Characterisation and genome sequence of the lytic Acinetobacter baumannii bacteriophage vB-AbaS-Loki

© 2017 Turner et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Acinetobacter baumannii has emerged as an important nosocomial pathogen in healthcare and community settings. While over 100 of Acinetobacter phages have been described in the literature, relatively few have been sequenced. This work describes the characterisation and genome annotation of a new lytic Acinetobacter siphovirus, vB-AbaS-Loki, isolated from activated sewage sludge. Sequencing revealed that Loki encapsulates a 41,308 bp genome, encoding 51 predicted open reading frames. Loki is most closely related to Acinetobacter phage IME-AB3 and more distantly related to Burkholderia phage KL1, Paracoccus phage vB-PmaS-IMEP1 and Pseudomonas phages vB-Pae-Kakheti25, vB-PaeS-SCH-Ab26 and PA73. Loki is characterised by a narrow host range, among the 40 Acinetobacter isolates tested, productive infection was only observed for the propagating host, A. baumannii ATCC 17978. Plaque formation was found to be dependent upon the presence of Ca2+ ions and adsorption to host cells was abolished upon incubation with a mutant of ATCC 17978 encoding a premature stop codon in lpxA. The complete genome sequence of vB-AbaS-Loki was deposited in the European Nucleotide Archive (ENA) under the accession number LN890663. Copyright

Linking biogeochemical processes and historic primary producer communities in the SE USA sinkhole lake form the mid-Holocene to present.

Many freshwater resources receive materials from human development causing a decrease in ecological services when compared to pre-disturbance periods. As a result, the understanding of eutrophication and limnological change has increased, but less attention has been given to systems under intense human impact that have not eutrophied so that drivers precluding eutrophication can be documented. The primary objective of this research was to reconstruct allochthonous inputs and in-lake processes for Long Pond, Georgia, USA from the mid Holocene to present and link them to primary producer community changes. Long Pond is a mesotrophic lake located in a highly altered watershed from agricultural and municipal land use and housing developments. A 5 m sediment core was collected from Long Pond, and organic matter, nutrients (C, N, P), metals (Al, Fe, Cu), and photosynthetic pigments were measured. Long Pond existed in three limnological states spanning the past ~6000 years. Prior to modern lacustrine conditions, Long Pond was a wetland/peat system that experienced the highest primary producer abundance recorded in the core. The modern lacustrine state began in the late Holocene and was characterized by increased connectivity with the surrounding watershed and low productivity. Human impacts began around 1900 AD and included high levels of phosphorus and metal deposition but moderate levels of primary producer abundance. As a result, in-lake dynamics are believed to be regulating the trophic status of Long Pond. Low concentrations of available phosphorus in the water column combined with high concentrations of sedimentary phosphorus may imply the binding of phosphorus to the sediments by certain materials such as aluminum and iron. Long Pond serves as an example of the complex in-lake processes that can occur from allochthonous inputs and autochthonous responses in lake systems thus complicating management decisions

Nitrogen-fixing populations of Planctomycetes and Proteobacteria are abundant in surface ocean metagenomes

Nitrogen fixation in the surface ocean impacts global marine nitrogen bioavailability and thus microbial primary productivity. Until now, cyanobacterial populations have been viewed as the main suppliers of bioavailable nitrogen in this habitat. Although PCR amplicon surveys targeting the nitrogenase reductase gene have revealed the existence of diverse non-cyanobacterial diazotrophic populations, subsequent quantitative PCR surveys suggest that they generally occur in low abundance. Here, we use state-of-the-art metagenomic assembly and binning strategies to recover nearly one thousand non-redundant microbial population genomes from the TARA Oceans metagenomes. Among these, we provide the first genomic evidence for non-cyanobacterial diazotrophs inhabiting surface waters of the open ocean, which correspond to lineages within the Proteobacteria and, most strikingly, the Planctomycetes. Members of the latter phylum are prevalent in aquatic systems, but have never been linked to nitrogen fixation previously. Moreover, using genome-wide quantitative read recruitment, we demonstrate that the discovered diazotrophs were not only widespread but also remarkably abundant (up to 0.3% of metagenomic reads for a single population) in both the Pacific Ocean and the Atlantic Ocean northwest. Our results extend decades of PCR-based gene surveys, and substantiate the importance of heterotrophic bacteria in the fixation of nitrogen in the surface ocean

The pediatric template of brain perfusion

Magnetic resonance imaging (MRI) captures the dynamics of brain development with multiple modalities that quantify both structure and function. These measurements may yield valuable insights into the neural patterns that mark healthy maturation or that identify early risk for psychiatric disorder. The Pediatric Template of Brain Perfusion (PTBP) is a free and public neuroimaging resource that will help accelerate the understanding of childhood brain development as seen through the lens of multiple modality neuroimaging and in relation to cognitive and environmental factors. The PTBP uses cross-sectional and longitudinal MRI to quantify cortex, white matter, resting state functional connectivity and brain perfusion, as measured by Arterial Spin Labeling (ASL), in 120 children 7–18 years of age. We describe the PTBP and show, as a demonstration of validity, that global summary measurements capture the trajectories that demarcate critical turning points in brain maturation. This novel resource will allow a more detailed understanding of the network-level, structural and functional landmarks that are obtained during normal adolescent brain development