Dark CO2 fixation by chemolithoautotrophic prokaryotes in the deep-water masses of the north-west coast of the Iberian Peninsule

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

Bacterial activity and community composition response to the size-reactivity of dissolved organic matter

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<0.05, n=9, Spearman Rank Order), particularly in the H+L incubations. Interestingly, LNA cell abundance was highly correlated with the slope ratio (SR) values (R=-0.8, P<0.05, n=9, Spearman Rank Order), indicating that bacteria belonging to the LNA population are tightly linked to the molecular weight or aromaticity of the DOM. Taken together, our results indicate differences in the bio-reactivity of the low and high molecular weight size classes of DOM associated to the phylogenetic composition of the bacterial communities

Lower prokaryotic leucine incorporation rates under in situ pressure than under decompressed conditions in the deep north Atlantic

Comunicación oralProkaryotic 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

Taurine: an energy "drink" for deep sea microbes

Presentación oralThe 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

Dissolved inorganic carbon fixation of Thaumarchaeota vs. Bacteria in the meso- and upper bathypelagic waters of the world’s oceans differentiated with the use of metabolic inhibitors

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

Nitrogen fixation in the upwelling region off NW Iberia

Comunicación oralPicoplankton are the most abundant organisms in the ocean, often dominate planktonic biomass and primary production, and they could represent a substantial contribution to the global export of carbon. Nowadays, we have a limited understanding about the factors that control the picoplankton community structure. A recent analysis indicates that light and temperature are the main factors explaining Prochlorococcus and Synechococcus distributions, whereas nutrient concentrations play a minor role (Flombaum et al., PNAS 2013). Methodological difficulties to quantify mixing in the marine enviroments have motivated the use of indirect approaches to determine the input of nutrients into the euphotic zone, however, nutrient concentrations are not necessarily a proxy of nutrient supply. We present a large data set, including open-ocean and coastal regions, of simultaneous measurements of picoplankton abundance, temperature and irradiance, together with estimates of nutrient supply. The transport of nutrients across the nutricline was computed combining nutrient concentrations and small-scale turbulence observations collected with a microstructure profiler. Our preliminary results indicate that nutrient supply also plays a role in the distribution of functional groups of picoplankton in the ocean

Diversity and abundance of planktonic communities in the deep waters off the galician coast (NW Spain)

Comunicación oralPlanktonic communities play pivotal roles within marine ecosystems, affecting their structure, functioning and services. Although they have been extensively studied in the epipelagic ocean, the knowledge about these communities in the dark ocean is rather short. In this study, we explored patterns of abundance and biomass of a wide variety of taxonomic groups from the prokaryotes to mesozooplankton in the epi-, meso- and bathypelagic waters off the Galician coast. As expected, ciliate and zooplankton abundances are depleted in the bathypelagic waters relative to abundances of prokaryotes and nanoflagellates. The rate of decrease of zooplankton biomass with depth is twice as that of prokaryotes and nanoflagellates, indicating that relative contribution of mesozooplancton to the total plankton biomass decreases with depth. Overall, the diversity of prokaryotes in the dark ocean is almost as high as in the epipelagic layer, although the phylotypes are different. The major fraction of epipelagic ciliates belongs to alloricate genera, whereas tintinnids dominate the deep ciliate populations. Small copepods were dominant in the epi- and meso-pelagic zone. By contrast, foraminiferans, big copepods and myctophic fishes were more abundant in the deep ocean

Temporal variability of diazotroph community composition in the upwelling region off NW Iberia

Knowledge of the ecology of N 2 -fixing (diazotrophic) plankton is mainly limited to oligotrophic (sub)tropical oceans. However, diazotrophs are widely distributed and active throughout the global ocean. Likewise, relatively little is known about the temporal dynamics of diazotrophs in productive areas. Between February 2014 and December 2015, we carried out 9 one-day samplings in the temperate northwestern Iberian upwelling system to investigate the temporal and vertical variability of the diazotrophic community and its relationship with hydrodynamic forcing. In downwelling conditions, characterized by deeper mixed layers and a homogeneous water column, non-cyanobacterial diazotrophs belonging mainly to nifH clusters 1G (Gammaproteobacteria) and 3 (putative anaerobes) dominated the diazotrophic community. In upwelling and relaxation conditions, affected by enhanced vertical stratification and hydrographic variability, the community was more heterogeneous vertically but less diverse, with prevalence of UCYN-A (unicellular cyanobacteria, subcluster 1B) and non-cyanobacterial diazotrophs from clusters 1G and 3. Oligotyping analysis of UCYN-A phylotype showed that UCYN-A2 sublineage was the most abundant (74%), followed by UCYN-A1 (23%) and UCYN-A4 (2%). UCYN-A1 oligotypes exhibited relatively low frequencies during the three hydrographic conditions, whereas UCYN-A2 showed higher abundances during upwelling and relaxation. Our findings show the presence of a diverse and temporally variable diazotrophic community driven by hydrodynamic forcing in an upwelling system.Xunta de Galicia | Ref. EM2013/021Ministerio de Economía, Industria y Competitividad | Ref. CTM2016-75451-C2-1-RMinisterio de Educación, Cultura y Deporte | Ref. FPU13/01674Ministerio de Educación, Cultura y Deporte | Ref. EST16/00142Universidad de Vigo | Ref. Axudas á investigación 201

Sample dilution and bacterial community composition influence empirical leucine-to-carbon conversion factors in surface waters of the world's oceans

Research articleThe transformation of leucine incorporation into prokaryotic carbon production rates requires the use of either theoretical or empirically determined conversion factors. Empirical leucine-to-carbon conversion factors (eCFs) vary widely across environments, and little is known about their potential controlling factors. We conducted 10 surface seawater manipulation experiments across the world’s oceans, where the growth of the natural prokaryotic assemblages was promoted by filtration (i.e. removal of grazers; F treatment) or filtration combined with dilution (i.e. relieving also resource competition; FD treatment). The impact of sunlight exposure was also evaluated in the FD treatments, and we did not find a significant effect on the eCFs. The eCFs varied from 0.09 to 1.47 kg C mol Leu-1 and were significantly lower in the filtered and diluted (FD) than in the filtered (F) treatments. Also, changes in bacterial community composition during the incubations, as assessed by Automated Ribosomal Intergenic Spacer Analysis (ARISA), were stronger in the FD than in the F treatments, as compared to unmanipulated controls. Thus, we discourage the common procedure of diluting samples (in addition to filtration) for eCFs determination. The eCFs in the filtered treatment were negatively correlated with the initial chlorophyll a concentration, picocyanobacterial abundance (mostly Prochlorococcus) and the percentage of heterotrophic prokaryotes with high nucleic acid content (%HNA). The latter two variables explained 80% of the eCFs variability in the F treatment, supporting the view that both Prochlorococcus and HNA prokaryotes incorporate leucine in substantial amounts although resulting into relatively low carbon production rates in the oligotrophic ocean.En prensa3,829

Factors controlling the community structure of picoplankton in contrasting marine environments

The effect of inorganic nutrients on planktonic assemblages has traditionally relied on concentrations rather than estimates of nutrient supply. We combined a novel dataset of hydrographic properties, turbulent mixing, nutrient concentration, and picoplankton community composition with the aims of (i) quantifying the role of temperature, light, and nitrate fluxes as factors controlling the distribution of autotrophic and heterotrophic picoplankton subgroups, as determined by flow cytometry, and (ii) describing the ecological niches of the various components of the picoplankton community. Data were collected at 97 stations in the Atlantic Ocean, including tropical and subtropical open-ocean waters, the northwestern Mediterranean Sea, and the Galician coastal upwelling system of the northwest Iberian Peninsula. A generalized additive model (GAM) approach was used to predict depth-integrated biomass of each picoplankton subgroup based on three niche predictors: sea surface temperature, averaged daily surface irradiance, and the transport of nitrate into the euphotic zone, through both diffusion and advection. In addition, niche overlap among different picoplankton subgroups was computed using nonparametric kernel density functions. Temperature and nitrate supply were more relevant than light in predicting the biomass of most picoplankton subgroups, except for Prochlorococcus and low-nucleic-acid (LNA) prokaryotes, for which irradiance also played a significant role. Nitrate supply was the only factor that allowed the distinction among the ecological niches of all autotrophic and heterotrophic picoplankton subgroups. Prochlorococcus and LNA prokaryotes were more abundant in warmer waters (>20 ∘C) where the nitrate fluxes were low, whereas Synechococcus and high-nucleic-acid (HNA) prokaryotes prevailed mainly in cooler environments characterized by intermediate or high levels of nitrate supply. Finally, the niche of picoeukaryotes was defined by low temperatures and high nitrate supply. These results support the key role of nitrate supply, as it not only promotes the growth of large phytoplankton, but it also controls the structure of marine picoplankton communities.Ministerio de Economía y Competitividad | Ref. CTM2012-30680Ministerio de Economía y Competitividad | Ref. CTM2008-0626I-C03-01Ministerio de Economía y Competitividad | Ref. REN2003-09532-C03-01Ministerio de Economía y Competitividad | Ref. CTM2004-05174 -C02Ministerio de Economía y Competitividad | Ref. CTM2011-25035Xunta de Galicia | Ref. 09MMA027604PRXunta de Galicia | Ref. EM2013/021European Commission | Ref. FP7, n. 261860Ministerio de Economía y Competitividad | Ref. FJCI-641 2015-2571