Proteorhodopsin-Bearing Bacteria in Antarctic Sea Ice

Abstract

Proteorhodopsins (PRs) are widespread bacterial integral membrane proteins that function as light-driven proton pumps. Antarctic sea ice supports a complex community of autotrophic algae, heterotrophic bacteria, viruses, and protists that are an important food source for higher trophic levels in ice-covered regions of the Southern Ocean. Here, we present the first report of PR-bearing bacteria, both dormant and active, in Antarctic sea ice from a series of sites in the Ross Sea using gene-specific primers. Positive PR sequences were generated from genomic DNA at all depths in sea ice, and these sequences aligned with the classes Alphaproteobacteria, Gammaproteobacteria, and Flavobacteria. The sequences showed some similarity to previously reported PR sequences, although most of the sequences were generally distinct. Positive PR sequences were also observed from cDNA reverse transcribed from RNA isolated from sea ice samples. This finding indicates that these sequences were generated from metabolically active cells and suggests that the PR gene is functional within sea ice. Both blue-absorbing and green-absorbing forms of PRs were detected, and only a limited number of blue-absorbing forms were found and were in the midsection of the sea ice profile in this study. Questions still remain regarding the protein's ecological functions, and ultimately, field experiments will be needed to establish the ecological and functional role of PRs in the sea ice ecosystem.

Winter diversity and expression of proteorhodopsin genes in a polar ocean

“…This is an important contribution to the understanding of PR diversity in polar waters as to our knowledge, previous polar studies yielded fewer clones (o50; Cottrell and Kirchman, 2009;Koh et al, 2010). This difference is likely a consequence of our use of seven pairs of degenerate primers versus only three used in previous Arctic studies.…”

“…Degenerated PR primers were modified from Atamna-Ismaeel et al (2008) and Koh et al (2010), with an expected PCR product size of B350 bp. An additional reverse primer (PR-R4) was created after in silico testing with the Fuzznuc web application (http://emboss.bioinformatics.nl/cgi-bin/emboss/ fuzznuc).…”

“…Consensus sequences were added to the 5 0 ends of primers to increase amplification Proteorhodopsin dynamics in a polar ocean D Nguyen et al efficiency (Bodaker et al, 2012). Six primer pairs from Koh et al (2010) were used in combination with a seventh pair using the additional reverse primer (Supplementary Information; Table 1). It should be noted that sequences representative of the actinorhodopsin-like LG1 and LG2 groups (Sharma et al, 2008(Sharma et al, , 2009) present a TWXXYP region at the 3 0 end and would not be amplified by our set of reverse primers that are based on GWXXYP (Atamna-Ismaeel et al, 2008) and SWXFY regions.…”

Expression of holo-proteorhodopsin in Synechocystis sp. PCC 6803

“…The gene encoding the first discovered member of this group was detected in the genome sequence of an uncultured γ-proteobacterium from oceanic waters (5). Since then, PRs have turned out to be highly abundant in the oceans (6)(7)(8)(9), and organisms containing them, including a cyanobacterium (10) can be found in many other habitats as well (7,(11)(12)(13). In vivo experiments have shown that pumping of protons by PR can lead to increases in growth rate under nutrient-limited conditions (6,14,15), production of ATP (16), increased fixation of CO 2 (6,17), and/or survival under starvation or stress conditions (16,(18)(19)(20).…”

Diversity of Arctic pelagic <i>Bacteria</i> with an emphasis on photoheterotrophs: a review

“…Antarctic PR sequences have been detected in coastal surface waters near Anvers Island, western Antarctic Peninsula (Béjà et al, 2000;Williams et al, 2012) and in sea ice and brine samples of the Ross Sea (Koh et al, 2010). Sequences analyses revealed that Antarctic PR showed similarity to previously reported PR sequences, although most of the sequences were generally distinct.…”