Antarctica: marine microorganisms and the global importance of the Southern Ocean
Marine microorganisms play a critical role in maintaining the planet in a habitable state for several reasons. The oceans have the highest cellular production rate of any ecosystem, and despite having low levels of nutrients maintain microbial numbers on the order of 1 × 105 cells mL−1 (Schut et al., 1997; Whitman et al., 1998). In the open ocean, bacteria and archaea dominate in terms of biomass and play an essential role in regulating the accumulation, export, re-mineralization, and transformation of the world's largest pool of organic carbon (Cole et al., 1988; Schut et al., 1997; Azam, 1998; Azam & Malfatti, 2007). Bacteria can contribute up to 90% of the cellular DNA (Paul et al., 1985), 40% of the planktonic carbon (Azam, 1998; Azam & Malfatti, 2007), perform up to 80% of the primary production (Ducklow, 1999), and have nutrient uptake potentials around 100 times faster than that of eucaryal phytoplankton (Blackburn et al., 1998). The fixation of carbon, nitrogen, and phosphorus by microorganisms and their conversion into particulate matter form the basis of the food web in the oceans. There are global consequences for these microbial processes since the downward flow of microbial particles is the most efficient means of transporting CO2 fixed by primary production to marine sediments, thus sequestering it from the atmosphere. The balance between particle degradation, regenerating CO2 via respiration, and burial directly impacts the trajectory of climate change.
The functions of the Southern Ocean are dependent on the existence of different water body masses, which can be distinguished based on the distribution of physico-chemical parameters and ocean currents (Whitworth, 1980; Orsi et al., 1995; Sokolov & Rintoul, 2002; Sokolov & Rintoul, 2009a, b). The nutrient-rich upper and lower Circumpolar Deep Waters is formed from the mixing of the deep waters from the Atlantic and Indian oceans with the cold sinking Antarctic Surface Waters (Fig. 2). Upwelling of Circumpolar Deep Waters returns nutrients to surface waters at lower latitudes, resulting in 75% of global primary production occurring north of 30°S (Sarmiento et al., 2004). The Antarctic Bottom Water, which originates in the Weddell and Ross seas, sinks and is pushed north becoming the driving force of the global conveyor belt. The Polar Front separates the cold Antarctic Surface Waters from the warmer waters of the Subantarctic Zone. Across the Polar Front, the water temperature abruptly changes by 1.5–2 °C over a distance of 30–50 km, marking the most pronounced biogeographic boundary in Antarctic waters (Chiba et al., 2001; Hunt et al., 2001; Esper and Zonneveld, 2002; Ward et al., 2003; Selje et al., 2004; Abell & Bowman, 2005a; Giebel et al., 2009; Weber & Deutsch, 2010; Jamieson et al., 2012; Wilkins et al., 2012.
Figure 2. Depiction of the main water bodies near Antarctica, and the Antarctic Circumpolar Current. Figure adapted from Rintoul (2000).
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Bounded by the Polar Front and the Antarctic continent, the Antarctic Circumpolar Current recirculates surface waters around the Antarctic continent and is integral to the seasonal cycles of sea ice formation and loss. Seasonal variation not only causes extreme changes in sea ice cover, but controls light levels and day length. As a result, phototrophic growth and biomass production are high in summer and very low in winter. Overall, bacteria are abundant in the Southern Ocean despite the low temperatures and seasonal variability in productivity and are a major pathway for carbon flow (Delille, 2004; Hessen et al., 2004).
It is expected that microbial communities that are unique to each water body (Esper & Zonneveld 2002; Ward et al., 2003; Selje et al., 2004; Abell & Bowman, 2005a) will be affected in a unique way by climate change and anthropogenic impact (Brown et al., 2012). Anthropogenic climate change appears to be pushing the Antarctic Circumpolar Current poleward (Fyfe & Saenko, 2005; Gille, 2008; Biastoch et al., 2009) due to warming and fresh water inputs (Böning et al., 2008). The Southern Ocean covers ~ 10% of the earth's surface area (Aronson et al., 2011), and due to the important role it plays in sequestering anthropogenic CO2 (Sabine et al., 2004; Mikaloff Fletcher et al., 2006) through both physiochemical processes and the ‘biological pump’ of CO2 fixation and export from the euphotic zone to the ocean depths (Thomalla et al., 2011), the changes taking place in Antarctic waters could have major global ecological consequences (Liu & Curry, 2010). This is emphasized by the fact that changes to ecosystems in the south polar region (e.g. Ross Sea) are likely to have similarities to those occurring in the north (e.g. western Arctic Ocean) (Kirchman et al., 2009). Predictions are that polar systems are generally very sensitive to environmental changes (Moline et al., 2004; Murray & Grzymski, 2007) with global warming expected to cause increased microbial activity and lower availability of energy and food for organisms higher up the food chain (Kirchman et al., 2009).
Many of the Antarctic marine zones (Fig. 1) have been sampled for the purpose of characterizing microbial communities using molecular approaches. A few transects have also been performed, comparing communities present in water bodies that represent different currents, temperatures, nutrient load, etc. A limited analysis of Southern Ocean sediment and deep water has been performed, but the majority of studies have been on surface waters. Sea ice communities have also been studied. However, the Southern Ocean is expansive with many environmental variables that may affect community composition. As a result, studies are still at the stage of establishing baseline values for diversity and community dynamics. Moreover, large-scale shotgun sequencing metagenomic surveys and associated functional studies (metaproteomics, metatranscriptomics) have only commenced recently (Table 2). Topics in this Southern Ocean section describe the main marine pelagic bacterial, archaeal, eucaryal, and viral taxa, inferring where known, the functional capacities and roles they play in biogeochemical cycles. The characteristics of sea ice communities are also described.
Table 2. Southern Ocean studies that used metagenomics, metaproteomics, or tag pyrosequencing
|Location||Methods||Notes||Reference||Fig. 1 map location|
|Kerguelen Islands and Antarctic Peninsula||Tag pyrosequencing of 16S rRNA genes||Sampled at multiple time points over an annual cycle||Ghiglione & Murray (2012)||Kerguelen Plateau; Antarctic Peninsula|
|Australian sector of Southern Ocean||Metagenomics (454 shotgun pyrosequencing)||Sampled along a longitudinal transect including multiple oceanic provinces||Wilkins et al. (2012)||Australian Sector|
|Australian sector of Southern Ocean||Metaproteomics and metagenomics (454 shotgun pyrosequencing)||Samples mainly coastal and metaproteomics performed on Flavobacteria-enriched sample||Williams et al. (2012b)||Australian Sector|
|Global, including samples from the Southern Ocean and Antarctic coastal waters||Metagenomics (454 shotgun pyrosequencing)||Global study of SAR11 biogeography including the Southern Ocean||Brown et al. (2012)||Australian Sector; Wilkes Land Coast; Prydz Bay; Vestfold and Larsemann Hills; Ross Sea|
|Palmer Station, Antarctic Peninsula||Metaproteomics||Complementary to metagenomic study of Grzymski et al. (2012)||Williams et al. (2012a)||Antarctic Peninsula|
|Palmer Station, Antarctic Peninsula||Metagenomics (shotgun library)||Complementary to metaproteomic study of Williams et al. (2012a)||Grzymski et al. (2012)||Antarctic Peninsula|
Alphaproteobacteria: SAR11: highly abundant with distinct biogeography
The SAR11 clade of Alphaproteobacteria is probably the most abundant class of marine microorganism worldwide (Morris et al., 2002). Candidatus ‘Pelagibacter ubique’ strain HTCC1062, the first and most intensively studied SAR11 isolate, has one of the smallest genomes and gene complements of any known free-living cell, and has a very small cell volume (Giovannoni et al., 2005). The small cell volume, streamlined genome, and use of ATP-binding cassette (ABC) nutrient-uptake transporter genes are all consistent with an oligotrophic lifestyle, scavenging a wide range of substrates using high-affinity, broad-specificity transporters (Giovannoni et al., 2005; Lauro et al., 2009; Sowell et al., 2009). SAR11 cells probably preferentially utilize low over high molecular weight (HMW) dissolved organic matter (DOM) (Malmstrom et al., 2005), and their relative contribution to uptake of DOM may decrease as substrate concentration increases (Alonso & Pernthaler, 2006). A consequence of this oligotrophic strategy is that SAR11 members are probably unable to take advantage of sudden nutrient influxes, such as during phytoplankton blooms to rapidly increase cell density (Tripp et al., 2008).
SAR11 has been consistently detected at high abundances in molecular surveys of the Southern Ocean. The surveys include open ocean regions as well as at depth and in coastal waters, and SAR11 is usually the dominant alphaproteobacterial, if not bacterial, group (García-Martínez and Rodríguez-Valera, 2000; López-García et al., 2001; Murray & Grzymski, 2007; Giebel et al., 2009; Murray et al., 2010; Straza et al., 2010; Piquet et al., 2011; Ghiglione & Murray, 2012; Jamieson et al., 2012), and appears to be more abundant in the epipelagic zone than at depth (Giebel et al., 2009).
SAR11 exhibits biogeographic partitioning in the Southern Ocean and is represented by two major phylotypes with a temperature-driven boundary in the region of the Polar Front (Brown et al., 2012). The clade appears to be more abundant in the Subantarctic and polar frontal zones than in the Antarctic Zone (Giebel et al., 2009; Ghiglione & Murray, 2012; Wilkins et al., 2012). This may be related to a competitive advantage of the oligotrophic SAR11 in the high nutrient-low chlorophyll (HNLC) Subantarctic Zone relative to the Antarctic Zone, where blooming phytoplankton lead to increased concentrations of HMW DOM and particulate organic matter.
SAR11 was found to account for the largest fraction of leucine uptake among all bacterial groups in continental shelf waters off the West Antarctic Peninsula, but a comparatively small fraction of protein uptake, consistent with a role as a low molecular weight (LMW) DOM specialist (Straza et al., 2010). In a 16S rRNA gene survey on the Kerguelen Plateau (Subantarctic Zone), SAR11 was found to be a dominant group in HNLC waters outside a phytoplankton bloom but less abundant within the bloom (West et al., 2008). A separate study of the same bloom found SAR11 had a markedly smaller relative contribution to bulk leucine incorporation within the bloom, suggesting it was not a major contributor to DOM degradation (Obernosterer et al., 2011). Interestingly, SAR11 did dominate in abundance and leucine incorporation at an additional site where a transient phytoplankton bloom had taken place, implying that a time lag occurred during the succession between the baseline HNLC and bloom populations. It was also reported that the SAR11 abundances at the bloom station began to climb toward nonbloom levels once the bloom had peaked and begun to decline. Consistent with this, the relative abundance of SAR11 has been found to weakly inversely correlate with chlorophyll a fluorescence levels in Australian Antarctic waters (Williams et al., 2012b).
In a coastal Antarctic Peninsula metaproteome, the SAR11 component was dominated by ABC transport proteins for the capture and uptake of labile substrates, especially taurine, polyamines and amino acids, and also included dimethylsulfoniopropionate (DMSP) demethylase (Williams et al., 2012a). In another study, despite an apparently negative correlation between SAR11 and blooming phytoplankton, only small seasonal changes in abundance were reported during an annual cycle at the Antarctic Peninsula and Kerguelen Island (Ghiglione and Murray, 2012). All of these above studies of SAR11 are consistent with the interpretation that SAR11 is a nonopportunistic oligotroph specializing in LMW DOC.
An interesting physiological feature of SAR11 is the expression of the retinal-binding pigment proteorhodopsin, which has been shown to act as a proton pump when exposed to light (Béjà et al., 2000) and has been implicated in photoheterotrophy. Proteorhodopsin may also perform nonenergetic functions such as photoregulatory sensing (Fuhrman et al., 2008), and constitutive expression may facilitate the phototrophic ability to immediately respond to cellular energy deficits caused by carbon starvation (Steindler et al., 2011). These latter characteristics may explain the unanticipated finding that, despite very low light levels in Antarctic waters during austral winter, proteorhodopsin was detected in the metaproteome throughout the annual cycle (Williams et al., 2012a).
Alphaproteobacteria: Roseobacter clade: Antarctic phylotypes and a role in phytoplankton bloom turnover
The Roseobacter clade is an abundant and ecologically significant group of marine Alphaproteobacteria, found at high (> 15%) abundance in most marine surface environments (Buchan & Moran, 2005 and references therein). Unlike some other major proteobacterial groups which are strongly associated with a particular ecological niche (e.g. the SAR11 clade), the Roseobacter clade has diverse metabolic abilities, with members capable (for example) of aerobic anoxygenic phototrophy (Béjà et al., 2002; Biebl et al., 2005), degradation of DMSP by at least two pathways (Moran et al., 2003; Miller & Belas, 2004), carbon monoxide oxidation (King, 2003) and heterotrophic utilization of a broad range of organic substrates (reviewed in Brinkhoff et al., 2008). Members of the Roseobacter clade are found in the planktonic fraction as well as in commensal association with phytoplankton and metazoans (reviewed in Buchan & Moran, 2005). These characteristics are reflected in the broad diversity of genomic traits exhibited by related members of the Roseobacter clade (Lauro et al., 2009) and the significant differences in gene content present between the cultured and uncultured members of the clade (Luo et al., 2012).
Several 16S rRNA gene-based studies have identified the Roseobacter Clade Affiliated (RCA) subgroup as ubiquitous and abundant in Southern Ocean surface waters and to a depth of at least 2200 m. They composed ~ 10–30% of surface bacteria (and the majority of the Roseobacter clade) in the Subantarctic and Antarctic Zones (Selje et al., 2004; Murray & Grzymski, 2007; Giebel et al., 2009; Manganelli et al., 2009; Ghiglione & Murray, 2012; Wilkins et al., 2012) and were a major fraction of the population in coastal waters (Murray & Grzymski, 2007; Koh et al., 2011). Two major RCA phylotypes appear to be present in the Southern Ocean and form the majority of the Roseobacter population. The phylotypes are strictly segregated by the Polar Front, coexisting only within the Polar Frontal Zone (Selje et al., 2004; Giebel et al., 2009) where they may outnumber even the SAR11 clade. There is some evidence that the Antarctic Zone RCA phylotype originates from the North Atlantic. North Atlantic Deep Water is formed by the sinking of dense, saline waters in the surface north Atlantic, and is transported to the Southern Ocean via global thermohaline circulation to become Circumpolar Deep Water (Callahan, 1972). Consistent with the upwelling of Circumpolar Deep Water in the Antarctic Zone south of the Polar Front, a global study of specifically amplified RCA 16S rRNA gene fragments found that the surface phylotype south of the Polar Front was identical to that found in the Arctic Ocean, while differing by 3 bp from the phylotype north of the Polar Front (Selje et al., 2004).
Little is known about the functional capabilities of RCA as only two isolated representatives have been described. Candidatus ‘Planktomarina temperata’ was isolated from the North Sea, where it was the dominant phylotype (Giebel et al., 2010). The identification of the pufM gene encoding a bacteriochlorophyll a subunit suggests this member of the RCA is capable of performing aerobic anoxygenic photosynthesis, a function that is potentially ecologically important (Giebel et al., 2010). An apparently heterotrophic RCA member was isolated from subtropical waters (Mayali et al., 2008). This strain was found to colonize and increase mortality of blooming dinoflagellates, but its photosynthetic potential was not investigated (Mayali et al., 2008).
Members of the Roseobacter clade, and particularly the RCA, have been strongly associated with phytoplankton blooms in the Southern Ocean. Two separate 16S rRNA gene-based studies of a naturally fertilized bloom at the Kerguelen Islands (Obernosterer et al., 2011; West et al., 2008) found that RCA and the Roseobacter NAC11-7 and NAC11-6 clusters were dominant bacterial OTUs within the bloom, suggesting they play a role in heterotrophic degradation of bloom products. However, unlike the other clusters, RCA representatives were also relatively abundant and metabolically active outside of the bloom. In Southern Ocean vertical profiles RCA abundances have been found to peak at the deep chlorophyll maximum, again suggesting an association with phytoplankton (Giebel et al., 2009; Obernosterer et al., 2011).
RCA abundance may follow seasonal cycles in the Southern Ocean. In the coastal current and Weddell Sea, RCA phylotypes have been found to reach a maximum of ~ 8% of all bacterial 16S rRNA gene sequences during winter but up to 36% during autumn (Giebel et al., 2009). In coastal waters off the Antarctic Peninsula and around the Kerguelen Islands, the proportion of RCA peaked in January and February (summer) (Ghiglione & Murray, 2012).
A metagenomic study of Southern Ocean waters off West Antarctica found that Roseobacter clade 16S rRNA gene sequences were much more abundant in summer than in winter, with Sulfitobacter sequences the most abundant within this clade (Grzymski et al., 2012). This is consistent with the association of the Roseobacter clade with phytoplankton (Moran et al., 2007). Nevertheless, Roseobacter clade representatives in these polar waters appear to be metabolically active in both seasons. Metaproteomic analysis of coastal Antarctic Peninsula waters revealed an emphasis on high-affinity uptake systems such as ABC and tripartite ATP-independent periplasmic (TRAP) systems for capturing labile nutrients such as sugars, polyamines, amino acids, and oligopeptides (Williams et al., 2012a).
Betaproteobacteria: roles in ammonia oxidation and C1 turnover
The Betaproteobacteria are a large and cosmopolitan class with a range of ecological roles in the global ocean (reviewed in Kirchman, 2008). While not found at high abundance (Gentile et al., 2006; Ghiglione & Murray, 2012; Lo Giudice et al., 2012; Jamieson et al., 2012), there is evidence that Betaproteobacteria perform significant ecological functions. Most known ammonia-oxidizing bacteria belong to the Betaproteobacteria (Head et al., 1993; Teske et al., 1994). Nitrosospira-like 16S rRNA gene sequences were detected in Ross Sea and Antarctic Peninsula surface waters, and the ribotype appeared to be similar to one found in the Arctic (Hollibaugh et al., 2002). A metagenomic survey also detected OTUs for Nitrosomonas europaea, Nitrosomonas eutropha, and Nitrosospira multiformis strains in Southern Ocean surface waters (Wilkins et al., 2012). However, ammonia-oxidizing archaea outnumbered ammonia-oxidizing bacteria at most sites (Wilkins et al., 2012), consistent with the view that the former are the major nitrifiers in the marine environment (Wuchter et al., 2006). Metagenomic and metaproteomic analyses of surface coastal waters off the Antarctic Peninsula also showed evidence for ammonia-oxidizing Betaproteobacteria performing Calvin cycle carbon fixation and ammonia oxidation during winter (Grzymski et al., 2012; Williams et al., 2012a).
The OM43 clade of Betaproteobacteria is associated with coastal phytoplankton blooms (Morris et al., 2006) and appears to be an obligate methylotroph capable of utilizing methanol and formaldehyde as carbon and energy sources (Giovannoni et al., 2008). As it has one of the smallest reported genomes for a free-living cell, OM43 seems to be highly specialized for this unusual niche (Mira et al., 2001). OM43 has been detected in a 16S rRNA gene library in a bloom in the Subantarctic Zone, where it was the only betaproteobacterial representative (West et al., 2008), and in a metaproteomic survey of Antarctic Peninsula coastal waters where methanol dehydrogenase from OM43 was detected (Williams et al., 2012a). Although the source of methanol in the marine environment is not known, it may be a byproduct of phytoplankton growth (Heikes et al., 2002), which would be consistent with the association of OM43 with coastal blooms. The capacity for methylotrophic growth is also consistent with the identification of methyltransferases from oligotrophic marine Gammaproteobacteria (OMG) and methanogenic Archaea in an Antarctic coastal water sample taken during a phytoplankton bloom (Williams et al., 2012b). Alternative sources of methanol are atmospheric deposition (Sinha et al., 2007) or photochemical degradation of organic material (Dixon et al., 2011). The latter is of particular relevance for Antarctic waters, given the high levels of solar irradiation during the austral summer. These possibilities indicate that OM43, and perhaps other C1 specialists, may play important roles in the Southern Ocean microbial loop.
Gammaproteobacteria: GSO-EOSA-1: dark carbon fixation, even at the surface
The GSO-EOSA-1 complex of sulfur-oxidizing Gammaproteobacteria, which includes the uncultivated ARCTIC96BD-19 and SUP05 lineages and cultivated chemoautotrophic clam symbionts, has been reported in global mesopelagic waters (Swan et al., 2011) and oxygen minimum zones (Walsh et al., 2009; Canfield et al., 2010). The GSO-EOSA-1 complex appears to be affiliated with the Thiotrichales branch of the Gammaproteobacteria (Williams et al., 2010). Four studies have recently identified GSO-EOSA-1 representatives at high abundance in coastal and Antarctic Zone waters (Ghiglione and Murray, 2012; Grzymski et al., 2012; Williams et al., 2012a; Wilkins, et al., 2012). A metagenomic survey of coastal waters at Palmer station (Antarctic Peninsula) found winter bacterioplankton to be dominated by Gammaproteobacteria (~ 20% of the winter library compared to ~ 3% of the summer library), falling into five closely related taxa that were affiliated with the GSO-EOSA-1 complex (Grzymski et al., 2012). Metaproteomic analysis of the same sites confirmed the abundance and seasonal pattern, and indicated that GSO-EOSA-1 appeared to be metabolically active at the surface in both summer and winter. In a latitudinal study from Hobart, Australia, to the Mertz Glacier, OTUs for GSO-EOSA-1 were found to be more abundant in the Antarctic Zone than in the Subantarctic Zone (Wilkins et al., 2012).
Genomic and metagenomic analyses of GSO-EOSA-1 representatives, particularly SUP05, have revealed their potential for carbon fixation using the Calvin cycle and sulfur oxidation, even in well-oxygenated waters (Walsh et al., 2009; Swan et al., 2011; Grzymski et al., 2012). Based on the characteristics of taxa identified, it was estimated that 18–37% of the winter bacterioplankton community has the potential to perform chemolithoautotrophy, including GSO-EOSA-1, suggesting that winter chemolithoautotrophy may contribute significantly to Southern Ocean carbon fixation (Grzymski et al., 2012).
Gammaproteobacteria: OMG: contributors to phytoplankton bloom remineralization
The OMG are physiologically diverse heterotrophs that belong to previously detected clades (OM60, BD1-7, KI89A, OM182, SAR92) (Cho & Giovannoni, 2004). Cultured OMG isolates appear to be oligotrophic (Cho & Giovannoni, 2004), although SAR92, a member of the OMG group, has been observed in nutrient-rich waters with high phytoplankton abundances (Pinhassi et al., 2005; Stingl et al., 2007). In the Southern Ocean, OTUs for SAR92 were far more abundant inside a bloom in the Kerguelen Islands and plateau region than in Subantarctic Zone waters outside the bloom, with abundance also declining with bloom age (West et al., 2008; Obernosterer et al., 2011). This is consistent with the growth of SAR92 being carbon limited (Stingl et al., 2007) and suggests that the OMG group may play an important role in degradation of organic carbon produced by phytoplankton blooms in the Southern Ocean.
The OMG group has also been detected in coastal Antarctic Peninsula and Kerguelen Islands waters (Ghiglione & Murray, 2012), and metagenome and metaproteome analyses of coastal waters at Palmer station where OMG were found to be more abundant in summer than in winter (Grzymski et al., 2012; Williams et al., 2012a). TonB-dependent receptor systems matching the OMG group were highly abundant in the Palmer metaproteome, indicating that this is the preferred uptake system for ambient substrates (Williams et al., 2012a). Certain OMG strains encode proteorhodopsin (HTCC2207, Stingl et al., 2007; HTCC2143, Oh et al., 2010b), and matches to these proteins were also identified in the metaproteome of both the summer and winter samples (Williams et al., 2012a).
Other Gammaproteobacteria: contributors to DOM turnover
Ant4D3, an uncultured gammaproteobacterium, was identified in fosmids from nearshore waters at Palmer station (Grzymski et al., 2006) and has since been reported as one of the most abundant proteobacterial groups in the Southern Ocean (West et al., 2008; Murray et al., 2010; Straza et al., 2010; Ghiglione & Murray, 2012). In waters off the western Antarctic Peninsula, Ant4D3 represented 10% of the total and 50% of the gammaproteobacterial community, and 68% of cells incorporating amino acids (Straza et al., 2010). Based on rRNA gene sequence data, the clade appeared to have low diversity (Straza et al., 2010). Similar to SAR86, Ant4D3 cells were more active in HNLC Subantarctic waters than in bloom conditions on the Kerguelen Plateau (West et al., 2008). In contrast, ~ 17% of excised 16S-DGGE bands from summer Antarctic Peninsula waters matched Ant4D3, dominating the Gammaproteobacteria and outnumbering those from winter Antarctic Peninsula and from Kerguelen Island waters (Ghiglione & Murray, 2012). Ant4D3 sequences were also abundant in a 16S rRNA gene library from waters in the vicinity of Antarctic icebergs (Murray et al., 2010). Little is known about the function and ecological role of Ant4D3, although it has been detected in Antarctic waters associated with a phytoplankton bloom (Williams et al., 2012b), and Arctic waters where it appeared to occupy a DOM utilization niche different from that of other major heterotrophs such as SAR11 (Nikrad et al., 2012).
Various other gammaproteobacterial groups (e.g. Oceanospirillales, Alteromonadales) have been detected in Southern Ocean waters, including bacteria with best matches to Neptuniibacter caesariensis, Marinomonas spp., Marinobacter aquaeolei, Colwellia psychrerythraea, and Pseudoalteromonas haloplanktis (Murray & Grzymski, 2007; Grzymski et al., 2012; Wilkins et al., 2012; Williams et al., 2012a). These are motile chemoorganotrophs that target labile substrates such as simple sugars, amino acids, organic acids, or (in the case of M. aquaeolei) hydrocarbons (Médigue et al., 2005; Methé et al., 2005; Arahal et al., 2007; Espinosa et al., 2010; Singer et al., 2011). Some marine Oceanospirillales possess genes for both carbon fixation (Calvin cycle) and sulfur oxidation (Swan et al., 2011).
CFB: algal detritus degradation
The CFB group is cosmopolitan and abundant in the global ocean (Glöckner et al., 1999). The abundance of CFB may be underrepresented in 16S rRNA gene libraries and FISH analyses due to probe specificity biased against CFB 16S rRNA (Cottrell & Kirchman, 2000; Eilers et al., 2000; Kirchman, 2002), with better estimates being achievable from shotgun metagenomic surveys (O'Sullivan et al., 2004; Cottrell et al., 2005).
The CFB class Flavobacteria appear to be abundant in both freshwater and marine environments (O'Sullivan et al., 2004; Cottrell et al., 2005) including the Southern Ocean (Abell & Bowman, 2005a; Williams et al., 2012b). The Flavobacteria often form a major fraction of planktonic taxa (Fandino et al., 2001) and are particularly prevalent in particle-attached communities (DeLong et al., 1993) and in association with phytoplankton blooms (Pinhassi et al., 2004). Isolated representatives have a well-described capacity to degrade HMW DOM, particularly biopolymers which may be recalcitrant to utilization by other bacterial heterotrophs (reviewed in Kirchman, 2002), suggesting they play an important role in remineralization of primary production products.
Flavobacteria in the Southern Ocean are strongly biogeographically partitioned. From 16S-DGGE analysis, the abundance and diversity of particle-attached Flavobacteria were higher in the nutrient- and phytoplankton-rich waters south of the Polar Front compared to HNLC Subantarctic waters (Abell & Bowman, 2005a). A large-scale metagenomic analysis that identified the Polar Front as a major biogeographic boundary found that CFB contributed a large fraction of the variance between the zones north and south of the Polar Front and that CFB were more abundant south of the front (Wilkins et al., 2012). This difference in abundance may be largely attributable to the low iron availability in the Subantarctic, which probably limits primary production (Boyd et al., 2007). Both natural and artificial iron fertilization events in the Subantarctic have resulted in high abundances of bacterial heterotrophs (Oliver et al., 2004; Christaki et al., 2008), and Flavobacteria have been identified as a major component of the bacterial response to blooms induced by natural iron input on the Kerguelen Plateau (West et al., 2008).
The higher abundance of Flavobacteria in the Antarctic Zone may also relate to their prevalence in sea ice (Brown & Bowman, 2001; Brinkmeyer et al., 2003), from which they would be released into Antarctic Zone waters during seasonal melting. Two groups, the uncultured agg58 cluster and the genus Polaribacter, appear to dominate flavobacterial populations and activity in the Southern Ocean (Abell & Bowman, 2005a, b; Murray & Grzymski 2007; West et al., 2008; Straza et al., 2010; Ducklow et al., 2011; Obernosterer et al., 2011; Ghiglione & Murray 2012). Members of the Polaribacter genus are gas-vacuolated, proteorhodopsin-containing Flavobacteria that are prevalent in Antarctic and Arctic seawater. Genomic analysis of Polaribacter sp. MED152 indicates it is genetically geared to utilize polymers obtained from algal detritus rather than labile exudates (González et al., 2008). Metagenomic analysis of Antarctic Peninsula coastal waters found Polaribacter-related sequences to be dominant in summer, consistent with them being associated with phytoplankton blooms and/or being seeded from melting sea ice (Grzymski et al., 2012). Flavobacterial proteins (including those with the best matches to Polaribacter spp.) were similarly much more abundant in the summer vs. winter metaproteome from the same sites, with components of TonB-dependent receptor systems predominating (Williams et al., 2012a).
A comparative metagenomics study of coastal East Antarctica samples found that the relative abundance of Flavobacteria (dominated by Polaribacter) positively correlated with chlorophyll a fluorescence, and the relative abundance of SAR11 inversely correlated with fluorescence and Flavobacteria abundance (Williams et al., 2012b). A metaproteomic assessment of the sample with highest relative abundance of Flavobacteria concluded that the Flavobacteria synthesized proteins for actively binding and exploiting algal-derived polymeric substrates (carbohydrates, polypeptides, lipids), while Alphaproteobacteria (SAR11, Rhodobacterales, SAR116) and Gammaproteobacteria (Ant4D3, OMG, Oceanospirillales + Alteromonadales) synthesized high-affinity uptake systems to utilize simple byproducts (sugars, acetate, ammonia) released from the degradation of the algal polymers (Williams et al., 2012b).
There is some evidence that planktonic and particle-attached Flavobacteria may include specific phylotypes. In a mesocosm experiment using 16S-DGGE to examine colonization of diatom detritus in Southern Ocean seawater, a large proportion of flavobacterial phylotypes present in the planktonic phase were found not to colonize detrital particles (Abell & Bowman, 2005b). This suggested that these phylotypes may grow more slowly, perhaps comprising a secondary group of colonizers that dominate when the more accessible detrital nutrients have been exhausted and the primary colonizers have secreted useful secondary metabolites. Consistent with this hypothesis, the analysis of single-cell genome sequencing data indicates that the majority of uncultured marine Flavobacteria are adapted to specialized ecological niches, while also possessing the genomic capacity to attach to particles and degrade biopolymers (Woyke et al., 2009). It is likely that size fractionating these communities will help to physically separate planktonic from particle-attached cells, and metagenomic analyses of the separate fractions should help to define phylogenetic and functional differences within the Flavobacteria (Williams et al., 2012b); this approach has proven useful for Antarctic lake (e.g. Lauro et al., 2011) and Southern Ocean (e.g. Wilkins et al., 2012) communities.
Other bacteria: members of the community that may play important roles
The Verrucomicrobia is a recently described bacterial phylum that is ubiquitous in the marine environment and appears to be composed of several physiologically distinct lineages (Freitas et al., 2012). A small number of representatives of Verrucomicrobia have been detected in the Southern Ocean (Gentile et al., 2006; Murray & Grzymski, 2007; West et al., 2008; Murray et al., 2010). More recently, 16S rRNA gene analysis identified higher numbers of Verrucomicrobia at a Kerguelen Island site relative to a site near Palmer Station on the Antarctic Peninsula (Ghiglione & Murray, 2012). In contrast, a metagenomic survey identified a larger number of OTUs for the verrucomicrobium Coraliomargarita akajimensis in Antarctic Zone compared to Subantarctic Zone waters (Wilkins et al., 2012).
Bacteria of the phylum Planctomycetes have been detected at low abundance in molecular surveys of the Southern Ocean (López-García et al., 2001; Abell & Bowman, 2005a; Gentile et al., 2006; Murray et al., 2010; Jamieson et al., 2012). Planctomycetes is emerging as a group of interest in marine microbial ecology, because they perform anaerobic ammonia oxidation (anammox) (Strous et al., 1999), and metaproteomic analysis indicates they may be active in coastal Antarctic Peninsula waters (Williams et al., 2012a). The metaproteome study also detected Nitrospirae proteins involved in nitrite oxidation and carbon fixation via the reductive tricarboxylic acid cycle (Williams et al., 2012a). These metaproteome data support a role for members of the Nitrospirae and Planctomycetes in completing nitrification using nitrite generated by ammonia-oxidizing archaea and bacteria in Antarctic waters.
Other bacterial groups that have been reported at low abundance in the Southern Ocean include Actinobacteria (Brinkmeyer et al., 2003; Abell & Bowman, 2005a; Gentile et al., 2006; Murray & Grzymski, 2007; Murray et al., 2010; Bolhuis et al., 2011; Ghiglione & Murray, 2012; Jamieson et al., 2012), Epsilonproteobacteria (Gentile et al., 2006; Murray & Grzymski, 2007), and Firmicutes (Murray & Grzymski, 2007; Murray et al., 2010; Lo Giudice et al., 2012). Little is known about their respective ecological roles, although Actinobacteria are known to associate with marine aggregates (Grossart et al., 2004), and their terrestrial counterparts have diverse HMW substrate degradation capabilities (reviewed in Kirchman, 2008). A strong negative correlation has been reported between actinobacterial abundance and latitude in a global survey using 16S rRNA gene libraries (Pommier et al., 2007), with higher abundances in tropical and subtropical waters.
Archaea: high abundance and novel properties
Following the discoveries in 1992 of new clades of Archaea in the marine environment (DeLong, 1992; Fuhrman et al., 1992), in 1994, Archaea were discovered in Antarctic coastal surface waters at high abundance (up to 34%) (DeLong et al., 1994). These discoveries helped to establish that Archaea were ubiquitous members of the environment, and not just unusual extremophiles (Cavicchioli, 2011). The majority of rRNA gene sequences from Antarctic waters were affiliated with the Marine Group I Crenarchaeota (MGI; also called Thaumarchaeota), while the remainder represented Group II Euryarchaeota (DeLong et al., 1994). Subsequent rRNA gene analyses verified that MGI are the most abundant Archaea in surface waters of coastal Antarctica, followed by Group II Euryarchaeota (Gerlache Strait, Massana et al., 1998; near Anvers Island, Murray et al., 1998). Further studies have demonstrated the widespread distribution of Antarctic marine Archaea both longitudinally and north and south of the Polar Front (Topping et al., 2006; Kalanetra et al., 2009; Jamieson et al., 2012; Wilkins et al., 2012). Archaea including MGI have also been identified in benthic sediments on the Antarctic coast (Bowman & McCuaig, 2003; Bowman et al., 2003).
In the Southern Ocean, total archaeal rRNA gene levels were found to decrease during spring (Massana et al., 1998) and summer (Murray et al., 1998) and to negatively correlate with chlorophyll a concentration (Murray et al., 1998). Consistent with this, MGI abundance was found to increase by 44% during winter (Church et al., 2003). MGI are able to perform ammonia-oxidizing chemolithoautotrophy (Ingalls et al., 2006; Berg et al., 2007, 2010). Ammonia-oxidizing MGI have been shown to be especially sensitive to photoinhibition (Merbt et al., 2012), which might account for their decline during periods of extended illumination. It has also been speculated that the decline of Archaea during spring/summer represents competition with nonarchaeal microorganisms during phytoplankton blooms (Massana et al., 1998) or that the majority of MGI are chemoautotrophic and therefore more competitive compared to heterotrophs during carbon-scarce winter conditions (Murray et al., 1998).
Metaproteomic analysis of winter coastal Antarctic Peninsula samples revealed that MGI proteins (most with best matches to the ammonia-oxidizer Nitrosopumilus maritimus) represented 30% of all archaeal plus bacterial proteins, and no MGI proteins were detected in the summer metaproteome (Williams et al., 2012a). The winter metaproteome included MGI proteins involved in the 3-hydroxypropionate/4-hydroxybutyrate cycle, the pathway used by ammonia-oxidizing MGI for carbon fixation (Berg et al., 2007, 2010), and proteins for ammonium uptake and ammonia oxidation. Based on the metagenomic and metaproteomic analyses, it was proposed that chemolithoautotrophic ammonia oxidation was performed by MGI and sulfur oxidation by Gammaproteobacteria (see Gammaproteobacteria: GSO-EOSA-1: dark carbon fixation, even at the surface, above), suggesting that these communities were likely to be the major drivers of carbon fixation in Antarctic waters during winter (Grzymski et al., 2012; Williams et al., 2012a).
Marine Group II Euryarchaeota include motile, proteorhodopsin-containing photoheterotrophs that specialize in protein and lipid degradation (Frigaard et al., 2006; Iverson et al., 2012). Marine Group II Euryarchaeota have been found in higher abundance in surface waters than at depth (Massana et al., 1998), and in waters off Anvers Island, numbers increased in autumn (Murray et al., 1998). However, there are little molecular data for Marine Group II Euryarchaeota, particularly seasonal data, and their importance in Southern Ocean ecosystem function is not clear.
It is noteworthy that primer design can greatly impact on the ability to effectively evaluate the abundance of any taxa, and this has particularly impacted on the detection and enumeration of Archaea. A striking example relates to the discovery of the marine hydrothermal Nanoarchaeum equitans, which was unable to be detected using archaeal probes (Huber et al., 2002), but when primers were designed from the 16S rRNA gene sequence present in the genome sequence, Nanoarchaeum species were identified in many environments around the globe (Casanueva et al., 2008). In the Southern Ocean, a summer transect between the Polar Front and the ice edge failed to identify DAPI-positive archaeal cells when Archaea-specific probes ARCH334 and ARCH915 were used (Simon et al., 1999). A similar outcome for samples from 3000 m depth at the Polar Front in the Drake Passage prompted the redesign of primers leading to the discovery of both a higher number and greater diversity of Archaea in the samples (López-García et al., 2001). While shotgun metagenomic avoids this problem, the issue is relevant for the design of primers employed for pyrotag sequencing, a cost-effective means of baselining community composition. This is particularly the case for the design of universal primers suitable for detecting Archaea, Bacteria, and Eucarya. This issue is well illustrated by the analysis of an Antarctic lake community where archaeal representation increased by many fold when standard universal primers were redesigned to better represent Archaea (R. Cavicchioli et al., unpublished results).
Virioplankton: crucial influence and much to be learned
The ‘viral shunt’, by which nutrients are released via lysis from marine microorganisms and returned to the dissolved and particulate pools, may mediate the flux of a quarter of all organic matter in the microbial loop (Wilhelm & Suttle, 1999), and the viral release of iron from bacterioplankton may be crucial for phytoplankton growth (Poorvin et al., 2004). Viral production, and by inference the viral shunt, has been shown to be highly active in HNLC Subantarctic (Evans et al., 2009), iron-fertilized Subantarctic (Weinbauer et al., 2009), and coastal waters, where virus-mediated carbon flux may account for 50–100% of all heterotrophic production (Guixa-Boixereu et al., 2002). Despite this crucial ecosystem role, molecular analysis of the diversity and function of Southern Ocean virioplankton is sparse.
Using probes for marker genes, both algal viruses and cyanophage have been detected in Southern Ocean waters (Short & Suttle, 2002, 2005). Cyanophage genes and proteins, and a major capsid protein from Phaeocystis pouchetii virus PpV01, were identified in coastal Antarctic Peninsula waters by metagenomic and metaproteomic analyses (Grzymski et al., 2012; Williams et al., 2012a). In a latitudinal study, OTUs for Ostreococcus viruses were found to be more abundant in Antarctic compared to Subantarctic Zone waters, and cyanophage were detected in all Southern Ocean samples examined (D. Wilkins et al., unpublished results). While preliminary, these studies suggest that the more abundant viruses in the Southern Ocean are predators of phytoplankton.
Antarctic sea ice communities: unique interactions between Bacteria, Archaea, Eucarya, and viruses
Sea ice is one of the largest and most climatically sensitive geophysical parameter on the planet. In the Antarctic and Southern Ocean region, sea ice ranges in extent from 3 × 106 km2 in summer to 18 × 106 km2 in winter (Parkinson, 2004). As resource availability in the Southern Ocean is strongly seasonal and related to the cycle of sea ice, the life history traits of the dominant macrofauna, including marine mammals, penguins, and various other seabirds, as well as benthic communities (Wing et al., 2012), are tightly synchronized with the presence of sea ice. Predicted changes in sea ice extent threaten to unravel the current synchronicity and may impact all levels of the food web. Several recent studies have already identified declines in polar species related to zones of decreasing sea ice extent (Anisimov et al., 2007; Schofield et al., 2010; Trathan et al., 2011).
The sea ice environment can be highly productive, despite being cold (0 to −35 °C) and highly saline (up to seven times seawater salinity). As an ecosystem, sea ice is characterized by a continuum of temperature, salinity, pH, light, and nutrient gradients, which arise due to the physical and chemical processes of ice formation, and it varies both spatially and temporally (Eicken, 2003; Mock & Thomas, 2005). Conditions are generally harshest at the ice surface where in situ temperatures are governed by air temperature (including wind regimes) and the extent of insulating snow cover. At the ice water interface, temperatures are stable at −2 °C buffered by the seawater, nutrient supply is constantly replenished through wave action, and UV radiation and photosynthetic light intensities are lower. This interface is the site of highest biological productivity. Exclusion of salt crystals during the freezing of seawater results in the formation of highly saline ‘brine’ channels within the ice matrix, and it is these channels that provide the habitat for organisms residing within the sea ice structure.
The first application of molecular biology methods to the sea ice microbial community (SIMCO) was the use of 16S rRNA gene sequencing to taxonomically characterize culture collections. This identified many novel stenopsychrophiles, including members of the Gammaproteobacteria genera Colwellia, Shewanella, Marinobacter, and Glaciecola (Bowman et al., 1998a), the Firmicutes genus Planococcus, and the CFB genera Psychroserpens (Bowman et al., 1997b), Gelidibacter (Bowman et al., 1997b), and Psychroflexus (Bowman et al., 1998b) (Fig. 1). Eurypsychrophiles isolated from sea ice include the Gammaproteobacteria genera Pseudoalteromonas, Psychrobacter (Bowman et al., 1997c), Halomonas, and Pseudomonas, the Alphaproteobacteria genera Hyphomonas and Sphingomonas (related to the Roseobacter clade), the Actinobacteria genus Arthrobacter, and the Firmicutes genera Planococcus and Halobacillus (Bowman et al., 1997a).
The use of cultivation-independent (16S rRNA gene sequencing of DNA extracted from sea ice) and cultivation-dependent methods led to the discovery that the majority of sea ice organisms are active (Brinkmeyer et al., 2003) and the dominant organisms are culturable. These features distinguish SIMCOs from other pelagic marine microbial communities where generally between 0.1% and 15% of organisms (Donachie et al., 2007) are readily cultivatable (Amann et al., 1995).
The main organisms identified from culture-independent surveys in both Antarctic and Arctic sea ice are members of the Alpha- and Gammaproteobacteria, CFB, Actinobacteria, Chlamydiales, and Verrucomicrobiales (Brown & Bowman, 2001; Brinkmeyer et al., 2003; Murray & Grzymski, 2007). Microbial communities are phylogenetically similar in sea ice in the southern and northern polar regions, highlighting that strong and common selection mechanisms take place during the development of SIMCOs (Brown & Bowman, 2001; Brinkmeyer et al., 2003).
Bacteria in SIMCOs are taxonomically and physiologically different to the community inhabiting the water column from which ice is formed. However, this is not the case for Archaea. In contrast to sea water where Archaea may be abundant (see 'Archaea: high abundance and novel properties' above), in sea ice, Archaea are either below detection (Brown & Bowman, 2001; Brinkmeyer et al., 2003; Murray & Grzymski, 2007) or comprise a very low abundance (Junge et al., 2004; Collins et al., 2010; Cowie et al., 2011). The most abundant archaeal taxa in sea ice are MGI that are similar to seawater members (Cowie et al., 2011), and the relatively low abundance, diverse members of the Euryarchaeota are also closely related to pelagic members. Similar to Bacteria, Archaea from the Antarctic are phylogenetically similar to those from the Arctic (Collins et al., 2010; Cowie et al., 2011).
Proteorhodopsin-containing bacteria have been isolated from Antarctic sea ice (e.g. Psychroflexus torquis, Bowman et al., 1998b), and the presence and in situ activity of photoresponsive genes for bacterial chlorophyll A (pufM) and proteorhodopsin have been confirmed (Koh et al., 2010, 2011), suggesting that the strong seasonal light regimes may play a direct role in structuring sea ice bacterial communities. However, the major phototrophs in sea ice are Eucarya.
The sea ice eucaryal community has generally been examined using traditional microscopy techniques and is composed of a diverse range of phototrophic, heterotrophic, and mixotrophic organisms including Stramenopiles (mainly diatoms), Alveolates, and metazoans that are incorporated into the ice matrix by physical scavenging of cells during ice formation (Garrison et al., 1983). Once incorporated, the community undergoes maturation based on the different physical and chemical properties it experiences in the sea ice. Hence, depending on factors such as position in the ice column, snow cover, light intensity, and nutrient supply, there is a large spatial heterogeneity, and habitat-specific communities develop (Gast et al., 2004).
Seasonal changes in physical and chemical properties also play a large role in shaping the sea ice eucaryal community, and community composition can vary significantly. For example, postwinter/early spring communities have been observed to comprise dinoflagellates, ciliates, cercozoans, Stramenopiles, Viridiplantae, haptophytes, and metazoans, or a dinoflagellate-dominated community, or a diatom-dominated community that developed after sea ice breakup (Piquet et al., 2008). Furthermore, at the end of winter, phototrophs may be essentially absent from sea ice, having been removed by extensive over-winter grazing (Bachy et al., 2011), although spatial heterogeneity can result in significantly different postwinter communities (Kramer et al., 2011). Evidence from Arctic sea ice suggests that communities inhabiting the ice/water interface are more similar to seawater communities than those entrained higher in the ice matrix, isolated from seawater intrusions (Bachy et al., 2011). These ice–water interface communities, generally dominated by phototrophic pennate diatoms, are the focus of numerical models aimed at estimating sea ice contributions to climate active compounds such as dimethyl sulfide (Elliot et al., 2012).
Although there are sea ice Eucarya such as Fragilariopsis cylindrus, which reside in the south and north polar regions (Lundholme & Hasle, 2008), the true nature of species bipolarity is unclear (Poulin et al., 2010) as there is a lack of molecular data with sufficient resolution to establish biogeography and sea ice vs. sea water speciation differences (Gast et al., 2004, 2006). The lack of taxonomic marker data for morphologically well-defined cultured Eucarya (e.g. Skvovgaard et al., 2005) also hinders assessment of claims of highly novel diversity in marine eucaryal microorganisms (e.g. López-García et al., 2001; Moon-van-de Staay et al., 2001; Gast et al., 2004).
Sea ice microorganisms produce compounds that interact with the ice matrix to enhance its habitability (Krembs et al., 2011). Algae and bacteria produce extracellular polymeric substances (Mock & Thomas, 2005) that can display antifreeze activity that inhibits ice recrystallization and increases salt retention in the sea ice matrix (Raymond, 2011). Salt retention translates to greater retention of other source water impurities including iron and nutrients critical for photosynthetic activity (Krembs et al., 2011). Genomic and transcriptomic analyses of the sea ice diatoms F. cylindrus (Krell et al., 2008; Bayer-Giraldi et al., 2010) and Chaetoceros neogracile (Gwak et al., 2010) have revealed the importance of novel antifreeze proteins in responding to cold stress. Genes encoding antifreeze proteins appear to have undergone horizontal gene transfer into the dominant metazoan calanoid copepod in Antarctic sea ice, Stephos longipes (Kiko, 2010). The proteins have high identity to a group of (putative) antifreeze proteins from diatoms, bacteria, and a snow mold, in contrast to a lack of homologs in any known metazoan lineage.
Viruses are present and may be highly abundant in sea ice, although the factors driving their distributions are not clear. Viral abundances have been observed ranging from 105 to 109 in Antarctic sea ice (Gowing et al., 2004; Patterson & Laybourn-Parry, 2012) and are greater than in the underlying seawater, suggesting active entrainment during ice formation or in situ production (Collins & Demming, 2011). When observed over a complete sea ice cycle, virus-to-bacterium ratios showed a clear seasonal pattern in Antarctica, with lowest values in winter (range 1.2–20.8) (Patterson & Laybourn-Parry, 2012). Temperature and salinity fluctuations within the brine channel system, the high abundance of viruses, and the predicted increased frequency of interactions between bacteria and viruses compared to seawater indicate that sea ice provides ‘natural transformation’ conditions and is a potential ‘hot spot’ for horizontal gene transfer (Kiko, 2010; Collins & Demming, 2011). Such conditions may also have promoted the transfer of antifreeze genes into copepods.
Antarctic microorganisms: a brief Southern Ocean perspective
The picoplankton in the surface waters of the Southern Ocean that encircle the Antarctic continent are dominated by Alphaproteobacteria, Gammaproteobacteria, Flavobacteria, and MGI. The Alphaproteobacteria consist mainly of the SAR11 and Roseobacter clades, with a metabolic preference for labile substrates, including those released by phytoplankton. Flavobacteria have metabolic preferences focused on more complex organic matter, although the relative roles of free-living vs. attached Flavobacteria in processing algal-derived organic matter are still poorly understood. Collectively, the Gammaproteobacteria have diverse metabolic capabilities, with members of the GSO-EOSA-1 complex serving as potentially important contributors to carbon fixation. The ammonia-oxidizing MGI associate with the prolonged periods of minimal light exposure during the long polar winter and are inferred to be major contributors to carbon fixation during this season. In summer, the high light availability and intensity drive algal oxygenic photoautotrophic carbon assimilation, a process that appears to be greatly influenced by viral activity. Sea ice contributes importantly to phytoplankton growth and provides a dynamic environment for a range of typically culturable bacteria.
While many taxa present in the Southern Ocean are found in temperate or tropical waters, the accumulation of metagenome data is beginning to resolve differences in phylotypes, such as those defined for the SAR11 clade (Brown et al., 2012). Large-scale metagenomics is also defining community-wide differences defined by major water body features, such as the Polar Front (Wilkins et al., 2012), and combined metagenome/metaproteome analyses are discovering how specific events (e.g. phytoplankton blooms and seasonal changes) affect both community composition and function (Grzymski et al., 2012; Williams et al., 2012a,b). In view of the continuing improvements in cost effectiveness offered by DNA sequencing technologies, there is a bright outlook for the application of pyrotag-sequencing diversity surveys, shotgun metagenomics of size-fractionated samples, and single-cell genomics of important individuals (Stepanauskas, 2012). In association with the application of functional omics approaches (metaproteomics, metatranscriptomics, stable isotope probing), the next 10 years should see major advances being made about the microbial communities and their responses to ecosystem perturbation from an expanded range of Southern Ocean locations and conditions; the targets of these studies should include an examination of seasonal influences and communities present in distinct water bodies, currents, fronts, and in specific oceanic regions and features (e.g. surface vs. depth, distinct photic zones such as the deep chlorophyll maximum, coastal vs. island/plateau vs. pelagic, phytoplankton blooms, sea ice, polynyas, and in the vicinity of glaciers and icebergs).