Fluconazole resistance in Candida albicans is induced by Pseudomonas aeruginosa quorum sensing

Microorganisms employ quorum sensing (QS) mechanisms to communicate with each other within microbial ecosystems. Emerging evidence suggests that intraspecies and interspecies QS plays an important role in antimicrobial resistance in microbial communities. However, the relationship between interkingdom QS and antimicrobial resistance is largely unknown. Here, we demonstrate that interkingdom QS interactions between a bacterium, Pseudomonas aeruginosa and a yeast, Candida albicans, induce the resistance of the latter to a widely used antifungal fluconazole. Phenotypic, transcriptomic, and proteomic analyses reveal that P. aeruginosa’s main QS molecule, N-(3-Oxododecanoyl)-L-homoserine lactone, induces candidal resistance to fluconazole by reversing the antifungal’s effect on the ergosterol biosynthesis pathway. Accessory resistance mechanisms including upregulation of C. albicans drug-efflux, regulation of oxidative stress response, and maintenance of cell membrane integrity, further confirm this phenomenon. These findings demonstrate that P. aeruginosa QS molecules may confer protection to neighboring yeasts against azoles, in turn strengthening their co-existence in hostile polymicrobial infection sites

Protecting the invisible: Establishing guideline values for copper toxicity to marine microbiomes

Understanding the rapid responses of marine microbiomes to environmental disturbances is paramount for supporting early assessments of harm to high-value ecosystems, such as coral reefs. Yet, management guidelines aimed at protecting aquatic life from environmental pollution remain exclusively defined for organisms at higher trophic levels. In this study, 16S rRNA gene amplicon sequencing was applied in conjunction with propidium monoazide for cell-viability assessment as a sensitive tool to determine taxon- and community-level changes in a seawater microbial community under copper (Cu) exposure. Bayesian model averaging was used to establish concentration-response relationships to evaluate the effects of copper on microbial composition, diversity, and richness for the purpose of estimating microbiome Hazard Concentration (mHCx) values. Predicted mHC5 values at which a 5 % change in microbial composition, diversity, and richness occurred were 1.05, 0.72, and 0.38 μg Cu L−1, respectively. Threshold indicator taxa analysis was applied across the copper concentrations to identify taxon-specific change points for decreasing taxa. These change points were then used to generate a Prokaryotic Sensitivity Distribution (PSD), from which mHCxdec values were derived for copper, suitable for the protection of 99, 95, 90, and 80 % of the marine microbiome. The mHC5dec guideline value of 0.61 μg Cu L−1, protective of 95 % of the marine microbial community, was lower than the equivalent Australian water quality guideline value based on eukaryotic organisms at higher trophic levels. This suggests that marine microbial communities might be more vulnerable, highlighting potential insufficiencies in their protection against copper pollution. The mHCx values proposed here provide approaches to quantitatively assess the effects of contaminants on microbial communities towards the inclusion of prokaryotes in future water quality guidelines

Multiple-beam pulse shaping and preamplification

Glass fusion laser systems typically use a master oscillator-power amplifier (MOPA) architecture, where control of the optical pulse temporal and spatial parameters is accomplished mainly in the master oscillator and low power optics. The pulses from this low power ``front end`` are amplified in the power amplifier, which modifies the pulse shape temporally and spatially. Nonlinear frequency conversion crystals following the amplifier further change the pulse before it reaches the target. To effectively control the optical pulse on target for different types of experiments, and compensate for nonlinearity in the preceding optics, the front end system must be versatile enough to easily control many pulse parameters over a large range. The front end pulse generation system described in this article represents a new approach to this problem. The proposed National Ignition Facility (NIF) has 192 beamlines, each of which requires an input pulse of up to 12 Joules in around 4 ns equivalent square pulse length. Considerations of laser architecture for supplying each of these beamlines from a central oscillator system were crucial in the design of the front end. Previous lasers have used bulk optics to split a single oscillator signal and report beams to multiple amplifier chains. A key idea in the current design is to replace bulk optic transport with fibers, eliminating large opto-mechanical subsystems. Another important concept is convenient pulse forming using low voltage integrated optic modulators. The integrated optic and fiber optic concepts resulted in the current pulse generation designs for NEF. An important advantage is that each of the beamlines can have an independently controlled temporal pulse shape, which provides for precise balance of instantaneous power on target

Comparative Genomic Analysis of the Class \u3ci\u3eEpsilonproteobacteria\u3c/i\u3e and Proposed Reclassification to Epsilonbacteraeota (phyl. nov.)

The Epsilonproteobacteria is the fifth validly described class of the phylum Proteobacteria, known primarily for clinical relevance and for chemolithotrophy in various terrestrial and marine environments, including deep-sea hydrothermal vents. As 16S rRNA gene repositories have expanded and protein marker analysis become more common, the phylogenetic placement of this class has become less certain. A number of recent analyses of the bacterial tree of life using both 16S rRNA and concatenated marker gene analyses have failed to recover the Epsilonproteobacteria as monophyletic with all other classes of Proteobacteria. In order to address this issue, we investigated the phylogenetic placement of this class in the bacterial domain using 16S and 23S rRNA genes, as well as 120 single-copy marker proteins. Single- and concatenated-marker trees were created using a data set of 4,170 bacterial representatives, including 98 Epsilonproteobacteria. Phylogenies were inferred under a variety of tree building methods, with sequential jackknifing of outgroup phyla to ensure robustness of phylogenetic affiliations under differing combinations of bacterial genomes. Based on the assessment of nearly 300 phylogenetic tree topologies, we conclude that the continued inclusion of Epsilonproteobacteria within the Proteobacteria is not warranted, and that this group should be reassigned to a novel phylum for which we propose the name Epsilonbacteraeota (phyl. nov.). We further recommend the reclassification of the order Desulfurellales (Deltaproteobacteria) to a novel class within this phylum and a number of subordinate changes to ensure consistency with the genome-based phylogeny. Phylogenomic analysis of 658 genomes belonging to the newly proposed Epsilonbacteraeota suggests that the ancestor of this phylum was an autotrophic, motile, thermophilic chemolithotroph that likely assimilated nitrogen from ammonium taken up from the environment or generated from environmental nitrate and nitrite by employing a variety of functional redox modules. The emergence of chemoorganoheterotrophic lifestyles in several Epsilonbacteraeota families is the result of multiple independent losses of various ancestral chemolithoautotrophic pathways. Our proposed reclassification of this group resolves an important anomaly in bacterial systematics and ensures that the taxonomy of Proteobacteria remains robust, specifically as genome-based taxonomies become more common

An adaptive optics system for solid-state laser systems used in inertial confinement fusion

Using adaptive optics the authors have obtained nearly diffraction-limited 5 kJ, 3 nsec output pulses at 1.053 {micro}m from the Beamlet demonstration system for the National Ignition Facility (NIF). The peak Strehl ratio was improved from 0.009 to 0.50, as estimated from measured wavefront errors. They have also measured the relaxation of the thermally induced aberrations in the main beam line over a period of 4.5 hours. Peak-to-valley aberrations range from 6.8 waves at 1.053 {micro}m within 30 minutes after a full system shot to 3.9 waves after 4.5 hours. The adaptive optics system must have enough range to correct accumulated thermal aberrations from several shots in addition to the immediate shot-induced error. Accumulated wavefront errors in the beam line will affect both the design of the adaptive optics system for NIF and the performance of that system

Microbial community characterization during anaerobic digestion of Scenedesmus spp. under mesophilic and thermophilic conditions

[EN] Microbial communities were thoroughly characterized in a mesophilic anaerobic membrane bioreactor (AnMBR) and a thermophilic continuous stirred tank reactor (CSTR), which were both treating recalcitrant microalgal biomass dominated by Scenedesmus. 16S rRNA amplicon sequencing analysis was performed when the AnMBR achieved 70% algal biodegradation and revealed high microbial diversity, probably due to the high solid retention time (SRT) of the AnMBR configuration. The bacterial community consisted of Chloroflexi (27.9%), WWE1 (19.0%) and Proteobacteria (15.4%) as the major phyla, followed by Spirochaetes (7.7%), Bacteroidetes (5.9%) and Firmicutes (3.6%). These phyla are known to exhibit proteolytic and cellulolytic capabilities required to degrade the Scenedesmus cell-wall. Methanosaeta was the most abundant methanogen detected in the AnMBR suggesting that methane was mainly produced by the acetoclastic pathway. In comparison, the thermophilic CSTR achieved 32.6% algal biodegradation, and its bacterial community had fewer Operational Taxonomic Units (977 OTUs) than the AnMBR (1396 OTUs), as is generally observed for high temperature biogas reactors. However, phyla with high hydrolytic potential were detected such as Firmicutes (34.6%) and the candidate taxon EM3 (38.7%) in the thermophilic CSTR. Although the functional metabolism of EM3 in anaerobic digesters is unknown, the high abundance of EM3 suggests that this taxon plays an important role in the thermophilic, anaerobic degradation of Scenedesmus. The abundant syntrophic bacteria and the detection of hydrogenotrophic methanogens in the thermophilic CSTR suggest that the hydrogenotrophic pathway was the dominant pathway for methane production in this reactor.This research has been supported by the Spanish Ministry of Economy and Competitiveness (MINECO, Project CTM2011-28595-C02-01/02), which is gratefully acknowledged. Support from The Research Council of Norway, grant number 228747 (BiogGasFuel), is also appreciated.Greses-Huerta, S.; Gaby, JC.; Aguado García, D.; Ferrer, J.; Seco Torrecillas, A.; Horn, SJ. (2017). Microbial community characterization during anaerobic digestion of Scenedesmus spp. under mesophilic and thermophilic conditions. Algal Research. 27:121-130. https://doi.org/10.1016/j.algal.2017.09.002S1211302

Atmospheric trace gases support primary production in Antarctic desert surface soil

LetterCultivation-independent surveys have shown that the desert soils of Antarctica harbour surprisingly rich microbial communities¹⁻³. Given that phototroph abundance varies across these Antarctic soils²·⁴, an enduring question is what supports life in those communities with low photosynthetic capacity³·⁵. Here we provide evidence that atmospheric trace gases are the primary energy sources of two Antarctic surface soil communities. We reconstructed 23 draft genomes from metagenomic reads, including genomes from the candidate bacterial phyla WPS-2 and AD3. The dominant community members encoded and expressed high-affinity hydrogenases, carbon monoxide dehydrogenases, and a RuBisCO lineage known to support chemosynthetic carbon fixation⁶·⁷. Soil microcosms aerobically scavenged atmospheric H₂ and CO at rates sufficient to sustain their theoretical maintenance energy and mediated substantial levels of chemosynthetic but not photosynthetic CO₂ fixation. We propose that atmospheric H₂, CO₂ and CO provide dependable sources of energy and carbon to support these communities, which suggests that atmospheric energy sources can provide an alternative basis for ecosystem function to solar or geological energy sources⁸·⁹. Although more extensive sampling is required to verify whether this process is widespread in terrestrial Antarctica and other oligotrophic habitats, our results provide new understanding of the minimal nutritional requirements for life and open the possibility that atmospheric gases support life on other planets.Mukan Ji, Chris Greening, Inka Vanwonterghem, Carlo R. Carere, Sean K. Bay, Jason A. Steen, Kate Montgomery, Thomas Lines, John Beardall, Josie van Dorst, Ian Snape, Matthew B. Stott, Philip Hugenholtz & Belinda C. Ferrar