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Surface microbial communities are exposed to seasonally changing environmental conditions, resulting in recurring patterns of community composition. However, knowledge on temporal dynamics of open ocean microbial communities remains scarce. Seasonal patterns and associations of taxa and oligotypes from surface and chlorophyll maximum layers in the western Mediterranean Sea were studied over a 2-year period. Summer stratification versus winter mixing governed not only the prokaryotic community composition and diversity but also the temporal dynamics and co-occurrence association networks of oligotypes. Flavobacteriales, Rhodobacterales, SAR11, SAR86, and Synechococcales oligotypes exhibited contrasting seasonal dynamics, and consequently, specific microbial assemblages and potential inter-oligotype connections characterized the different seasons. In addition, oligotypes composition and dynamics differed between surface and deep chlorophyll maximum (DCM) prokaryotic communities, indicating depth-related environmental gradients as a major factor affecting association networks between closely related taxa. Taken together, the seasonal and depth specialization of oligotypes suggest temporal dynamics of community composition and metabolism, influencing ecosystem function and global biogeochemical cycles. Moreover, our results indicate highly specific associations between microbes, pointing to keystone ecotypes and fine-tuning of the microbes realized niche.

1st Iberian Ecological Society Meeting (2019); XIV Congreso Nacional de la Asociación Española de Ecología Terrestre (AEET), Ecology: an integrative science in the Anthropocene, 4-7 February 2019, Barcelona, Spain, Marine phytoplankton produce dimethylsulfoniopropionate (DMSP), which, upon release into the ambient water, is mainly degradedby Bacteria either via the DMSP cleavage or demethylation pathway. It has been hypothesized that the extent of DMSP demethylationdepends on DMSP availability and bacterial sulfur demand, which could lead to potential niche differentiation of the demethylatingbacterial community. In this study, we determined DMSP concentrations in marine snow and the ambient water over a seasonalcycle. Subsequently, we linked these DMSP concentrations to the abundance of Bacteria harboring the dmdA gene encoding the en-zyme that catalyzes the demethylation reaction. In marine snow, DMSP concentrations were up to four times higher than in the am-bient water and three times higher in marine snow in summer than in winter. Certain subclades of demethylating Bacteria weredetected only in the ambient water and some of them exhibited strong seasonal dynamics. The demethylating bacterial communityin marine snow expressed weaker seasonal dynamics than in the ambient water. The strong correlation of the representative oligo-types of the demethylating bacterial subclades with DMSP concentrations suggest a distinct and fine-tuned niche partitioning amongdemethylating bacterial subclades. Our results reveal a pronounced seasonal variability and spatial heterogeneity in DMSP concen-trations and the associated demethylating bacterial community and point to the occurrence of specific oligotypes with differentaffinities for DMSP in coastal waters where marine snow is present

Viruses are an abundant, diverse and dynamic component of marine and terrestrial ecosystems. In the ocean, viruses play a key role in the biogeochemical cycles and controlling microbial abundance, diversity and evolution. Recent metagenomics studies assessed the structure of the viral community in the upper ocean. However, little is known about the compositional changes in viral communities along the deep ocean conveyor belt. To assess potential changes in the viral community in the global deepwater circulation system, water samples were collected in the core of the North Atlantic Deep Water (NADW) (∼2,500 m) and Pacific Antarctic Bottom Water (∼4,000 m). Microbial and viral abundance were evaluated by flow cytometry. Subsequently, flow cytometry was used to sort virus-like particles and next generation sequencing was applied to build DNA libraries from the sorted virus populations. The viral communities were highly diverse across different oceanic regions with high dissimilarity between samples. Only 18% of the viral protein clusters were shared between the NADW and the Pacific Antarctic Bottom Water. Few viral groups, mainly associated with uncultured environmental and uncultured Mediterranean viruses were ubiquitously distributed along the global deep-water circulation system. Thus, our results point to a few groups of widely distributed abundant viruses in addition to the presence of rare and diverse types of viruses at a local scale.

Viruses are an abundant, diverse and dynamic component of marine and terrestrial ecosystems. In the ocean, viruses play a key role in the biogeochemical cycles and controlling microbial abundance, diversity and evolution. Recent metagenomics studies assessed the structure of the viral community in the upper ocean. However, little is known about the compositional changes in viral communities along the deep ocean conveyor belt. To assess potential changes in the viral community in the global deep-water circulation system, water samples were collected in the core of the North Atlantic Deep Water (NADW) (∼2,500 m) and Pacific Antarctic Bottom Water (∼4,000 m). Microbial and viral abundance were evaluated by flow cytometry. Subsequently, flow cytometry was used to sort virus-like particles and next generation sequencing was applied to build DNA libraries from the sorted virus populations. The viral communities were highly diverse across different oceanic regions with high dissimilarity between samples. Only 18% of the viral protein clusters were shared between the NADW and the Pacific Antarctic Bottom Water. Few viral groups, mainly associated with uncultured environmental and uncultured Mediterranean viruses were ubiquitously distributed along the global deep-water circulation system. Thus, our results point to a few groups of widely distributed abundant viruses in addition to the presence of rare and diverse types of viruses at a local scale.

Messenger RNA can provide valuable insights into the variability of metabolic processes of microorganisms. However, due to uncertainties that include the stability of RNA, its application for activity profiling of environmental samples is questionable. We explored different factors affecting the decay rate of transcripts of three marine bacterial isolates using qPCR and determined mRNA half-life time of specific bacterial taxa and of functional genes by metatranscriptomics of a coastal environmental prokaryotic community. The half-life time of transcripts from 11 genes from bacterial isolates ranged from 1 to 46 min. About 80% of the analysed transcripts exhibited half-live times shorter than 10 min. Significant differences were found in the half-life time between mRNA and rRNA. The halflife time of mRNA obtained from a coastal metatranscriptome ranged from 9 to 400 min. The shortest half-life times of the metatranscriptome corresponded to transcripts from the same clusters of orthologous groups (COGs) in all bacterial classes. The prevalence of short mRNA half-life time in genes related to defence mechanisms and motility indicate a tight connection of RNA decay rate to environmental stressors. The short half-life time of RNA and its high variability needs to be considered when assessing metatranscriptomes especially in environmental samples.

To elucidate the potential for nitrification and denitrification processes in a high latitude deep oxygen minimum zone (OMZ) we determined the abundance and community composition of the main microbial players in the aerobic and anaerobic (anammox) ammonium oxidation and denitrification processes in the Gulf of Alaska throughout the water column. Within the dominant bacterial groups, Flavobacterales, Rhodobacterales, Actinomarinales, and SAR86 were more abundant in epipelagic waters and decreased with depth, whereas SAR11, SAR324, Marinimicrobia, and Thiomicrospirales increased their contribution to the bacterial community with depth. Nitrosopumilaceae also increased with depth and dominated the OMZ and bathypelagic archaeal communities. Euryarchaeota Marine Group II exhibited an opposite depth pattern to Nitrosopumilaceae, whereas Marine Group III and Woesearchaeota were more abundant in the bathypelagic realm. Candidatus Brocadia contributed 70–100% of the anammox bacterial community throughout the water column. Archaeal ammonia oxidizers (AOA) dominated the microbial community involved in the nitrogen cycle. Two AOA ecotypes, the high ammonia (HAC) and low ammonia (LAC)-AOA, characterized by distinct genes for aerobic ammonia oxidation (amoA) and for denitrification (nirK), exhibited a distinct distribution pattern related to depth and ammonia concentrations. HAC-AOA dominated in epipelagic (80.5 ± 28.3% of total AOA) oxygenated and ammonia-rich waters, and LAC-AOA dominated in the OMZ (90.9 ± 5.1%) and bathypelagic waters (85.5 ± 13.5%), characterized by lower oxygen and ammonia concentrations. Bacterial denitrifiers (3.7 ± 6.9 bacterial nirK gene mL−1) and anaerobic ammonia oxidizers (78 ± 322 anammox 16S rRNA genes L−1) were low in abundance under the oxygen conditions in the Gulf of Alaska throughout the water column. The widespread distribution of bacterial denitrifiers and anaerobic ammonia oxidizers in low abundances reveals a reservoir of genetic and metabolic potential ready to colonize the environment under the predicted increase of OMZs in the ocean. Taken together, our results reinforce the niche partitioning of archaeal ammonia oxidizers based on their distinct metabolic characteristics resulting in the dominance of LAC-AOA in a high latitude deep OMZ. Considering the different ecological roles and functions of the two archaeal ecotypes, the expansion of the zones dominated by the LAC-ecotype might have implications for the nitrogen cycle in the future ocean.

Global environmental changes are challenging the structure and functioning of ecosystems. However, a mechanistic understanding of how global environmental changes will affect ecosystems is still lacking. The complex and interacting biological and physical processes spanning vast temporal and spatial scales that constitute an ecosystem make this a formidable problem. A unifying framework based on ecological theory, that considers fundamental and realized niches, combined with metabolic, evolutionary, and climate change studies, is needed to provide the mechanistic understanding required to evaluate and forecast the future of marine communities, ecosystems, and their services.

Zooplankton and microbes play a key role in the ocean's biological cycles by releasing and consuming copious amounts of particulate and dissolved organic matter. Additionally, zooplankton provide a complex microhabitat rich in organic and inorganic nutrients in which bacteria thrive. In this study, we assessed the phylogenetic composition and metabolic potential of microbial communities associated with crustacean zooplankton species collected in the North Atlantic. Using Illumina sequencing of the 16S rRNA gene we found significant differences between the microbial communities associated with zooplankton and those inhabiting the surrounding seawater. Metagenomic analysis of the zooplankton-associated microbial community revealed a highly specialized bacterial community able to exploit zooplankton as microhabitat and thus, mediating biogeochemical processes generally underrepresented in the open ocean. The zooplankton-associated bacterial community is able to colonize the zooplankton's internal and external surfaces by using a large set of adhesion mechanisms and to metabolize complex organic compounds released or exuded by the zooplankton such as chitin, taurine and other complex molecules. Moreover, the high number of genes involved in iron and phosphorus metabolisms in the zooplankton-associated microbiome suggests that this zooplankton-associated bacterial community mediates specific biogeochemical processes (through the proliferation of specific taxa) that are generally underrepresented in the ambient waters. This article is protected by copyright. All rights reserved.

Bulk dark dissolved inorganic carbon (DIC) fixation rates were determined and compared to microbial heterotrophic production in subsurface, meso- and bathypelagic Atlantic waters off the Galician coast (NW Iberian margin). DIC fixation rates were slightly higher than heterotrophic production throughout the water column, however, more prominently in the bathypelagic waters. Microautoradiography combined with catalyzed reporter deposition fluorescence in situhybridization (MICRO-CARD-FISH) allowed us to identify several microbial groups involved in dark DIC uptake. The contribution of SAR406 (Marinimicrobia), SAR324 (Deltaproteobacteria) and Alteromonas (Gammaproteobacteria) to the dark DIC fixation was significantly higher than that of SAR202 (Chloroflexi) and Thaumarchaeota, in agreement with their contribution to microbial abundance. Q-PCR on the gene encoding for the ammonia monooxygenase subunit A (amoA) from the putatively high versus low ammonia concentration ecotypes revealed their depth-stratified distribution pattern. Taken together, our results indicate that chemoautotrophy is widespread among microbes in the dark ocean, particularly in bathypelagic waters. This chemolithoautotrophic biomass production in the dark ocean, depleted in bio-available organic matter, might play a substantial role in sustaining the dark ocean's food web.

Original research paper, Taurine (Tau), an amino acid-like compound, is present in almost all marine metazoans including crustacean zooplankton. It plays an important physiological role in these organisms and is released into the ambient water throughout their life cycle. However, limited information is available on the release rates by marine organisms, the concentrations and turnover of Tau in the ocean. We determined dissolved free Tau concentrations throughout the water column and its release by abundant crustacean mesozooplankton at two open ocean sites (Gulf of Alaska and North Atlantic). At both locations, the concentrations of dissolved free Tau were in the low nM range (up to 15.7 nM) in epipelagic waters, declining sharply in the mesopelagic to about 0.2 nM and remaining fairly stable throughout the bathypelagic waters. Pacific amphipod–copepod assemblages exhibited lower dissolved free Tau release rates per unit biomass (0.8 ± 0.4 μmol g−1 C-biomass h−1) than Atlantic copepods (ranging between 1.3 ± 0.4 μmol g−1 C-biomass h−1 and 9.5 ± 2.1 μmol g−1 C-biomass h−1), in agreement with the well-documented inverse relationship between biomass-normalized excretion rates and body size. Our results indicate that crustacean zooplankton might contribute significantly to the dissolved organic matter flux in marine ecosystems via dissolved free Tau release. Based on the release rates and assuming steady state dissolved free Tau concentrations, turnover times of dissolved free Tau range from 0.05 d to 2.3 d in the upper water column and are therefore similar to those of dissolved free amino acids. This rapid turnover indicates that dissolved free Tau is efficiently consumed in oceanic waters, most likely by heterotrophic bacteria., Austrian Science Fund, MINECO, Xunta de Galicia, US National Science Fund, 3,385

Poster, Mixing zones and boundaries between different water masses are "hot spots" of marine biodiversity and activity. We aimed to investigate the effects of water mass mixing in the dark-ocean microbial communities by collecting and incubating natural bacterial communities from the Mediterranean Water (MW; at 1000 m depth), the Subpolar Modal Water (SPMW, 500m) and the Labrador Sea Water (LSW, 1800 m), and comparing them with artificially mixed communities. Mixing experiment 1 consisted of incubating at in sity conditions the original LSW and MW communities, plus a mixture of both (MIX1, dilution 1:1), whereas the Mixing experiment 2 included the original prokaryotic communities from SPMW and MW and a mixture of both (MIX2, dilution 1:1). Bacterial abundance and activity was monitored every 24 h over 8 days, while bacterial community composition and DOM characterization were assessed at the beginning (day 0), middle (day 4) and at the end of the experiment (day 8). Live prokaryotic cell abundance was higher in the MIX1 and MIX2 treatments as compared to the original communities. Moreover, MIX bacteria showed slightly higher leucine incorporation rates than MW or LSW. These metabolic responses were accompanied by changes in the optical properties of DOM, suggesting a change in the dynamics of the organic matter. Taken together, our results indicate differences in the bio-reactvity of the organic matter after mixing as compared to the original water masses that could influence the composition and activity of the bacterial community.

Viruses are abundant, diverse and dynamic compo-nents of the marine environments and play a signi?-cant role in the ocean biogeochemical cycles. Toassess potential variations in the relation betweenviruses and microbes in different geographic regionsand depths, viral and microbial abundance and pro-duction were determined throughout the watercolumn along a latitudinal transect in the South Atlan-tic Ocean. Path analysis was used to examine therelationships between several abiotic and bioticparameters and the different microbial and viral popu-lations distinguished by ?ow cytometry.The depth-integrated contribution of microbial andviral abundance to the total microbial and viralbiomass differed signi?cantly among the differentprovinces. Additionally, the virus-to-microbe ratioincreased with depth and decreased laterally towardsthe more productive regions. Our data revealed thatthe abundance of phytoplankton and microbes is themain controlling factor of the viral populations in theeuphotic and mesopelagic layers, whereas in thebathypelagic realm, viral abundance was only weaklyrelated to the biotic and abiotic variables. The relativecontribution of the three viral populations distin-guished by ?ow cytometry showed a clear geographi-cal pattern throughout the water column, suggestingthat these populations are composed of distinct taxa

In marine ecosystems, Thaumarchaeota are most likely the major ammonia oxidizers. While ammonia concentrations vary by about two orders of magnitude in the oceanic water column, archaeal ammonia oxidizers (AOA) vary by only one order of magnitude from surface to bathypelagic waters. Thus, the question arises whether the key enzyme responsible for ammonia oxidation, ammonia monooxygenase (amo), exhibits different affinities to ammonia along the oceanic water column and consequently, whether there are different ecotypes of AOA present in the oceanic water column. We determined the abundance and phylogeny of AOA based on their amoA gene. Two ecotypes of AOA exhibited a distribution pattern reflecting the reported availability of ammonia and the physico-chemical conditions throughout the Atlantic, and from epi- to bathypelagic waters. The distinction between these two ecotypes was not only detectable at the nucleotide level. Consistent changes were also detected at the amino acid level. These changes include substitutions of polar to hydrophobic amino acid, and glycine substitutions that could have an effect on the configuration of the amo protein and thus, on its activity. Although we cannot identify the specific effect, the ratio of non-synonymous to synonymous substitutions (dN/dS) between the two ecotypes indicates a strong positive selection between them. Consequently, our results point to a certain degree of environmental selection on these two ecotypes that have led to their niche specialization.

Poster communication, Our results provide evidence for the significant contribution to chemolithotrophy by specific archaeal and bacterial groups in the dark ocean.

Heterotrophic bacteria respond dynamically to variations in organic matter availability in the dark ocean. However, our knowledge on how the differences in sized and/or reactivity of dissolved organic matter (DOM) affect the bacterial community dynamics is still scarce. Our study aims to investigate the response of bacterial activity and community composition to the degradability of filtered and of size-fractionated DOM. A natural bacterial community isolated from Mediterrean Water (MW; at 1000 m depth) was inoculated in seawater from the same location subjected to three different treatments: 0.2µm-filtered seawater (control), low molecular weight fraction (LMW) obtained by ultrafiltration, and the combination of low and high molecular weight fractions at the original ratio (H+L). Bacterial abundance and activity was monitored every 24h over 6 days, while bacterial community composition and DOM characterization were assessed at the beginning (day 0), middle (day 4) and at the end of the experiment (day 6). Low (LNA) and high nucleic acid content (HNA) bacterial abundance, as well as leucine incorporation rates, were consistently higher in the H+L incubations than in the LMW treatments, indicating different reactivity of the two organic matter size fractions. Moreover, actively respiring cells, estimated as CTC-positive cells, highly correlated to humic-like substances (FDOM-M; R=0.7, P

Recent studies suggest that the prokaryotes inhabiting the dark ocean present higher chemolithoautotrophic activity than assumed previously. These chemolithoautotrophic microbes incorporate dissolved inorganic carbon (DIC) as carbon source for biomass production and use reduced inorganic compound as an energy source. We have quantified DIC fixation in the meso- and bathypelagic waters of the northwestern coast of the Iberian Peninsula, ranging from 1.04 to 46.83 mmol C m-2 d-1. Combining microautoradiography and fluorescence in situ hybridization (MICRO-CARD-FISH), we confirmed that both Thaumarchaeota and some bacterial groups such as SAR-11, SAR-202, SAR-406, Alteromonas take up bicarbonate uptake, particularly in the mesopelagic waters. Quantitative PCR analyses clearly showed a higher abundance of thaumarchaeal 16S and low ammonia concentration (LAC)- amoA genes in meso- and lower bathypelagic waters than in surface waters. In contrast, high ammonia concentration (HAC)- amoA genes dominated the subsurface samples. Taken together, both genomic and physiological evidences indicate that some archaeal and bacterial groups may be significant contributors to dark ocean chemoautolithotrophy.

Comunicación oral Prokaryotic activity and community composition is highly depth-stratified in the oceanic water column reflecting the increasing recalcitrance of dissolved organic matter and decreasing temperature with depth. The role of increasing hydrostatic pressure in controlling deep ocean microbial activity is less well-studied. To determine the influence in hydrostatic pressure on heterotrophic microbial activity, an in situ incubator was deployed in the North Atlantic Ocean at a depth between 500 to 2000 m. The in situ incubator was programmed to collect and incubate prokaryotes under the water after adding 3H-leucine and to fix a certain volume of the incubated samples at specific time intervals (3 to 10 h depending on the depth). Prokaryotic leucine incorporation obtained under in situ pressure conditions was generally lower than that on decompressed samples incubated on board. Ratios of in situ prokaryotic leucine incorporation to decompressed conditions decreased with increasing depth. Our results suggest that bulk heterotrophic prokaryotic production in the deep sea might be lower than expected.

Presentación oral The wide use of –omics approaches has led to the discovery of novel metabolic pathways in uncultivated marine bacteria. For example, metagenomic and –proteomic studies revealed that taurine might be an important substrate for heterotrophic marine bacteria. Taurine, an organic acid, is widely produced by marine metazoans and some phytoplankton albeit its concentration and turnover in the ocean has not been determined yet. In this study, we determined the role of taurine as carbon and energy source throughout the water column of the open North Atlantic from the epipelagic to the bathypelagic realm. Bulk uptake and respiration of taurine were measured and microautoradiography was combined with catalyzed reporter deposition fluorescence in situ hybridization to evaluate taurine uptake by specific phylogenetic groups. A shift between the dominant use of taurine as a carbon source from the epi- and mesopelagic (about 40% of taurine respired) to the bathypelagic (76% respired) realm was observed. Taken together, our results indicate that taurine is effectively used by marine prokaryotes, especially in the mesopelagic environment where zooplankton, a potential source for taurine, reside during the day.

Macroecological patterns are found in animals and plants, but also in micro-organisms.Macroecological and biogeographic distribution patterns in marine Archaea, however,have not been studied yet. Ammonia-oxidizing Archaea (AOA) show a bipolar distribution(i.e. similar communities in the northernmost and the southernmost locations,separated by distinct communities in the tropical and gyral regions) throughout theAtlantic, detectable from epipelagic to upper bathypelagic layers (

Recent studies suggest that the dark ocean prokaryotes fix inorganic carbon at rates substantially higher than assumed. We have studied the contribution of Archaea vs. Bacteria to total prokaryotic fixation of dissolved inorganic carbon (DIC) in the meso- and upper bathypelagic waters of the world’s oceans during the Malaspina circumnavigation expedition carried out between December 2010 and July 2011. We used the metabolic inhibitor Erythromycin, an antibiotic specifically inhibiting growth of Bacteria but not affecting Archaea. Bacteria dominated throughout the water column in the three major ocean basins (54% of the total DAPI counts), decreasing in their relative contribution to total prokaryotic abundance from the surface to the meso- and bathypelagic waters. By contrast, the relative contribution of Thaumarchaeota was generally higher in the meso- and bathypelagic layers than in the surface waters (up to 29% of the total DAPI counts in the Pacific Ocean). Averaged over the entire water column, Thaumarchaeota contributed 8%, 33% and 18% to the total prokaryotic DIC fixation in the Indian, Pacific and Atlantic Ocean, respectively. The contribution of Thaumarchaeota to total prokaryotic DIC fixation increased with depth, particularly in the Atlantic below 1000 m depth and in the lower mesopelagic zone of the Pacific Ocean. Preliminary results from an station in the Atlantic Ocean, combining microautoradiography and fluorescence in situ hybridization (MICRO-CARD-FISH), confirmed that both Thaumarchaeota and some bacterial groups such as SAR 324 take up DIC. Thaumarchaeota and SAR 324 accounted for 7 % and 12% of DIC-positive DAPI-stained cells, respectively, as revealed by MICRO-CARD-FISH. Our results suggest that some phylogenetic groups may be significant contributors to the dark ocean chemoautotrophy.

Recently, evidence suggests that dark CO2 fixation in the pelagic realm of the ocean does not only occur in the suboxic and anoxic water bodies but also in the oxygenated meso- and bathypelagic waters of the North Atlantic. To elucidate the significance and phylogeny of the key organisms mediating dark CO2 fixation in the tropical Atlantic, we quantified functional genes indicative for CO2 fixation. We used a Q-PCR-based assay targeting the bifunctional acetyl-CoA/propionyl-CoA carboxylase (accA subunit), a key enzyme powering inter alia the 3-hydroxypropionate/4-hydroxybutyrate cycle (HP/HB) and the archaeal ammonia monooxygenase (amoA). Quantification of accA-like genes revealed a consistent depth profile in the upper mesopelagial with increasing gene abundances from subsurface layers towards the oxygen minimum zone (OMZ), coinciding with an increase in archaeal amoA gene abundance. Gene abundance profiles of metabolic marker genes (accA, amoA) were correlated with thaumarchaeal 16S rRNA gene abundances as well as CO2 fixation rates to link the genetic potential to actual rate measurements. AccA gene abundances correlated with archaeal amoA gene abundance throughout the water column (r2=0.309, P

We collected surface- and deep-water samples (maximum depth 300m) during the springsummer transition in the coastal Arctic along a transect in the Kongsfjorden (Ny-angstrom lesund, Spitsbergen, Norway) to determine the structure of the active versus total marine bacterioplankton community using different approaches. Catalysed reporter depositionfluorescence in situ hybridization combined with microautoradiography (MICROCARDFISH) was used to determine the abundance and activity of different bacterial groups. The bacterial communities were dominated by members of Alphaproteobacteria followed by Bacteroidetes, whereas Gammaproteobacteria were present at low abundance but exhibited a high percentage of active cells taking up leucine. The clone libraries of 16S rRNA genes (16S rDNA) and 16S rRNA from two different depths were used to decipher the bacterial community structure. Independently of the type of clone libraries analysed (16S rDNA- or 16S rRNA-based), four major and four minor taxonomic groups were detected. The bacterioplankton community was mainly dominated at both the DNA and the RNA levels by Alphaproteobacteria followed by Gammaproteobacteria. The Rhodobacteriaceae were the most abundant members of the Alphaproteobacteria in both DNA and RNA clone libraries, followed by the SAR11 clade, which was only detectable at the 16S rDNA level. Moreover, there was a general agreement between the results obtained with both techniques, although some specific phylogenetic groups, such as SAR11 and Roseobacter, deviated substantially from this relation. These discrepancies are most likely linked to different physiological states among members of the bacterioplankton community. Combined, MICROCARDFISH and DNA and RNA clone libraries, however, allowed for accurately quantifying different bacterial groups and their activity as well as a detailed phylogenetic insight into the fractions of present versus metabolically active bacterial groups.

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 similar to 50% to total prokaryotes throughout the water column. Marine Crenarchaeota Group I (MCGI) accounted for similar to 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 similar to 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.

Microbial communities in Arctic coastal waters experience dramatic changes in environmental conditions during the spring to summer transition period, potentially leading to major variations in the relationship between viral and prokaryotic communities. To document these variations, a number of physico-chemical and biological parameters were determined during the ice-melting season in the coastal Arctic (Kongsfjorden, Ny-Alesund, Spitsbergen). The bacterial and viral abundance increased during the spring to summer transition period, probably associated to the increase in temperature and the development of a phytoplankton bloom. The increase in viral abundance was less pronounced than the increase in prokaryotic abundance; consequently, the viral to prokaryotic abundance ratio decreased. The bacterial and viral communities were stratified as determined by Automated Ribosomal Intergenic Spacer Analysis and Randomly Amplified Polymorphic DNA-PCR respectively. Both the bacterial and viral communities were characterized by a relatively low number of operational taxonomic units (OTUs). Despite the apparent low complexity of the bacterial and viral communities, the link between these two communities was weak over the melting season, as suggested by the different trends of prokaryotic and viral abundance during the sampling period. This weak relationship between the two communities might be explained by UV radiation and suspended particles differently affecting the viruses and prokaryotes in the coastal Arctic during this period. Based on our results, we conclude that the viral and bacterial communities in the Arctic were strongly affected by the variability of the environmental conditions during the transition period between spring and summer.

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, 6