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Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype
Zomer, A.; Ingham, C.J.; von Meijenfeldt, F. A.B.; Escobar Doncel, A.; van de Kerkhof, G.T.; Hamidjaja, R.; Schouten, S.; Schertel, L.; Müller, K. H.; Catón, L.; Hahnke, R.L.; Bolhuis, H.; Vignolini, S.; Dutilh, B.E. (2024). Structural color in the bacterial domain: The ecogenomics of a 2-dimensional optical phenotype. Proc. Natl. Acad. Sci. U.S.A. 121(29): e2309757121. https://dx.doi.org/10.1073/pnas.2309757121
In: Proceedings of the National Academy of Sciences of the United States of America. The Academy: Washington, D.C.. ISSN 0027-8424; e-ISSN 1091-6490, meer
Peer reviewed article  
Beschikbaar in  Auteurs 
Author keywords
    bacterial genomics; optics; photonic crystal; iridescence; living nanostructures
Auteurs  Top 
  • Zomer, A.
  • Ingham, C.J.
  • von Meijenfeldt, F. A.B., meer
  • Escobar Doncel, A.
  • van de Kerkhof, G.T.
  • Hamidjaja, R.
  • Schouten, S.
  • Schertel, L.
  • Müller, K. H.
  • Catón, L.
  • Hahnke, R.L.
  • Bolhuis, H., meer
  • Vignolini, S.
  • Dutilh, B.E.
Abstract
    Structural color is an optical phenomenon resulting from light interacting with nanostructured materials. Although structural color (SC) is widespread in the tree of life, the underlying genetics and genomics are not well understood. Here, we collected and sequenced a set of 87 structurally colored bacterial isolates and 30 related strains lacking SC. Optical analysis of colonies indicated that diverse bacteria from at least two different phyla (Bacteroidetes and Proteobacteria) can create two-dimensional packing of cells capable of producing SC. A pan-genome-wide association approach was used to identify genes associated with SC. The biosynthesis of uroporphyrin and pterins, as well as carbohydrate utilization and metabolism, was found to be involved. Using this information, we constructed a classifier to predict SC directly from bacterial genome sequences and validated it by cultivating and scoring 100 strains that were not part of the training set. We predicted that SCr is widely distributed within gram-negative bacteria. Analysis of over 13,000 assembled metagenomes suggested that SC is nearly absent from most habitats associated with multicellular organisms except macroalgae and is abundant in marine waters and surface/air interfaces. This work provides a large-scale ecogenomics view of SC in bacteria and identifies microbial pathways and evolutionary relationships that underlie this optical phenomenon.
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