TABLE 1

Rhodopsins from environmental samplesa

Sampling site(s)No. of rhodopsinsTaxon (clade)MethodologyRhodopsinReference
Monterey Bay, East Pacific1Gammaproteobacteria (SAR86)Metagenomics, BACsPR28
Monterey Bay, East Pacific; HOT, Antarctica6ProteobacteriaPR gene clone sequencingPR96
East Mediterranean Sea; Red Sea30ProteobacteriaPR gene clone sequencingPR94
HOTS, Pacific; East Pacific; Antarctica5Alphaproteobacteria, GammaproteobacteriaMetagenomics, genomic library, BACsPR52
Red Sea; Pacific2Gammaproteobacteria (SAR86)Metagenomics, BACsPR36
HOTS, Pacific17Archaea (marine group II Euryarchaeota)Metagenomics, fosmid libraryPR69
Gulf of Maine, Northwest Atlantic2BacteroidetesCell sorting, SAGsPR68
HOTS, Pacific16PlanctomycetalesMetagenomics, fosmid and BAC library sequencingPR56
Monterey Bay, East Pacific16BetaproteobacteriaMetagenomics, fosmid and BAC library sequencingPR56
Atlantic to Pacific2,674MultiplebMetagenomics. sequencingPR84
Freshwater, Panama56MultipleMetagenomics. sequencingPR84
North Atlantic91MultiplePR gene clone sequencing, qPCRPR92
Freshwater (multiple)66Alphaproteobacteria (LD12), BacteroidetesPR gene clone sequencingPR163
Great Lakes, Canada69ActinobacteriaMetagenomics. sequencingActR164
China Sea140BacteroidetesPR gene clone sequencing qPCRPR104
Chukchi and Beaufort Sea, Arctic Ocean54MultiplePR gene clone sequencing, qPCRPR105
Lakes, Canada69Actinobacteria (acI, Luna)ActR gene clone sequencingActR82
North Sea117Alphaproteobacteria, Gammaproteobacteria, BacteroidetesPR gene clone sequencing, qPCRPR93
Antarctica, sea ice52Proteobacteria, BacteroidetesPR gene clone sequencingPR165
West Mediterranean Sea39ArchaeaMetagenomics, sequencing, fosmid libraryPR70
Freshwater lakes119Actinobacteria (multiple)Cell sorting, SAGsActR, PR81
High mountain lake91MultiplePR gene clone sequencingPR166
Puget Sound, Pacific1Archaea (marine group II Euryarchaeota)Metagenomics, sequencing (genome assembly)PR71
Leaf surfaces, Israel156MultipleMetagenomics, sequencingMultiple167
Northeast Pacific Ocean3Diatoms, haptophytes(Meta)transcriptomicsXR154
Gulf of Maine; Mediterranean; Pacific; Atlantic26Proteobacteria, Bacteroidetes, ArchaeaCell sorting, SAGsPR54
Red Sea12Bacteria, Archaea, virusMetagenomics, sequencingMultiple103
Sargasso Sea782Proteobacteria, BacteroidetesMetagenomics, sequencingPR64
Beaufort Sea, Arctic Ocean187Proteobacteria, BacteroidetesPR gene clone sequencing, qPCRPR106
Arctic permafrost1Firmicutes (Exiguobacterium)BR gene clone sequencingBR72
  • a Abbreviations: BACs, bacterial artificial chromosomes; qPCR, quantitative PCR; SAGs, single amplified genomes; PR, proteorhodopsin; ActR, actinorhodopsin; XR, xanthorhodopsin; BR, bacteriorhodopsin.

  • b Bacteria from multiple classes or phyla.