Short-term temporal variations of heterotrophic bacterial abundance and production in the open NW Mediterranean Sea

International audienceWe present the vertical and temporal dynamics of total vs. particle-attached bacterial abundance and activity over a 5 week period under summer to autumn transition in NW Mediterranean Sea. By comparison to previous investigations in the same area but during different seasons, we found that total bacterial biomass and production values were consistent with the hydrological conditions of the summer-fall transition. At a weekly time scale, total bacterial biomass and production in the euphotic layers was significantly correlated with phytoplanktonic biomass. At an hourly time scale, total bacterial biomass responded very rapidly to chlorophyll-a fluctuations, suggesting a tight coupling between phytoplankton and bacteria for resource partitioning during summer-autumn transition. In contrast, no influence of diel changes on bacterial parameters was detected. Episodic events such as coastal water intrusions had a significant positive effect on total bacterial abundance and production, whereas we could not detect any influence of short wind events whatever the magnitude. Finally, we show that particle-attached bacteria can represent a large proportion (until 49%) of the total bacterial activity in the euphotic layer but display rapid and sporadic changes at hourly time scales. This study underlines the value of large datasets covering different temporal scales to clarify the biogeochemical role of bacteria in the cycling of organic matter in open seawater

Seasonal to hour variation scales in abundance and production of total and particle-attached bacteria in the open NW Mediterranean Sea (0–1000 m)

We present the vertical and temporal dynamics of total <i>vs.</i> particle-attached bacterial abundance and activity over a 5 week period under summer to autumn transition in NW Mediterranean Sea. At a weekly time scale, total bacterial biomass and production in the euphotic layers was significantly correlated with phytoplanktonic biomass. At an hourly time scale, total bacterial biomass responded very rapidly to chlorophyll <i>a</i> fluctuations, suggesting a tight coupling between phytoplankton and bacteria for resource partitioning during the summer-autumn transition. In contrast, no influence of diel changes on bacterial parameters was detected. Episodic events such as coastal water intrusions had a significant positive effect on total bacterial abundance and production, whereas we could not detect any influence of short wind events whatever the magnitude. Finally, we show that particle-attached bacteria can represent a large proportion (up to 49%) of the total bacterial activity in the euphotic layer but display rapid and sporadic changes at hourly time scales. In the mesopelagic layers, bacterial abundance and production linearly decreased with depth, except some production peaks at 400–750 m. This study underlines the value of large datasets covering different temporal scales to clarify the biogeochemical role of bacteria in the cycling of organic matter in open seawater

Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

Bacterioplankton plays a central role in energy and matter fluxes in the sea, yet the factors that constrain its variation in marine systems are still poorly understood. Here we use the explanatory power of direct multivariate gradient analysis to evaluate the driving forces exerted by environmental parameters on bacterial community distribution in the water column. We gathered and analysed data from a one month sampling period from the surface to 1000 m depth at the JGOFS-DYFAMED station (NW Mediterranean Sea). This station is characterized by very poor horizontal advection currents which makes it an ideal model to test hypotheses on the causes of vertical stratification of bacterial communities. Capillary electrophoresis single strand conformation polymorphism (CE-SSCP) fingerprinting profiles analyzed using multivariate statistical methods demonstrated a vertical zonation of bacterial assemblages in three layers, above, in or just below the chlorophyll maximum and deeper, that remained stable during the entire sampling period. Through the use of direct gradient multivariate ordination analyses we demonstrate that a complex array of biogeochemical parameters is the driving force behind bacterial community structure shifts in the water column. Physico-chemical parameters such as phosphate, nitrate, salinity and to a lesser extent temperature, oxygen, dissolved organic carbon and photosynthetically active radiation acted in synergy to explain bacterial assemblages changes with depth. Analysis of lipid biomarkers of organic matter sources and fates suggested that bacterial community structure in the surface layers was in part explained by lipids of chloroplast origin. Further detailed analysis of pigment-based phytoplankton diversity gave evidence of a compartmentalized influence of several phytoplankton groups on bacterial community structure in the first 150 m depth

Sedimentological imprint on subseafloor microbial communities in Western Mediterranean Sea Quaternary sediments

An interdisciplinary study was conducted to evaluate the relationship between geological and paleoenvironmental parameters and the bacterial and archaeal community structure of two contrasting subseafloor sites in the Western Mediterranean Sea (Ligurian Sea and Gulf of Lion). Both depositional environments in this area are well-documented from paleoclimatic and paleooceanographic point of views. Available data sets allowed us to calibrate the investigated cores with reference and dated cores previously collected in the same area, and notably correlated to Quaternary climate variations. DNA-based fingerprints showed that the archaeal diversity was composed by one group, Miscellaneous Crenarchaeotic Group (MCG), within the Gulf of Lion sediments and of nine different lineages (dominated by MCG, South African Gold Mine Euryarchaeotal Group (SAGMEG) and <i>Halobacteria</i>) within the Ligurian Sea sediments. Bacterial molecular diversity at both sites revealed mostly the presence of the classes <i>Alphaproteobacteria</i>, <i>Betaproteobacteria</i> and <i>Gammaproteobacteria</i> within <i>Proteobacteria</i> phylum, and also members of <i>Bacteroidetes</i> phylum. The second most abundant lineages were <i>Actinobacteria</i> and <i>Firmicutes</i> at the Gulf of Lion site and <i>Chloroflexi</i> at the Ligurian Sea site. Various substrates and cultivation conditions allowed us to isolate 75 strains belonging to four lineages: <i>Alpha-</i>, <i>Gammaproteobacteria</i>, <i>Firmicutes</i> and <i>Actinobacteria</i>. In molecular surveys, the <i>Betaproteobacteria</i> group was consistently detected in the Ligurian Sea sediments, characterized by a heterolithic facies with numerous turbidites from a deep-sea <i>levee</i>. Analysis of relative betaproteobacterial abundances and turbidite frequency suggested that the microbial diversity was a result of main climatic changes occurring during the last 20 ka. Statistical direct multivariate canonical correspondence analyses (CCA) showed that the availability of electron acceptors and the quality of electron donors (indicated by age) strongly influenced the community structure. In contrast, within the Gulf of Lion core, characterized by a homogeneous lithological structure of upper-slope environment, most detected groups were <i>Bacteroidetes</i> and, to a lesser extent, <i>Betaproteobacteria</i>. At both site, the detection of <i>Betaproteobacteria</i> coincided with increased terrestrial inputs, as confirmed by the geochemical measurements (Si, Sr, Ti and Ca). In the Gulf of Lion, geochemical parameters were also found to drive microbial community composition. Taken together, our data suggest that the palaeoenvironmental history of erosion and deposition recorded in the Western Mediterranean Sea sediments has left its imprint on the sedimentological context for microbial habitability, and then indirectly on structure and composition of the microbial communities during the late Quaternary

Lateral Gene Expression in Drosophila Early Embryos Is Supported by Grainyhead-Mediated Activation and Tiers of Dorsally-Localized Repression

The general consensus in the field is that limiting amounts of the transcription factor Dorsal establish dorsal boundaries of genes expressed along the dorsal-ventral (DV) axis of early Drosophila embryos, while repressors establish ventral boundaries. Yet recent studies have provided evidence that repressors act to specify the dorsal boundary of intermediate neuroblasts defective (ind), a gene expressed in a stripe along the DV axis in lateral regions of the embryo. Here we show that a short 12 base pair sequence (“the A-box”) present twice within the ind CRM is both necessary and sufficient to support transcriptional repression in dorsal regions of embryos. To identify binding factors, we conducted affinity chromatography using the A-box element and found a number of DNA-binding proteins and chromatin-associated factors using mass spectroscopy. Only Grainyhead (Grh), a CP2 transcription factor with a unique DNA-binding domain, was found to bind the A-box sequence. Our results suggest that Grh acts as an activator to support expression of ind, which was surprising as we identified this factor using an element that mediates dorsally-localized repression. Grh and Dorsal both contribute to ind transcriptional activation. However, another recent study found that the repressor Capicua (Cic) also binds to the A-box sequence. While Cic was not identified through our A-box affinity chromatography, utilization of the same site, the A-box, by both factors Grh (activator) and Cic (repressor) may also support a “switch-like” response that helps to sharpen the ind dorsal boundary. Furthermore, our results also demonstrate that TGF-β signaling acts to refine ind CRM expression in an A-box independent manner in dorsal-most regions, suggesting that tiers of repression act in dorsal regions of the embryo

Boronic Acid Transition State Inhibitors as Potent Inactivators of KPC and CTX-M β-Lactamases: Biochemical and Structural Analyses

Design of novel beta-lactamase inhibitors (BLIs) is one of the currently accepted strategies to combat the threat of cephalosporin and carbapenem resistance in Gram-negative bacteria. Boronic acid transition state inhibitors (BATSIs) are competitive, reversible BLIs that offer promise as novel therapeutic agents. In this study, the activities of two alpha-amido-beta-triazolylethaneboronic acid transition state inhibitors (S02030 and MB_076) targeting representative KPC (KPC-2) and CTX-M (CTX-M-96, a CTX-M-15-type extended-spectrum beta-lactamase [ESBL]) beta-lactamases were evaluated. The 50% inhibitory concentrations (IC(50)s) for both inhibitors were measured in the nanomolar range (2 to 135 nM). For S02030, the k(2)/K for CTX-M-96 (24,000 M-1 s(-1)) was twice the reported value for KPC-2 (12,000 M-1 s(-1)); for MB_076, the k(2)/K values ranged from 1,200 M-1 s(-1) (KPC-2) to 3,900 M-1 s(-1) (CTX-M-96). Crystal structures of KPC-2 with MB_076 (1.38-& ANGS; resolution) and S02030 and the in silico models of CTX-M-96 with these two BATSIs show that interaction in the CTX-M-96-S02030 and CTX-M-96-MB_076 complexes were overall equivalent to that observed for the crystallographic structure of KPC-2-S02030 and KPC-2-MB_076. The tetrahedral interaction surrounding the boron atom from S02030 and MB_076 creates a favorable hydrogen bonding network with S70, S130, N132, N170, and S237. However, the changes from W105 in KPC-2 to Y105 in CTX-M-96 and the missing residue R220 in CTX-M-96 alter the arrangement of the inhibitors in the active site of CTX-M-96, partially explaining the difference in kinetic parameters. The novel BATSI scaffolds studied here advance our understanding of structure-activity relationships (SARs) and illustrate the importance of new approaches to beta-lactamase inhibitor design

Learning to teach data journalism: Innovation, influence and constraints

Journalism education has tended to respond slowly to developments in digital journalism, such as data journalism, despite or because of close links with the industry. This paper examines the obstacles to innovation in journalism education with particular reference to data journalism, drawing on the literature, a review of stakeholders and course documents, and the author’s reflections on developing a data journalism module as part of a new MA programme. It highlights the complexities linked to the particular demands of data journalism, and identifies critical issues around student satisfaction; reputation and job/career outcomes; relevance, currency and appeal; programme management; and coherence. Rather than holding it back, more specialized socialization could assist journalism education to innovate effectively, the author suggests

The closure of the Rocas Verdes Basin and early tectono-metamorphic evolution of the Magallanes Fold-and-Thrust Belt, southern Patagonian Andes (52–54°S)

The hinterland Western Domain of the Magallanes Fold-and-Thrust Belt (MFTB) between 52°-54°S is part of a poorly studied region of the southernmost Andean Cordillera. This domain consists of NNW-SSE trending tectonic slices of pre-Jurassic basement units and Late Jurassic-Early Cretaceous ophiolitic complexes and volcano-sedimentary successions of the Rocas Verdes Basin (RVB). New detrital zircon UPb ages of metatuffs and metapsammopelites constrain episodes of Late Jurassic rift-related volcanism (ca. 160 Ma) followed by Early Cretaceous sedimentation (ca. 125 Ma) during the opening of the RVB. Shear bands developed in the RVB units further record the initial phases of the Andean Orogeny. The 30-km wide thrust stack located on top of the Eastern Tobífera Thrust consists of mylonitic metatuffs, metapelites and metabasalts with a NE-verging brittle-ductile S1* foliation. Phengite-bearing metatuffs commonly record pressure-temperature (P-T) conditions between ~3–6 kbar and ~ 210–460 °C, consistent with underthrusting of the RVB beneath the parautochthonous magmatic arc in the west. Peak metamorphic conditions of ~6 kbar and 460 °C are derived from a metapsammopelitic schist with textures of contact metamorphism overprinting early mylonitic structures (at least S1*). A back-arc quartz-diorite, intruded at ca. 83 Na, is in contact with the metapsammopelites and constrain the minimum age of deformation at deep crustal depths. Campanian-Maastrichtian (ca. 70–73 Ma) 40Ar/39Ar phengite dates from a mylonitic metapelite indicate the timing of thrusting and backthrusting during the initial uplift of the underthrusted crustal stack. These findings reveal a ~ 400 km along-strike connection of mylonite belts in a continent-verging thrust structure that became active at the onset of the Andean orogeny during the closure of the Rocas Verdes back-arc marginal basin

Bacterial diversity and community composition from seasurface to subseafloor

© The International Society for Microbial Ecology, 2015. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in ISME Journal 10 (2016): 979–989, doi:10.1038/ismej.2015.175.We investigated compositional relationships between bacterial communities in the water column and those in deep-sea sediment at three environmentally distinct Pacific sites (two in the Equatorial Pacific and one in the North Pacific Gyre). Through pyrosequencing of the v4–v6 hypervariable regions of the 16S ribosomal RNA gene, we characterized 450 104 pyrotags representing 29 814 operational taxonomic units (OTUs, 97% similarity). Hierarchical clustering and non-metric multidimensional scaling partition the samples into four broad groups, regardless of geographic location: a photic-zone community, a subphotic community, a shallow sedimentary community and a subseafloor sedimentary community (greater than or equal to1.5 meters below seafloor). Abundance-weighted community compositions of water-column samples exhibit a similar trend with depth at all sites, with successive epipelagic, mesopelagic, bathypelagic and abyssopelagic communities. Taxonomic richness is generally highest in the water-column O2 minimum zone and lowest in the subseafloor sediment. OTUs represented by abundant tags in the subseafloor sediment are often present but represented by few tags in the water column, and represented by moderately abundant tags in the shallow sediment. In contrast, OTUs represented by abundant tags in the water are generally absent from the subseafloor sediment. These results are consistent with (i) dispersal of marine sedimentary bacteria via the ocean, and (ii) selection of the subseafloor sedimentary community from within the community present in shallow sediment.This study was funded by the Biological Oceanography Program of the US National Science Foundation (grant OCE-0752336) and by the NSF-funded Center for Dark Energy Biosphere Investigations (grant NSF-OCE-0939564)