| 1. |
- Baltar, Federico, et al.
(author)
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High dissolved extracellular enzymatic activity in the deep Central Atlantic Ocean
- 2010
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In: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 58:3, s. 287-302
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Journal article (peer-reviewed)abstract
- The distribution of prokaryotic abundance (PA), prokaryotic heterotrophic production (PHP), and suspended particulate organic material (POM), as well as total and dissolved (operationally defined as passing through 0.2 mu m pore size filters) potential extracellular enzymatic activities (EEA; alpha- and beta-glucosidase [AGase and BGase], leucine aminopeptidase [LAPase], and alkaline phosphatase [APase]) were determined in the meso- and bathypelagic waters of the (sub)tropical Atlantic along an eastern zonal transatlantic transect and a western N-S transect. Significant differences between both transects were found for POM concentration but not for PA, PHP (except in the subsurface and oxygen minimum layer), and dissolved and total EEA. PHP decreased by 3 orders of magnitude from the lower euphotic zone to bathypelagic waters, while PA and cell-specific PHP decreased only by 1 and 2 orders of magnitude, respectively. The proportion of the dissolved to the total EEA was high in the dark ocean for all the enzymes, ranging from 54 to 100, 56 to 100, 65 to 100 and 57 to 97 % for AGase, BGase, LAPase and APase, respectively. The kinetic parameters (V-max, and K-m) of both the dissolved and total fractions of LAPase and APase were very similar throughout the water column, suggesting a similar origin for both dissolved and particulate EEA. Significant correlations of both dissolved and total EEA were found with prokaryotic metabolism and the POM pool. Based on the previous notion that the fraction of dissolved EEA is higher in particle-attached than in free-living microbes, our results suggest that microbial activity in the dark ocean occurs mainly on colloidal and particulate material. This is in agreement with recent genomic evidence. However, these colloidal and particulate materials are prone to disruption during the sampling process. Hence, more selective sampling techniques are needed to specifically collect these deep-water aggregates that probably represent hotspots of microbial activity in the deep ocean.
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| 2. |
- Sarmento, Hugo, et al.
(author)
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Phytoplankton species-specific release of dissolved free amino acids and their selective consumption by bacteria
- 2013
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In: Limnology and Oceanography. - : Wiley. - 0024-3590 .- 1939-5590. ; 58:3, s. 1123-1135
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Journal article (peer-reviewed)abstract
- Despite representing only a small fraction of the ocean's dissolved organic matter pool, dissolved free amino acids (DFAA) have high turnover rates and are major nitrogen and carbon sources for bacterioplankton. Both phytoplankton and bacterioplankton assimilate and release DFAA, but their consumption and production are difficult to quantify in nature due to their short residence times (min) as dissolved monomers. We segregated DFAA production by phytoplankton and bacterial consumption by measuring individual DFAA concentrations in four axenic phytoplankton cultures during the exponential growth phase, and also after 4 d incubations in the presence of a natural bacterioplankton community. The amounts and composition of the DFAA pool varied widely among phytoplankton species. The proportion of dissolved organic carbon attributed to DFAA varied among cultures. The picoeukaryotic prasinophyte, Micromonas pusilla, released higher amounts of DFAA than the other species tested (diatoms and dinoflagellate), especially alanine, which has been reported as the dominant individual DFAA in some oligotrophic environments. Community structure of heterotrophic prokaryotes responded to differences in the quality of organic matter released among microalgal species, with Roseobacter-related bacteria responding strongly to exudate composition. Our results demonstrate the specificity of DFAA extracellular release among several algal species and their preferential uptake by members of bacterial communities.
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| 3. |
- Alonso-Saez, Laura, et al.
(author)
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Leucine-to-carbon empirical conversion factor experiments: does bacterial community structure have an influence?
- 2010
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 12:11, s. 2988-2997
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Journal article (peer-reviewed)abstract
- The suitability of applying empirical conversion factors (eCFs) to determine bacterial biomass production remains unclear because seawater cultures are usually overtaken by phylotypes that are not abundant in situ. While eCFs vary across environments, it has not been tested whether differences in eCFs are driven by changes in bacterial community composition or by in situ environmental conditions. We carried out seawater cultures throughout a year to analyse the correlation between eCFs and bacterial community structure, analysed by catalysed reporter deposition fluorescence in situ hybridization. Gammaproteobacteria usually dominated seawater cultures, but their abundance exhibited a wide range (25–73% of cell counts) and significantly increased with inorganic nutrient enrichment. Flavobacteria were less abundant but increased up to 40% of cells counts in winter seawater cultures, when in situ chlorophyll a was high. The correlations between eCFs and the abundance of the main broad phylogenetic groups (Gamma-, Alphaproteobacteria and Flavobacteria) were significant, albeit weak, while more specific groups (Alteromonadaceae and Rhodobacteraceae) were not significantly correlated. Our results show that the frequent development of the fast-growing group Alteromonadaceae in seawater cultures does not strongly drive the observed variations in eCFs. Rather, the results imply that environmental conditions and the growth of specific phylotypes interact to determine eCFs.
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| 4. |
- Baltar, Federico, et al.
(author)
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Bacterial Versus Archaeal Origin of Extracellular Enzymatic Activity in the Northeast Atlantic Deep Waters
- 2013
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In: Microbial Ecology. - Springer-Verlag : Springer Science and Business Media LLC. - 0095-3628 .- 1432-184X. ; 65:2, s. 277-288
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Journal article (peer-reviewed)abstract
- We determined the total and dissolved extracellularenzymatic activity (EEA) of α-glucosidase and β-glucosidase(AGase and BGase), alkaline phosphatase (APase) and leucineaminopeptidase (LAPase) activities in the epi-, meso- andbathypelagic waters of the subtropical Northeast Atlantic.EEA was also determined in treatments in which bacterialEEAwas inhibited by erythromycin. Additionally, EEA decayexperiments were performed with surface and deep waters todetermine EEA lifetimes in both water masses. The proportionof dissolved to total EEA (66–89 %, 44–88 %, 57–82 % and86–100 % for AGase, BGase, APase and LAPase, respectively)was generally higher than the cell-associated (i.e.,particulate) EEA. The percentage of dissolved to total EEAwas inversely proportional to the percentage of erythromycininhibitedto total EEA. Since erythromycin-inhibited plusdissolved EEA equaled total EEA, this tentatively suggeststhat cell-associated EEA in the open oceanic water column isalmost exclusively of bacterial origin. The decay constants ofdissolved EEAwere in the range of 0.002–0.048 h−1 dependingon the type of extracellular enzyme, temperature and depthin the water column. Although dissolved EEA can have differentorigins, the major contribution of Bacteria to cellassociatedEEA and the long life-time of dissolved EEAsuggest that Bacteria—and not mesophilic Archaea—areessentially the main producers of EEA in the open subtropicalNortheast Atlantic down to bathypelagic layers.
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| 5. |
- Baltar, Federico, 1982-, et al.
(author)
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Mesoscale eddies: hot-spots for prokaryotic diversity and function in the ocean
- 2010
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In: The ISME Journal. - : Springer Science and Business Media LLC. - 1751-7362 .- 1751-7370. ; 4, s. 975-988
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Journal article (peer-reviewed)abstract
- To investigate the effects of mesoscale eddies on prokaryotic assemblage structure and activity, we sampled two cyclonic eddies (CEs) and two anticyclonic eddies (AEs) in the permanent eddy-field downstream the Canary Islands. The eddy stations were compared with two far-field (FF) stations located also in the Canary Current, but outside the influence of the eddy field. The distribution of prokaryotic abundance (PA), bulk prokaryotic heterotrophic activity (PHA), various indicators of single-cell activity (such as nucleic acid content, proportion of live cells, and fraction of cells actively incorporating leucine), as well as bacterial and archaeal community structure were determined from the surface to 2000 m depth. In the upper epipelagic layer (0–200 m), the effect of eddies on the prokaryotic community was more apparent, as indicated by the higher PA, PHA, fraction of living cells, and percentage of active cells incorporating leucine within eddies than at FF stations. Prokaryotic community composition differed also between eddy and FF stations in the epipelagic layer. In the mesopelagic layer (200–1000 m), there were also significant differences in PA and PHA between eddy and FF stations, although in general, there were no clear differences in community composition or single-cell activity. The effects on prokaryotic activity and community structure were stronger in AE than CE, decreasing with depth in both types of eddies. Overall, both types of eddies show distinct community compositions (as compared with FF in the epipelagic), and represent oceanic ‘hotspots’ of prokaryotic activity (in the epi- and mesopelagic realms).
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| 6. |
- Baltar, Federico, et al.
(author)
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Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical Northeast Atlantic Ocean.
- 2012
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In: Applied and Environmental Microbiology. - 0099-2240 .- 1098-5336. ; 78:9, s. 3309-3316
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Journal article (peer-reviewed)abstract
- 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 (0-200 m) and mesopelagic (200-1000 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 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, prokaryotic to nanoflagellate abundance ratio) than in the epipelagic (i.e., bulk activity, nucleic acid content and nanoflagellate abundance) waters. Our results show that the mesopelagic realm in the NE Atlantic is, in terms of microbial activity, more heterogeneous than its epipelagic counterpart, probably linked to mesoscale hydrographical variations.
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| 7. |
- Baltar, Federico, et al.
(author)
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Prokaryotic carbon utilization in the dark ocean: : growth efficiency, leucine-to-carbon conversion factors, and their relation
- 2010
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In: Aquatic Microbial Ecology. - : Inter-Research Science Center. - 0948-3055 .- 1616-1564. ; 60:3, s. 227-232
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Journal article (peer-reviewed)abstract
- Experiments were conducted in the mesopelagic subtropical northeast Atlantic Ocean to determine the range of variability in the prokaryotic leucine-to-carbon conversion factor (CF), and prokaryotic growth efficiency (PGE). The way prokaryotic heterotrophic production (PHP) is calcu- lated directly influences PGE (variations of PGE between 1 and 31% were found for a single sample). The empirically obtained deep-water CFs showed a 7-fold variability (0.13 to 0.85 kg C mol–1 Leu), but were always lower than the theoretical CF of 1.55 kg C mol–1 Leu assuming no isotope dilution. Empirically determined CFs were highly correlated to PGE, suggesting that both parameters are rep- resentations of the same basic metabolic processes. Overall, the PGEs obtained in this study suggest that mesopelagic prokaryotic assemblages can sometimes be as important in carbon processing as their epipelagic counterparts.
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| 8. |
- Baltar, Federico, et al.
(author)
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Significance of non-sinking particulate organic carbon and dark CO2 fixation to heterotrophic carbon demand in the mesopelagic Atlantic
- 2010
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In: Geophysical Research Letters. - 0094-8276 .- 1944-8007. ; 37, s. L09602-
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Journal article (peer-reviewed)abstract
- It is generally assumed that sinking particulate organic carbon (POC) constitutes the main source of organic carbon supply to the deep ocean's food webs. However, a major discrepancy between the rates of sinking POC supply (collected with sediment traps) and the prokaryotic organic carbon demand (the total amount of carbon required to sustain the heterotrophic metabolism of the prokaryotes; i.e., production plus respiration, PCD) of deep-water communities has been consistently reported for the dark realm of the global ocean. While the amount of sinking POC flux declines exponentially with depth, the concentration of suspended, buoyant non-sinking POC (nsPOC; obtained with oceanographic bottles) exhibits only small variations with depth in the (sub) tropical Northeast Atlantic. Based on available data for the North Atlantic we show here that the sinking POC flux would contribute only 4-12% of the PCD in the mesopelagic realm (depending on the primary production rate in surface waters). The amount of nsPOC potentially available to heterotrophic prokaryotes in the mesopelagic realm can be partly replenished by dark dissolved inorganic carbon fixation contributing between 12% to 72% to the PCD daily. Taken together, there is evidence that the mesopelagic microheterotrophic biota is more dependent on the nsPOC pool than on the sinking POC supply. Hence, the enigmatic major mismatch between the organic carbon demand of the deep-water heterotrophic microbiota and the POC supply rates might be substantially smaller by including the potentially available nsPOC and its autochthonous production in oceanic carbon cycling models. Citation: Baltar, F., J. Aristegui, E. Sintes, J. M. Gasol, T. Reinthaler, and G. J. Herndl (2010), Significance of non-sinking particulate organic carbon and dark CO2 fixation to heterotrophic carbon demand in the mesopelagic northeast Atlantic.
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| 9. |
- Gómez-Consarnau, Laura, et al.
(author)
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Structuring of bacterioplankton communities by specific dissolved organic carbon compounds
- 2012
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In: Environmental Microbiology. - : Wiley. - 1462-2912 .- 1462-2920. ; 14:9, s. 2361-2378
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Journal article (peer-reviewed)abstract
- The main role of microorganisms in the cycling of the bulk dissolved organic carbon pool in the ocean is well established. Nevertheless, it remains unclear if particular bacteria preferentially utilize specific carbon compounds and whether such compounds have the potential to shape bacterial community composition. Enrichment experiments in the Mediterranean Sea, Baltic Sea and the North Sea (Skagerrak) showed that different low-molecular-weight organic compounds, with a proven importance for the growth of marine bacteria (e.g. amino acids, glucose, dimethylsulphoniopropionate, acetate or pyruvate), in most cases differentially stimulated bacterial growth. Denaturing gradient gel electrophoresis fingerprints and 16S rRNA gene sequencing revealed that some bacterial phylotypes that became abundant were highly specific to enrichment with specific carbon compounds (e.g. Acinetobacter sp. B1-A3 with acetate or Psychromonas sp. B3-U1 with glucose). In contrast, other phylotypes increased in relative abundance in response to enrichment with several, or all, of the investigated carbon compounds (e.g. Neptuniibacter sp. M2-A4 with acetate, pyruvate and dimethylsulphoniopropionate, and Thalassobacter sp. M3-A3 with pyruvate and amino acids). Furthermore, different carbon compounds triggered the development of unique combinations of dominant phylotypes in several of the experiments. These results suggest that bacteria differ substantially in their abilities to utilize specific carbon compounds, with some bacteria being specialists and others having a more generalist strategy. Thus, changes in the supply or composition of the dissolved organic carbon pool can act as selective forces structuring bacterioplankton communities.
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| 10. |
- Lekunberri, Itziar, et al.
(author)
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The phylogenetic and ecological context of cultured and whole genome-sequenced planktonic bacteria from the coastal NW Mediterranean Sea
- 2014
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In: Systematic and Applied Microbiology. - : Elsevier BV. - 0723-2020 .- 1618-0984. ; 37:3, s. 216-228
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Journal article (peer-reviewed)abstract
- Microbial isolates are useful models for physiological and ecological studies and can also be used to reassemble genomes from metagenomic analyses. However, the phylogenetic diversity that can be found among cultured marine bacteria may vary significantly depending on the isolation. Therefore, this study describes a set of 136 bacterial isolates obtained by traditional isolation techniques from the Blanes Bay Microbial Observatory, of which seven strains have had the whole genome sequenced. The complete set was compared to a series of environmental sequences obtained by culture-independent techniques (60 DGGE sequences and 303 clone library sequences) previously obtained by molecular methods. In this way, each isolate was placed in both its "ecological" (time of year, nutrient limitation, chlorophyll and temperature values) context or setting, and its "phylogenetic" landscape (i.e. similar organisms that were found by culture-independent techniques, when they were relevant, and when they appeared). Nearly all isolates belonged to the Gammaproteobacteria, Alphaproteobacteria, or the Bacteroidetes (70, 40 and 20 isolates, respectively). Rarefaction analyses showed similar diversity patterns for sequences from isolates and molecular approaches, except for Alphaproteobacteria where cultivation retrieved a higher diversity per unit effort. Approximately 30% of the environmental clones and isolates formed microdiversity clusters constrained at 99% 16S rRNA gene sequence identity, but the pattern was different in Bacteroidetes (less microdiversity) than in the other main groups. Seventeen cases (12.5%) of nearly complete (98-100%) rRNA sequence identity between isolates and environmental sequences were found: nine in the Alphaproteobacteria, five in the Gammaproteobacteria, and three in the Bacteroidetes, indicating that cultivation could be used to obtain at least some organisms representative of the various taxa detected by molecular methods. Collectively, these results illustrated the largely unexplored potential of culturing on standard media for complementing the study of microbial diversity by culture-independent techniques and for obtaining phylogenetically distinct model organisms from natural seawater.
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