Cyanobacteria colonize a variety of polar terrestrial ecospheres including rocks, glaciers, ice shelves, streams, ponds and lakes [41,42,43,44,45]. Phototrophs in these environments are generally psychrotolerant and exhibit an assortment of cold-protection mechanisms and slow growth rates to endure freeze-thaw cycles. The intracellular accumulation of salts to sustain osmotic balance, variation in DNA repair mechanisms and the use of photo-complexes are additional strategies that terrestrial cyanobacteria employ in extreme cold environments [44,46,47]. Picocyanobacteria such as Synechococcus and Prochlorococcus are the most abundant phototropic cells in the World’s oceans [48]. Despite this significant contribution to primary production, these cells are small, 0.5–1.5 µm and, in the case of Prochlorococcus, remained undetected until 1986 when they were discovered using flow cytometry [49]. Importantly, the abundance of marine cyanobacteria decreases rapidly south of latitude 40° [50,51,52] and this has been attributed to eco-physiological factors such as temperature, salinity and nutrient requirements [44].

Considering their prevalence in cold terrestrial environments, the apparent absence of cyanobacteria within sea ice is, however, unexpected. Interestingly, Synechococcus was detected from coastal waters off East Antarctica in 1989 using microscopy and pigment chemistry [53] and a decade later, cyanobacterial-like pigments (phycoerythrin and phycocyanin) were detected for the first time within the ice matrix using flow cytometry [54]. Pigment-based confirmation is questionable however as phycoerythrin and phycocyanin are also present in other algae including Cryptophytes which are common during Antarctic coastal blooms [54]. To potentially validate these earlier findings, a multi-method molecular analysis was recently carried out on fast-ice cores extracted from sites spanning 300 km in the Ross Sea region of Antarctica [55]. Clone libraries were constructed from the 16S rDNA gene, the internal transcribed sequence (ITS) region and the cyanobacterial core RNA polymerase (rpoC). Analysis of all sections of extracted ice did not reveal the presence of Synechococcus sp., Prochlorococcus sp., or any other marine cyanobacteria-related species. Additional screening was carried out using ligation detection reaction-based microarray, which can detect as little as 1 fmol of DNA [56]. Data from the ITS and microarray analysis of these sea ice samples showed close affiliation to the freshwater cyanobacteria Phormidium sp. and Cylindrospermopsis sp., respectively [55], but the closest Antarctic relative was an uncultured cyanobacteria clone from the nearby meromictic Lake Fryxell [42]. Aerobiology studies conducted in the Antarctic [57,58] and the Arctic [59] suggested that much of the biological material present in the air originates locally. Harding et al. [59] observed that >47% of the operational taxonomic units (OTUs) in Arctic snow samples were from previously reported local cyanobacteria [45,60]. Given that Terra Nova Bay is situated in a katabatic wind cross-zone [61], it is likely that the cyanobacterial propagules identified by Koh et al. [55] were wind-transported from nearby freshwater ponds or terrestrial soil and incorporated into the ice during seasonal formation. Despite earlier anecdotal findings, molecular-based evidence now confirms that cyanobacteria do not play a significant role in sea ice ecosystem dynamics.

Phototropic metabolism is a feature of four other eubacterial phyla (i.e., Proteobacteria, Chlorobi, Chloroflexi and Firmicutes). Unlike cyanobacteria, these phototrophs utilize the most ancient form of photosynthesis: anoxygenic photosynthesis [62]. This pathway is important for nitrogen-fixation, and cells with bacteriochlorophyll (bchl) also play an important role in the microbial loop [63,64]. The presence of highly diverse anoxygenic phototrophic bacterial communities in marine environments now suggests that non-chlorophyll-a phototrophy may be a more common life history strategy than previously realized. For example, the Proteobacteria contain the largest group of anoxyphototrophs [65], which were thought to be strictly anaerobic until three decades ago when the first aerobic representative was identified [66]. In both aerobic and anaerobic taxa, bchl-a is the primary light-harvesting pigment and absorbs red light at 770 to 880 nm and blue light at ~385nm [67,68,69]. This provides a useful contrast to the chlorophyll-a present in cyanobacteria and algae, which absorbs at 430 nm and 665 nm (Figure 3).

The aerobic anoxygenic phototrophic (AAnP) bacteria are a diverse group of prokaryotes with respect to their functionality, physiology, and morphology [69]. These are obligate aerobes with unusually high concentrations of carotenoids, low cellular contents of bchl-a and a distinct lack of the light-harvesting complex II [38,39]. In the anaerobic phototrophic bacteria (AnPB), the puf operon coding for the bchl is repressed by both oxygen and high light [70]. However, in the AAnP, the expression of the puf operon is not limited by oxygen, but it is still repressed by strong light [37,71,72]. Despite these physiological differences, both AnPB and AAnPs have a similar photosynthetic apparatus and similar electron carriers and structural polypeptides [73]. The close correlation between AAnPs and oxygenic phototrophs in the euphotic zone may indicate that these cells contribute to a light-controlled component of the microbial redox cycle [38]. Several molecular studies based on the genes of the puf operon have been carried out in tropical, temperate and polar marine environments [74,75,76,77,78,79] and these organisms have been estimated to account for up to 10% of the energy production in the upper layers of the water column [38,80] in most temperate and tropical oceans.

There is some evidence to suggest that AAnP bacteria are absent at high latitudes [81] and are genetically distinct from their freshwater counterparts [82,83]. However, positive pufM [64,73] clonal sequences were detected from extracted DNA and messenger RNA transcripts from the lower sections of Antarctic annual fast-ice as well as the underlying water column [84]. All clones grouped with the cultured α-Proteobacteria [39,74]. No β- and δ-Proteobacteria AAnPs were detected in the sea ice, matching the observations of Karr et al. [82] at Lake Fryxell. In fact, all the sea ice and seawater clones were likely α-Proteobacteria Roseobacter-clade affiliated [84], which could constitute ~20% of the Southern Ocean bacterial community [85,86], given that Roseobacter denitrificans is able to illicit specific defence systems against photo-oxidative stress [87]. More importantly, their presence in RNA extracts indicates that bacteria within the sea ice are actively expressing the gene for bchl synthesis.

AAnPs may constitute only ~0.05% of the prokaryotic abundance in the Western Antarctic waters [80], however the ease with which AAnPs were found within sea ice suggests that their relative proportion may be higher in ice-associated microbial communities. Results obtained by quantitative PCR suggest that Bchl OTUs may comprise up to 10% of the sea ice bacterial community [88], although further work is clearly needed to ascertain the ecological significance of this metabolic pathway.

The discovery of phototrophic energy generated via proteorhodopsin (PR) was a major finding in microbial ecology [89]. PRs are retinal binding bacterial integral membrane proteins that belong to the microbial rhodopsin super-family of proteins and function as light-driven proton pumps [89,90]. Unlike Bchl, PR cells do not generate cellular reducing power through NADPH, however ATP is produced upon light stimulation without the evolution of oxygen or fixation of inorganic carbon. Since the first reported PR sequence was obtained in 2000 [89], many other PR-bearing bacteria have been identified in environments ranging from freshwater lakes to the deep marine biosphere [91,92,93,94,95,96]. PR genes appear to be abundant in the genomes of oceanic bacteria [95], accounting for 13% of the prokaryotic community in the Mediterranean Sea and Red Sea and 70% in the Sargasso Sea [94,95,97,98]. Importantly, in vitro studies have demonstrated proton pumping and increased growth rates of PR-bearing bacteria under illuminated conditions [99,100,101,102]. Recently, PR in Candidatus Pelagibacter ubique was reported to play a critical role in a cellular response that maintains cell function during periods of carbon starvation [102]. These observations suggest that harvesting light energy via PR may be important in marine environments [103], but again the ecological significance of this metabolic pathway is currently unknown.

Sea ice bacteria that express the PR gene were described for the first time in 2010 [104]. PR-bearing representatives from the classes α-Proteobacteria, γ-Proteobacteria and Flavobacteria were present throughout the fast-ice in the Ross Sea region of Antarctica. Complementary DNA (cDNA) generated from RNA samples suggested that PR bacteria were metabolically active at the time of sampling. The bulk of the positive cDNA samples were collected from the middle and bottom part of the ice matrix, which possibly indicates that PR bacteria favor the lower light intensity and relatively stable temperatures found in the bottom half of the ice. Essentially, as light penetrates deeper into the ice matrix, the more energetic blue light predominates [105]. A stratified distribution of different forms of PR-bacteria in marine waters has been observed previously [106,107], and this has been attributed to a single-residue switch mechanism whereby the presence of leucine or glutamine at amino acid position 105 determines whether the protein absorbs in the green or blue wavelength [106]. Koh et al. [104] found both blue-absorbing (BPR) and green-absorbing (GPR) forms, but BPR were found primarily in the middle of the ice where red and green wavelengths of the solar spectrum are relatively low [105]. Conversely, GPR appear to be distributed throughout the ice, but their highest concentrations were at the ice/water interface [104], where, due to the presence of eukaryotic chl-a, the only available light is green.