Differential recruitment of opportunistic taxa leads to contrasting abilities in carbon processing by bathypelagic and surface microbial communities.

Different factors affect the way dissolved organic matter (DOM) is processed in the ocean water column, including environmental conditions and the functional capabilities of the communities. Recent studies have shown that bathypelagic prokaryotes are metabolically flexible, but whether this versatility translates into a higher ability to process DOM has been barely explored. Here we performed a multifactorial transplant experiment to compare the growth, activity and changes in DOM quality in surface and bathypelagic waters inoculated with either surface or bathypelagic prokaryotic communities. The effect of nutrient additions to surface waters was also explored. Despite no differences in the cell abundance of surface and deep ocean prokaryotes were observed in any of the treatments, in surface waters with nutrients the heterotrophic production of surface prokaryotes rapidly decreased. Conversely, bathypelagic communities displayed a sustained production throughout the experiment. Incubations with surface prokaryotes always led to a significant accumulation of recalcitrant compounds, which did not occur with bathypelagic prokaryotes, suggesting they have a higher ability to process DOM. These contrasting abilities could be explained by the recruitment of a comparatively larger number of opportunistic taxa within the bathypelagic assemblages, which likely resulted in a broader community capability of substrate utilization.

Sinking particles promote vertical connectivity in the ocean microbiome.

The sinking of organic particles formed in the photic layer is a main vector of carbon export into the deep ocean. Although sinking particles are heavily colonized by microbes, so far it has not been explored whether this process plays a role in transferring prokaryotic diversity from surface to deep oceanic layers. Using Illumina sequencing of the 16S rRNA gene, we explore here the vertical connectivity of the ocean microbiome by characterizing marine prokaryotic communities associated with five different size fractions and examining their compositional variability from surface down to 4,000 m across eight stations sampled in the Atlantic, Pacific, and Indian Oceans during the Malaspina 2010 Expedition. Our results show that the most abundant prokaryotes in the deep ocean are also present in surface waters. This vertical community connectivity seems to occur predominantly through the largest particles because communities in the largest size fractions showed the highest taxonomic similarity throughout the water column, whereas free-living communities were more isolated vertically. Our results further suggest that particle colonization processes occurring in surface waters determine to some extent the composition and biogeography of bathypelagic communities. Overall, we postulate that sinking particles function as vectors that inoculate viable particle-attached surface microbes into the deep-sea realm, determining to a considerable extent the structure, functioning, and biogeography of deep ocean communities.

Major imprint of surface plankton on deep ocean prokaryotic structure and activity.

Deep ocean microbial communities rely on the organic carbon produced in the sunlit ocean, yet it remains unknown whether surface processes determine the assembly and function of bathypelagic prokaryotes to a larger extent than deep-sea physicochemical conditions. Here, we explored whether variations in surface phytoplankton assemblages across Atlantic, Pacific and Indian ocean stations can explain structural changes in bathypelagic (ca. 4,000 m) free-living and particle-attached prokaryotic communities (characterized through 16S rRNA gene sequencing), as well as changes in prokaryotic activity and dissolved organic matter (DOM) quality. We show that the spatial structuring of prokaryotic communities in the bathypelagic strongly followed variations in the abundances of surface dinoflagellates and ciliates, as well as gradients in surface primary productivity, but were less influenced by bathypelagic physicochemical conditions. Amino acid-like DOM components in the bathypelagic reflected variations of those components in surface waters, and seemed to control bathypelagic prokaryotic activity. The imprint of surface conditions was more evident in bathypelagic than in shallower mesopelagic (200-1,000 m) communities, suggesting a direct connectivity through fast-sinking particles that escape mesopelagic transformations. Finally, we identified a pool of endemic deep-sea prokaryotic taxa (including potentially chemoautotrophic groups) that appear less connected to surface processes than those bathypelagic taxa with a widespread vertical distribution. Our results suggest that surface planktonic communities shape the spatial structure of the bathypelagic microbiome to a larger extent than the local physicochemical environment, likely through determining the nature of the sinking particles and the associated prokaryotes reaching bathypelagic waters.

Spatial variability of marine bacterial and archaeal communities along the particulate matter continuum.

Biotic and abiotic particles shape the microspatial architecture that defines the microbial aquatic habitat, being particles highly variable in size and quality along oceanic horizontal and vertical gradients. We analysed the prokaryotic (bacterial and archaeal) diversity and community composition present in six distinct particle size classes ranging from the pico- to the microscale (0.2 to 200 µm). Further, we studied their variations along oceanographic horizontal (from the coast to open oceanic waters) and vertical (from the ocean surface into the meso- and bathypelagic ocean) gradients. In general, prokaryotic community composition was more variable with depth than in the transition from the coast to the open ocean. Comparing the six size-fractions, distinct prokaryotic communities were detected in each size-fraction, and whereas bacteria were more diverse in the larger size-fractions, archaea were more diverse in the smaller size-fractions. Comparison of prokaryotic community composition among particle size-fractions showed that most, but not all, taxonomic groups have a preference for a certain size-fraction sustained with depth. Species sorting, or the presence of diverse ecotypes with distinct size-fraction preferences, may explain why this trend is not conserved in all taxa.

Patterns of prokaryotic activity along the marine planktonic matter continuum.

Prokaryotic abundance and activity are commonly assessed by dividing them into two size-fractions: free-living and attached to particles. Nevertheless, organic matter, essential for the growth of heterotrophic prokaryotes, is present in the environment in a continuum of sizes, from purely dissolved to large particles. Therefore, defining the activity of the prokaryotic community would be more accurate by considering all the distinct size fractions. To achieve this, we measured prokaryotic abundance (PA), heterotrophic prokaryotic activity (as leucine incorporation) and extracellular enzyme activities at a coastal site in the NW Mediterranean Sea. We conducted measurements in both bulk seawater and size fractionated samples sequentially passing through 5 different filter types: 0.2-0.8-3-5-10 µm pore size. Our results indicate that the fraction <0.8 µm contained the highest percentage of cells (91.6 ± 1.1 %) and leucine incorporation rates (72.2 ± 3.5 %). Most of the extracellular enzyme activity appeared in the dissolved fraction (<0.2 µm; 19.8-79.4 %), yet the specific activity of the enzymes (per cell activity) was 100-1000 times higher in the particulate (>0.8 µm) than in the free-living (0.2-0.8 µm) fraction. The size fraction with highest specific activities for leucine incorporation and most of the enzyme activities (ß-glucosidase, esterase, Leu-aminopeptidase and alkaline phosphatase) was the 5-10 µm fraction. In contrast, the higher specific chitobiase activity in the >10 µm fraction, suggests that the prokaryotic community colonizing large particles might be more specialized in the hydrolysis of organic matter of zooplanktonic origin than the community colonizing smaller particles.

Particulate and dissolved fluorescent organic matter fractionation and composition: Abiotic and ecological controls in the Southern Ocean.

Phytoplankton-derived organic matter sustains heterotrophic marine life in regions away from terrestrial inputs such as the Southern Ocean. Fluorescence spectroscopy has long been used to characterize the fluorescent organic matter (FOM) pool. However, most studies focus only in the dissolved FOM fraction (FDOM) disregarding the contribution of particles. In order to assess the dynamics and drivers of the dissolved and particulate fractions of FOM, we used a Lagrangian approach to follow the time evolution of phytoplankton proliferations at four different sites in the Southern Ocean and compared the FOM in filtered and unfiltered seawater aliquots. We found that filtration had little effects on FOM visible spectrum fluorescence intensities, implying that most of this signal was due to dissolved fluorophores. On the other hand, protein-like fluorescence was strongly supressed by filtration, with fluorescence of particles accounting for up to 90 % of the total protein-like FOM. Photobleaching was identified as the main driver of visible FDOM composition, which was better described by indices of phytoplankton photoacclimation than by measurements of the incident solar radiation dose. In contrast, protein-like FOM intensity and fractionation were primarily related to abundance, composition and physiological state of phytoplankton proliferations. The chlorophyll a concentration from non-diatom phytoplankton explained 91 % of the particulate protein-like FOM variability. The proportion of protein-like fluorescence found in the dissolved phase was predicted by the combination of potential viral and grazing pressures, which accounted for 51 and 29 % of its variability, respectively. Our results show that comparing FOM measurements from filtered and unfiltered seawater provides relevant information on the taxonomic composition and cell integrity of phytoplankton communities. A better understanding of the commonly overlooked FOM fractionation process is essential for the implementation of in situ fluorescence sensors and will also help us better understand the processes that govern OM cycling in marine systems.

Seasonal Variation of Bacterial Diversity Along the Marine Particulate Matter Continuum.

Seasonal dynamics of ocean prokaryotic communities in the free-living fraction have been widely described, but less is known about the seasonality of prokaryotes inhabiting marine particles. We describe the seasonality of bacterial communities in the particulate matter continuum by sampling monthly over two years in a temperate oligotrophic coastal ecosystem and using a serial filtration (including six size-fractions spanning from 0.2 to 200 µm). We observed that bacterial communities in the particulate matter continuum had annual changes following harmonic seasonal oscillations, where alpha, beta, and gamma diversity increased during the warm period and decreased during the cold period. Communities in each size-fraction changed gradually over time, being the communities in larger size-fractions the ones with stronger annual changes. Annual community changes were driven mainly by day length and sea surface temperature, and each size-fraction was additionally affected by other variables (e.g., smaller size-fractions by dissolved PO4 and larger size-fractions by turbidity). While some taxonomic groups mantained their preference for a given size fraction during most of the year, others varied their distribution into different size fractions over time, as e.g., SAR11, which increased its presence in particles during the cold period. Our results indicate that the size-fractionation scheme provides novel seasonal patterns that are not possible to unveil by analyzing only free-living bacteria, and that help to better understand the temporal dynamics of prokaryotes.

Microbial responses to perfluoroalkyl substances and perfluorooctanesulfonate (PFOS) desulfurization in the Antarctic marine environment.

Perfluorooctanesulfonate (PFOS) and perfluorooctanoate (PFOA) acids are ubiquitous in the oceans, including remote regions, and are toxic to fish and mammals. The impact to the lowest trophic levels of the food web, however, remains unknown. We challenged natural bacterial communities inhabiting Antarctic coastal waters (Deception Island) with PFOS and PFOA concentrations ranging from 2 ng/L to 600 ng/L that selected for tolerant taxa. After 48 h, concentrations of PFOS decreased by more than 50% and sulfur metabolism-related transcripts were significantly enriched in the treatments suggesting desulfurization of PFOS. Conversely, no significant differences were found between initial and final PFOA concentrations. Gammaproteobacteria and Roseobacter, two abundant groups of marine bacteria, increased their relative activity after 24 h of incubation, whereas Flavobacteriia became the main contributor in the treatments after 6 days. Community activities (extracellular enzyme activity and absolute number of transcripts) were higher in the treatments than in the controls, while bacterial abundances were lower in the treatments, suggesting a selection of PFOS and PFOA tolerant community in the exposed treatments. Our results show a direct effect of PFOS and PFOA exposure on the composition and functionality of natural Antarctic marine microbial communities. While no evidence of defluorination of PFOS or PFOA was detected, probable desulfurization of PFOS depicts a direct link with the sulfur biogeochemistry of the ocean.

Seasonal impact of grazing, viral mortality, resource availability and light on the group-specific growth rates of coastal Mediterranean bacterioplankton.

Estimation of prokaryotic growth rates is critical to understand the ecological role and contribution of different microbes to marine biogeochemical cycles. However, there is a general lack of knowledge on what factors control the growth rates of different prokaryotic groups and how these vary between sites and along seasons at a given site. We carried out several manipulation experiments during the four astronomical seasons in the coastal NW Mediterranean in order to evaluate the impact of grazing, viral mortality, resource competition and light on the growth and loss rates of prokaryotes. Gross and net growth rates of different bacterioplankton groups targeted by group-specific CARD-FISH probes and infrared microscopy (for aerobic anoxygenic phototrophs, AAP), were calculated from changes in cell abundances. Maximal group-specific growth rates were achieved when both predation pressure and nutrient limitation were experimentally minimized, while only a minimal effect of viral pressure on growth rates was observed; nevertheless, the response to predation removal was more remarkable in winter, when the bacterial community was not subjected to nutrient limitation. Although all groups showed increases in their growth rates when resource competition as well as grazers and viral pressure were reduced, Alteromonadaceae consistently presented the highest rates in all seasons. The response to light availability was generally weaker than that to the other factors, but it was variable between seasons. In summer and spring, the growth rates of AAP were stimulated by light whereas the growth of the SAR11 clade (likely containing proteorhodopsin) was enhanced by light in all seasons. Overall, our results set thresholds on bacterioplankton group-specific growth and mortality rates and contribute to estimate the seasonally changing contribution of various bacterioplankton groups to the function of microbial communities. Our results also indicate that the least abundant groups display the highest growth rates, contributing to the recycling of organic matter to a much greater extent than what their abundances alone would predict.

Annual changes of bacterial mortality due to viruses and protists in an oligotrophic coastal environment (NW Mediterranean).

The impact of viruses and protists on bacterioplankton mortality was examined monthly during 2 years (May 2005-April 2007) in an oligotrophic coastal environment (NW Mediterranean Sea). We expected that in such type of system, (i) bacterial losses would be caused mainly by protists, and (ii) lysogeny would be an important type of virus-host interaction. During the study period, viruses and grazers together were responsible for 50.6 +/- 40.1% day(-1) of bacterial standing stock losses (BSS) and 59.7 +/- 44.0% day(-1) of bacterial production losses (BP). Over the first year (May 2005-April 2006), protists were the principal cause of bacterial mortality, removing 29.9 +/- 20.4% day(-1) of BSS and 33.9 +/- 24.3% day(-1) of BP, whereas viral lysis removed 13.5 +/- 17.0% day(-1) of BSS and 12.3 +/- 12.3% day(-1) of BP. During the second year (May 2006-April 2007), viruses caused comparable bacterial losses (29.2 +/- 14.8% day(-1) of BSS and 40.9 +/- 20.7% day(-1) of BP) to protists (28.6 +/- 25.5% day(-1) of BSS and 32.4 +/- 20.0% day(-1) of BP). In 37% of cases higher losses of BP due to viruses than due to protists were found. Lysogenic infection was detected in 11 of 24 samplings. Contrary to our expectations, lytic infections dominated over the two years, and viruses resulted to be a significant source of bacterial mortality in this oligotrophic site.

Modulation of microbial growth and enzymatic activities in the marine environment due to exposure to organic contaminants of emerging concern and hydrocarbons.

Organic pollutants are continuously being introduced in seawater with uncharacterized impacts on the engines of the marine biogeochemical cycles, the microorganisms. The effects on marine microbial communities were assessed for perfluoroalkyl substances, organophosphate esters flame retardants and plasticizers, polycyclic aromatic hydrocarbons, and n-alkanes. Dose-response experiments were performed at three stations and at three depths in the NW Mediterranean with contrasted nutrient and pollutant concentrations. In these experiments, the microbial growth rates, the abundances of the main bacterial groups, measured by Catalyzed Reporter Deposition Fluorescence In Situ Hybridization (CARD-FISH), and extracellular enzymatic activities, were quantified. Increasing concentrations of organic pollutants (OPs) promoted different responses in the communities that were compound, organism and nutrient availability (trophic status). The largest differences between OP treatments and controls in the growth rates of both heterotrophic and phototrophic microbial groups were observed in seawater from the deep chlorophyll maxima. Furthermore, there was a compound specific stimulation of different extracellular enzymatic activities after the exposure to OPs. Our results revealed that marine microbial communities reacted not only to hydrocarbons, known to be used as a carbon source, but also to low concentrations of organic pollutants of emerging concern in a complex manner, reflecting the variability of various environmental variables. Multiple linear regressions suggested that organic pollutants modulated the bacterial growth and extracellular enzymatic activities, but this modulation was of lower magnitude than the observed pronounced response of the microbial community to nutrient availability.

Seasonal dynamics of transparent exopolymer particles (TEP) and their drivers in the coastal NW Mediterranean Sea.

Transparent Exopolymer Particles (TEPs) are a subclass of organic particles with high impact in biogeochemical and ecological processes, such as the biological carbon pump, air-sea interactions, or the microbial loop. However, the complexity in production and consumption makes TEP dynamics hardly predictable, calling for the need of descriptive studies about the in situ dynamics of these particles. We followed monthly TEP dynamics and combined them with a dataset of environmental variables during three years in a coastal site of the oligotrophic North Western Mediterranean (Blanes Bay). TEP concentration, ranging from 11.3 to 289.1µgXGeqL-1 (average 81.7±11.7µgXGeqL-1), showed recurrent peaks in early summer (June-July). TEP were temporally disconnected from chlorophyll a maxima, that occurred in late winter and early spring (maxima 1.21µgL-1), but they were significantly related to the abundance of specific phytoplankton groups (diatoms and dinoflagellates) and also coincided with periods of low nutrient concentrations. The fraction of particulate organic carbon in the form of TEP (the TEP:POC and TEP:PM ratios) were also highest in early summer, indicating that TEP-enriched particles of low density accumulate in surface waters during stratified periods. We hypothesize that the accumulation of these particles affects the microbial food web by enhancing the activity of specific prokaryotic extracellular enzymes (esterase, ß-glucosidase and alkaline phosphatase) and promoting the abundance of heterotrophic nanoflagellates.

Antarctic sea ice region as a source of biogenic organic nitrogen in aerosols.

Climate warming affects the development and distribution of sea ice, but at present the evidence of polar ecosystem feedbacks on climate through changes in the atmosphere is sparse. By means of synergistic atmospheric and oceanic measurements in the Southern Ocean near Antarctica, we present evidence that the microbiota of sea ice and sea ice-influenced ocean are a previously unknown significant source of atmospheric organic nitrogen, including low molecular weight alkyl-amines. Given the keystone role of nitrogen compounds in aerosol formation, growth and neutralization, our findings call for greater chemical and source diversity in the modelling efforts linking the marine ecosystem to aerosol-mediated climate effects in the Southern Ocean.

Out of Thin Air: Microbial Utilization of Atmospheric Gaseous Organics in the Surface Ocean.

Volatile and semi-volatile gas-phase organic carbon (GOC) is a largely neglected component of the global carbon cycle, with poorly resolved pools and fluxes of natural and anthropogenic GOC in the biosphere. Substantial amounts of atmospheric GOC are exchanged with the surface ocean, and subsequent utilization of specific GOC compounds by surface ocean microbial communities has been demonstrated. Yet, the final fate of the bulk of the atmospheric GOC entering the surface ocean is unknown. Our data show experimental evidence of efficient use of atmospheric GOC by marine prokaryotes at different locations in the NE Subtropical Atlantic, the Arctic Ocean and the Mediterranean Sea. We estimate that between 2 and 27% of the prokaryotic carbon demand was supported by GOC with a major fraction of GOC inputs being consumed within the mixed layer. The role of the atmosphere as a key vector of organic carbon subsidizing marine microbial metabolism is a novel link yet to be incorporated into the microbial ecology of the surface ocean as well as into the global carbon budget.

Trends in Ostreopsis proliferation along the Northern Mediterranean coasts.

Harmful benthic microalgae blooms represent an emergent phenomenon in temperate zones, causing health, ecological and economic concern. The main goal of this work was to compile records of Ostreopsis at large temporal and spatial scales, in order to study the relationship between cell abundances, the periodicity and intensity of the blooms and the role of sea water temperature in 14 Spanish, French, Monegasque and Italian sites located along the northern limits of the Mediterranean Sea. General trends were observed in the two considered basins: the north-western Mediterranean Sea, in which higher cell abundances were mostly recorded in mid-summer (end of July), and the northern Adriatic Sea where they occur in early fall (end of September). The sea-water temperature does not seem to be a primary driver, and the maximal abundance periods were site and year specific. Such results represent an important step in the understanding of harmful benthic microalgae blooms in temperate areas, and provide a good base for policy makers and managers in the attempt to monitor and forecast benthic harmful microalgae blooms.