Comparative Genomics Reveals Adaptation by Alteromonas sp. SN2 to Marine Tidal-Flat Conditions: Cold Tolerance and Aromatic Hydrocarbon Metabolism

Alteromonas species are globally distributed copiotrophic bacteria in marine habitats. Among these, sea-tidal flats are distinctive: undergoing seasonal temperature and oxygen-tension changes, plus periodic exposure to petroleum hydrocarbons. Strain SN2 of the genus Alteromonas was isolated from hydrocarbon-contaminated sea-tidal flat sediment and has been shown to metabolize aromatic hydrocarbons there. Strain SN2's genomic features were analyzed bioinformatically and compared to those of Alteromonas macleodii ecotypes: AltDE and ATCC 27126. Strain SN2's genome differs from that of the other two strains in: size, average nucleotide identity value, tRNA genes, noncoding RNAs, dioxygenase gene content, signal transduction genes, and the degree to which genes collected during the Global Ocean Sampling project are represented. Patterns in genetic characteristics (e.g., GC content, GC skew, Karlin signature, CRISPR gene homology) indicate that strain SN2's genome architecture has been altered via horizontal gene transfer (HGT). Experiments proved that strain SN2 was far more cold tolerant, especially at 5°C, than the other two strains. Consistent with the HGT hypothesis, a total of 15 genomic islands in strain SN2 likely confer ecological fitness traits (especially membrane transport, aromatic hydrocarbon metabolism, and fatty acid biosynthesis) specific to the adaptation of strain SN2 to its seasonally cold sea-tidal flat habitat

Millimeter-wave Signature of Strange Matter Stars

One of the most important questions in the study of compact objects is the nature of pulsars, including whether they consist of neutron matter or strange quark matter (SQM). However, few mechanisms for distinguishing between these two possibilities have been proposed. The purpose of this paper is to show that a strange star (one made of SQM) will have a vibratory mode with an oscillation frequency of approximately 250 GHz (millimeter wave). This mode corresponds to motion of the center of the expected crust of normal matter relative to the center of the strange quark core, without distortion of either. Radiation from currents generated in the crust at the mode frequency would be a SQM signature. We also consider effects of stellar rotation, estimate power emission and signal-to-noise ratio, and discuss briefly possible mechanisms for exciting the mode.Comment: 13 pages, Latex, one figur

Infiltration of Sulfate to Enhance Sulfate Reduction of Petroleum Hydrocarbons

The lack of sufficient electron acceptors, particularly sulfate, can limit the rate of biodegradation of petroleum hydrocarbons (PHCs). Hence there is a growing interest by remediation practitioners to deliver sulfate to a PHC impacted saturated zone to enhance biodegradation. When shallow contamination is present in a relatively permeable aquifer and site constraints allow, a cost-effective approach is to apply sulfate on the ground surface. In this investigation a pilot-scale experiment was conducted to increase our understanding of the delivery of sulfate using a surface-based method and the resulting impact on a shallow PHC contaminated aquifer. A surficial infiltration pond positioned on the ground surface above a well-characterized residual PHC source zone was used to control sulfate dosing. A high-resolution network near the infiltration pond and downgradient of the source zone was employed to monitor relevant geochemical indicators and PHC concentrations. Compound specific isotope analysis (CSIA) was used to identify biodegradation patterns and to investigate the occurrence of microbial sulfate reduction. Selected metabolites and reverse-transcriptase quantitative polymerase chain reaction analyses of expressed biodegradation genes (as mRNA) were also used to characterize the response of indigenous microorganisms (especially sulfate reducing bacteria) to the added sulfate. Three sulfate application episodes (5000 L each) at various Na 2 SO 4 concentrations were allowed to infiltrate under a constant hydraulic head. Although the applied sulfate solution was impacted by density driven advection, detailed monitoring data indicated that the sulfate-enriched water mixed with up-gradient groundwater as it migrated downward through the residual PHC zone and formed a co-mingled downgradient plume with the dissolved PHC compounds. The enrichment of δ 34 S of sulfate in conjunction with a decrease in sulfate concentration showed the occurrence of sulfate reduction due to the applied sulfate. Increased dissolved inorganic carbon (DIC) concentrations associated with a shift toward more depleted values of δ 13 C of DIC was indicative of an input of isotopically depleted DIC from biodegradation of benzene, toluene and o-xylene (BTX). Despite fluctuations in the BTX concentrations, the CSIA data for BTX showed that these compounds were biodegraded. The biomarker data provided supporting evidence that toluene and o-xylene were undergoing anaerobic biodegradation due to sulfate reduction. This study provides insight into factors controlling surface-based delivery of sulfate to shallow PHC impacted groundwater systems, and the value of isotopic and molecular-biological procedures to augment conventional monitoring tools

Microbial community dynamics and stability during an ammonia-induced shift to syntrophic acetate oxidation

Anaerobic digesters rely on the diversity and distribution of parallel metabolic pathways mediated by complex syntrophic microbial communities to maintain robust and optimal performance. Using mesophilic swine waste digesters, we experimented with increased ammonia loading to induce a shift from aceticlastic methanogenesis to an alternative acetate-consuming pathway of syntrophic acetate oxidation. In comparison with control digesters, we observed shifts in bacterial 16S rRNA gene content and in functional gene repertoires over the course of the digesters' 3-year operating period. During the first year, under identical startup conditions, all bioreactors mirrored each other closely in terms of bacterial phylotype content, phylogenetic structure, and evenness. When we perturbed the digesters by increasing the ammonia concentration or temperature, the distribution of bacterial phylotypes became more uneven, followed by a return to more even communities once syntrophic acetate oxidation had allowed the experimental bioreactors to regain stable operation. The emergence of syntrophic acetate oxidation coincided with a partial shift from aceticlastic to hydrogenotrophic methanogens. Our 16S rRNA gene analysis also revealed that acetate-fed enrichment experiments resulted in communities that did not represent the bioreactor community. Analysis of shotgun sequencing of community DNA suggests that syntrophic acetate oxidation was carried out by a heterogeneous community rather than by a specific keystone population with representatives of enriched cultures with this metabolic capacity

Microbial life in the deep terrestrial subsurface

The distribution and function of microorganisms is a vital issue in microbial ecology. The US Department of Energy`s Program, ``Microbiology of the Deep Subsurface,`` concentrates on establishing fundamental scientific information about organisms at depth, and the use of these organisms for remediation of contaminants in deep vadose zone and groundwater environments. This investigation effectively extends the Biosphere hundreds of meters into the Geosphere and has implications to a variety of subsurface activities

A Unified Model of the GABA(A) Receptor Comprising Agonist and Benzodiazepine Binding Sites

We present a full-length α(1)β(2)γ(2) GABA receptor model optimized for agonists and benzodiazepine (BZD) allosteric modulators. We propose binding hypotheses for the agonists GABA, muscimol and THIP and for the allosteric modulator diazepam (DZP). The receptor model is primarily based on the glutamate-gated chloride channel (GluCl) from C. elegans and includes additional structural information from the prokaryotic ligand-gated ion channel ELIC in a few regions. Available mutational data of the binding sites are well explained by the model and the proposed ligand binding poses. We suggest a GABA binding mode similar to the binding mode of glutamate in the GluCl X-ray structure. Key interactions are predicted with residues α(1)R66, β(2)T202, α(1)T129, β(2)E155, β(2)Y205 and the backbone of β(2)S156. Muscimol is predicted to bind similarly, however, with minor differences rationalized with quantum mechanical energy calculations. Muscimol key interactions are predicted to be α(1)R66, β(2)T202, α(1)T129, β(2)E155, β(2)Y205 and β(2)F200. Furthermore, we argue that a water molecule could mediate further interactions between muscimol and the backbone of β(2)S156 and β(2)Y157. DZP is predicted to bind with interactions comparable to those of the agonists in the orthosteric site. The carbonyl group of DZP is predicted to interact with two threonines α(1)T206 and γ(2)T142, similar to the acidic moiety of GABA. The chlorine atom of DZP is placed near the important α(1)H101 and the N-methyl group near α(1)Y159, α(1)T206, and α(1)Y209. We present a binding mode of DZP in which the pending phenyl moiety of DZP is buried in the binding pocket and thus shielded from solvent exposure. Our full length GABA(A) receptor is made available as Model S1

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio