Jesús M Arrieta | King Abdullah University of Science and Technology (KAUST) (original) (raw)

Papers by Jesús M Arrieta

Research paper thumbnail of Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

Molecular Ecology, 2015

The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been... more The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL (<0.8 μm) and PA (0.8 - 20 μm) prokaryotes at 30 stations distributed worldwide within the bathypelagic oceanic realm (2,150 - 4,000 m depth) using high throughput sequencing of the small subunit ribosomal RNA gene (16S rRNA). A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary time-scale. As a consequence, PA and FL communities had clear alpha- and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association to particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean. This article is protected by copyright. All rights reserved.

Research paper thumbnail of Enhanced viral production and infection of bacterioplankton during an iron-induced phytoplankton bloom in the Southern Ocean

Limnology and Oceanography, 2009

; followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment exp... more ; followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Although viral abundance increased in a rather constant way during the course of the experiment inside the patch, the production of bacterial viruses and the fraction of infected cells in bacterioplankton exhibited pronounced maxima on days 7 and 21. In contrast, these parameters remained fairly constant outside the Fe-fertilized patch. Viral production was also stimulated directly after the Fe-enrichment. Within the Fe-replete patch, viral abundance and production was on average 2-and 3-fold, respectively, higher than outside the patch. On average 40% of the bacteria contained viruses in a lytic stage inside the Fe-replete patch compared to 21% outside the patch. About 11-12% of the bacteria contained a viral genome inducible with mitomycin C in both inside and outside the patch. Randomly amplified polymorphic desoxyribonucleic acid polymerase chain reaction analysis suggested the development of a specific viral community in the patch. Although short-term stimulation of viral production was likely due to increased bacterial activity, the long-term stimulation was likely also influenced by an increased encounter rate between bacterial viruses and hosts. Viral lysis was responsible for most of the bacterioplankton mortality in the patch. Overall, most of the bacterial carbon production entered the detrital or dissolved organic matter pool via the viral shunt in the patch.

Research paper thumbnail of Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean

Frontiers in microbiology, 2014

Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of... more Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 10(4) and 1.6 × 10(7) microbes per m(2) of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m(2) every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days...

Research paper thumbnail of Deep carbon export from a Southern Ocean iron-fertilized diatom bloom

Research paper thumbnail of Biogeneration of chromophoric dissolved organic matter by bacteria and krill in the Southern Ocean

Limnology and Oceanography, 2009

Chromophoric dissolved organic matter (CDOM), the optically active fraction of dissolved organic ... more Chromophoric dissolved organic matter (CDOM), the optically active fraction of dissolved organic matter, is primarily generated by pelagic organisms in the open ocean. In this study, we experimentally determined the quantity and spectral quality of CDOM generated by bacterioplankton using two different substrates (with and without photoproducts) and by Antarctic krill Euphausia superba and evaluated their potential contributions to CDOM dynamics in the peninsular region of the Southern Ocean. CDOM was generated by bacteria in all experiments, and the presence of photoproducts influenced both the quantity and the spectral quality of the resultant CDOM. We confirmed a direct link between bacterial production and CDOM generation, which yielded in situ CDOM duplication times from 31 to 33 d. Antarctic krill as a direct source of CDOM was also confirmed experimentally. We estimated that CDOM generation by krill would lead to CDOM duplication times from 0.48 to 0.80 d within krill swarms. Our findings highlight the potential significance of bacteria and Antarctic krill swarms in the generation of CDOM and underscore the dynamic nature of CDOM in this area.

Research paper thumbnail of Enhanced viral production and infection of bacterioplankton during an iron-induced phytoplankton bloom in the Southern Ocean

Limnology and Oceanography, 2009

We followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment ex... more We followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Although viral abundance increased in a rather constant way during the course of the experiment inside the patch, the production of bacterial viruses and the fraction of infected cells in bacterioplankton exhibited pronounced maxima on days 7 and 21. In contrast, these parameters remained fairly constant outside the Fe-fertilized patch. Viral production was also stimulated directly after the Fe-enrichment. Within the Fe-replete patch, viral abundance and production was on average 2-and 3-fold, respectively, higher than outside the patch. On average 40% of the bacteria contained viruses in a lytic stage inside the Fe-replete patch compared to 21% outside the patch. About 11-12% of the bacteria contained a viral genome inducible with mitomycin C in both inside and outside the patch. Randomly amplified polymorphic desoxyribonucleic acid polymerase chain reaction analysis suggested the development of a specific viral community in the patch. Although short-term stimulation of viral production was likely due to increased bacterial activity, the long-term stimulation was likely also influenced by an increased encounter rate between bacterial viruses and hosts. Viral lysis was responsible for most of the bacterioplankton mortality in the patch. Overall, most of the bacterial carbon production entered the detrital or dissolved organic matter pool via the viral shunt in the patch.

Research paper thumbnail of Consequences of UV-enhanced community respiration for plankton metabolic balance

Limnology and Oceanography, 2014

The net community production (NCP) of plankton communities affects their role as sources or sinks... more The net community production (NCP) of plankton communities affects their role as sources or sinks of atmospheric CO 2 . Most estimates of NCP have been made by enclosing communities in bottles, generally glass borosilicate, that remove ultraviolet (UV)B and part of UVA wavelengths. A series of experiments were conducted to test whether NCP values from communities incubated excluding UVB (+ part of UVA) radiation (i.e., in glass borosilicate) differ from those of communities receiving the full solar radiation spectrum (i.e., incubated with quartz bottles) and to explore the effect of UV radiation on the respiration rates and bacterial production in these communities. Plankton NCP tended to be 43% lower, on average, when the rates were measured under full solar radiation than when UVB (+ part of UVA) was removed. Dark respiration was significantly enhanced after exposure to the full solar spectrum for most communities, showing lower values when previously incubated in a light environment free of UVB (250%) or in the dark (262%). Bacterial production was inhibited by natural sunlight but increased, as observed for community respiration, when transferred to the dark. Communities previously exposed to full solar spectrum showed the greatest increase in bacterial production when allowed to recover in the dark. The net result of these responses were an increase in community respiration and decline in net community production over 24 h, indicating that UVB radiation plays a major role in the metabolic balance of the ocean's surface ecosystem.

Research paper thumbnail of Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica)

Frontiers in Microbiology, 2012

Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known... more Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes, and leaves) by Denaturing Gradient Gel Electrophoresis (DGGE). A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units) were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ, and δ subclasses) and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

Research paper thumbnail of Experimental Assessment of Temperature Thresholds for Arctic Phytoplankton Communities

Estuaries and Coasts, 2014

We examined the responses of two different natural arctic plankton communities to warming in an a... more We examined the responses of two different natural arctic plankton communities to warming in an attempt to find temperature thresholds for abrupt changes in growth or biomass. We conducted two experiments in situ using two different plankton communities; incubation temperatures represented the annual variation in these Arctic waters plus 3-4°C to account for the potential warming expected for the Arctic Ocean during the twenty-first century. We evaluated changes in nutrient and chlorophyll a concentrations, primary production, cell abundances, and growth rates as well as cell biovolume and percentage of living cells for the main groups found during our study. Phytoplankton communities were composed of diatoms, Phaeocystis sp., Micromonas, as well as other flagellates. Results indicate a decrease in chlorophyll a concentration and growth rate at the highest temperatures tested. We also found a differing effect on cell abundance and growth rates depending on the taxonomic group or cell size: diatom abundance decreased with warming while small-sized phytoplankton showed an increasing trend at the intermediate temperature treatments. Biovolume estimates also tended to decrease with increasing temperature. We find a perceptible change in trends at intermediate temperature treatments for most of the parameters which suggests a possible thermal threshold around 5-6°C for the arctic plankton communities examined here.

Research paper thumbnail of The oligotrophic ocean is heterotrophic

Annual review of marine science, 2013

Incubation (in vitro) and incubation-free (in situ) methods, each with their own advantages and l... more Incubation (in vitro) and incubation-free (in situ) methods, each with their own advantages and limitations, have been used to derive estimates of net community metabolism in the oligotrophic subtropical gyres of the open ocean. The hypothesis that heterotrophic communities are prevalent in most oligotrophic regions is consistent with the available evidence and supported by scaling relationships showing that heterotrophic communities prevail in areas of low gross primary production, low chlorophyll a, and warm water, conditions found in the oligotrophic ocean. Heterotrophic metabolism can prevail where heterotrophic activity is subsidized by organic carbon inputs from the continental shelf or the atmosphere and from nonphotosynthetic autotrophic and mixotrophic metabolic pathways. The growth of the oligotrophic regions is likely to be tilting the metabolic balance of the ocean toward a greater prevalence of heterotrophic communities.

Research paper thumbnail of Response to: "Interpreting the Results of Oceanic Mesoscale Enrichment Experiments: Caveats and Lessons from Limnology and Coastal Ecology

Limnology and Oceanography, 2007

Research paper thumbnail of Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean

Frontiers in microbiology, 2014

Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of... more Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 10(4) and 1.6 × 10(7) microbes per m(2) of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m(2) every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days...

Research paper thumbnail of Global abundance of planktonic heterotrophic protists in the deep ocean

The ISME Journal, 2014

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remin... more The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72 ± 19 cells ml À 1 in mesopelagic waters down to 11 ± 1 cells ml À 1 in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml À 1 . The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

Research paper thumbnail of Marine Biodiversity and Gene Patents

Research paper thumbnail of Microbial diversity in the deep sea and the underexplored "rare biosphere

Proceedings of the National Academy of Sciences, 2006

The evolution of marine microbes over billions of years predicts that the composition of microbia... more The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This ''rare biosphere'' is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

Research paper thumbnail of The impact of ice melting on bacterioplankton in the Arctic Ocean

Polar Biology, 2010

Global warming and the associated ice melt are leading to an increase in the organic carbon in th... more Global warming and the associated ice melt are leading to an increase in the organic carbon in the Arctic Ocean. We evaluated the effects of ice melt on bacterioplankton at 21 stations in the Greenland Sea and Arctic Ocean in the summer of 2007, when a historical minimum of Arctic ice coverage was measured. Polar Surface Waters, which have a low temperature and low salinity and originate mainly from melted ice, contained a very low abundance of bacteria (7.01 9 10 5 ± 2.20 9 10 5 cells ml -1 ); however, these bacteria had high specific bacterial production (2.40 ± 1.61 fmol C bac -1 d -1 ) compared to those in Atlantic Waters. Specifically, bacterioplankton in Polar Surface Waters showed a preference for utilizing carbohydrates and had significantly higher specific activities of the glycosidases assayed, i.e. b-glucosidase, xylosidase, arabinosidase and cellobiosidase. Furthermore, bacterioplankton in Polar Sea Waters showed preferential growth on some of the carbohydrates in the Biolog Ecoplate, such as D-cellobiose and N-acetyl-D-glucosamine. Our results suggest that climate change and the associated melting of Arctic ice might induce changes in bacterioplankton functional diversity by enhancing the turnover of carbohydrates. Since organic aggregates are largely composed of polysaccharides, higher solubilization of aggregates might modify the carbon cycle, weaken the biological pump and have biogeochemical and ecological implications for the future Arctic Ocean.

Research paper thumbnail of Effect of ice melting on bacterial carbon fluxes channelled by viruses and protists in the Arctic Ocean

Polar Biology, 2010

During the last few years, extensive sea ice melting in the Arctic due to climate change has been... more During the last few years, extensive sea ice melting in the Arctic due to climate change has been detected, which could potentially modify the organic carbon fluxes in these waters. In this study, the effect of sea ice melting on bacterial carbon channelling by phages and protists has been evaluated in the northern Greenland Sea and Arctic Ocean. Grazing on bacteria by protists was evaluated using the FLB disappearance method. Lysis of bacteria due to viral infections was measured using the virus reduction approach. Losses of bacterial production caused by protists (PMM BP ) dominated losses caused by viruses (VMM BP ) throughout the study. Lysogenic viral production was detected in 7 out of 21 measurements and constituted from 33.9 to 100.0% of the total viral production. Significantly higher PMM BP and lower VMM BP were detected in waters affected by ice melting compared with unaffected waters. Consequently, significantly more bacterial carbon was channelled to the higher trophic levels in affected waters (13.05 ± 5.98 lgC l -1 day -1 ) than in unaffected waters (8.91 ± 8.33 lgC l -1 day -1 ). Viruses channelled 2.63 ± 2.45 lgC l -1 day -1 in affected waters and 4.27 ± 5.54 lgC l -1 day -1 in unaffected waters. We conclude that sea ice melting in the Arctic could modify the carbon flow through the microbial food web. This process may be especially important in the case of massive sea ice melting due to climate change.

Research paper thumbnail of Response of bacterioplankton to iron fertilization in the Southern Ocean

Limnology and Oceanography, 2004

We studied the bacterial response to Fe fertilization over 3 weeks during the second iron-enrichm... more We studied the bacterial response to Fe fertilization over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Bacterial abundance in the Fe-fertilized patch increased over the first 12 d following Fe release and remained about twice as high as outside the Fe-fertilized patch until the end of the experiment. Bacterial production peaked a few days after each of the three Fe releases inside the Fe-fertilized patch, reaching rates two to three times higher than outside the patch. Besides the peaks in leucine and thymidine incorporation following Fe release, bacterial production was not significantly higher inside the patch than outside, suggesting direct limitation of bacterial growth by Fe. Bacterial aminopeptidase activity roughly followed the increase in bacterial abundance, whereas cell-specific ␣and ␤-glucosidase were higher inside the Fe-fertilized patch. The diversity of ␤-glucosidases was determined by capillary electrophoresis zymography. The different ␤-glucosidases showed much higher activity levels inside the patch than in the surrounding waters, and three additional ␤-glucosidases constituting ϳ55% of the total ␤-glucosidase activity were present inside the Fe-fertilized patch from day 9 onward. No major changes in response to Fe fertilization were detected in the phylogenetic composition of the bacterioplankton community, as determined by 16S rDNA fingerprinting, indicating a remarkable adaptation of the bacterioplankton community to episodic iron inputs. This stability on the phylogenetic level is contrasted by the dramatic qualitative and quantitative changes in ectoenzymatic activity.

Research paper thumbnail of Changes in bacterial beta-glucosidase diversity during a coastal phytoplankton bloom

Limnology and Oceanography, 2002

Bacterial enzymatic hydrolysis of high molecular weight organic matter is the rate-limiting step ... more Bacterial enzymatic hydrolysis of high molecular weight organic matter is the rate-limiting step in the bacterially mediated carbon cycling in the global ocean. Despite the importance of this process, only bulk measurements of these hydrolytic activities are available, and the dynamics and diversity of the ectohydrolases involved in the cleavage of high molecular weight organic matter are poorly understood. In this study we monitored the dynamics of bacterial ␤-glucosidase diversity during the wax and wane of a coastal phytoplankton bloom using a newly developed capillary electrophoretic assay. Up to eight different ␤-glucosidases were detected in a single sample and 11 over the whole study period, revealing a previously unnoticed ␤-glucosidase diversity. A close link was found between the temporal succession of ␤-glucosidase diversity and bacterioplankton species richness as determined by terminal-restriction fragment length polymorphism analysis. This indicates that the regulation of the ␤-glucosidase activity and diversity was driven by shifts in the bacterial community structure rather than by simple induction of enzyme expression within a stable bacterioplankton community.

Research paper thumbnail of Long-term records of trace metal content of western Mediterranean seagrass ( Posidonia oceanica ) meadows: Natural and anthropogenic contributions

Journal of Geophysical Research, 2010

1] We discuss Al, Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn contents in seagrass Posidonia ocean... more 1] We discuss Al, Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn contents in seagrass Posidonia oceanica rhizomes from the Balearic Archipelago for the last 3 decades. Time series of metal concentration in P. oceanica were measured by dating rhizomes using retrospective procedures. The highest concentrations of Al (174.73 mg g −1 ), Cd (3.56 mg g −1 ), Cr (1.34 mg g −1 ), Cu (32.15 mg g −1 ), Pb (8.51 mg g −1 ), and Zn (107.14 mg g −1 ) were measured in meadows located around the largest and most densely populated island (Mallorca Island). There was a general tendency for Ag concentration to decrease with time (up to 80% from 1990 to 2005 in sample from Mallorca Island), which could be attributed to a reduction of the anthropogenic sources. Nickel and Zn concentrations were the unique elements that showed a consistent temporal trend in all samples, increasing their concentrations since year 1996 at all studied stations; this trend matched with the time series of UV-absorbing aerosols particles in the air (i.e., aerosols index) over the Mediterranean region (r 2 : 0.78, p < 0.001 for Cabrera Island), suggesting that P. oceanica could be an efficient recorder of dust events. A comparison of enrichment factors in rhizomes relative to average crustal material indicates that suspended aerosol is also the most likely source for Cr and Fe to P. oceanica. Citation: Tovar-Sánchez, A., J. Serón, N. Marbà, J. M. Arrieta, and C. M. Duarte (2010), Long-term records of trace metal content of western Mediterranean seagrass (Posidonia oceanica) meadows: Natural and anthropogenic contributions, J. Geophys.

Research paper thumbnail of Particle-association lifestyle is a phylogenetically conserved trait in bathypelagic prokaryotes

Molecular Ecology, 2015

The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been... more The free-living (FL) and particle-attached (PA) marine microbial communities have repeatedly been proved to differ in their diversity and composition in the photic ocean and also recently in the bathypelagic ocean at a global scale. However, although high taxonomic ranks exhibit preferences for a PA or FL mode of life, it remains poorly understood whether two clear lifestyles do exist and how these are distributed across the prokaryotic phylogeny. We studied the FL (&amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;amp;lt;0.8 μm) and PA (0.8 - 20 μm) prokaryotes at 30 stations distributed worldwide within the bathypelagic oceanic realm (2,150 - 4,000 m depth) using high throughput sequencing of the small subunit ribosomal RNA gene (16S rRNA). A high proportion of the bathypelagic prokaryotes were mostly found either attached to particles or freely in the surrounding water but rarely in both types of environments. In particular, this trait was deeply conserved through their phylogeny suggesting that the deep-ocean particles and the surrounding water constitute two highly distinct niches and that transitions from one to the other have been rare at an evolutionary time-scale. As a consequence, PA and FL communities had clear alpha- and beta-diversity differences that exceeded the global-scale geographical variation. Our study organizes the bathypelagic prokaryotic diversity into a reasonable number of ecologically coherent taxa regarding their association to particles, a first step for understanding which are the microbes responsible for the processing of the dissolved and particulate pools of organic matter that have a very different biogeochemical role in the deep ocean. This article is protected by copyright. All rights reserved.

Research paper thumbnail of Enhanced viral production and infection of bacterioplankton during an iron-induced phytoplankton bloom in the Southern Ocean

Limnology and Oceanography, 2009

; followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment exp... more ; followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Although viral abundance increased in a rather constant way during the course of the experiment inside the patch, the production of bacterial viruses and the fraction of infected cells in bacterioplankton exhibited pronounced maxima on days 7 and 21. In contrast, these parameters remained fairly constant outside the Fe-fertilized patch. Viral production was also stimulated directly after the Fe-enrichment. Within the Fe-replete patch, viral abundance and production was on average 2-and 3-fold, respectively, higher than outside the patch. On average 40% of the bacteria contained viruses in a lytic stage inside the Fe-replete patch compared to 21% outside the patch. About 11-12% of the bacteria contained a viral genome inducible with mitomycin C in both inside and outside the patch. Randomly amplified polymorphic desoxyribonucleic acid polymerase chain reaction analysis suggested the development of a specific viral community in the patch. Although short-term stimulation of viral production was likely due to increased bacterial activity, the long-term stimulation was likely also influenced by an increased encounter rate between bacterial viruses and hosts. Viral lysis was responsible for most of the bacterioplankton mortality in the patch. Overall, most of the bacterial carbon production entered the detrital or dissolved organic matter pool via the viral shunt in the patch.

Research paper thumbnail of Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean

Frontiers in microbiology, 2014

Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of... more Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 10(4) and 1.6 × 10(7) microbes per m(2) of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m(2) every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days...

Research paper thumbnail of Deep carbon export from a Southern Ocean iron-fertilized diatom bloom

Research paper thumbnail of Biogeneration of chromophoric dissolved organic matter by bacteria and krill in the Southern Ocean

Limnology and Oceanography, 2009

Chromophoric dissolved organic matter (CDOM), the optically active fraction of dissolved organic ... more Chromophoric dissolved organic matter (CDOM), the optically active fraction of dissolved organic matter, is primarily generated by pelagic organisms in the open ocean. In this study, we experimentally determined the quantity and spectral quality of CDOM generated by bacterioplankton using two different substrates (with and without photoproducts) and by Antarctic krill Euphausia superba and evaluated their potential contributions to CDOM dynamics in the peninsular region of the Southern Ocean. CDOM was generated by bacteria in all experiments, and the presence of photoproducts influenced both the quantity and the spectral quality of the resultant CDOM. We confirmed a direct link between bacterial production and CDOM generation, which yielded in situ CDOM duplication times from 31 to 33 d. Antarctic krill as a direct source of CDOM was also confirmed experimentally. We estimated that CDOM generation by krill would lead to CDOM duplication times from 0.48 to 0.80 d within krill swarms. Our findings highlight the potential significance of bacteria and Antarctic krill swarms in the generation of CDOM and underscore the dynamic nature of CDOM in this area.

Research paper thumbnail of Enhanced viral production and infection of bacterioplankton during an iron-induced phytoplankton bloom in the Southern Ocean

Limnology and Oceanography, 2009

We followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment ex... more We followed the viral response to Fe-enrichment over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Although viral abundance increased in a rather constant way during the course of the experiment inside the patch, the production of bacterial viruses and the fraction of infected cells in bacterioplankton exhibited pronounced maxima on days 7 and 21. In contrast, these parameters remained fairly constant outside the Fe-fertilized patch. Viral production was also stimulated directly after the Fe-enrichment. Within the Fe-replete patch, viral abundance and production was on average 2-and 3-fold, respectively, higher than outside the patch. On average 40% of the bacteria contained viruses in a lytic stage inside the Fe-replete patch compared to 21% outside the patch. About 11-12% of the bacteria contained a viral genome inducible with mitomycin C in both inside and outside the patch. Randomly amplified polymorphic desoxyribonucleic acid polymerase chain reaction analysis suggested the development of a specific viral community in the patch. Although short-term stimulation of viral production was likely due to increased bacterial activity, the long-term stimulation was likely also influenced by an increased encounter rate between bacterial viruses and hosts. Viral lysis was responsible for most of the bacterioplankton mortality in the patch. Overall, most of the bacterial carbon production entered the detrital or dissolved organic matter pool via the viral shunt in the patch.

Research paper thumbnail of Consequences of UV-enhanced community respiration for plankton metabolic balance

Limnology and Oceanography, 2014

The net community production (NCP) of plankton communities affects their role as sources or sinks... more The net community production (NCP) of plankton communities affects their role as sources or sinks of atmospheric CO 2 . Most estimates of NCP have been made by enclosing communities in bottles, generally glass borosilicate, that remove ultraviolet (UV)B and part of UVA wavelengths. A series of experiments were conducted to test whether NCP values from communities incubated excluding UVB (+ part of UVA) radiation (i.e., in glass borosilicate) differ from those of communities receiving the full solar radiation spectrum (i.e., incubated with quartz bottles) and to explore the effect of UV radiation on the respiration rates and bacterial production in these communities. Plankton NCP tended to be 43% lower, on average, when the rates were measured under full solar radiation than when UVB (+ part of UVA) was removed. Dark respiration was significantly enhanced after exposure to the full solar spectrum for most communities, showing lower values when previously incubated in a light environment free of UVB (250%) or in the dark (262%). Bacterial production was inhibited by natural sunlight but increased, as observed for community respiration, when transferred to the dark. Communities previously exposed to full solar spectrum showed the greatest increase in bacterial production when allowed to recover in the dark. The net result of these responses were an increase in community respiration and decline in net community production over 24 h, indicating that UVB radiation plays a major role in the metabolic balance of the ocean's surface ecosystem.

Research paper thumbnail of Endophytic bacterial community of a Mediterranean marine angiosperm (Posidonia oceanica)

Frontiers in Microbiology, 2012

Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known... more Bacterial endophytes are crucial for the survival of many terrestrial plants, but little is known about the presence and importance of bacterial endophytes of marine plants. We conducted a survey of the endophytic bacterial community of the long-living Mediterranean marine angiosperm Posidonia oceanica in surface-sterilized tissues (roots, rhizomes, and leaves) by Denaturing Gradient Gel Electrophoresis (DGGE). A total of 26 Posidonia oceanica meadows around the Balearic Islands were sampled, and the band patterns obtained for each meadow were compared for the three sampled tissues. Endophytic bacterial sequences were detected in most of the samples analyzed. A total of 34 OTUs (Operational Taxonomic Units) were detected. The main OTUs of endophytic bacteria present in P. oceanica tissues belonged primarily to Proteobacteria (α, γ, and δ subclasses) and Bacteroidetes. The OTUs found in roots significantly differed from those of rhizomes and leaves. Moreover, some OTUs were found to be associated to each type of tissue. Bipartite network analysis revealed differences in the bacterial endophyte communities present on different islands. The results of this study provide a pioneering step toward the characterization of the endophytic bacterial community associated with tissues of a marine angiosperm and reveal the presence of bacterial endophytes that differed among locations and tissue types.

Research paper thumbnail of Experimental Assessment of Temperature Thresholds for Arctic Phytoplankton Communities

Estuaries and Coasts, 2014

We examined the responses of two different natural arctic plankton communities to warming in an a... more We examined the responses of two different natural arctic plankton communities to warming in an attempt to find temperature thresholds for abrupt changes in growth or biomass. We conducted two experiments in situ using two different plankton communities; incubation temperatures represented the annual variation in these Arctic waters plus 3-4°C to account for the potential warming expected for the Arctic Ocean during the twenty-first century. We evaluated changes in nutrient and chlorophyll a concentrations, primary production, cell abundances, and growth rates as well as cell biovolume and percentage of living cells for the main groups found during our study. Phytoplankton communities were composed of diatoms, Phaeocystis sp., Micromonas, as well as other flagellates. Results indicate a decrease in chlorophyll a concentration and growth rate at the highest temperatures tested. We also found a differing effect on cell abundance and growth rates depending on the taxonomic group or cell size: diatom abundance decreased with warming while small-sized phytoplankton showed an increasing trend at the intermediate temperature treatments. Biovolume estimates also tended to decrease with increasing temperature. We find a perceptible change in trends at intermediate temperature treatments for most of the parameters which suggests a possible thermal threshold around 5-6°C for the arctic plankton communities examined here.

Research paper thumbnail of The oligotrophic ocean is heterotrophic

Annual review of marine science, 2013

Incubation (in vitro) and incubation-free (in situ) methods, each with their own advantages and l... more Incubation (in vitro) and incubation-free (in situ) methods, each with their own advantages and limitations, have been used to derive estimates of net community metabolism in the oligotrophic subtropical gyres of the open ocean. The hypothesis that heterotrophic communities are prevalent in most oligotrophic regions is consistent with the available evidence and supported by scaling relationships showing that heterotrophic communities prevail in areas of low gross primary production, low chlorophyll a, and warm water, conditions found in the oligotrophic ocean. Heterotrophic metabolism can prevail where heterotrophic activity is subsidized by organic carbon inputs from the continental shelf or the atmosphere and from nonphotosynthetic autotrophic and mixotrophic metabolic pathways. The growth of the oligotrophic regions is likely to be tilting the metabolic balance of the ocean toward a greater prevalence of heterotrophic communities.

Research paper thumbnail of Response to: "Interpreting the Results of Oceanic Mesoscale Enrichment Experiments: Caveats and Lessons from Limnology and Coastal Ecology

Limnology and Oceanography, 2007

Research paper thumbnail of Resolving the abundance and air-sea fluxes of airborne microorganisms in the North Atlantic Ocean

Frontiers in microbiology, 2014

Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of... more Airborne transport of microbes may play a central role in microbial dispersal, the maintenance of diversity in aquatic systems and in meteorological processes such as cloud formation. Yet, there is almost no information about the abundance and fate of microbes over the oceans, which cover >70% of the Earth's surface and are the likely source and final destination of a large fraction of airborne microbes. We measured the abundance of microbes in the lower atmosphere over a transect covering 17° of latitude in the North Atlantic Ocean and derived estimates of air-sea exchange of microorganisms from meteorological data. The estimated load of microorganisms in the atmospheric boundary layer ranged between 6 × 10(4) and 1.6 × 10(7) microbes per m(2) of ocean, indicating a very dynamic air-sea exchange with millions of microbes leaving and entering the ocean per m(2) every day. Our results show that about 10% of the microbes detected in the boundary layer were still airborne 4 days...

Research paper thumbnail of Global abundance of planktonic heterotrophic protists in the deep ocean

The ISME Journal, 2014

The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remin... more The dark ocean is one of the largest biomes on Earth, with critical roles in organic matter remineralization and global carbon sequestration. Despite its recognized importance, little is known about some key microbial players, such as the community of heterotrophic protists (HP), which are likely the main consumers of prokaryotic biomass. To investigate this microbial component at a global scale, we determined their abundance and biomass in deepwater column samples from the Malaspina 2010 circumnavigation using a combination of epifluorescence microscopy and flow cytometry. HP were ubiquitously found at all depths investigated down to 4000 m. HP abundances decreased with depth, from an average of 72 ± 19 cells ml À 1 in mesopelagic waters down to 11 ± 1 cells ml À 1 in bathypelagic waters, whereas their total biomass decreased from 280±46 to 50±14 pg C ml À 1 . The parameters that better explained the variance of HP abundance were depth and prokaryote abundance, and to lesser extent oxygen concentration. The generally good correlation with prokaryotic abundance suggested active grazing of HP on prokaryotes. On a finer scale, the prokaryote:HP abundance ratio varied at a regional scale, and sites with the highest ratios exhibited a larger contribution of fungi molecular signal. Our study is a step forward towards determining the relationship between HP and their environment, unveiling their importance as players in the dark ocean's microbial food web.

Research paper thumbnail of Marine Biodiversity and Gene Patents

Research paper thumbnail of Microbial diversity in the deep sea and the underexplored "rare biosphere

Proceedings of the National Academy of Sciences, 2006

The evolution of marine microbes over billions of years predicts that the composition of microbia... more The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of deep water masses of the North Atlantic and diffuse flow hydrothermal vents are one to two orders of magnitude more complex than previously reported for any microbial environment. A relatively small number of different populations dominate all samples, but thousands of low-abundance populations account for most of the observed phylogenetic diversity. This ''rare biosphere'' is very ancient and may represent a nearly inexhaustible source of genomic innovation. Members of the rare biosphere are highly divergent from each other and, at different times in earth's history, may have had a profound impact on shaping planetary processes.

Research paper thumbnail of The impact of ice melting on bacterioplankton in the Arctic Ocean

Polar Biology, 2010

Global warming and the associated ice melt are leading to an increase in the organic carbon in th... more Global warming and the associated ice melt are leading to an increase in the organic carbon in the Arctic Ocean. We evaluated the effects of ice melt on bacterioplankton at 21 stations in the Greenland Sea and Arctic Ocean in the summer of 2007, when a historical minimum of Arctic ice coverage was measured. Polar Surface Waters, which have a low temperature and low salinity and originate mainly from melted ice, contained a very low abundance of bacteria (7.01 9 10 5 ± 2.20 9 10 5 cells ml -1 ); however, these bacteria had high specific bacterial production (2.40 ± 1.61 fmol C bac -1 d -1 ) compared to those in Atlantic Waters. Specifically, bacterioplankton in Polar Surface Waters showed a preference for utilizing carbohydrates and had significantly higher specific activities of the glycosidases assayed, i.e. b-glucosidase, xylosidase, arabinosidase and cellobiosidase. Furthermore, bacterioplankton in Polar Sea Waters showed preferential growth on some of the carbohydrates in the Biolog Ecoplate, such as D-cellobiose and N-acetyl-D-glucosamine. Our results suggest that climate change and the associated melting of Arctic ice might induce changes in bacterioplankton functional diversity by enhancing the turnover of carbohydrates. Since organic aggregates are largely composed of polysaccharides, higher solubilization of aggregates might modify the carbon cycle, weaken the biological pump and have biogeochemical and ecological implications for the future Arctic Ocean.

Research paper thumbnail of Effect of ice melting on bacterial carbon fluxes channelled by viruses and protists in the Arctic Ocean

Polar Biology, 2010

During the last few years, extensive sea ice melting in the Arctic due to climate change has been... more During the last few years, extensive sea ice melting in the Arctic due to climate change has been detected, which could potentially modify the organic carbon fluxes in these waters. In this study, the effect of sea ice melting on bacterial carbon channelling by phages and protists has been evaluated in the northern Greenland Sea and Arctic Ocean. Grazing on bacteria by protists was evaluated using the FLB disappearance method. Lysis of bacteria due to viral infections was measured using the virus reduction approach. Losses of bacterial production caused by protists (PMM BP ) dominated losses caused by viruses (VMM BP ) throughout the study. Lysogenic viral production was detected in 7 out of 21 measurements and constituted from 33.9 to 100.0% of the total viral production. Significantly higher PMM BP and lower VMM BP were detected in waters affected by ice melting compared with unaffected waters. Consequently, significantly more bacterial carbon was channelled to the higher trophic levels in affected waters (13.05 ± 5.98 lgC l -1 day -1 ) than in unaffected waters (8.91 ± 8.33 lgC l -1 day -1 ). Viruses channelled 2.63 ± 2.45 lgC l -1 day -1 in affected waters and 4.27 ± 5.54 lgC l -1 day -1 in unaffected waters. We conclude that sea ice melting in the Arctic could modify the carbon flow through the microbial food web. This process may be especially important in the case of massive sea ice melting due to climate change.

Research paper thumbnail of Response of bacterioplankton to iron fertilization in the Southern Ocean

Limnology and Oceanography, 2004

We studied the bacterial response to Fe fertilization over 3 weeks during the second iron-enrichm... more We studied the bacterial response to Fe fertilization over 3 weeks during the second iron-enrichment experiment (EisenEx) in the Southern Ocean. Bacterial abundance in the Fe-fertilized patch increased over the first 12 d following Fe release and remained about twice as high as outside the Fe-fertilized patch until the end of the experiment. Bacterial production peaked a few days after each of the three Fe releases inside the Fe-fertilized patch, reaching rates two to three times higher than outside the patch. Besides the peaks in leucine and thymidine incorporation following Fe release, bacterial production was not significantly higher inside the patch than outside, suggesting direct limitation of bacterial growth by Fe. Bacterial aminopeptidase activity roughly followed the increase in bacterial abundance, whereas cell-specific ␣and ␤-glucosidase were higher inside the Fe-fertilized patch. The diversity of ␤-glucosidases was determined by capillary electrophoresis zymography. The different ␤-glucosidases showed much higher activity levels inside the patch than in the surrounding waters, and three additional ␤-glucosidases constituting ϳ55% of the total ␤-glucosidase activity were present inside the Fe-fertilized patch from day 9 onward. No major changes in response to Fe fertilization were detected in the phylogenetic composition of the bacterioplankton community, as determined by 16S rDNA fingerprinting, indicating a remarkable adaptation of the bacterioplankton community to episodic iron inputs. This stability on the phylogenetic level is contrasted by the dramatic qualitative and quantitative changes in ectoenzymatic activity.

Research paper thumbnail of Changes in bacterial beta-glucosidase diversity during a coastal phytoplankton bloom

Limnology and Oceanography, 2002

Bacterial enzymatic hydrolysis of high molecular weight organic matter is the rate-limiting step ... more Bacterial enzymatic hydrolysis of high molecular weight organic matter is the rate-limiting step in the bacterially mediated carbon cycling in the global ocean. Despite the importance of this process, only bulk measurements of these hydrolytic activities are available, and the dynamics and diversity of the ectohydrolases involved in the cleavage of high molecular weight organic matter are poorly understood. In this study we monitored the dynamics of bacterial ␤-glucosidase diversity during the wax and wane of a coastal phytoplankton bloom using a newly developed capillary electrophoretic assay. Up to eight different ␤-glucosidases were detected in a single sample and 11 over the whole study period, revealing a previously unnoticed ␤-glucosidase diversity. A close link was found between the temporal succession of ␤-glucosidase diversity and bacterioplankton species richness as determined by terminal-restriction fragment length polymorphism analysis. This indicates that the regulation of the ␤-glucosidase activity and diversity was driven by shifts in the bacterial community structure rather than by simple induction of enzyme expression within a stable bacterioplankton community.

Research paper thumbnail of Long-term records of trace metal content of western Mediterranean seagrass ( Posidonia oceanica ) meadows: Natural and anthropogenic contributions

Journal of Geophysical Research, 2010

1] We discuss Al, Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn contents in seagrass Posidonia ocean... more 1] We discuss Al, Ag, Cd, Co, Cr, Cu, Fe, Mn, Ni, Pb, and Zn contents in seagrass Posidonia oceanica rhizomes from the Balearic Archipelago for the last 3 decades. Time series of metal concentration in P. oceanica were measured by dating rhizomes using retrospective procedures. The highest concentrations of Al (174.73 mg g −1 ), Cd (3.56 mg g −1 ), Cr (1.34 mg g −1 ), Cu (32.15 mg g −1 ), Pb (8.51 mg g −1 ), and Zn (107.14 mg g −1 ) were measured in meadows located around the largest and most densely populated island (Mallorca Island). There was a general tendency for Ag concentration to decrease with time (up to 80% from 1990 to 2005 in sample from Mallorca Island), which could be attributed to a reduction of the anthropogenic sources. Nickel and Zn concentrations were the unique elements that showed a consistent temporal trend in all samples, increasing their concentrations since year 1996 at all studied stations; this trend matched with the time series of UV-absorbing aerosols particles in the air (i.e., aerosols index) over the Mediterranean region (r 2 : 0.78, p < 0.001 for Cabrera Island), suggesting that P. oceanica could be an efficient recorder of dust events. A comparison of enrichment factors in rhizomes relative to average crustal material indicates that suspended aerosol is also the most likely source for Cr and Fe to P. oceanica. Citation: Tovar-Sánchez, A., J. Serón, N. Marbà, J. M. Arrieta, and C. M. Duarte (2010), Long-term records of trace metal content of western Mediterranean seagrass (Posidonia oceanica) meadows: Natural and anthropogenic contributions, J. Geophys.