Abstract
Proteorhodopsins (PR) are phylogenetically diverse and highly expressed proton pumps in marine bacterial communities. The phylogenetic diversity and in situ expression of the main PR groups in polar off-shore, coastal and estuarine waters is poorly known and their abundance has not yet been reported. Here, we show that PR gene sequences of the southern Beaufort Sea including MacKenzie shelf and estuary are mainly affiliated to Gammaproteobacteria, Alphaproteobacteria, and Bacteroidetes. Substantial overlap (78%) between DNA- and cDNA-based librairies indicated in situ PR transcription within a large fraction of PR-containing community. Sets of specific qPCR primers were designed to measure the absolute abundances of the major PR types. Spatial and depth profiles showed that PR-containing bacteria were abundant throughout the photic zone, comprising up to 45% of total bacteria. Although their abundance varied greatly with location and depth, Alphaproteobacteria predominated in the PR community in all water masses, with SAR11 as the major PR type. Low nutrient concentrations rather than light were the environmental drivers that best explained the abundance and distribution of arctic PR types. Together, our data suggests that PR-based phototrophy could be the major phototrophic prokaryotic process during the Arctic Ocean summer.
Highlights
Proteorhodopsins (PRs) are prokaryotic retinal-binding integral membrane proteins that function as light-driven proton pumps
After its initial discovery on a large genomic fragment derived from an uncultured marine gammaproteobacterium of the SAR86 clade (Béjà et al, 2000), PRs have been found in a diversity of bacterial groups notably in the SAR11 clade, one of the most common clades in the oceans (Giovannoni et al, 2005)
Of a total of 617 PR gene sequences retrieved along the transect covering the North Pacific Ocean to the Beaufort Sea, 306 were obtained from DNA and 311 from cDNA libraries. 72 distinct operational taxonomic units (OTUs) were identified after clustering sequences at 82% amino acid sequence similarity (Campbell et al, 2008)
Summary
Proteorhodopsins (PRs) are prokaryotic retinal-binding integral membrane proteins that function as light-driven proton pumps. After its initial discovery on a large genomic fragment derived from an uncultured marine gammaproteobacterium of the SAR86 clade (Béjà et al, 2000), PRs have been found in a diversity of bacterial groups notably in the SAR11 clade, one of the most common clades in the oceans (Giovannoni et al, 2005) They have been identified in the alphaproteobacterial SAR116 clade (Oh et al, 2010; Grote et al, 2011) the gammaproteobacterial clade SAR92 (Stingl et al, 2007b), in Roseobacter clade and Bacteroidetes species (Gómez-Consarnau et al, 2007; González et al, 2008; Riedel et al, 2010; Yoshizawa et al, 2012) and in marine planktonic Archaea (Frigaard et al, 2006). Some close homologs to PR are found in brackish, freshwater and sea ice environments (Atamna-Ismaeel et al, 2008; Koh et al, 2010)
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