Effect of Activated Carbon Amendment on Bacterial Community Structure and Functions in a PAH Impacted Urban Soil

ABSTRACT: We collected urban soil samples impacted by polycyclic aromatic hydrocarbons (PAHs) from a sorbent-based remediation field trial to address concerns about unwanted side-effects of 2 % powdered (PAC) or granular (GAC) activated carbon amendment on soil microbiology and pollutant biodegradation. After three years, total microbial cell counts and respiration rates were highest in the GAC amended soil. The predominant bacterial community structure derived from denaturing gradient gel electrophoresis (DGGE) shifted more strongly with time than in response to AC amendment. DGGE band sequencing revealed the presence of taxa with closest affiliations either to known PAH degraders, e.g. Rhodococcus jostii RHA-1, or taxa known to harbor PAH degraders, e.g. Rhodococcus erythropolis, in all soils. Quantification by real-time polymerase chain reaction yielded similar dioxygenases gene copy numbers in unamended, PAC-, or GACamended soil. PAH availability assessments in batch tests showed th

Seasonal dynamics of active SAR11 ecotypes in the oligotrophic Northwest Mediterranean Sea

A seven-year oceanographic time series in NW Mediterranean surface waters was combined with pyrosequencing of ribosomal RNA (16S rRNA) and ribosomal RNA gene copies (16S rDNA) to examine the environmental controls on SAR11 ecotype dynamics and potential activity. SAR11 diversity exhibited pronounced seasonal cycles remarkably similar to total bacterial diversity. The timing of diversity maxima was similar across narrow and broad phylogenetic clades and strongly associated with deep winter mixing. Diversity minima were associated with periods of stratification that were low in nutrients and phytoplankton biomass and characterised by intense phosphate limitation (turnover time80%) by SAR11 Ia. A partial least squares (PLS) regression model was developed that could reliably predict sequence abundances of SAR11 ecotypes (Q2=0.70) from measured environmental variables, of which mixed layer depth was quantitatively the most important. Comparison of clade-level SAR11 rRNA:rDNA signals with leucine incorporation enabled us to partially validate the use of these ratios as an in-situ activity measure. However, temporal trends in the activity of SAR11 ecotypes and their relationship to environmental variables were unclear. The strong and predictable temporal patterns observed in SAR11 sequence abundance was not linked to metabolic activity of different ecotypes at the phylogenetic and temporal resolution of our study

Diversity of bacterial communities on sunken woods in the Mediterranean Sea

7 páginas, 4 figuras, 1 tabla.Sunken woods are very rich and diverse ecosystems supporting large macrofaunal diversity and representing a source of carbon and energy for any heterotrophic organism able to consume plant material, and those relying on specialized microbial taxa. However, relatively little is known about the microbial communities that degrade sunken woods and produce reduced compounds that serve as energy sources for chemosynthetic lifestyles. The purpose of this study was to explore the bacterial diversity developing on and within sunken woods in a NW Mediterranean submarine canyon and its adjacent slope by using 16S rRNA genes survey. We described communities from Pine wood immerged at 1200 m deep in the Blanes Canyon and its adjacent open slope, as well as from material filling wood boring bivalve burrows. We demonstrate that bacterial communities were very different from each other in each of the three wood ecosystems. These highly diverse wood communities contained all the major bacterial phyla, but Alphaproteobacteria and Deltaproteobacteria were dominant in the open slope and the canyon, respectively. The burrows had more Gamma- and Epsilonproteobacteria. In summary, highly diverse bacterial communities with potentially wide metabolic capabilities colonized wood sunken in the Blanes Canyon and its adjacent open slopes in the Mediterranean Sea.The work of P.E.G. is supported by the Agence Nationale de la Recherche (ANR) project MICADO (ANR-11JSV7- 003-01). The GDRE DIWOOD (CNRS European Research Group on sunken woods and associated fauna) supported the Master’s project of Sandrine Bessette. The present work was developed within the framework of the RECS II (REN2002- 04556-C02-01), PROMETEO (CTM 2007-66316-C02-02/MAR) and DOS MARES (CTM2010-21810-C03-03/MAR) projects funded by the Spanish MICINN, and is a contribution of the 3rd and 4th authors to the Consolidated Research Group 2009SGR665 of the Generalitat de Catalunya.Peer reviewe

Microbial communities associated with the degradation of oak wood in the Blanes submarine canyon and its adjacent open slope (NW Mediterranean)

7 páginas, 5 figuras, 2 tablas.Submarine canyons can trap and concentrate organic falls, like terrestrial debris, including wood. Sunken wood creates a unique ecosystem in the deep sea, which base, i.e. the microbial communities directly degrading this wood, remains poorly studied. Our aim was thus to examine the wood degrading microbial community by comparing oak samples experimentally deployed in experimental mooring arrays in the Blanes Canyon (BC) and its adjacent open slope (NW Mediterranean Sea). We analyzed the microbial community by parallel tag pyrosequencing of the16S rRNA genes from wood samples recovered from different depths after 9 and 12 months of deployment. In this first study of the phylogenetic description of wood associated microbial community by high throughput molecular techniques, we found that the microbial diversity was higher in samples from BC compared to the open slope. The structure of the communities were, however, not significantly different from each other, although we observed an apparent clustering according to time of immersion. Furthermore, an in depth taxonomic analysis revealed that Alphaproteobacteria was the dominant microbial taxa, with the Roseobacter clade seeming to have a specialized role in the degradation of oak in BC and its adjacent slope.The research conducted by SKF and PEG is supported by the Agence Nationale de la Recherche (ANR) through the MICADO project (ANR-11-JSV7-003-01).The present work was developed within the PROMETEO (CTM 2007- 66316-C02-02/MAR), DOS MARES (CTM2010-21810-C03-03/ MAR) and HERMIONE (European Community FP7/2007-2013, grant agreement n 226354) projects, and is a contribution of CR and DM to the Consolidated Research Group 2009SRG665 of the ‘‘Generalitat de Catalunya’’. CR was supported by a JAE postdoctoral fellowship. This work was also funded by CNRS and by the UMPC-Fondation TOTAL chair ‘Extreme marine environments, biodiversity and global change’. The LECOB group is part of the GDRE DIWOOD research network supported by CNRS.Peer reviewe

Microbial Communities in Sunken Wood Are Structured by Wood-Boring Bivalves and Location in a Submarine Canyon

9 páginas, 3 figuras, 2 tablas.The cornerstones of sunken wood ecosystems are microorganisms involved in cellulose degradation. These can either be free-living microorganisms in the wood matrix or symbiotic bacteria associated with wood-boring bivalves such as emblematic species of Xylophaga, the most common deep-sea woodborer. Here we use experimentally submerged pine wood, placed in and outside the Mediterranean submarine Blanes Canyon, to compare the microbial communities on the wood, in fecal pellets of Xylophaga spp. and associated with the gills of these animals. Analyses based on tag pyrosequencing of the 16S rRNA bacterial gene showed that sunken wood contained three distinct microbial communities. Wood and pellet communities were different from each other suggesting that Xylophaga spp. create new microbial niches by excreting fecal pellets into their burrows. In turn, gills of Xylophaga spp. contain potential bacterial symbionts, as illustrated by the presence of sequences closely related to symbiotic bacteria found in other wood eating marine invertebrates. Finally, we found that sunken wood communities inside the canyon were different and more diverse than the ones outside the canyon. This finding extends to the microbial world the view that submarine canyons are sites of diverse marine life.The work of PE Galand and SK Fagervold was supported by the Agence Nationale de la Recherche (ANR) project MICADO (ANR-11JSV7-003-01). The present work was developed within the framework of the projects PROMETEO (CTM2007-66316-C02-01/MAR) and DOSMARES (CTM2010-21810-C03-03). This paper is also a contribution of D Martin and C Romano to the CRG 2009SRG665 funded by the Generalitat de Catalunya. ANJ was funded within the DIWOOD research project by the Max Planck Gesellschaft; CB was funded within the Cluster of Excellence 0The Ocean in the Earth System0 at Marum, Bremen, by the German Research Foundation (DFG).Peer reviewe

Transfer of 7 Organic UV Filters from Sediment to the Ragworm <i>Hediste diversicolor</i>: Bioaccumulation of Benzophenone-3 and Further Proof of Octocrylene Metabolism

Organic UV filters are continuously released in aquatic ecosystems due to their widespread use, especially in touristic coastal environments. Generally, organic UV filters are poorly soluble in water and tend to accumulate in the sediment compartment. This represents a conceivable risk for sediment-dwelling organisms and a potential for transfer of the UV filters up the food chain. This study aimed to assess the potential transfer of seven UV filters including benzophenone-3 (BP3), bis-ethylhexyloxyphenol methoxyphenyl triazine (BEMT), butyl methoxydibenzoylmethane (BM), methylene bis-benzotriazolyl tetramethylbutylphenol (MBBT), 2-ethylhexyl salicylate (ES), diethylhexyl butamido triazone (DBT), and octocrylene (OC) from artificial spiked sediment (10 µg.g−1 dry weight) to sediment-dwelling worms. All UV filters were detected in the worms after 28 days of exposure, but only BP3 was apparently bioaccumulated, with a biota sediment accumulation factor (BSAF) of 12.38 ± 4.65. However, metabolomic profiling revealed that OC was metabolized by the worms into 11 fatty acid conjugates, demonstrating that OC did also accumulate in the worms in the form of OC–fatty acid conjugates. Here, the sole quantification of the parent organic UV filter underestimated the accumulation factor and the exposure of organisms. In general, it is therefore important to pair the conventional method (BSAF calculus) with other techniques, such as metabolomics, to assess the actual potential for bioaccumulation of xenobiotics including transformed xenobiotics