The SAR11 Group of Alpha-Proteobacteria Is Not Related to the Origin of Mitochondria

Although free living, members of the successful SAR11 group of marine alpha-proteobacteria contain a very small and A+T rich genome, two features that are typical of mitochondria and related obligate intracellular parasites such as the Rickettsiales. Previous phylogenetic analyses have suggested that Candidatus Pelagibacter ubique, the first cultured member of this group, is related to the Rickettsiales+mitochondria clade whereas others disagree with this conclusion. In order to determine the evolutionary position of the SAR11 group and its relationship to the origin of mitochondria, we have performed phylogenetic analyses on the concatenation of 24 proteins from 5 mitochondria and 71 proteobacteria. Our results support that SAR11 group is not the sistergroup of the Rickettsiales+mitochondria clade and confirm that the position of this group in the alpha-proteobacterial tree is strongly affected by tree reconstruction artefacts due to compositional bias. As a consequence, genome reduction and bias toward a high A+T content may have evolved independently in the SAR11 species, which points to a different direction in the quest for the closest relatives to mitochondria and Rickettsiales. In addition, our analyses raise doubts about the monophyly of the newly proposed Pelagibacteraceae family

Going Deeper: Metagenome of a Hadopelagic Microbial Community

The paucity of sequence data from pelagic deep-ocean microbial assemblages has severely restricted molecular exploration of the largest biome on Earth. In this study, an analysis is presented of a large-scale 454-pyrosequencing metagenomic dataset from a hadopelagic environment from 6,000 m depth within the Puerto Rico Trench (PRT). A total of 145 Mbp of assembled sequence data was generated and compared to two pelagic deep ocean metagenomes and two representative surface seawater datasets from the Sargasso Sea. In a number of instances, all three deep metagenomes displayed similar trends, but were most magnified in the PRT, including enrichment in functions for two-component signal transduction mechanisms and transcriptional regulation. Overrepresented transporters in the PRT metagenome included outer membrane porins, diverse cation transporters, and di- and tri-carboxylate transporters that matched well with the prevailing catabolic processes such as butanoate, glyoxylate and dicarboxylate metabolism. A surprisingly high abundance of sulfatases for the degradation of sulfated polysaccharides were also present in the PRT. The most dramatic adaptational feature of the PRT microbes appears to be heavy metal resistance, as reflected in the large numbers of transporters present for their removal. As a complement to the metagenome approach, single-cell genomic techniques were utilized to generate partial whole-genome sequence data from four uncultivated cells from members of the dominant phyla within the PRT, Alphaproteobacteria, Gammaproteobacteria, Bacteroidetes and Planctomycetes. The single-cell sequence data provided genomic context for many of the highly abundant functional attributes identified from the PRT metagenome, as well as recruiting heavily the PRT metagenomic sequence data compared to 172 available reference marine genomes. Through these multifaceted sequence approaches, new insights have been provided into the unique functional attributes present in microbes residing in a deeper layer of the ocean far removed from the more productive sun-drenched zones above

Chemical composition and in vitro antimicrobial activity of the essential oils of flower heads and leaves of Santolina rosmarinifolia L. form Romania

The essential oils of the flower heads and leaves of Santolina rosmarinifolia L. (Compositae) cultivated in Romania were obtained through hydrodistillation and analysed by GC-MS. Forty-two components were identified, representing 92.3-94.0% of the whole composition of the samples. Their in vitro antimicrobial activity against gram-positive and gram-negative bacteria strains and the fungus Candida albicans was determined using the agar-diffusion method and the broth dilution method

Fluorescent bacteria for colloidal iron biosensors

This research was focused on the possibility of iron sensing by means of bacterial cultures. The effect of ferric and ferrous ions on Pseudomonas aeruginosa, which has the ability to uptake the environmental iron in the form of complex iron compositions named siderophores, characterized by luminescent features, was studied. The different sensitivity to the iron from oxide compounds in comparison to the iron from chlorides and sulfate was emphasized by means of fluorescence measurements. It could be stated that Pseudomonas aeruginosa, from human body specimens could be the biological component of an iron biosensor for ferrofluid traces reminiscent after the administration for medical purposes

Statistical Analysis of the Preparatory Phase of the Mw8.1 Iquique Earthquake, Chile

The 2014 Iquique seismic crisis in Chile, culminating with a Mw 8.1 earthquake on 1 April, highlights a complex unlocking of the Northern Chilean subduction that has been considered a seismic gap since 1877. During the year preceding this event, at least three clusters of seismic activity have been reported: in July 2013 and January and March 2014. Recent studies have proposed large-scale slab deformation as a potential trigger for the megathrust earthquake, and these clusters possibly indicate aseismic slip transients accompanying the progressive destabilization of the plate contact. However, no evidence of gradual unlocking of the interface or transient deformation has yet been found in the seismicity rate. To address this question, we develop a dense earthquake catalog covering 15 months preceding the mainshock and derived from the continuous waveform data set recorded by the Integrated Plate Boundary Observatory Chile (IPOC) and Iquique Local Network (ILN) networks. After declustering the seismicity, a space-time analysis highlights a large-scale acceleration of the seismicity along the interface accompanied by a deceleration of intermediate-depth earthquakes. We demonstrate the existence of a seismic quiescence downdip of the mainshock rupture before the July 2013 cluster. We propose that this seismic quiescence potentially highlights fluid circulation and/or aseismic motion along upper-plate crustal fault(s)

Physics-based seismic input for engineering applications: a case study in the Aterno river valley, Central Italy

In this paper, we present 3D physics-based numerical simulations, in the nearsource region at the regional scale, of the 2009, April 6, L’Aquila earthquake (central Italy), based on improved models of the Aterno river basin geology and source kinematics. The simulations were carried out by an open-source code, SPEED, based on a discontinuous Galerkin spectral element method. The numerical mesh of the Aterno basin was built on a detailed subsurface geological model and on the evaluation of the dynamic properties of the soils. The source model was selected among the kinematic solutions available in the literature as the one that fits best the near-source observations. Broadband ground motions were then generated through a hybrid method, combining 3D low frequency waveforms with high-frequency stochastic synthetics. To provide an example of application as seismic input to earthquake engineering analyses in the time domain, results of this approach were used for 2D site response analyses at Castelnuovo, a village severely damaged by the earthquake, and in the neighborhood of which no seismic record was available. SPEED simulation satisfactorily reproduces the recorded accelerograms in the frequency range 0.1–0.7 Hz. The site response analysis at the local scale shows that the amplification of the hill is more significant at its natural frequency, due to topographic and stratigraphic factors, than at the peak of the seismic input simulated by SPEED, that is at about 3 s along the fault-normal component. The presented application supports the conclusion that 3D physics-based numerical simulations do have the potential to become an alternative for determination of input ground motion for earthquake engineering analyses, especially for those scenarios for which real records are not available