Latitudinal trends of Crenarchaeota and Bacteria in the meso- and bathypelagic water masses of the Eastern North Atlantic

The distribution and activity of the bulk picoplankton community and, using microautoradiography combined with catalysed reported deposition fluorescence in situ hybridization (MICRO-CARD-FISH), of the major prokaryotic groups (Bacteria, marine Crenarchaeota Group I and marine Euryarchaeota Group II) were determined in the water masses of the subtropical North Atlantic. The bacterial contribution to total picoplankton abundance was fairly constant, comprising approximately 50% of DAPI-stainable cells. Marine Euryarchaeota Group II accounted always for < 5% of DAPI-stainable cells. The percentage of total picoplankton identified as marine Crenarchaeota Group I was approximately 5% in subsurface waters (100 m depth) and between 10% and 20% in the oxygen minimum layer (250-500 m) and deep waters [North East Atlantic Deep Water (NEADW) and Lower Deep Water (LDW), 2750-4800 m depth]. Single-cell activity, determined via a quantitative MICRO-CARD-FISH approach and taking only substrate-positive cells into account, ranged from 0.05 to 0.5 amol D-aspartic acid (Asp) cell(-1) day(-1) and 0.1-2 amol L-Asp cell(-1) day(-1), slightly decreasing with depth. In contrast, the D-Asp:L-Asp cell-specific uptake ratio increased with depth. By combining data reported previously using the same method as applied here and data reported here, we found a decreasing relative abundance of marine Crenarchaeota Group I throughout the meso- and bathypelagic water column from 65 degrees N to 5 degrees N in the eastern basin of the North Atlantic. Thus, the relative contribution of marine Crenarchaeota Group I to deep-water prokaryotic communities might be more variable than previous studies have suggested. This apparent variability in the contribution of marine Crenarchaeota Group I to total picoplankton abundance might be related to successions and ageing of deep-water masses in the large-scale meridional ocean circulation and possibly, the appearance of crenarchaeotal clusters other than the marine Crenarchaeota Group I in the (sub)tropical North Atlantic.     

Latitudinal distribution of prokaryotic picoplankton populations in the Atlantic Ocean

Members of the prokaryotic picoplankton are the main drivers of the biogeochemical cycles over large areas of the world's oceans. In order to ascertain changes in picoplankton composition in the euphotic and twilight zones at an ocean basin scale we determined the distribution of 11 marine bacterial and archaeal phyla in three different water layers along a transect across the Atlantic Ocean from South Africa (32.9°S) to the UK (46.4°N) during boreal spring. Depth profiles down to 500 m at 65 stations were analysed by catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) and automated epifluorescence microscopy. There was no obvious overall difference in microbial community composition between the surface water layer and the deep chlorophyll maximum (DCM) layer. There were, however, significant differences between the two photic water layers and the mesopelagic zone. SAR11 (35 ± 9%) and Prochlorococcus (12 ± 8%) together dominated the surface waters, whereas SAR11 and Crenarchaeota of the marine group I formed equal proportions of the picoplankton community below the DCM (both ～15%). However, due to their small cell sizes Crenarchaeota contributed distinctly less to total microbial biomass than SAR11 in this mesopelagic water layer. Bacteria from the uncultured Chloroflexi‐related clade SAR202 occurred preferentially below the DCM (4–6%). Distinct latitudinal distribution patterns were found both in the photic zone and in the mesopelagic waters: in the photic zone, SAR11 was more abundant in the Northern Atlantic Ocean (up to 45%) than in the Southern Atlantic gyre (～25%), the biomass of Prochlorococcus peaked in the tropical Atlantic Ocean, and Bacteroidetes and Gammaproteobacteria bloomed in the nutrient‐rich northern temperate waters and in the Benguela upwelling. In mesopelagic waters, higher proportions of SAR202 were present in both central gyre regions, whereas Crenarchaeota were clearly more abundant in the upwelling regions and in higher latitudes. Other phylogenetic groups such as the Planctomycetes, marine group II Euryarchaeota and the uncultured clades SAR406, SAR324 and SAR86 rarely exceeded more than 5% of relative abundance.     

Viral abundance, decay, and diversity in the meso- and bathypelagic waters of the north atlantic

To elucidate the potential importance of deep-water viruses in controlling the meso- and bathypelagic picoplankton community, the abundance, decay rate, and diversity of the virioplankton community were determined in the meso- and bathypelagic water masses of the eastern part of the subtropical North Atlantic. Viral abundance averaged 1.4 x 10(6) ml(-1) at around 100 m of depth and decreased only by a factor of 2 at 3,000 to 4,000 m of depth. In contrast, picoplankton abundance decreased by 1 order of magnitude to the Lower Deep Water (LDW; 3,500- to 5,000-m depth). The virus-to-picoplankton ratio increased from 9 at about 100 m of depth to 110 in the LDW. Mean viral decay rates were 3.5 x 10(-3) h(-1) between 900 m and 2,750 m and 1.1 x 10(-3) h(-1) at 4,000 m of depth, corresponding to viral turnover times of 11 and 39 days, respectively. Pulsed-field gel electrophoresis fingerprints obtained from the viral community between 2,400 m and 4,000 m of depth revealed a maximum of only four bands from 4,000 m of depth. Based on the high viral abundance and the low picoplankton production determined via leucine incorporation, we conclude that the viral production calculated from the viral decay is insufficient to maintain the high viral abundance in the deep North Atlantic. Rather, we propose that substantial allochthonous viral input or lysogenic or pseudolysogenic production is required to maintain the high viral abundance detected in the meso- and bathypelagic North Atlantic. Consequently, deep-water prokaryotes are apparently far less controlled in their abundance and taxon richness by lytic prokaryotic phages than the high viral abundance and the virus-to-picoplankton ratio would suggest.     

Viral Abundance, Decay, and Diversity in the Meso- and Bathypelagic Waters of the North Atlantic

To elucidate the potential importance of deep-water viruses in controlling the meso- and bathypelagic picoplankton community, the abundance, decay rate, and diversity of the virioplankton community were determined in the meso- and bathypelagic water masses of the eastern part of the subtropical North Atlantic. Viral abundance averaged 1.4 × 10⁶ ml⁻¹ at around 100 m of depth and decreased only by a factor of 2 at 3,000 to 4,000 m of depth. In contrast, picoplankton abundance decreased by 1 order of magnitude to the Lower Deep Water (LDW; 3,500- to 5,000-m depth). The virus-to-picoplankton ratio increased from 9 at about 100 m of depth to 110 in the LDW. Mean viral decay rates were 3.5 × 10⁻³ h⁻¹ between 900 m and 2,750 m and 1.1 × 10⁻³ h⁻¹ at 4,000 m of depth, corresponding to viral turnover times of 11 and 39 days, respectively. Pulsed-field gel electrophoresis fingerprints obtained from the viral community between 2,400 m and 4,000 m of depth revealed a maximum of only four bands from 4,000 m of depth. Based on the high viral abundance and the low picoplankton production determined via leucine incorporation, we conclude that the viral production calculated from the viral decay is insufficient to maintain the high viral abundance in the deep North Atlantic. Rather, we propose that substantial allochthonous viral input or lysogenic or pseudolysogenic production is required to maintain the high viral abundance detected in the meso- and bathypelagic North Atlantic. Consequently, deep-water prokaryotes are apparently far less controlled in their abundance and taxon richness by lytic prokaryotic phages than the high viral abundance and the virus-to-picoplankton ratio would suggest.     

Water mass-specificity of bacterial communities in the North Atlantic revealed by massively parallel sequencing

Bacterial assemblages from subsurface (100 m depth), meso- (200-1000 m depth) and bathy-pelagic (below 1000 m depth) zones at 10 stations along a North Atlantic Ocean transect from 60°N to 5°S were characterized using massively parallel pyrotag sequencing of the V6 region of the 16S rRNA gene (V6 pyrotags). In a dataset of more than 830,000 pyrotags, we identified 10,780 OTUs of which 52% were singletons. The singletons accounted for less than 2% of the OTU abundance, whereas the 100 and 1000 most abundant OTUs represented 80% and 96% respectively of all recovered OTUs. Non-metric Multi-Dimensional Scaling and Canonical Correspondence Analysis of all the OTUs excluding the singletons revealed a clear clustering of the bacterial communities according to the water masses. More than 80% of the 1000 most abundant OTUs corresponded to Proteobacteria of which 55% were Alphaproteobacteria, mostly composed of the SAR11 cluster. Gammaproteobacteria increased with depth and included a relatively large number of OTUs belonging to Alteromonadales and Oceanospirillales. The bathypelagic zone showed higher taxonomic evenness than the overlying waters, albeit bacterial diversity was remarkably variable. Both abundant and low-abundance OTUs were responsible for the distinct bacterial communities characterizing the major deep-water masses. Taken together, our results reveal that deep-water masses act as bio-oceanographic islands for bacterioplankton leading to water mass-specific bacterial communities in the deep waters of the Atlantic.     

Contribution of Archaea to total prokaryotic production in the deep Atlantic Ocean

Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.     

Distribution of marine viruses and their potential hosts in Prydz Bay and adjacent Southern Ocean,Antarctic

Viruses play a key role in all marine ecosystems, and yet little is known of their distribution in Antarctic waters, especially in bathypelagic waters (>1000 m). In this study, the abundance and distribution of viruses and their potential hosts from the surface to the bottom of Prydz Bay, Antarctic, was investigated using flow cytometry. Viruses and autotrophs were abundant in nearshore and continental shelf waters, while heterotrophic bacteria and picoeukaryotes were abundant in offshore waters. Virus and bacteria abundances generally decreased with increasing depth but increased slightly just above the seafloor. Within the water column, maximum virus numbers coincided with the maximum values of chlorophyll a (when greater than 0.1 μg l^?1), in the surface and subsurface (25 m). In the open ocean, however, virus abundance usually correlated with bacterial abundance at greater depths (50, 300 and 500 m) where the surface chlorophyll a concentration was lower than 0.1 μg l^?1. Viral abundance was correlated with the host cell abundance, and this was different in different pelagic zones (bacteria and autotrophs (i.e., chlorophyll a concentration) in the epipelagic waters, picoeukaryotes and bacteria in mesopelagic waters and bacteria in bathypelagic waters). Principle component analysis and Pearson correlation analysis indicated that there was a close relationship between virus abundance and chlorophyll a, bacteria and nutrients (NO₂ + NO₃, phosphate and silicate), and picoeukaryote abundance was mainly correlated with water depth and salinity.     

Community differentiation and population enrichment of Sargasso Sea bacterioplankton in the euphotic zone of a mesoscale mode‐water eddy

Eddies are mesoscale oceanographic features (～ 200 km diameter) that can cause transient blooms of phytoplankton by shifting density isoclines in relation to light and nutrient resources. To better understand how bacterioplankton respond to eddies, we examined depth‐resolved distributions of bacterial populations across an anticyclonic mode‐water eddy in the Sargasso Sea. Previous work on this eddy has documented elevated phytoplankton productivity and diatom abundance within the eddy centre with coincident bacterial productivity and biomass maxima. We illustrate bacterial community shifts within the eddy centre, differentiating populations uplifted along isopycnals from those enriched or depleted at horizons of enhanced bacterial and primary productivity. Phylotypes belonging to the Roseobacter, OCS116 and marine Actinobacteria clades were enriched in the eddy core and were highly correlated with pigment‐based indicators of diatom abundance, supporting developing hypotheses that members of these clades associate with phytoplankton blooms. Typical mesopelagic clades (SAR202, SAR324, SAR406 and SAR11 IIb) were uplifted within the eddy centre, increasing bacterial diversity in the lower euphotic zone. Typical surface oligotrophic clades (SAR116, OM75, Prochlorococcus and SAR11 Ia) were relatively depleted in the eddy centre. The biogeochemical context of a bloom‐inducing eddy provides insight into the ecology of the diverse uncultured bacterioplankton dominating the oligotrophic oceans.     

Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical northeast atlantic ocean

We analyzed the regional distribution of bulk heterotrophic prokaryotic activity (leucine incorporation) and selected single-cell parameters (cell viability and nucleic acid content) as parameters for microbial functioning, as well as bacterial and archaeal community structure in the epipelagic (0 to 200 m) and mesopelagic (200 to 1,000 m) subtropical Northeast Atlantic Ocean. We selectively sampled three contrasting regions covering a wide range of surface productivity and oceanographic properties within the same basin: (i) the eddy field south of the Canary Islands, (ii) the open-ocean NE Atlantic Subtropical Gyre, and (iii) the upwelling filament off Cape Blanc. In the epipelagic waters, a high regional variation in hydrographic parameters and bacterial community structure was detected, accompanied, however, by a low variability in microbial functioning. In contrast, mesopelagic microbial functioning was highly variable between the studied regions despite the homogeneous abiotic conditions found therein. More microbial functioning parameters indicated differences among the three regions within the mesopelagic (i.e., viability of cells, nucleic acid content, cell-specific heterotrophic activity, nanoflagellate abundance, prokaryote-to-nanoflagellate abundance ratio) than within the epipelagic (i.e., bulk activity, nucleic acid content, and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the Northeast Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations.     

Contribution of Archaea to Total Prokaryotic Production in the Deep Atlantic Ocean

Fluorescence in situ hybridization (FISH) in combination with polynucleotide probes revealed that the two major groups of planktonic Archaea (Crenarchaeota and Euryarchaeota) exhibit a different distribution pattern in the water column of the Pacific subtropical gyre and in the Antarctic Circumpolar Current system. While Euryarchaeota were found to be more dominant in nearsurface waters, Crenarchaeota were relatively more abundant in the mesopelagic and bathypelagic waters. We determined the abundance of archaea in the mesopelagic and bathypelagic North Atlantic along a south-north transect of more than 4,000 km. Using an improved catalyzed reporter deposition-FISH (CARD-FISH) method and specific oligonucleotide probes, we found that archaea were consistently more abundant than bacteria below a 100-m depth. Combining microautoradiography with CARD-FISH revealed a high fraction of metabolically active cells in the deep ocean. Even at a 3,000-m depth, about 16% of the bacteria were taking up leucine. The percentage of Euryarchaeota and Crenarchaeaota taking up leucine did not follow a specific trend, with depths ranging from 6 to 35% and 3 to 18%, respectively. The fraction of Crenarchaeota taking up inorganic carbon increased with depth, while Euryarchaeota taking up inorganic carbon decreased from 200 m to 3,000 m in depth. The ability of archaea to take up inorganic carbon was used as a proxy to estimate archaeal cell production and to compare this archaeal production with total prokaryotic production measured via leucine incorporation. We estimate that archaeal production in the mesopelagic and bathypelagic North Atlantic contributes between 13 to 27% to the total prokaryotic production in the oxygen minimum layer and 41 to 84% in the Labrador Sea Water, declining to 10 to 20% in the North Atlantic Deep Water. Thus, planktonic archaea are actively growing in the dark ocean although at lower growth rates than bacteria and might play a significant role in the oceanic carbon cycle.     

Microbes mediating the sulfur cycle in the Atlantic Ocean and their link to chemolithoautotrophy

Only about 10%–30% of the organic matter produced in the epipelagic layers reaches the dark ocean. Under these limiting conditions, reduced inorganic substrates might be used as an energy source to fuel prokaryotic chemoautotrophic and/or mixotrophic activity. The aprA gene encodes the alpha subunit of the adenosine-5′-phosphosulfate (APS) reductase, present in sulfate-reducing (SRP) and sulfur-oxidizing prokaryotes (SOP). The sulfur-oxidizing pathway can be coupled to inorganic carbon fixation via the Calvin–Benson–Bassham cycle. The abundances of aprA and cbbM, encoding RuBisCO form II (the key CO₂ fixing enzyme), were determined over the entire water column along a latitudinal transect in the Atlantic from 64°N to 50°S covering six oceanic provinces. The abundance of aprA and cbbM genes significantly increased with depth reaching the highest abundances in meso- and upper bathypelagic layers. The contribution of cells containing these genes also increased from mesotrophic towards oligotrophic provinces, suggesting that under nutrient limiting conditions alternative energy sources are advantageous. However, the aprA/cbbM ratios indicated that only a fraction of the SOP is associated with inorganic carbon fixation. The aprA harbouring prokaryotic community was dominated by Pelagibacterales in surface and mesopelagic waters, while Candidatus Thioglobus, Chromatiales and the Deltaproteobacterium_SCGC dominated the bathypelagic realm. Noticeably, the contribution of the SRP to the prokaryotic community harbouring aprA gene was low, suggesting a major utilization of inorganic sulfur compounds either as an energy source (occasionally coupled with inorganic carbon fixation) or in biosynthesis pathways.     

Protist Community Grazing on Prokaryotic Prey in Deep Ocean Water Masses

Oceanic protist grazing at mesopelagic and bathypelagic depths, and their subsequent effects on trophic links between eukaryotes and prokaryotes, are not well constrained. Recent studies show evidence of higher than expected grazing activity by protists down to mesopelagic depths. This study provides the first exploration of protist grazing in the bathypelagic North Atlantic Deep Water (NADW). Grazing was measured throughout the water column at three stations in the South Atlantic using fluorescently-labeled prey analogues. Grazing in the deep Antarctic Intermediate water (AAIW) and NADW at all three stations removed 3.79% ± 1.72% to 31.14% ± 8.24% of the standing prokaryote stock. These results imply that protist grazing may be a significant source of labile organic carbon at certain meso- and bathypelagic depths.     

Bacterial Diversity in the South Adriatic Sea during a Strong,Deep Winter Convection Year

The South Adriatic Sea is the deepest part of the Adriatic Sea and represents a key area for both the Adriatic Sea and the deep eastern Mediterranean. It has a role in dense water formation for the eastern Mediterranean deep circulation cell, and it represents an entry point for water masses originating from the Ionian Sea. The biodiversity and seasonality of bacterial picoplankton before, during, and after deep winter convection in the oligotrophic South Adriatic waters were assessed by combining comparative 16S rRNA sequence analysis and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH). The picoplankton communities reached their maximum abundance in the spring euphotic zone when the maximum value of the chlorophyll a in response to deep winter convection was recorded. The communities were dominated by Bacteria, while Archaea were a minor constituent. A seasonality of bacterial richness and diversity was observed, with minimum values occurring during the winter convection and spring postconvection periods and maximum values occurring under summer stratified conditions. The SAR11 clade was the main constituent of the bacterial communities and reached the maximum abundance in the euphotic zone in spring after the convection episode. Cyanobacteria were the second most abundant group, and their abundance strongly depended on the convection event, when minimal cyanobacterial abundance was observed. In spring and autumn, the euphotic zone was characterized by Bacteroidetes and Gammaproteobacteria. Bacteroidetes clades NS2b, NS4, and NS5 and the gammaproteobacterial SAR86 clade were detected to co-occur with phytoplankton blooms. The SAR324, SAR202, and SAR406 clades were present in the deep layer, exhibiting different seasonal variations in abundance. Overall, our data demonstrate that the abundances of particular bacterial clades and the overall bacterial richness and diversity are greatly impacted by strong winter convection.     

Cell density inversely regulates D- and L-aspartate levels in rat pheochromocytoma MPT1 cells

In a previous report (FEBS Lett. 434 (1998) 231), we demonstrated for the first time that D-aspartate (D-Asp) is synthesized in rat pheochromocytoma 12 (PC12) cells. This unique amino acid is believed to act as a novel messenger in mammalian cell regulation. However, the dynamics of D-Asp homeostasis in mammalian cells is yet to be elucidated. In this communication, we demonstrate that D-Asp is also synthesized in MPT1 cells (a subclone of PC12 cells) and that the D- and L-Asp levels in cells are regulated by cell density of the culture. Our data show that D-Asp levels increase, while in contrast, L-Asp levels decrease as a function of increased cell density. Conversely, in PC12 cells, which do not express the glutamate transporter involved in the incorporation of D- and L-Asp into cells, L-Asp levels decrease upon cell density increase while D-Asp concentrations remain almost unchanged. The results indicate that the biochemical behaviors of D- and L-Asp in mammalian cells are distinct and that the cellular levels of these stereoisomers appear to be under different control mechanisms.     

Uptake of Dissolved Organic Carbon by Gammaproteobacterial Subgroups in Coastal Waters of the West Antarctic Peninsula

Heterotrophic bacteria are well known to be key players in the turnover of dissolved organic material (DOM) in the oceans, but the relationship between DOM uptake and bacterial clades is still not well understood. Here we explore the turnover and single-cell use of glucose, an amino acid mixture, N-acetylglucosamine (NAG), and protein by gammaproteobacterial clades in coastal waters of the West Antarctic Peninsula in summer and fall. More than 60% of the cells within two closely related gammaproteobacterial clades, Ant4D3 and Arctic96B-16, were active in using the amino acid mixture, protein, and NAG. In contrast, an average of only 7% of all SAR86 cells used amino acids and protein even in summer when DOM use was high. In addition to DOM uptake within a group, we explored the contribution of the three gammaproteobacterial groups to total community uptake of a compound. SAR86 contributed 5- to 10-fold less than the other gammaproteobacterial subgroups to the uptake of all compounds. We found that the overall contribution of the Ant4D3 clade to DOM uptake was highest, whereas the SAR86 clade contributed the least to DOM turnover in West Antarctic Peninsula waters. Our results suggest that the low growth activity of a bacterial clade leads to low abundance, fewer active cells and a low contribution to the turnover of DOM components.     

Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic

Prokaryotic extracellular enzymatic activity, abundance, heterotrophic production and respiration were determined in the meso- and bathypelagic (sub)tropical North Atlantic. While prokaryotic heterotrophic production (PHP) decreased from the lower euphotic layer to the bathypelagic waters by two orders of magnitude, prokaryotic abundance and cell-specific PHP decreased only by one order of magnitude. In contrast to cell-specific PHP, cell-specific extracellular enzymatic activity (alpha- and beta-glucosidase, leucine aminopeptidase, alkaline phosphatase) increased with depth as did cell-specific respiration rates. Cell-specific alkaline phosphatase activity increased from the intermediate water masses to the deep waters up to fivefold. Phosphate concentrations, however, varied only by a factor of two between the different water masses, indicating that phosphatase activity is not related to phosphate availability in the deep waters. Generally, cell-specific extracellular enzymatic activities were inversely related to cell-specific prokaryotic leucine incorporation. Thus, it is apparent that the utilization of deep ocean organic matter is linked to higher cell-specific extracellular enzymatic activity and respiration and lower cell-specific PHP than in surface waters.     

Prevalence of the Chloroflexi-related SAR202 bacterioplankton cluster throughout the mesopelagic zone and deep ocean

Since their initial discovery in samples from the north Atlantic Ocean, 16S rRNA genes related to the environmental gene clone cluster known as SAR202 have been recovered from pelagic freshwater, marine sediment, soil, and deep subsurface terrestrial environments. Together, these clones form a major, monophyletic subgroup of the phylum Chloroflexi: While members of this diverse group are consistently identified in the marine environment, there are currently no cultured representatives, and very little is known about their distribution or abundance in the world's oceans. In this study, published and newly identified SAR202-related 16S rRNA gene sequences were used to further resolve the phylogeny of this cluster and to design taxon-specific oligonucleotide probes for fluorescence in situ hybridization. Direct cell counts from the Bermuda Atlantic time series study site in the north Atlantic Ocean, the Hawaii ocean time series site in the central Pacific Ocean, and along the Newport hydroline in eastern Pacific coastal waters showed that SAR202 cluster cells were most abundant below the deep chlorophyll maximum and that they persisted to 3600 m in the Atlantic Ocean and to 4000 m in the Pacific Ocean, the deepest samples used in this study. On average, members of the SAR202 group accounted for 10.2% (+/-5.7%) of all DNA-containing bacterioplankton between 500 and 4000 m.     

Prevalence of the Chloroflexi-Related SAR202 Bacterioplankton Cluster throughout the Mesopelagic Zone and Deep Ocean

Since their initial discovery in samples from the north Atlantic Ocean, 16S rRNA genes related to the environmental gene clone cluster known as SAR202 have been recovered from pelagic freshwater, marine sediment, soil, and deep subsurface terrestrial environments. Together, these clones form a major, monophyletic subgroup of the phylum Chloroflexi. While members of this diverse group are consistently identified in the marine environment, there are currently no cultured representatives, and very little is known about their distribution or abundance in the world's oceans. In this study, published and newly identified SAR202-related 16S rRNA gene sequences were used to further resolve the phylogeny of this cluster and to design taxon-specific oligonucleotide probes for fluorescence in situ hybridization. Direct cell counts from the Bermuda Atlantic time series study site in the north Atlantic Ocean, the Hawaii ocean time series site in the central Pacific Ocean, and along the Newport hydroline in eastern Pacific coastal waters showed that SAR202 cluster cells were most abundant below the deep chlorophyll maximum and that they persisted to 3,600 m in the Atlantic Ocean and to 4,000 m in the Pacific Ocean, the deepest samples used in this study. On average, members of the SAR202 group accounted for 10.2% (±5.7%) of all DNA-containing bacterioplankton between 500 and 4,000 m.     

Contribution of Crenarchaeota and Bacteria to autotrophy in the North Atlantic interior

Marine Crenarchaeota are among the most abundant groups of prokaryotes in the ocean and recent reports suggest that they oxidize ammonia as an energy source and inorganic carbon as carbon source, while other studies indicate that Crenarchaeota use organic carbon and hence, live heterotrophically. We used catalysed reporter deposition fluorescence in situ hybridization (CARD‐FISH) to determine the crenarchaeal and bacterial contribution to total prokaryotic abundance in the (sub)tropical Atlantic. Bacteria contributed ～50% to total prokaryotes throughout the water column. Marine Crenarchaeota Group I (MCGI) accounted for ～5% of the prokaryotes in subsurface waters (100 m depth) and between 10 and 20% in the oxygen minimum layer (250–500 m depth) and deep waters (North East Atlantic Deep Water). The fraction of both MCGI and Bacteria fixing inorganic carbon, determined by combining microautoradiography with CARD‐FISH (MICRO‐CARD‐FISH), decreased with depth, ranging from ～30% in the oxygen minimum zone to < 10% in the intermediate waters (Mediterranean Sea Outflow Water, Antarctic Intermediate Water). In the deeper water masses, however, MCGI were not taking up inorganic carbon. Using quantitative MICRO‐CARD‐FISH to determine autotrophy activity on a single cell level revealed that MCGI are incorporating inorganic carbon (0.002–0.1 fmol C cell^?1 day^?1) at a significantly lower rate than Bacteria (0.01–0.6 fmol C cell^?1 day^?1). Hence, it appears that MCGI contribute substantially less to autotrophy than Bacteria. Taking the stoichiometry of nitrification together with our findings suggests that MCGI might not dominate the ammonia oxidation step in the mesopelagic waters of the ocean to that extent as the reported dominance of archaeal over bacterial amoA would suggest.     

Community Structure and Function of Planktonic Crenarchaeota: Changes with Depth in the South China Sea

Marine Crenarchaeota represent a widespread and abundant microbial group in marine ecosystems. Here, we investigated the abundance, diversity, and distribution of planktonic Crenarchaeota in the epi-, meso-, and bathypelagic zones at three stations in the South China Sea (SCS) by analysis of crenarchaeal 16S rRNA gene, ammonia monooxygenase gene amoA involved in ammonia oxidation, and biotin carboxylase gene accA putatively involved in archaeal CO₂ fixation. Quantitative PCR analyses indicated that crenarchaeal amoA and accA gene abundances varied similarly with archaeal and crenarchaeal 16S rRNA gene abundances at all stations, except that crenarchaeal accA genes were almost absent in the epipelagic zone. Ratios of the crenarchaeal amoA gene to 16S rRNA gene abundances decreased ~2.6 times from the epi- to bathypelagic zones, whereas the ratios of crenarchaeal accA gene to marine group I crenarchaeal 16S rRNA gene or to crenarchaeal amoA gene abundances increased with depth, suggesting that the metabolism of Crenarchaeota may change from the epi- to meso- or bathypelagic zones. Denaturing gradient gel electrophoresis profiling of the 16S rRNA genes revealed depth partitioning in archaeal community structures. Clone libraries of crenarchaeal amoA and accA genes showed two clusters: the “shallow” cluster was exclusively derived from epipelagic water and the “deep” cluster was from meso- and/or bathypelagic waters, suggesting that niche partitioning may take place between the shallow and deep marine Crenarchaeota. Overall, our results show strong depth partitioning of crenarchaeal populations in the SCS and suggest a shift in their community structure and ecological function with increasing depth.