is at least partly due to differences in microbial community composition and activity, and hence their variable capacity to perform certain biotransformation reactions. Particularly, the presence and activity of nitrifiers has been linked to improved biotransformation of a range of micropollutants. 

In this project, we want to further clarify the role of nitrifiers in micropollutant biotransformation. Specifically, we ask what types of biotransformation reactions are catalyzed by nitrifiers, what are the relative roles of nitrifying archaea and bacteria in catalyzing those reactions, and what is the relative importance of heterotrophic microorganisms relative to nitrifying organisms. To address these questions we study the biotransformation extent and products for certain pertinent chemical classes in different inhibition and pure culture experiments.

Publications

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      authors => protected'Johnson, D. R.; Helbling, D. E.; Men, Y.; Fenner,&n
         bsp;K.' (82 chars)
      title => protected'Can meta-omics help to establish causality between contaminant biotransforma
         tions and genes or gene products?' (109 chars)
      journal => protected'Environmental Science: Water Research and Technology' (52 chars)
      year => protected2015 (integer)
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      issue => protected'3' (1 chars)
      startpage => protected'272' (3 chars)
      otherpage => protected'278' (3 chars)
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      description => protected'There is increasing interest in using meta-omics association studies to inve
         stigate contaminant biotransformations. The general strategy is to character
         ize the complete set of genes, transcripts, or enzymes from <I>in situ</I> e
         nvironmental communities and use the abundances of particular genes, transcr
         ipts, or enzymes to establish associations with the communities' potential t
         o biotransform one or more contaminants. The associations can then be used t
         o generate hypotheses about the underlying biological causes of particular b
         iotransformations. While meta-omics association studies are undoubtedly powe
         rful, they have a tendency to generate large numbers of non-causal associati
         ons, making it potentially difficult to identify the genes, transcripts, or 
         enzymes that cause or promote a particular biotransformation. In this perspe
         ctive, we describe general scenarios that could lead to pervasive non-causal
          associations or conceal causal associations. We next explore our own publis
         hed data for evidence of pervasive non-causal associations. Finally, we eval
         uate whether causal associations could be identified despite the discussed l
         imitations. Analysis of our own published data suggests that, despite their 
         limitations, meta-omics association studies might still be useful for improv
         ing our understanding and predicting the contaminant biotransformation capac
         ities of microbial communities.' (1399 chars)
      serialnumber => protected'2053-1400' (9 chars)
      doi => protected'10.1039/c5ew00016e' (18 chars)
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Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?

There is increasing interest in using meta-omics association studies to investigate contaminant biotransformations. The general strategy is to characterize the complete set of genes, transcripts, or enzymes from in situ environmental communities and use the abundances of particular genes, transcripts, or enzymes to establish associations with the communities' potential to biotransform one or more contaminants. The associations can then be used to generate hypotheses about the underlying biological causes of particular biotransformations. While meta-omics association studies are undoubtedly powerful, they have a tendency to generate large numbers of non-causal associations, making it potentially difficult to identify the genes, transcripts, or enzymes that cause or promote a particular biotransformation. In this perspective, we describe general scenarios that could lead to pervasive non-causal associations or conceal causal associations. We next explore our own published data for evidence of pervasive non-causal associations. Finally, we evaluate whether causal associations could be identified despite the discussed limitations. Analysis of our own published data suggests that, despite their limitations, meta-omics association studies might still be useful for improving our understanding and predicting the contaminant biotransformation capacities of microbial communities.
Johnson, D. R.; Helbling, D. E.; Men, Y.; Fenner, K. (2015) Can meta-omics help to establish causality between contaminant biotransformations and genes or gene products?, Environmental Science: Water Research and Technology, 1(3), 272-278, doi:10.1039/c5ew00016e, Institutional Repository