Global distribution of a chlorophyll f cyanobacterial marker

ISME J. 2020 Sep;14(9):2275-2287. doi: 10.1038/s41396-020-0670-y. Epub 2020 May 26.


Some cyanobacteria use light outside the visible spectrum for oxygenic photosynthesis. The far-red light (FRL) region is made accessible through a complex acclimation process that involves the formation of new phycobilisomes and photosystems containing chlorophyll f. Diverse cyanobacteria ranging from unicellular to branched-filamentous forms show this response. These organisms have been isolated from shaded environments such as microbial mats, soil, rock, and stromatolites. However, the full spread of chlorophyll f-containing species in nature is still unknown. Currently, discovering new chlorophyll f cyanobacteria involves lengthy incubation times under selective far-red light. We have used a marker gene to detect chlorophyll f organisms in environmental samples and metagenomic data. This marker, apcE2, encodes a phycobilisome linker associated with FRL-photosynthesis. By focusing on a far-red motif within the sequence, degenerate PCR and BLAST searches can effectively discriminate against the normal chlorophyll a-associated apcE. Even short recovered sequences carry enough information for phylogenetic placement. Markers of chlorophyll f photosynthesis were found in metagenomic datasets from diverse environments around the globe, including cyanobacterial symbionts, hypersaline lakes, corals, and the Arctic/Antarctic regions. This additional information enabled higher phylogenetic resolution supporting the hypothesis that vertical descent, as opposed to horizontal gene transfer, is largely responsible for this phenotype's distribution.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Antarctic Regions
  • Arctic Regions
  • Chlorophyll A
  • Chlorophyll* / analogs & derivatives
  • Cyanobacteria* / genetics
  • Light
  • Photosynthesis
  • Phylogeny


  • chlorophyll f
  • Chlorophyll
  • Chlorophyll A