TABLE 1.
Rhodopsins from environmental samplesa
| Sampling site(s) | No. of rhodopsins | Taxon (clade) | Methodology | Rhodopsin | Reference |
|---|---|---|---|---|---|
| Monterey Bay, East Pacific | 1 | Gammaproteobacteria (SAR86) | Metagenomics, BACs | PR | 28 |
| Monterey Bay, East Pacific; HOT, Antarctica | 6 | Proteobacteria | PR gene clone sequencing | PR | 96 |
| East Mediterranean Sea; Red Sea | 30 | Proteobacteria | PR gene clone sequencing | PR | 94 |
| HOTS, Pacific; East Pacific; Antarctica | 5 | Alphaproteobacteria, Gammaproteobacteria | Metagenomics, genomic library, BACs | PR | 52 |
| Red Sea; Pacific | 2 | Gammaproteobacteria (SAR86) | Metagenomics, BACs | PR | 36 |
| HOTS, Pacific | 17 | Archaea (marine group II Euryarchaeota) | Metagenomics, fosmid library | PR | 69 |
| Gulf of Maine, Northwest Atlantic | 2 | Bacteroidetes | Cell sorting, SAGs | PR | 68 |
| HOTS, Pacific | 16 | Planctomycetales | Metagenomics, fosmid and BAC library sequencing | PR | 56 |
| Monterey Bay, East Pacific | 16 | Betaproteobacteria | Metagenomics, fosmid and BAC library sequencing | PR | 56 |
| Atlantic to Pacific | 2,674 | Multipleb | Metagenomics. sequencing | PR | 84 |
| Freshwater, Panama | 56 | Multiple | Metagenomics. sequencing | PR | 84 |
| North Atlantic | 91 | Multiple | PR gene clone sequencing, qPCR | PR | 92 |
| Freshwater (multiple) | 66 | Alphaproteobacteria (LD12), Bacteroidetes | PR gene clone sequencing | PR | 163 |
| Great Lakes, Canada | 69 | Actinobacteria | Metagenomics. sequencing | ActR | 164 |
| China Sea | 140 | Bacteroidetes | PR gene clone sequencing qPCR | PR | 104 |
| Chukchi and Beaufort Sea, Arctic Ocean | 54 | Multiple | PR gene clone sequencing, qPCR | PR | 105 |
| Lakes, Canada | 69 | Actinobacteria (acI, Luna) | ActR gene clone sequencing | ActR | 82 |
| North Sea | 117 | Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes | PR gene clone sequencing, qPCR | PR | 93 |
| Antarctica, sea ice | 52 | Proteobacteria, Bacteroidetes | PR gene clone sequencing | PR | 165 |
| West Mediterranean Sea | 39 | Archaea | Metagenomics, sequencing, fosmid library | PR | 70 |
| Freshwater lakes | 119 | Actinobacteria (multiple) | Cell sorting, SAGs | ActR, PR | 81 |
| High mountain lake | 91 | Multiple | PR gene clone sequencing | PR | 166 |
| Puget Sound, Pacific | 1 | Archaea (marine group II Euryarchaeota) | Metagenomics, sequencing (genome assembly) | PR | 71 |
| Leaf surfaces, Israel | 156 | Multiple | Metagenomics, sequencing | Multiple | 167 |
| Northeast Pacific Ocean | 3 | Diatoms, haptophytes | (Meta)transcriptomics | XR | 154 |
| Gulf of Maine; Mediterranean; Pacific; Atlantic | 26 | Proteobacteria, Bacteroidetes, Archaea | Cell sorting, SAGs | PR | 54 |
| Red Sea | 12 | Bacteria, Archaea, virus | Metagenomics, sequencing | Multiple | 103 |
| Sargasso Sea | 782 | Proteobacteria, Bacteroidetes | Metagenomics, sequencing | PR | 64 |
| Beaufort Sea, Arctic Ocean | 187 | Proteobacteria, Bacteroidetes | PR gene clone sequencing, qPCR | PR | 106 |
| Arctic permafrost | 1 | Firmicutes (Exiguobacterium) | BR gene clone sequencing | BR | 72 |
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.