Multiple energy sources and metabolic strategies sustain microbial diversity in Antarctic desert soils

Numerous diverse microorganisms reside in the cold desert soils of continental Antarctica, though we lack a holistic understanding of the metabolic processes that sustain them. Here, we profile the composition, capabilities, and activities of the microbial communities in 16 physicochemically diverse mountainous and glacial soils. We assembled 451 metagenome-assembled genomes from 18 microbial phyla and inferred through Bayesian divergence analysis that the dominant lineages present are likely native to Antarctica. In support of earlier findings, metagenomic analysis revealed that the most abundant and prevalent microorganisms are metabolically versatile aerobes that use atmospheric hydrogen to support aerobic respiration and sometimes carbon fixation. Surprisingly, however, hydrogen oxidation in this region was catalyzed primarily by a phylogenetically and structurally distinct enzyme, the group 1l [NiFe]-hydrogenase, encoded by nine bacterial phyla. Through gas chromatography, we provide evidence that both Antarctic soil communities and an axenic Bacteroidota isolate (Hymenobacter roseosalivarius) oxidize atmospheric hydrogen using this enzyme. Based on ex situ rates at environmentally representative temperatures, hydrogen oxidation is theoretically sufficient for soil communities to meet energy requirements and, through metabolic water production, sustain hydration. Diverse carbon monoxide oxidizers and abundant methanotrophs were also active in the soils. We also recovered genomes of microorganisms capable of oxidizing edaphic inorganic nitrogen, sulfur, and iron compounds and harvesting solar energy via microbial rhodopsins and conventional photosystems. Obligately symbiotic bacteria, including Patescibacteria, Chlamydiae, and predatory Bdellovibrionota, were also present. We conclude that microbial diversity in Antarctic soils reflects the coexistence of metabolically flexible mixotrophs with metabolically constrained specialists.DATA AVAILABILTY: All amplicon sequencing data, raw metagenomes, metagenomic assemblies, and metagenome-assembled genomes were deposited to the National Center for Biotechnology Information (NCBI) Sequence Read Archive under the BioProject accession no. PRJNA630822. All other study data are included in the article and/or supporting information.An Australian Research Council Discovery Early Career Researcher Award (ARC DECRA) Fellowship, an Australian Antarctic Division grant, a South African National Antarctic Program grant, a National Health & Medical Research Council Emerging Leadership 2 (NHMRC EL2) Fellowship, an Australian Government Research Training Stipend Scholarship, a Monash International Tuition Scholarship, a Monash Postgraduate Publications Award, a South African National Antarctic Programme (SANAP) postdoctoral grant.https://www.pnas.orghj2022BiochemistryGeneticsMicrobiology and Plant Patholog

Genomic analysis and relatedness of P2-like phages of the Burkholderia cepacia complex

<p>Abstract</p> <p>Background</p> <p>The <it>Burkholderia cepacia </it>complex (BCC) is comprised of at least seventeen Gram-negative species that cause infections in cystic fibrosis patients. Because BCC bacteria are broadly antibiotic resistant, phage therapy is currently being investigated as a possible alternative treatment for these infections. The purpose of our study was to sequence and characterize three novel BCC-specific phages: KS5 (vB_BceM-KS5 or vB_BmuZ-ATCC 17616), KS14 (vB_BceM-KS14) and KL3 (vB_BamM-KL3 or vB_BceZ-CEP511).</p> <p>Results</p> <p>KS5, KS14 and KL3 are myoviruses with the A1 morphotype. The genomes of these phages are between 32317 and 40555 base pairs in length and are predicted to encode between 44 and 52 proteins. These phages have over 50% of their proteins in common with enterobacteria phage P2 and so can be classified as members of the <it>Peduovirinae </it>subfamily and the "P2-like viruses" genus. The BCC phage proteins similar to those encoded by P2 are predominantly structural components involved in virion morphogenesis. As prophages, KS5 and KL3 integrate into an AMP nucleosidase gene and a threonine tRNA gene, respectively. Unlike other P2-like viruses, the KS14 prophage is maintained as a plasmid. The P2 <it>E+E' </it>translational frameshift site is conserved among these three phages and so they are predicted to use frameshifting for expression of two of their tail proteins. The <it>lysBC </it>genes of KS14 and KL3 are similar to those of P2, but in KS5 the organization of these genes suggests that they may have been acquired via horizontal transfer from a phage similar to λ. KS5 contains two sequence elements that are unique among these three phages: an IS<it>Bmu</it>2-like insertion sequence and a reverse transcriptase gene. KL3 encodes an EcoRII-C endonuclease/methylase pair and Vsr endonuclease that are predicted to function during the lytic cycle to cleave non-self DNA, protect the phage genome and repair methylation-induced mutations.</p> <p>Conclusions</p> <p>KS5, KS14 and KL3 are the first BCC-specific phages to be identified as P2-like. As KS14 has previously been shown to be active against <it>Burkholderia cenocepacia in vivo</it>, genomic characterization of these phages is a crucial first step in the development of these and similar phages for clinical use against the BCC.</p

Optimisation de la mesure de figures de pôles en diffraction X

Les conditions optimales de mesure de figures de pôles ont été recherchées en utilisant différentes variantes de montage (utilisation d'un monochromateur, détecteur en énergie dispersive, incidence réduite) et en analysant divers matériaux (alliage de cuivre, acier bas carbone, couches minces de TiN). La qualité des données mesurées dans chaque cas est estimée à partir des coefficients de compatibilité calculés.The best conditions for measuring pole figures have been sought by using several kinds of difraction arrangement (use of a monochromator, energy dispersive detector, reduced incidence) and by analysing several materials (copper alloy, low carbon steel, TiN thin films). The quality of the measured data is estimated from the compatibility coefficients which are calculated in each case

Poor prognostic factors in complex regional pain syndrome 1: a Delphi survey

OBJECTIVE: A major challenge in the management of patients with complex regional pain syndrome 1 is identifying those individuals who are at risk of developing severe problems. Data from large follow-up studies providing empirical evidence are largely lacking. The goal of this study was to obtain an expert-agreed priority list of parameters that are correlated with a poor prognosis. METHODS: In a two-round Delphi survey, experts were asked to list those parameters that they considered to be strongly associated with a poor prognosis (first round) and to weight parameters that they believed to be most relevant for poor prognosis (second round). Median ratings and interquartile ranges were calculated. Rates > 7 and interquartile ranges < 3 depicted important and expert-agreed parameters. RESULTS: Thirty-nine experts compiled a list of 254 items. Twenty-eight experts reached a consensus on 49 important items associated with poor prognosis. They primarily agreed on clinical manifestations of complex regional pain syndrome 1. Psychosocial factors were considered less important. CONCLUSION: The findings of this study indicate that poor prognosis for complex regional pain syndrome 1 is primarily dependent on clinical manifestations. While evidence suggests that psychosocial factors may play a role in the development of the condition, their role in poor prognosis appears to be less important