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  • 1.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Gasol, Josep M
    Herndl, Gerhard J
    Microbial functioning and community structure variability in the mesopelagic and epipelagic waters of the subtropical Northeast Atlantic Ocean.2012In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 78, no 9, p. 3309-3316Article in journal (Refereed)
    Abstract [en]

    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.

  • 2.
    Baltar, Federico
    et al.
    Facultad de Ciencias del Mar, Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira,.
    Arístegui, Javier
    Facultad de Ciencias del Mar, Universidad de Las Palmas de Gran Canaria, Campus Universitario de Tafira,.
    Gasol, Josep M.
    Herndl, Gerhard J.
    Prokaryotic carbon utilization in the dark ocean: : growth efficiency, leucine-to-carbon conversion factors, and their relation2010In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 60, no 3, p. 227-232Article in journal (Refereed)
    Abstract [en]

    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.

     

  • 3.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Gasol, Josep M.
    Lekunberri, Itziar
    Herndl, Gerhard J.
    Mesoscale eddies: hot-spots for prokaryotic diversity and function in the ocean2010In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 4, p. 975-988Article in journal (Refereed)
    Abstract [en]

    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).

  • 4.
    Baltar, Federico
    et al.
    Univ Las Palmas Gran Canaria, Fac Ciencias Mar, Las Palmas Gran Canaria 35017, Spain.
    Arístegui, Javier
    Gasol, Josep M.
    Sintes, Eva
    Herndl, Gerhard J.
    Evidence of prokaryotic metabolism on suspended particulate organic matter in the dark waters of the (sub)tropical North Atlantic2009In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 54, no 1, p. 182-193Article in journal (Refereed)
    Abstract [en]

    The distribution of prokaryotic abundance (PA), respiratory activity (ETS), heterotrophic production (PHP), and suspended particulate (POM) and dissolved (DOM) organic matter was determined in the meso- and bathypelagic waters of the (sub) tropical North Atlantic. PA decreased by one order of magnitude from the lower euphotic zone to the bathypelagic waters, while ETS decreased by two and PHP by three orders of magnitude. On a section following the Mid-Atlantic Ridge from 35 degrees N to 5 degrees N, ETS below 1000-m depth increased southwards up to three-fold. This latitudinal gradient in the deep waters was paralleled by a six-fold increase in Particulate Organic Carbon (POC), whereas no trend was apparent in the DOM distribution. Significant correlations between POM and ETS were obtained in the water masses between 1000-m and 3000-m depth, the Antarctic Intermediate Water and the North East Atlantic Deep Water. A strong imbalance in the dark ocean was found between prokaryotic carbon demand (estimated through two different approaches) and the carbon sinking flux derived from sediment-trap records corrected with Th-230. The imbalance was greater when deeper in the water column, suggesting that the suspended carbon pool must account for most of the carbon deficit. Our results, together with other recent findings discussed in this paper, indicate that microbial life in the dark ocean is likely more dependent on slowly sinking or buoyant, laterally advected suspended particles than hitherto assumed. 

  • 5.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Gasol, Josep M.
    Sintes, Eva
    van Aken, Hendrik M.
    Herndl, Gerhard J.
    High dissolved extracellular enzymatic activity in the deep Central Atlantic Ocean2010In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 58, no 3, p. 287-302Article in journal (Refereed)
    Abstract [en]

    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.

  • 6.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Las Palmas Gran Canaria, Inst Oceanog & Cambio Global, Gran Canaria 35214, Spain.
    Arístegui, Javier
    Universidad de Las Palmas de Gran Canaria.
    Gasol, Josep M.
    Yokokawa, Taichi
    Royal Netherlands Institute for Sea Research.
    Herndl, Gerhard J.
    University of Vienna.
    Bacterial Versus Archaeal Origin of Extracellular Enzymatic Activity in the Northeast Atlantic Deep Waters2013In: Microbial Ecology, ISSN 0095-3628, E-ISSN 1432-184X, Vol. 65, no 2, p. 277-288Article in journal (Refereed)
    Abstract [en]

    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.

  • 7.
    Baltar, Federico
    et al.
    Univ Las Palmas Gran Canaria, Fac Ciencias Mar, Las Palmas Gran Canaria 35017, Spain.
    Arístegui, Javier
    Herndl, Gerhard J
    Gasol, Josep M
    Hernández-León, Santiago
    Strong coast-ocean and surface-depth gradients in prokaryotic assemblage structure and activity in a coastal transition zone region2007In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 50, no 1, p. 63-74Article in journal (Refereed)
    Abstract [en]

    The distribution of marine Crenarchaeota Group 1, marine Euryarchaeota Group II and some major groups of Bacteria (SAR 11, Roseobacter, Gammaproteobacteria and Bacteroidetes) was investigated in the North Atlantic water column (surface to 2000 m depth) along a transect from the coastal waters of the NW African upwelling to the offshore waters of the Canary Coastal Transition Zone (CTZ). Catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) was used to describe the prokaryotic assemblages. Bulk picoplankton abundance and leucine incorporation were determined. Pronounced changes in prokaryotic assemblage composition were observed from the coast to the open ocean and at the deep chlorophyll maximum (DCM) with decreasing bulk heterotrophic activity. All bacterial groups decreased in absolute abundances from the coast to the open ocean; both archaeal groups increased towards the open ocean. Prokaryotic abundance and activity decreased 2 and 3 orders of magnitude, respectively, from the surface to 2000 m. Prokaryotic growth rates were high in the mesopelagic zone (similar to 0.13 d(-)1), compared to other reports from the central North Atlantic. SARI 1 in total picoplankton abundance decreased from 42 % in the DCM to 4 % at 2000 m, while marine Crenarchaeota Group I increased from 1 % in the DCM to 39 % in the oxygen minimum layer. A clear influence of the different intermediate water masses was observed on the bulk heterotrophic picoplankton activity, with lower leucine incorporation rates corresponding to layers where patches of Antarctic Intermediate Water were detected. Coast-ocean and surface-depth gradients in bulk prokaryotic abundance and production and assemblage composition were comparable to changes observed in basin-scale studies, pinpointing the CTZs as regions of strong variability in microbial diversity and metabolism. 

  • 8.
    Baltar, Federico
    et al.
    Univ Las Palmas Gran Canaria, Fac Ciencias Mar, Las Palmas Gran Canaria 35017, Spain .
    Arístegui, Javier
    Montero, María F.
    Espino, Minerva
    Gasol, Josep M.
    Herndl, Gerhard J.
    Mesoscale variability modulates seasonal changes in the trophic structure of nano- and picoplankton communities across the NW Africa-Canary Islands transition zone2009In: Progress in Oceanography, ISSN 0079-6611, E-ISSN 1873-4472, Vol. 83, no 1-4, p. 180-188Article in journal (Refereed)
    Abstract [en]

    The variability of picoplankton and nanoplankton autotrophic (A) and heterotrophic (H) communities was studied along a zonal gradient extending from the NW African shelf to 500 km offshore in two contrasting seasons of the year: early spring (spring) and summer (summer). Plankton abundance was significantly higher in summer than in spring. In particular, heterotrophic prokaryotes (HP) and Prochlorococcus (Proc) were an order of magnitude more abundant in summer, presumably due to a higher loading of dissolved organic matter and higher temperatures. The average ratio of A to H biomass was lower during the summer. Over the African shelf, picoplankton was lowest during summer, while both the autotrophic and heterotrophic nanoflagellates (ANF and HNF) showed the highest abundances. In contrast, in spring, the highest abundance of Picoeukaryotes (PE) and Synechococcus (Syn) was found over or close to the shelf. The offshore sampling sections intersected a complex area of strong mesoscale variability, which affected the plankton distribution. In summer, the entrainment of an upwelling filament around a cyclonic eddy provoked the increase of HP and Syn abundances by about one order of magnitude over the surrounding waters, while PE were more abundant over the core of the eddy (probably due to nutrient pumping). In spring, HP and Syn were more abundant at the boundaries of an anticyclonic eddy and in the filament (where PE also increased). Proc abundance increased up to one order of magnitude in the core of the eddy and in the eddy-oceanic waters front. ANF and HNF showed the highest abundances in the filament and the eddy. in summary, although seasonality affects the background variability in microplankton communities, the mesoscale variability found in the Canary Islands transition zone strongly modulates the patterns of distribution, abundances and changes in community structure, altering the A to H ratio and concomitantly playing a key role modifying the carbon pathways within the food web in the region. 

  • 9.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Sintes, Eva
    Reinthaler, Thomas
    Gasol, Josep M.
    Herndl, Gerhard J.
    Significance of non-sinking particulate organic carbon and dark CO2 fixation to heterotrophic carbon demand in the mesopelagic Atlantic2010In: Geophysical Research Letters, ISSN 0094-8276, E-ISSN 1944-8007, Vol. 37, p. L09602-Article in journal (Refereed)
    Abstract [en]

    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.

  • 10.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Cell-free extracellular enzymatic activity is linked to seasonal temperature changes: a case study in the Baltic Sea2016In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 13, no 9, p. 2815-2821Article in journal (Refereed)
    Abstract [en]

    Extracellular enzymatic activities (EEA) are a crucial step on the degradation of organic matter. Dissolved (cell-free) extracellular enzymes in seawater can make up a significant contribution of the bulk EEA. However, the factors controlling the proportion of dissolved EEA in the marine environment remain unknown. Here we studied the seasonal changes in the proportion of dissolved relative to total EEA (of alkaline phosphatase [APase], β-glucosidase, [BGase], and leucine aminopeptidase, [LAPase]), in the Baltic Sea for 18 months. The proportio n of dissolved EEA ranged between 37-100%, 0-100%, 34-100% for APase, BGase and LAPase, respectively. A consistent seasonal pattern in the proportion of dissolved EEA was found among all the studied enzymes, with values up to 100% during winter and <40% du ring summer. A significant negative relation was found between the 21proportion of dissolved EEA and temperature, indicating that temperature might be a critical factor controlling the proportion of dissolved relative to total EEA in marine environments. Our results suggest a strong decoupling of hydrolysis rates from mi crobial dynamics in cold waters. This implies that under cold conditions, cell-free enzymes can contribute to substrate availability at large distances from the producing cell, increasing the dissociation between the hydrolysis of organic compounds and the actual microbes producing the enzymes. This also indicates that global warming could come to affect the hydrolysis of organic matter by reducing the hydrolytic activity of cell-free enzymes.

  • 11.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Lindh, Markus V.
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Parparov, Arkadi
    Israel Oceanographic and Limnological Research.
    Berman, Tom
    Israel Oceanographic and Limnological Research.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Prokaryotic community structure and respiration during long-term incubations2012In: MicrobiologyOpen, ISSN 2045-8827, E-ISSN 2045-8827, Vol. 1, no 2, p. 214-224Article in journal (Refereed)
    Abstract [en]

    Despite the importance of incubation assays for studies inmicrobial ecology that frequentlyrequire long confinement times, few reports are available in which changesin the assemblage structure of aquatic prokaryotes were monitored during longtermincubations.We measured rates of dissolved organic carbon degradation andmicrobial respiration by consumption of dissolved oxygen (DO) in four experimentswith Lake Kinneret near-surface water and, concomitantly, we analyzed thevariability in prokaryotic community structure during long-term dark bottle incubations.During the first 24 h, therewere only minor changes in bacterial communitycomposition. Thereafter there were marked changes in the prokaryotic communitystructure during the incubations. In contrast, oxygen consumption rates (a proxyfor both respiration and dissolved organic carbon degradation rates) remained stablefor up to 10–23 days. This study is one of the first to examine closely the phylogeneticchanges that occur in the microbial community of untreated freshwaterduring long-term (days) incubations in dark, sealed containers. Novel informationon the diversity of the main bacterial phylotypes that may be involved in dissolvedorganic matter degradation in lake Kinneret is also provided. Our results suggestthat, under certain ecological settings, constant community metabolic rates can bemaintained as a result of shifts in community composition.

  • 12.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lekunberri, Itziar
    Univ Vienna, Austria ; Inst Catala Recerca Aigua, Spain.
    Reinthaler, Thomas
    Univ Vienna, Austria.
    Herndl, Gerhard J.
    Univ Vienna, Austria ; Univ Utrecht, Netherlands.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Prokaryotic Responses to Ammonium and Organic Carbon Reveal Alternative CO2 Fixation Pathways and Importance of Alkaline Phosphatase in the Mesopelagic North Atlantic2016In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 7, article id 1670Article in journal (Refereed)
    Abstract [en]

    To decipher the response of mesopelagic prokaryotic communities to input of nutrients, we tracked changes in prokaryotic abundance, extracellular enzymatic activities, heterotrophic production, dark dissolved inorganic carbon (DIC) fixation, community composition (16S rRNA sequencing) and community gene expression (metatranscriptomics) in 3 microcosm experiments with water from the mesopelagic North Atlantic. Responses in 3 different treatments amended with thiosulfate, ammonium or organic matter (i.e., pyruvate plus acetate) were compared to unamended controls. The strongest stimulation was found in the organic matter enrichments, where all measured rates increased >10-fold. Strikingly, in the organic matter treatment, the dark DIC fixation rates-assumed to be related to autotrophic metabolisms-were equally stimulated as all the other heterotrophic-related parameters. This increase in DIC fixation rates was paralleled by an up-regulation of genes involved in DIC assimilation via anaplerotic pathways. Alkaline phosphatase was the metabolic rate most strongly stimulated and its activity seemed to be related to cross-activation by nonpartner histidine kinases, and/or the activation of genes involved in the regulation of elemental balance during catabolic processes. These findings suggest that episodic events such as strong sedimentation of organic matter into the mesopelagic might trigger rapid increases of originally rare members of the prokaryotic community, enhancing heterotrophic and autotrophic carbon uptake rates, ultimately affecting carbon cycling. Our experiments highlight a number of fairly unstudied microbial processes of potential importance in mesopelagic waters that require future attention.

  • 13.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Wageningen University, The Netherlands.
    Unrein, Fernando
    Institut de Ciències del Mar CSIC, Spain.
    Catala, Philippe
    Pierre-and-Marie-Curie University, France.
    Hornak, Karel
    Biology Centre of the Academy of Sciences of the Czech Republic, Czech Republic.
    Simek, Karel
    Biology Centre of the Academy of Sciences of the Czech Republic, Czech Republic.
    Vaque, Dolors
    Institut de Ciències del Mar CSIC, Spain.
    Massana, Ramon
    Institut de Ciències del Mar CSIC, Spain.
    Gasol, Josep M.
    Institut de Ciències del Mar CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Marine bacterial community structure resilience to changes in protist predation under phytoplankton bloom conditions2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 3, p. 568-581Article in journal (Refereed)
    Abstract [en]

    To test whether protist grazing selectively affects the composition of aquatic bacterial communities, we combined high-throughput sequencing to determine bacterial community composition with analyses of grazing rates, protist and bacterial abundances and bacterial cell sizes and physiological states in a mesocosm experiment in which nutrients were added to stimulate a phytoplankton bloom. A large variability was observed in the abundances of bacteria (from 0.7 to 2.4 x 10(6) cells per ml), heterotrophic nanoflagellates (from 0.063 to 2.7 x 10(4) cells per ml) and ciliates (from 100 to 3000 cells per l) during the experiment (similar to 3-, 45- and 30-fold, respectively), as well as in bulk grazing rates (from 1 to 13 x 10(6) bacteria per ml per day) and bacterial production (from 3 to 379 mu g per Cl per day) (1 and 2 orders of magnitude, respectively). However, these strong changes in predation pressure did not induce comparable responses in bacterial community composition, indicating that bacterial community structure was resilient to changes in protist predation pressure. Overall, our results indicate that peaks in protist predation (at least those associated with phytoplankton blooms) do not necessarily trigger substantial changes in the composition of coastal marine bacterioplankton communities.

  • 14.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Palovaara, Joakim
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Vila-Costa, Maria
    Univ Barcelona, Spain.
    Salazar, Guillem
    CSIC, Spain.
    Calvo, Eva
    CSIC, Spain.
    Pelejero, Carles
    CSIC, Spain ; Inst Catalana Recerca & Estudis Avancats, Spain.
    Marrase, Celia
    CSIC, Spain.
    Gasol, Josep M.
    CSIC, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Response of rare, common and abundant bacterioplankton to anthropogenic perturbations in a Mediterranean coastal site2015In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 91, no 6, article id UNSP fiv058Article in journal (Refereed)
    Abstract [en]

    Bacterioplankton communities are made up of a small set of abundant taxa and a large number of low-abundant organisms (i.e. 'rare biosphere'). Despite the critical role played by bacteria in marine ecosystems, it remains unknown how this large diversity of organisms are affected by human-induced perturbations, or what controls the responsiveness of rare compared to abundant bacteria. We studied the response of a Mediterranean bacterioplankton community to two anthropogenic perturbations (i.e. nutrient enrichment and/or acidification) in two mesocosm experiments (in winter and summer). Nutrient enrichment increased the relative abundance of some operational taxonomic units (OTUs), e.g. Polaribacter, Tenacibaculum, Rhodobacteraceae and caused a relative decrease in others (e.g. Croceibacter). Interestingly, a synergistic effect of acidification and nutrient enrichment was observed on specific OTUs (e.g. SAR86). We analyzed the OTUs that became abundant at the end of the experiments and whether they belonged to the rare (<0.1% of relative abundance), the common (0.1-1.0% of relative abundance) or the abundant (>1% relative abundance) fractions. Most of the abundant OTUs at the end of the experiments were abundant, or at least common, in the original community of both experiments, suggesting that ecosystem alterations do not necessarily call for rare members to grow.

  • 15.
    Baltar, Federico
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Reinthaler, Thomas
    University of Vienna, Austria.
    Herndl, Gerhard J.
    University of Vienna, Austria ; Royal Netherlands Institute for Sea Research (NIOZ), The Netherlands.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Major Effect of Hydrogen Peroxide on Bacterioplankton Metabolism in the Northeast Atlantic2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 4, article id e61051Article in journal (Refereed)
    Abstract [en]

    Reactive oxygen species such as hydrogen peroxide have the potential to alter metabolic rates of marine prokaryotes, ultimately impacting the cycling and bioavailability of nutrients and carbon. We studied the influence of H2O2 on prokaryotic heterotrophic production (PHP) and extracellular enzymatic activities (i.e., beta-glucosidase [BGase], leucine aminopeptidase [LAPase] and alkaline phosphatase [APase]) in the subtropical Atlantic. With increasing concentrations of H2O2 in the range of 100-1000 nM, LAPase, APase and BGase were reduced by up to 11, 23 and 62%, respectively, in the different water layers. Incubation experiments with subsurface waters revealed a strong inhibition of all measured enzymatic activities upon H2O2 amendments in the range of 10-500 nM after 24 h. H2O2 additions also reduced prokaryotic heterotrophic production by 36-100% compared to the rapid increases in production rates occurring in the unamended controls. Our results indicate that oxidative stress caused by H2O2 affects prokaryotic growth and hydrolysis of specific components of the organic matter pool. Thus, we suggest that oxidative stress may have important consequences on marine carbon and energy fluxes.

  • 16.
    Baltar, Federico
    et al.
    Univ Las Palmas Gran Canaria, Fac Ciencias Mar, Las Palmas Gran Canaria 35017, Spain.
    Sintes, Eva
    van Aken, Hendrik M.
    Gasol, Josep M.
    Arístegui, Javier
    Herndl, Gerhard J.
    Prokaryotic extracellular enzymatic activity in relation to biomass production and respiration in the meso- and bathypelagic waters of the (sub)tropical Atlantic2009In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 11, no 8, p. 1998-2014Article in journal (Refereed)
    Abstract [en]

    P>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. 

  • 17. Boras, Julia
    et al.
    Sala, Montse M.
    Baltar, Federico
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Arístegui, Javier
    Duarte, Carlos M.
    Vaqué, D.
    Effect of viruses and protists on bacteria in eddies of the Canary Current region (subtropical Northeast Atlantic).2010In: Limnology and Oceanography, ISSN 0024-3590, E-ISSN 1939-5590, Vol. 55, no 2, p. 885-898Article in journal (Refereed)
    Abstract [en]

    The effect of oceanic eddies on microbial processes, with emphasis on bacterial losses due to protists and phages, was examined in the Canary Current region (subtropical northeast Atlantic) through the water column (down to 1000 m) during August 2006. Sampling stations were located in cyclonic and anticyclonic eddies, as well as in regions situated outside the influence of the eddy field (far-field stations). In the euphotic zone, in cyclonic eddies losses of bacteria due to viruses and protists were from 25.6% to 69.8%, and from not detected to 46.8% of bacterial production (BP) d(-1), respectively. In anticyclonic eddies, these values ranged from 20.6% to 90.2% of BP d(-1) for viruses, and from 8.0% to 79.4% of BP d(-1) for protists. At far-field stations, losses of bacteria ranged from 48.7% to 66.9% for viruses, and from not detected to 44.8% for protists. In addition, covering all stations and depths (from the epipelagic to the bathypelagic layer), bacterial losses due to viruses were significantly higher than losses by protists, and did not differ significantly among depths except for the stations situated in anticyclonic eddies, where they were significantly higher in the epipelagic layer. Lysogenic infection was more frequent at anticyclonic stations, where the highest pressure of protists on bacteria was observed. Because of the importance of viral activity, we suggest that lysis products from bacteria may be a source of regenerated nutrients in the surface of the oligotrophic ocean, in addition to the input of nutrients upwelled by eddies.

  • 18.
    Bunse, Carina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Israelsson, Stina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Martínez-García, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universidade de Vigo, Spain.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Muthusamy, Sarala Devi
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pontiller, Benjamin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Karlsson, Christofer M. G.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Seasonality and co-occurrences of free-living Baltic Sea bacterioplanktonManuscript (preprint) (Other academic)
  • 19. Burd, Adrian B.
    et al.
    Hansell, D. A.
    Steinberg, D. K.
    Anderson, T. R.
    Arístegui, J.
    Baltar, Federico
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Beaupré, S. R.
    Beusseler, K. O.
    DeHairs, F.
    Jackson, G. A.
    Kadko, D.
    Koppelmann, R.
    Lampitt, R. S.
    Nagata, T.
    Reinthaler, T.
    Robinson, C.
    Tamburini, C.
    Tanaka, T.
    Assessing the Apparent Imbalance Between Geochemical and Biochemical Indicators of Meso- and Bathypelagic Biological Activity: What the @$#! is wrong with present calculations of carbon budgets?2010In: Deep-sea research. Part II, Topical studies in oceanography, ISSN 0967-0645, E-ISSN 1879-0100, Vol. 57, no 16, p. 1557-1571Article in journal (Refereed)
    Abstract [en]

    Metabolic activity in the water column below the euphotic zone is ultimately fuelled by the vertical flux of organic material from the surface. Over time, the deep ocean is presumably at steady state, with sources and sinks balanced. But recently compiled global budgets and intensive local field studies suggest that estimates of metabolic activity in the dark ocean exceed the influx of organic substrates. This imbalance indicates either the existence of unaccounted sources of organic carbon or that metabolic activity in the dark ocean is being over-estimated. Budgets of organic carbon flux and metabolic activity in the dark ocean have uncertainties associated with environmental variability, measurement capabilities, conversion parameters, and processes that are not well sampled. We present these issues and quantify associated uncertainties where possible, using a Monte Carlo analysis of a published data set to determine the probability that the imbalance can be explained purely by uncertainties in measurements and conversion factors. A sensitivity analysis demonstrates that the bacterial growth efficiencies and assumed cell carbon contents have the greatest effects on the magnitude of the carbon imbalance. Two poorly quantified sources, lateral advection of particles and a population of slowly settling particles, are discussed as providing a means of closing regional carbon budgets. Finally, we make recommendations concerning future research directions to reduce important uncertainties and allow a better determination of the magnitude and causes of the unbalanced carbon budgets. (C) 2010 Elsevier Ltd. All rights reserved.

  • 20. Gasol, Josep M.
    et al.
    Alonso-Sáez, Laura
    Vaqué, D.
    Baltar, Federico
    Univ Las Palmas Gran Canaria, Fac Ciencias Mar, Las Palmas Gran Canaria 35017, Spain .
    Calleja, María L.
    Duarte, Carlos M.
    Arístegui, Javier
    Mesopelagic prokaryotic bulk and single-cell heterotrophic activity and community composition in the NW Africa-Canary Islands coastal-transition zone2009In: Progress in Oceanography, ISSN 0079-6611, E-ISSN 1873-4472, Vol. 83, p. 189-196Article in journal (Refereed)
    Abstract [en]

    Mesopelagic prokaryotic communities have often been assumed to be relatively inactive in comparison to those from epipelagic waters, and therefore unresponsive to the presence of nearby upwelled waters. We have studied the zonal (shelf-ocean), latitudinal, and depth (epipelagic-mesopelagic) variability of microbial assemblages in the NW Africa-Canary Islands coastal-transition zone (CTZ). Vertical profiles of bacterial bulk and single-cell activity through the epi- and mesopelagic waters were combined with point measurements of bacterial respiration, leucine-to-carbon conversion factors and leucine-to-thymidine incorporation ratios. The overall picture that emerges from our study is that prokaryotes in the mesopelagic zone of this area are less abundant than in the epipelagic but have comparable levels of activity. The relationship between prokaryotes and heterotrophic nanoflagellates, their main predators, remains constant throughout the water column, further contradicting the assumption that deep ocean bacterial communities are mostly inactive. Both bulk and single-cell activity showed clear differences between stations, with higher mesopelagic activities closer to the shelf or affected by upwelling features. We also tested whether differences in microbial function between stations could be related to differences in bacterial community structure, and conclude that bacterial communities are very similar at similar depths in the deep ocean, even if the stations present order-of-magnitude differences in bacterial function. 

  • 21. Herndl, Gerhard J.
    et al.
    Agogué, Helene
    Baltar, Federico
    Royal Netherlands Inst Sea Res, Dept Biol Oceanog, NL-1790 AB Den Burg, Netherlands.
    Reinthaler, Thomas
    Sintes, Eva
    Varela, Marta M.
    Regulation of aquatic microbial processes: the ‘microbial loop’ of the sunlit surface waters and the dark ocean dissected2008In: Aquatic Microbial Ecology, ISSN 0948-3055, E-ISSN 1616-1564, Vol. 53, no Sp. Iss. 1, p. 59-68Article in journal (Refereed)
    Abstract [en]

    Our understanding of microbial food web interactions in the ocean is essentially based on research performed in the euphotic layer, where the interactions between phytoplankton and prokaryotic plankton, mainly heterotrophic Bacteria, are well established. In the euphotic layer, particularly in meso- and eutrophic waters, prokaryotic plankton are mainly top-down controlled by bacterivorous flagellates and viruses, affecting metabolically active, fast growing populations more than dormant stages. In the meso- and bathypelagic realm of the ocean, however, prokaryotic plankton are thought to be mainly bottom-up controlled, because the heterotrophic component of the prokaryotic community is limited by the availability of organic carbon. However, deep-water prokaryotes exhibit a number of peculiarities compared to prokaryotes in the euphotic layer, among which are a large genome size and a gene repertoire indicative of a predominately surface-attached mode of life. This indicates that deep-water prokaryotic activity might be primarily associated with particles. Our present knowledge indicates that the microbial communities and their interactions in the deep ocean are likely very different from those known from surface waters. Increasing efforts to shed light on the microbial biota of the ocean's interior will likely lead to the discovery of novel metabolic pathways in prokaryotes and to the resolution of the current discrepancy between the geochemical evidence of remineralization rates of organic matter and actual measurements. 

  • 22.
    Israelsson, Stina
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Bertos-Fortis, Mireia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Fridolfsson, Emil
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindehoff, Elin
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lindh, Markus V.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Lund University.
    Martinez-Garcia, Sandra
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Universidade de Vigo, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Seasonal dynamics of Baltic Sea plankton activities: heterotrophic bacterial function under different biological and environmental conditionsManuscript (preprint) (Other academic)
  • 23.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Figueroa, Daniela
    Umeå University.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. University of Otago, New Zealand.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Agneta
    Umeå University.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Transplant experiments uncover Baltic Sea basin-specific responses in bacterioplankton community composition and metabolic activities2015In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 6, article id 223Article in journal (Refereed)
    Abstract [en]

    Anthropogenically induced changes in precipitation are projected to generate increased river runoff to semi-enclosed seas, increasing loads of terrestrial dissolved organic matter and decreasing salinity. To determine how bacterial community structure and functioning adjust to such changes, we designed microcosm transplant experiments with Baltic Proper (salinity 7.2) and Bothnian Sea (salinity 3.6) water. Baltic Proper bacteria generally reached higher abundances than Bothnian Sea bacteria in both Baltic Proper and Bothnian Sea water, indicating higher adaptability. Moreover, Baltic Proper bacteria growing in Bothnian Sea water consistently showed highest bacterial production and beta-glucosidase activity. These metabolic responses were accompanied by basin-specific changes in bacterial community structure. For example, Baltic Proper Pseudomonas and Limnobacter populations increased markedly in relative abundance in Bothnian Sea water, indicating a replacement effect. In contrast, Roseobacter and Rheinheimera populations were stable or increased in abundance when challenged by either of the waters, indicating an adjustment effect. Transplants to Bothnian Sea water triggered the initial emergence of particular Burkholderiaceae populations, and transplants to Baltic Proper water triggered Alteromonadaceae populations. Notably, in the subsequent re-transplant experiment, a priming effect resulted in further increases to dominance of these populations. Correlated changes in community composition and metabolic activity were observed only in the transplant experiment and only at relatively high phylogenetic resolution. This suggested an importance of successional progression for interpreting relationships between bacterial community composition and functioning. We infer that priming effects on bacterial community structure by natural episodic events or climate change induced forcing could translate into long-term changes in bacterial ecosystem process rates.

  • 24.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Riemann, Lasse
    Marine Biological Section, Department of Biology, University of Copenhagen, Helsingør, Denmark.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Romero-Oliva, Claudia
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Salomon, Paulo
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Granéli, Edna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Consequences of increased temperature and acidification on bacterioplankton community composition during a mesocosm spring bloom in the Baltic Sea2013In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 5, no 2, p. 252-262Article in journal (Refereed)
    Abstract [en]

    Despite the paramount importance of bacteria for biogeochemical cycling of carbon and nutrients, little is known about the potential effects of climate change on these key organisms. The consequences of the projected climate change on bacterioplankton community dynamics were investigated in a Baltic Sea spring phytoplankton bloom mesocosm experiment by increasing temperature with 3°C and decreasing pH by approximately 0.4 units via CO2 addition in a factorial design. Temperature was the major driver of differences in community composition during the experiment, as shown by denaturing gradient gel electrophoresis (DGGE) of amplified 16S rRNA gene fragments. Several bacterial phylotypes belonging to Betaproteobacteria were predominant at 3°C but were replaced by members of the Bacteriodetes in the 6°C mesocosms. Acidification alone had a limited impact on phylogenetic composition, but when combined with increased temperature, resulted in the proliferation of specific microbial phylotypes. Our results suggest that although temperature is an important driver in structuring bacterioplankton composition, evaluation of the combined effects of temperature and acidification is necessary to fully understand consequences of climate change for marine bacterioplankton, their implications for future spring bloom dynamics, and their role in ecosystem functioning.

  • 25.
    Lindh, Markus V.
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Sjöstedt, Johanna
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Andersson, Anders F.
    KTH Royal Inst Technol, Sweden.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Hugerth, Luisa
    KTH Royal Inst Technol, Sweden.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Muthusamy, Sarala Devi
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Legrand, Catherine
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Disentangling seasonal bacterioplankton population dynamics by high-frequency sampling2015In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 17, no 7, p. 2459-2476Article in journal (Refereed)
    Abstract [en]

    Multiyear comparisons of bacterioplankton succession reveal that environmental conditions drive community shifts with repeatable patterns between years. However, corresponding insight into bacterioplankton dynamics at a temporal resolution relevant for detailed examination of variation and characteristics of specific populations within years is essentially lacking. During 1 year, we collected 46 samples in the Baltic Sea for assessing bacterial community composition by 16S rRNA gene pyrosequencing (nearly twice weekly during productive season). Beta-diversity analysis showed distinct clustering of samples, attributable to seemingly synchronous temporal transitions among populations (populations defined by 97% 16S rRNA gene sequence identity). A wide spectrum of bacterioplankton dynamics was evident, where divergent temporal patterns resulted both from pronounced differences in relative abundance and presence/absence of populations. Rates of change in relative abundance calculated for individual populations ranged from 0.23 to 1.79 day(-1). Populations that were persistently dominant, transiently abundant or generally rare were found in several major bacterial groups, implying evolution has favoured a similar variety of life strategies within these groups. These findings suggest that high temporal resolution sampling allows constraining the timescales and frequencies at which distinct populations transition between being abundant or rare, thus potentially providing clues about physical, chemical or biological forcing on bacterioplankton community structure.

  • 26.
    Muthusamy, Sarala Devi
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    González, José M.
    Univ La Laguna, Dept Microbiol, Tenerife, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dynamics of metabolic activities and gene expression in the Roseobacter clade bacterium Phaeobacter sp. MED193 during growth with thiosulfate2014In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 80, no 22, p. 6933-6942Article in journal (Refereed)
    Abstract [en]

    Metagenomic analyses of surface seawater reveal that genes for sulfur oxidation are widespread in bacterioplankton communities. However, little is known about the metabolic processes used to exploit the energy potentially gained from inorganic sulfur oxidation in oxic seawater. We therefore studied the sox gene system containing Roseobacter clade isolate Phaeobacter sp. strain MED193 in acetate minimal medium with and without thiosulfate. The addition of thiosulfate enhanced the bacterial growth yields up to 40% in this strain. Concomitantly, soxB and soxY gene expression increased about 8-fold with thiosulfate and remained 11-fold higher than that in controls through stationary phase. At stationary phase, thiosulfate stimulated protein synthesis and anaplerotic CO2 fixation rates up to 5- and 35-fold, respectively. Several genes involved in anaplerotic CO2 fixation (i.e., pyruvate carboxylase, propionyl coenzyme A [CoA], and crotonyl-CoA carboxylase) were highly expressed during active growth, coinciding with high CO2 fixation rates. The high expression of key genes in the ethylmalonyl-CoA pathway suggests that this is an important pathway for the utilization of two-carbon compounds in Phaeobacter sp. MED193. Overall, our findings imply that Roseobacter clade bacteria carrying sox genes can use their lithotrophic potential to gain additional energy from sulfur oxidation for both increasing their growth capacity and improving their long-term survival.

  • 27.
    Muthusamy, Sarala Devi
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Lundin, Daniel
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Branca, Rui Miguel Mamede
    Sci Life Lab, Stockholm ; Karolinska Institutet.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Otago, New Zealand.
    Gonzalez, Jose M.
    Univ La Laguna, Spain.
    Lehtio, Janne
    Sci Life Lab, Stockholm ; Karolinska Institutet.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Comparative proteomics reveals signature metabolisms of exponentially growing and stationary phase marine bacteria2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 6, p. 2301-2319Article, review/survey (Refereed)
    Abstract [en]

    Much of the phenotype of a microorganism consists of its repertoire of metabolisms and how and when its proteins are deployed under different growth conditions. Hence, analyses of protein expression could provide important understanding of how bacteria adapt to different environmental settings. To characterize the flexibility of proteomes of marine bacteria, we investigated protein profiles of three important marine bacterial lineages - Oceanospirillaceae (Neptuniibacter caesariensis strain MED92), Roseobacter (Phaeobacter sp. MED193) and Flavobacteria (Dokdonia sp. MED134) - during transition from exponential to stationary phase. As much as 59-80% of each species' total proteome was expressed. Moreover, all three bacteria profoundly altered their expressed proteomes during growth phase transition, from a dominance of proteins involved in translation to more diverse proteomes, with a striking appearance of enzymes involved in different nutrient-scavenging metabolisms. Whereas the three bacteria shared several overarching metabolic strategies, they differed in important details, including distinct expression patterns of membrane transporters and proteins in carbon and phosphorous metabolism and storage compounds. These differences can be seen as signature metabolisms - metabolisms specific for lineages. These findings suggest that quantitative proteomics can inform about the divergent ecological strategies of marine bacteria in adapting to changes in environmental conditions.

  • 28. Nagata, Toshi
    et al.
    Tamburini, C.
    Arístegui, Javier
    Baltar, Federico
    Linnaeus University, Faculty of Science and Engineering, School of Natural Sciences.
    Bochdansky, A.
    Fonda-Unami, S.
    Fukuda, H.
    Gogou, A.
    Hansell, D. A.
    Hansman, R. L.
    Herndl, Gerhard J.
    Panagiotopoulos, C.
    Reinthaler, Thomas
    Sohrin, R.
    Verdugo, P.
    Yamada, N.
    Yamashita, Y.
    Yokokawa, T.
    Bartlett, D. H.
    Emerging concepts on microbial processes in the bathypelagic ocean – ecology, biogeochemistry and genomics2010In: Deep-sea research. Part II, Topical studies in oceanography, ISSN 0967-0645, E-ISSN 1879-0100, Vol. 57, no 16, p. 1519-1536Article in journal (Refereed)
    Abstract [en]

    This paper synthesizes recent findings regarding microbial distributions and processes in the bathypelagic ocean (depth > 1000 m). Abundance, production and respiration of prokaryotes reflect supplies of particulate and dissolved organic matter to the bathypelagic zone. Better resolution of carbon fluxes mediated by deep microbes requires further testing on the validity of conversion factors. Archaea, especially marine Crenarchaeota Group I, are abundant in deep waters where they can fix dissolved inorganic carbon. Viruses appear to be important in the microbial loop in deep waters, displaying remarkably high virus to prokaryote abundance ratios in some oceanic regions. Sequencing of 18S rRNA genes revealed a tremendous diversity of small-sized protists in bathypelagic waters. Abundances of heterotrophic nanoflagellates (HNF) and ciliates decrease with depth more steeply than prokaryotes; nonetheless, data indicated that HNF consumed half of prokaryote production in the bathypelagic zone. Aggregates are important habitats for deep-water microbes, which produce more extracellular enzymes (on a per-cell basis) than surface communities. The theory of marine gel formation provides a framework to unravel complex interactions between microbes and organic polymers. Recent data on the effects of hydrostatic pressure on microbial activities indicate that bathypelagic microbial activity is generally higher under in situ pressure conditions than at atmospheric pressures. High-throughput sequencing of 16S rRNA genes revealed a remarkable diversity of Bacteria in the bathypelagic ocean. Metagenomics and comparative genomics of piezophiles reveal not only the high diversity of deep sea microbes but also specific functional attributes of these piezophilic microbes, interpreted as an adaptation to the deep water environment. Taken together, the data compiled on bathypelagic microbes indicate that, despite high-pressure and low-temperature conditions, microbes in the bathypelagic ocean dynamically interact with complex mixtures of organic matter, responding to changes in the ocean's biogeochemical state.

  • 29.
    Palovaara, Joakim
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Akram, Neelam
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Baltar, Federico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Bunse, Carina
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Forsberg, Jeremy
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Pedrós-Alió, Carlos
    CSIC, Inst Ciencies Mar, Spain.
    González, José M.
    Univ La Laguna, Spain.
    Pinhassi, Jarone
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Stimulation of growth by proteorhodopsin phototrophy involves regulation of central metabolic pathways in marine planktonic bacteria2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 35, p. E3650-E3658Article in journal (Refereed)
    Abstract [en]

    Proteorhodopsin (PR) is present in half of surface ocean bacterioplankton, where its light-driven proton pumping provides energy to cells. Indeed, PR promotes growth or survival in different bacteria. However, the metabolic pathways mediating the light responses remain unknown. We analyzed growth of the PR-containing Dokdonia sp. MED134 (where light-stimulated growth had been found) in seawater with low concentrations of mixed [yeast extract and peptone (YEP)] or single (alanine, Ala) carbon compounds as models for rich and poor environments. We discovered changes in gene expression revealing a tightly regulated shift in central metabolic pathways between light and dark conditions. Bacteria showed relatively stronger light responses in Ala compared with YEP. Notably, carbon acquisition pathways shifted toward anaplerotic CO2 fixation in the light, contributing 31 +/- 8% and 24 +/- 6% of the carbon incorporated into biomass in Ala and YEP, respectively. Thus, MED134 was a facultative double mixotroph, i.e., photo- and chemotrophic for its energy source and using both bicarbonate and organic matter as carbon sources. Unexpectedly, relative expression of the glyoxylate shunt genes (isocitrate lyase and malate synthase) was >300-fold higher in the light-but only in Ala-contributing a more efficient use of carbon from organic compounds. We explored these findings in metagenomes and metatranscriptomes and observed similar prevalence of the glyoxylate shunt compared with PR genes and highest expression of the isocitrate lyase gene coinciding with highest solar irradiance. Thus, regulatory interactions between dissolved organic carbon quality and central metabolic pathways critically determine the fitness of surface ocean bacteria engaging in PR phototrophy.

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