title: Abundant proteorhodopsin genes in the North Atlantic Ocean.
abstract: Proteorhodopsin (PR) is a light-driven proton pump that has been found in a variety of marine bacteria, including Pelagibacter ubique, a member of the ubiquitous SAR11 clade. The goals of this study were to explore the diversity of PR genes and to estimate their abundance in the North Atlantic Ocean using quantitative polymerase chain reaction (QPCR). We found that PR genes in the western portion of the Sargasso Sea could be grouped into 27 clusters, but five clades had the most sequences. Sets of specific QPCR primers were designed to examine the abundance of PR genes in the following four of the five clades: SAR11 (P. ubique and other SAR11 Alphaproteobacteria), BACRED17H8 (Alphaproteobacteria), HOT2C01 (Alphaproteobacteria) and an uncultured subgroup of the Flavobacteria. Two groups (SAR11 and HOT2C01) dominated PR gene abundance in oligotrophic waters, but were significantly less abundant in nutrient- and chlorophyll-rich waters. The other two groups (BACRED17H8 and Flavobacteria subgroup NASB) were less abundant in all waters. Together, these four PR gene types were found in 50% of all bacteria in the Sargasso Sea. We found a significant negative correlation between total PR gene abundance and nutrients and chlorophyll but no significant correlation with light intensity for three of the four PR types in the depth profiles north of the Sargasso Sea. Our data suggest that PR is common in the North Atlantic Ocean, especially in SAR11 bacteria and another marine alphaproteobacterial group (HOT2C01), and that these PR-bearing bacteria are most abundant in oligotrophic waters.
authors.affiliation: College of Marine and Earth Studies, University of Delaware, Lewes, DE 19958, USA.
authors.forename: Barbara J
authors.initials: BJ
authors.lastname: Campbell
authors.forename: Lisa A
authors.initials: LA
authors.lastname: Waidner
authors.forename: Matthew T
authors.initials: MT
authors.lastname: Cottrell
authors.forename: David L
authors.initials: DL
authors.lastname: Kirchman
mesh_terms: D020561:Alphaproteobacteria / Q000235:genetics* / Q000378:metabolism; D001267:Atlantic Ocean; D002734:Chlorophyll / Q000378:metabolism; D000077194:Chlorophyll A; D004777:Environment; D005417:Flavobacterium / Q000235:genetics* / Q000378:metabolism; D005787:Gene Frequency; D005798:Genes, Bacterial; D014644:Genetic Variation; D016680:Genome, Bacterial; D010802:Phylogeny; D016133:Polymerase Chain Reaction / Q000379:methods; D012243:Rhodopsin / Q000096:biosynthesis / Q000235:genetics* / Q000378:metabolism; D025604:Rhodopsins, Microbial; D012623:Seawater / Q000382:microbiology*
chemical_list: D025604:Rhodopsins, Microbial; C413548:proteorhodopsin; D002734:Chlorophyll; D012243:Rhodopsin; D000077194:Chlorophyll A