Response of archaeal communities to oil spill in bioturbated mudflat sediments.

The response of archaeal community to oil spill with the combined effect of the bioturbation activity of the polychaetes Hediste diversicolor was determined in mudflat sediments from the Aber-Benoît basin (Brittany, French Atlantic coast), maintained in microcosms. The dynamics of the archaeal community was monitored by combining comparative terminal restriction fragment length polymorphism (T-RFLP) fingerprints and sequence library analyses based on 16S rRNA genes and 16S cDNA. Methanogens were also followed by targeting the mcrA gene. Crenarchaeota were always detected in all communities irrespective of the addition of H. diversicolor and/or oil. In the presence of oil, modifications of archaeal community structures were observed. These modifications were more pronounced when H. diversicolor was added resulting in a more diverse community especially for the Euryarchaeota and Thaumarchaeota. The analysis of mcrA transcripts showed a specific structure for each condition since the beginning of the experiment. Overall, oiled microcosms showed different communities irrespective of H. diversicolor addition, while similar hydrocarbon removal capacities were observed.

A valuable experimental setup to model exposure to Legionella's aerosols generated by shower-like systems.

The mechanism underlying Legionella aerosolization and entry into the respiratory tract remains poorly documented. In previous studies, we characterized the aerodynamic behaviour of Legionella aerosols and assessed their regional deposition within the respiratory tract using a human-like anatomical model. The aim of this study was to assess whether this experimental setup could mimic the exposure to bioaerosols generated by showers. To achieve this objective we performed experiments to measure the mass median aerodynamic diameter (MMAD) as well as the emitted dose and the physiological state of the airborne bacteria generated by a shower and two nebulizers (vibrating-mesh and jet nebulizers). The MMADs of the dispersed bioaerosols were characterized using a 12-stage cascade low-pressure impactor. The amount of dispersed airborne bacteria from a shower was quantified using a Coriolis® Delta air sampler and compared to the airborne bacteria reaching the thoracic region in the experimental setup. The physiological state and concentration of airborne Legionella were assessed by qPCR for total cells, culture for viable and cultivable Legionella (VC), and flow cytometry for viable but non-cultivable Legionella (VBNC). In summary, the experimental setup developed appears to mimic the bioaerosol emission of a shower in terms of aerodynamic size distribution. Compared to the specific case of a shower used as a reference in this study, the experimental setup developed underestimates by 2 times (when the jet nebulizer is used) or overestimates by 43 times (when the vibrating-mesh nebulizer is used) the total emitted dose of airborne bacteria. To our knowledge, this report is the first showing that an experimental model mimics so closely an exposure to Legionella aerosols produced by showers to assess human lung deposition and infection in well-controlled and safe conditions.

Deposition pattern of aerosolized Legionella using an ex vivo human-porcine respiratory model.

Legionella are bacteria responsible for severe lung pathologies. However how they enter and are deposited within the respiratory tract remains poorly documented. Data using animal testing led to the establishment of mathematical models allowing the estimation of aerosol dispersion risks. But direct extrapolation to humans is questionable and experimental models more physiologically representative of the inhalation route are welcome. The aim of this study was to develop a model as close as possible to the human anatomy and physiology allowing determining the deposition pattern of aerosolized Legionella while limiting in vivo experiments. To that purpose, we adapted the chimeric respiratory tract model we previously developed. This original model consisted of a replica of the human upper respiratory airways made by additive manufacturing connected to ex vivo porcine lungs ventilated by passive expansion, as for humans in physiological conditions. These experiments didn't imply specific animal sacrifices as pigs were bred for human consumption and lungs were considered as wastes by the slaughterhouse. Fluorescent Legionella were aerosolized and visualized using Cellvizio® Lab (probe-based confocal fluorescence microscope). Legionella were found in the whole respiratory tract. Broncho-alveolar lavages were also performed and the amount of Legionella reaching the thoracic region was quantified by culture and qPCR. Legionella were found preferentially in the left upper lobe compared to the right lower lobe. To our knowledge, it is the first time that experiments mimicking so closely human exposure by inhalation are performed while limiting animal experiments and providing a model for further Legionella infectious risk assessment.

Dynamic of sulphate-reducing microorganisms in petroleum-contaminated marine sediments inhabited by the polychaete Hediste diversicolor.

The behaviour of sulphate-reducing microbial community was investigated at the oxic-anoxic interface (0-2 cm) of marine sediments when submitted to oil and enhanced bioturbation activities by the addition of Hediste diversicolor. Although total hydrocarbon removal was not improved by the addition of H. diversicolor, terminal restriction fragment length polymorphism (T-RFLP) analyses based on dsrAB (dissimilatory sulphite reductase) genes and transcripts showed different patterns according to the presence of H. diversicolor which favoured the abundance of dsrB genes during the early stages of incubation. Complementary DNA (cDNA) dsrAB libraries revealed that in presence of H. diversicolor, most dsrAB sequences belonged to hydrocarbonoclastic Desulfobacteraceae, suggesting that sulphate-reducing microorganisms (SRMs) may play an active role in hydrocarbon biodegradation in sediments where the reworking activity is enhanced. Furthermore, the presence of dsrAB sequences related to sequences found associated to environments with high dinitrogen fixation activity suggested potential N2 fixation by SRMs in bioturbated-polluted sediments.

Structure of hydrocarbonoclastic nitrate-reducing bacterial communities in bioturbated coastal marine sediments.

The organisation of denitrifying microorganisms in oil-polluted bioturbated sediments was investigated in mesocosms under conditions as closer as possible to that observed in the environment. Molecular and culture-dependent approaches revealed that denitrifying Gammaproteobacteria were abundant in oil-polluted and bioturbated sediments suggesting that they may play a key role in hydrocarbon degradation in the environment. T-RFLP and gene libraries analyses targeting nirS gene showed that denitrifying microbial communities structure was slightly affected by either the addition of Hediste diversicolor or crude oil revealing the metabolic versatility of denitrifying microorganisms. From oil-polluted sediments, distinct denitrifying hydrocarbonoclastic bacterial consortia were obtained by enrichment cultures on high molecular weight polyaromatic hydrocarbons (PAHs) (dibenzothiophene, fluoranthene, pyrene and chrysene) under nitrate-reducing conditions. Interestingly, molecular characterisation of the consortia showed that the denitrifying communities obtained from oiled microcosms with addition of H. diversicolor were different to that observed without H. diversicolor addition, especially with fluoranthene and chrysene revealing the bacterial diversity involved in the degradation of these PAHs.

Impact of oil on bacterial community structure in bioturbated sediments.

Oil spills threaten coastlines where biological processes supply essential ecosystem services. Therefore, it is crucial to understand how oil influences the microbial communities in sediments that play key roles in ecosystem functioning. Ecosystems such as sediments are characterized by intensive bioturbation due to burrowing macrofauna that may modify the microbial metabolisms. It is thus essential to consider the bioturbation when determining the impact of oil on microbial communities. In this study, an experimental laboratory device maintaining pristine collected mudflat sediments in microcosms closer to true environmental conditions--with tidal cycles and natural seawater--was used to simulate an oil spill under bioturbation conditions. Different conditions were applied to the microcosms including an addition of: standardized oil (Blend Arabian Light crude oil, 25.6 mg.g⁻¹ wet sediment), the common burrowing organism Hediste (Nereis) diversicolor and both the oil and H. diversicolor. The addition of H. diversicolor and its associated bioturbation did not affect the removal of petroleum hydrocarbons. After 270 days, 60% of hydrocarbons had been removed in all microcosms irrespective of the H. diversicolor addition. However, 16S-rRNA gene and 16S-cDNA T-RFLP and RT-PCR-amplicon libraries analysis showed an effect of the condition on the bacterial community structure, composition, and dynamics, supported by PerMANOVA analysis. The 16S-cDNA libraries from microcosms where H. diversicolor was added (oiled and un-oiled) showed a marked dominance of sequences related to Gammaproteobacteria. However, in the oiled-library sequences associated to Deltaproteobacteria and Bacteroidetes were also highly represented. The 16S-cDNA libraries from oiled-microcosms (with and without H. diversicolor addition) revealed two distinct microbial communities characterized by different phylotypes associated to known hydrocarbonoclastic bacteria and dominated by Gammaproteobacteria and Deltaproteobacteria. In the oiled-microcosms, the addition of H. diversicolor reduced the phylotype-richness, sequences associated to Actinobacteria, Firmicutes and Plantomycetes were not detected. These observations highlight the influence of the bioturbation on the bacterial community structure without affecting the biodegradation capacities.

Enhanced structural and functional genome elucidation of the arsenite-oxidizing strain Herminiimonas arsenicoxydans by proteomics data.

The arsenite-oxidizing strain Herminiimonas arsenicoxydans proteome was investigated with gel electrophoresis and tandem mass spectrometry analyses. The comparison of experimental and theoretical M(r) and pI, as well as that of peptide sequences identified by MS and predicted protein sequences, allowed the correction of five protein annotations. More importantly, the functional analysis of SDS- and 2D-PAGE proteome maps obtained in the presence of arsenic, combined with partial transcriptomic results indicate that H. arsenicoxydans expressed genes and proteins required not only for arsenic detoxification or stress response but also involved in motility, exopolysaccharide synthesis, phosphate import or energetic metabolism. This study provides therefore new insights into the adaptation processes of H. arsenicoxydans in response to arsenic.