Comparison of cells synthesizing functional rhodopsins or genomes containing rhodopsin genes, quantified by different methodsa

Sample from <0.8-μm-size fraction% of:
Cells with rhodopsins (TIRF)bGenomes with SAR-PR (qPCR)cGenomes with LG1 (qPCR)cGenomes with rhodopsins (metagenomes)dGenomes with SAR-PR (metagenomes)Genomes with actinorhodopsin (metagenomes)
15 ppt salinity1539.80.751076323
31 ppt salinity40.31220.7774364
  • a Since the TIRF microscopy and qPCR analyses were only performed on filtered samples (cells of <0.8 μm), only the small-size-fraction metagenomic data are included here. Note that “actinorhodopsins” in the last column includes all rhodopsins identified in Actinobacteria (15).

  • b Percentage of cells with functional rhodopsins, calculated as 100 × (cells with fluorescence at 561 nm/DAPI-stained cells).

  • c Percentage of genomes encoding SAR-PR or LG1-type rhodopsins, as estimated by qPCR analysis. Calculated as 100 × (copies of rhodopsin/[copies of 16S/1.9]).

  • d Percentage of genomes encoding any rhodopsin gene, estimated from metagenomics data. Calculated as 100 × (number of assembled rhodopsin genes/number of assembled rplB genes).