By coupling DNA-SIP and pyrosequencing approaches, we identified Cycloclasticus sp. as a keystone degrader of polycyclic aromatic hydrocarbons (PAH) despite being a member of the ‘rare biosphere’ in ...NW Mediterranean seawaters. We discovered novel PAH-degrading bacteria (Oceanibaculum sp., Sneathiella sp.) and we identified other groups already known to possess this function (Alteromonas sp., Paracoccus sp.). Together with Cycloclasticus sp., these groups contributed to potential in situ phenanthrene degradation at a rate >0.5 mg l−1 day−1, sufficient to account for a considerable part of PAH degradation. Further, we characterized the PAH-tolerant bacterial communities, which were much more diverse in the polluted site by comparison to unpolluted marine references. PAH-tolerant bacteria were also members of the rare biosphere, such as Glaciecola sp. Collectively, these data show the complex interactions between PAH-degraders and PAH-tolerant bacteria and provide new insights for the understanding of the functional ecology of marine bacteria in polluted waters.
•We surveyed the PAH-degraders and the PAH-tolerant bacteria in coastal seawaters.•Coupling DNA stable isotope probing and pyrosequencing approaches.•Identification of keystone PAH-degraders, discovering novel PAH-degrading bacteria.•Rare bacterial biosphere as a ‘seed bank’ to withstand marine oil spill events.
Capsule: Role of the rare biosphere as a ‘seed bank’ to support the environment to withstand pollution events. Identification of keystone PAH-degraders and PAH-tolerant bacteria.
Summary
Open‐ocean convection is a fundamental process for thermohaline circulation and biogeochemical cycles that causes spectacular mixing of the water column. Here, we tested how much the ...depth‐stratified prokaryotic communities were influenced by such an event, and also by the following re‐stratification. The deep convection event (0–1500 m) that occurred in winter 2010–2011 in the NW Mediterranean Sea resulted in a homogenization of the prokaryotic communities over the entire convective cell, resulting in the predominance of typical surface Bacteria, such as Oceanospirillale and Flavobacteriales. Statistical analysis together with numerical simulation of vertical homogenization evidenced that physical turbulence only was not enough to explain the new distribution of the communities, but acted in synergy with other parameters such as exported particulate and dissolved organic matters. The convection also stimulated prokaryotic abundance (+21%) and heterotrophic production (+43%) over the 0–1500 m convective cell, and resulted in a decline of cell‐specific extracellular enzymatic activities (−67%), thus suggesting an intensification of the labile organic matter turnover during the event. The rapid re‐stratification of the prokaryotic diversity and activities in the intermediate layer 5 days after the intense mixing indicated a marked resilience of the communities, apart from the residual deep mixed water patch.
Biostimulation through the addition of inorganic nutrients has been the most widely practiced bioremediation strategy in oil-polluted marine waters. However, little attention has so far been paid to ...the microbial food web and the impact of top-down control that directly or indirectly influences the success of the bioremediation. We designed a mesocosm experiment using pre-filtered (<50 μm) surface seawater from the Bay of Banyuls-sur-Mer (North-Western Mediterranean Sea) and examined the top-down effect exerted by heterotrophic nanoflagellates (HNF) and virus-like particles (VLP) on prokaryotic abundance, activity and diversity in the presence or absence of diesel fuel. Prokaryotes, HNF and VLP abundances showed a predator–prey succession, with a co-development of HNF and VLP. In the polluted system, we observed a stronger impact of viral lysis on prokaryotic abundances than in the control. Analysis of the diversity revealed that a bloom of Vibrio sp. occurred in the polluted mesocosm. That bloom was rapidly followed by a less abundant and more even community of predation-resistant bacteria, including known hydrocarbon degraders such as Oleispira spp. and Methylophaga spp. and opportunistic bacteria such as Percisivirga spp., Roseobacter spp. and Phaeobacter spp. The shift in prokaryotic dominance in response to viral lysis provided clear evidence of the 'killing the winner' model. Nevertheless, despite clear effects on prokaryotic abundance, activity and diversity, the diesel degradation was not impacted by top-down control. The present study investigates for the first time the functioning of a complex microbial network (including VLP) using a nutrient-based biostimulation strategy and highlights some key processes useful for tailoring bioremediation.
We evaluated the relative impact of anthropogenic polycyclic aromatic hydrocarbons (PAHs) among biogeochemical variables on total, metabolically active, and PAH bacterial communities in summer and ...winter in surface microlayer (SML) and subsurface seawaters (SSW) across short transects along the NW Mediterranean coast from three harbors, one wastewater effluent, and one nearshore observatory reference site. At both seasons, significant correlations were found between dissolved total PAH concentrations and PAH-degrading bacteria that formed a gradient from the shore to nearshore waters. Accumulation of PAH degraders was particularly high in the SML, where PAHs accumulated. Harbors and wastewater outfalls influenced drastically and in a different way the total and active bacterial community structure, but they only impacted the communities from the nearshore zone (<2 km from the shore). By using direct multivariate statistical analysis, we confirmed the significant effect of PAH concentrations on the spatial and temporal dynamic of total and active communities in this area, but this effect was putted in perspective by the importance of other biogeochemical variables.
The 2009–2010 period was marked by an episode of intense drought known as the El Niño Modoki event. Sampling of the Términos Lagoon (Mexico) was carried out in November 2009 in order to understand ...the influence of these particular environmental conditions on organic matter fluxes within the lagoon's pelagic ecosystem and, more specifically, on the relationship between phyto- and bacterioplankton communities. The measurements presented here concern biogeochemical parameters (nutrients, dissolved and particulate organic matter POM, and dissolved polycyclic aromatic hydrocarbons PAHs), phytoplankton (biomass and photosynthesis), and bacteria (diversity and abundance, including PAH degradation bacteria and ectoenzymatic activities). During the studied period, the water column of the Términos Lagoon functioned globally as a sink and, more precisely, as a nitrogen assimilator. This was due to the high production of particulate and dissolved organic matter (DOM), even though exportation of autochthonous matter to the Gulf of Mexico was weak. We found that bottom-up control accounted for a large portion of the variability of phytoplankton productivity. Nitrogen and phosphorus stoichiometry mostly accounted for the heterogeneity in phytoplankton and free-living prokaryote distribution in the lagoon. In the eastern part, we found a clear decoupling between areas enriched in dissolved inorganic nitrogen near the Puerto Real coastal inlet and areas enriched in phosphate (PO4) near the Candelaria estuary. Such a decoupling limited the potential for primary production, resulting in an accumulation of dissolved organic carbon and nitrogen (DOC and DON, respectively) near the river mouths. In the western part of the lagoon, maximal phytoplankton development resulted from bacterial activity transforming particulate organic phosphorus (PP) and dissolved organic phosphorus (DOP) to available PO4 and the coupling between Palizada River inputs of nitrate (NO3) and PP. The Chumpan River contributed only marginally to PO4 inputs due to its very low contribution to overall river inputs. The highest dissolved total PAH concentrations were measured in the El Carmen Inlet, suggesting that the anthropogenic pollution of the zone is probably related to the oil-platform exploitation activities in the shallow waters of the southern of the Gulf of Mexico. We also found that a complex array of biogeochemical and phytoplanktonic parameters were the driving force behind the geographical distribution of bacterial community structure and activities. Finally, we showed that nutrients brought by the Palizada River supported an abundant bacterial community of PAH degraders, which are of significance in this important oil-production zone.
Pollution history has often been proposed to explain site-dependent bioremediation efficiencies, but this hypothesis has been poorly explored. Here, bacteria and their heterotrophic nanoflagellates ...(HNF) predators originating from pristine and chronically oil-polluted coastal sites were subjected to crude oil ± nutrients or emulsifier amendments. The addition of crude oil had a more visible effect on bacteria originating from the pristine site with a higher increase in the activity of given OTU and inactivation of other petroleum-sensitive bacteria, as revealed by DNA and RNA-based comparison. Such changes resulted in a delay in microbial growth and in a lower bacterial degradation of the more complex hydrocarbons. Biostimulation provoked a selection of different bacterial community assemblages and stirred metabolically active bacteria. This resulted in a clear increase of the peak of bacteria and their HNF predators and higher oil degradation, irrespective of the pollution history of the site.
► Oil had a more visible effect on the OLIG compared to POLL bacterial communities. ► Bacteria originated from the pristine site adapted to oil input after a lag period. ► PAH were more degraded in the POLL site. ► Biostimulation stirred the response of bacteria and HNF to oil pollution. ► HNF controlled bacteria within less than 48 h of the height of their outbreak.
Computer modeling is used widely to predict inhaled aerosol deposition in the human lung based on definition of the input conditions describing the aerosol characteristics, the breathing pattern and ...the airway anatomy of the subject. Validation of the models is limited by the lack of detailed experimental data. Three dimensional imaging data provides an opportunity to address this unmet need. Radioactive aerosol was administered to each of 11 healthy male subjects on two occasions under carefully monitored input conditions. Input parameters varied were particle size, depth of breathing, carrier gas and posture. The aerosol distribution was measured by combined single photon emission computed tomography and X-ray computer tomography (SPECT/CT). Airway anatomy was determined by high resolution CT imaging. The distribution of deposition was determined by a combination of 2D and 3D analysis and described in terms of the percentage of inhaled aerosol deposited in sections of the respiratory tract and in both spatial and anatomical sub-divisions within each lung. The percentage deposition in the conducting airways was also assessed by 24h clearance. A set of imaging data of aerosol deposition has been produced in which the input parameters of inhalation are well described. The parameters were varied in a controlled manner to allow the sensitivity of predictive models to different factors to be tested. An initial analysis of the data is presented which will act as a guide that other centers can use to compare their own methodology. This data is considered to be of great potential value to computer modelers of aerosol deposition in validating their models.
► In-vivo 3D images of aerosol deposition acquired with controlled input conditions. ► 3D deposition pattern correlated to high resolution anatomical images. ► Initial analysis of experimental data presented. ► Image data and conditions of aerosol delivery available via the internet. ► Data invaluable to modelers of aerosol deposition in validating predictions.
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