Discovering functional novelty in metagenomes: examples from light-mediated processes

J Bacteriol. 2009 Jan;191(1):32-41. doi: 10.1128/JB.01084-08. Epub 2008 Oct 10.


The emerging coverage of diverse habitats by metagenomic shotgun data opens new avenues of discovering functional novelty using computational tools. Here, we apply three different concepts for predicting novel functions within light-mediated microbial pathways in five diverse environments. Using phylogenetic approaches, we discovered two novel deep-branching subfamilies of photolyases (involved in light-mediated repair) distributed abundantly in high-UV environments. Using neighborhood approaches, we were able to assign seven novel functional partners in luciferase synthesis, nitrogen metabolism, and quorum sensing to BLUF domain-containing proteins (involved in light sensing). Finally, by domain analysis, for RcaE proteins (involved in chromatic adaptation), we predict 16 novel domain architectures that indicate novel functionalities in habitats with little or no light. Quantification of protein abundance in the various environments supports our findings that bacteria utilize light for sensing, repair, and adaptation far more widely than previously thought. While the discoveries illustrate the opportunities in function discovery, we also discuss the immense conceptual and practical challenges that come along with this new type of data.

Publication types

  • Review

MeSH terms

  • Bacteria / classification
  • Bacteria / genetics*
  • Bacteria / growth & development
  • Bacteria / radiation effects
  • Bacterial Proteins / genetics
  • Ecosystem
  • Environment
  • Genes / radiation effects*
  • Genome, Bacterial
  • Genomics / methods*
  • Light
  • Phylogeny
  • Plants / classification
  • Plants / genetics
  • Ultraviolet Rays


  • Bacterial Proteins