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In 2005, a team of Polish archaeologists discovered three Coptic codices, two on papyrus and one on parchment, in the rubbish dump of a hermitage at Sheik Abd el-Gurna, Egypt. While the parchment codex and the remains of the bindings of the papyrus ones have been conserved, the text blocks of the papyrus codices were opened and disassembled and after being disinfected remained untouched for nearly 15 years, until the current project started. Currently, all three books are stored in the collection of the Coptic Museum in Cairo. Our team undertook the conservation of and archaeometric research on the papyrus codices. The first of the books contains the Canons of Pseudo-Basil, while the second is an Encomium of St. Pisenthios. Both codices have been palaeographically dated to the seventh-eighth centuries CE. In this paper, we describe our project and present the results of the work carried out on the Canons of Pseudo-Basil. Our work involved photography in transmitted light, measurements of the thickness of the papyrus leaves, and digital microscopy under three-light illumination. These measurements allowed us to determine the types of the inks and characterize the papyrus writing substrate. For conservation, we used a novel method developed in the Egyptian Museum in Berlin that comprises suspending papyrus folios on a translucent, extremely thin Japanese paper inside glass frames without the use of adhesives.In 2005, a team of Polish archaeologists discovered three Coptic codices, two on papyrus and one on parchment, in the rubbish dump of a hermitage at Sheik Abd el-Gurna, Egypt. While the parchment codex and the remains of the bindings of the papyrus ones have been conserved, the text blocks of the papyrus codices were opened and disassembled and after being disinfected remained untouched for nearly 15 years, until the current project started. Currently, all three books are stored in the collection of the Coptic Museum in Cairo. Our team undertook the conservation of and archaeometric research on the papyrus codices. The first of the books contains the Canons of Pseudo-Basil, while the second is an Encomium of St. Pisenthios. Both codices have been palaeographically dated to the seventh-eighth centuries CE. In this paper, we describe our project and present the results of the work carried out on the Canons of Pseudo-Basil. Our work involved photography in transmitted light, measurements of the thickness of the papyrus leaves, and digital microscopy under three-light illumination. These measurements allowed us to determine the types of the inks and characterize the papyrus writing substrate. For conservation, we used a novel method developed in the Egyptian Museum in Berlin that comprises suspending papyrus folios on a translucent, extremely thin Japanese paper inside glass frames without the use of adhesives.
Microscopic knowledge of the structural, energetic, and electronic properties of scandium fluoride is still incomplete despite the relevance of this material as an intermediate for the manufacturing of Al−Sc alloys. In a work based on first-principles calculations and X-ray spectroscopy, we assess the stability and electronic structure of six computationally predicted ScF3 polymorphs, two of which correspond to experimentally resolved single-crystal phases. In the theoretical analysis based on density functional theory (DFT), we identify similarities among the polymorphs based on their formation energies, chargedensity distribution, and electronic properties (band gaps and density of states). We find striking analogies between the results obtained for the ow- and high-temperature phases of the material, indirectly confirming that the transition occurring between them mainly consists of a rigid rotation of the lattice. With this knowledge, we examine the X-ray absorption spectra from the Sc and F K-edge contrasting firstprinciples results obtained from the solution of the Bethe−Salpeter equation on top of all-electron DFT with high-energy-resolution fluorescence detection measurements. Analysis of the computational results sheds light on the electronic origin of the absorption maxima and provides information on the prominent excitonic effects that characterize all spectra. A comparison with measurements confirms that the sample is mainly composed of the high- and low-temperature polymorphs of ScF3. However, some fine details in the experimental results suggest that the probed powder sample may contain defects and/or residual traces of metastable polymorphs.
Bacterial biofilms can pose a serious health risk to humans and are less susceptible
to antibiotics and disinfection than planktonic bacteria. Here, a novel method
for biofilm eradication based on antimicrobial photodynamic therapy utilizing
a nanoparticle in conjunction with a BODIPY derivative as photosensitizer was
developed. Reactive oxygen species are generated upon illumination with
visible light and lead to a strong, controllable and persistent eradication of
both planktonic bacteria and biofilms. One of the biggest challenges in biofilm
eradication is the penetration of the antimicrobial agent into the biofilm and
its matrix. A biocompatible hydrophilic nanoparticle was utilized as a delivery
system for the hydrophobic BODIPY dye and enabled its accumulation within the
biofilm. This key feature of delivering the antimicrobial agent to the site of action
where it is activated resulted in effective eradication of all tested biofilms. Here,
3 bacterial species that commonly form clinically relevant pathogenic biofilms
were selected: Escherichia coli, Staphylococcus aureus and Streptococcus
mutans. The development of this antimicrobial photodynamic therapy tool for
biofilm eradication takes a promising step towards new methods for the much
needed treatment of pathogenic biofilms.
Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to nonmethanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens.
Numerous genus-level lineages appear to be present exclusively in arthropods,suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological nichesprovided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.
Pseudomonas aeruginosa is an opportunistic pathogen of considerable medical importance, owing to its pronounced antibiotic tolerance and association with cystic fibrosis and other life-threatening diseases. The aim of this study was to highlight the genes responsible for P. aeruginosa biofilm tolerance to antibiotics and thereby identify potential new targets for the development of drugs against biofilm-related infections. By developing a novel screening approach and utilizing a public P. aeruginosa transposon insertion library, several biofilm-relevant genes were identified. The Pf phage gene (PA0720) and flagellin gene (fliC) conferred biofilm-specific tolerance to gentamicin. Compared with the reference biofilms, the biofilms formed by PA0720 and fliC mutants were completely eliminated with a 4-fold-lower gentamicin concentration. Furthermore, the mreC, pprB, coxC, and PA3785 genes were demonstrated to play major roles in enhancing biofilm tolerance to gentamicin. The analysis of biofilm-relevant genes performed in this study provides important novel insights into the understanding of P. aeruginosa antibiotic tolerance, which will facilitate the detection of antibiotic resistance and the development of antibiofilm strategies against P. aeruginosa.
Research on per- and polyfluoroalkyl substances (PFAS) frequently incorporates organofluorine measurements, particularly because they could support a class-based approach to regulation. However, standardized methods for organofluorine analysis in a broad suite of matrices are currently unavailable, including a method for extractable organofluorine (EOF) measured using combustion ion chromatography (CIC). Here, we report the results of an international interlaboratory comparison. Seven laboratories representing academia, government, and the private sector measured paired EOF and PFAS concentrations in groundwater and eel (Anguilla rostrata) from a site contaminated by aqueous film-forming foam. Among all laboratories, targeted PFAS could not explain all EOF in groundwater but accounted for most EOF in eel. EOF results from all laboratories for at least one replicate extract fell within one standard deviation of the interlaboratory mean for groundwater and five out of seven laboratories for eel. PFAS spike mixture recoveries for EOF measurements in groundwater and eel were close to the criterion (±30%) for standardized targeted PFAS methods. Instrumental operation of the CIC such as replicate sample injections was a major source of measurement uncertainty. Blank contamination and incomplete inorganic fluorine removal may introduce additional uncertainties. To elucidate the presence of unknown organofluorine using paired EOF and PFAS measurements, we recommend that analysts carefully consider confounding methodological uncertainties such as differences in precision between measurements, data processing steps such as blank subtraction and replicate analyses, and the relative recoveries of PFAS and other fluorine compounds.
Adipokinetic hormone (AKH) is a neuropeptide produced in the insect corpora cardiaca that plays an essential role in mobilising carbohydrates and lipids from the fat body to the haemolymph. AKH acts by binding to a rhodopsin-like G protein-coupled receptor (GPCR), the adipokinetic hormone receptor (AKHR). In this study, we tackle AKH ligand and receptor gene evolution as well as the evolutionary origins of AKH gene paralogues from the order Blattodea (termites and cockroaches). Phylogenetic analyses of AKH precursor sequences point to an ancient AKH gene duplication event in the common ancestor of Blaberoidea, yielding a new group of putative decapeptides. In total, 16 different AKH peptides from 90 species were obtained. Two octapeptides and seven putatively novel decapeptides are predicted for the first time. AKH receptor sequences from 18 species, spanning solitary cockroaches and subsocial wood roaches as well as lower and higher termites, were subsequently acquired using classical molecular methods and in silico approaches employing transcriptomic data. Aligned AKHR open reading frames revealed 7 highly conserved transmembrane regions, a typical arrangement for GPCRs.
Phylogenetic analyses based on AKHR sequences support accepted relationships among termite, subsocial (Cryptocercus spp.) and solitary cockroach lineages to a large extent, while putative post-translational modification sites do not greatly differ between solitary and subsocial roaches and social termites. Our study provides important information not only for AKH and AKHR functional research but also for further analyses interested in their development as potential candidates for biorational pest control agents against invasive termites and cockroaches.
Excessive discharge of quaternary ammoniumdisinfectants such as benzalkonium chloride (BAC) into aquatic systems can trigger several physiological responses in environmental microorganisms. In this study, we isolated a less-susceptible strain of Aeromonas hydrophila to BAC, designated as INISA09, froma wastewater treatment plant in Costa Rica. We characterized its phenotypic response upon exposure to three dierent concentrations of BAC and characterizedmechanisms related to its resistance using genomic and proteomic approaches. The genome of the strain, mapped against 52 dierent sequenced A. hydrophila strains, consists of approximately 4.6Mb with 4,273 genes. We found a massive genome rearrangement and thousands of missense mutations compared to the reference strain A. hydrophila ATCC 7966.
We identified 15,762 missense mutations mainly associated with transport, antimicrobial resistance, and outer membrane proteins.
In addition, a quantitative proteomic analysis revealed a significant upregulation of several efflux pumps and the downregulation of porins when the strain was exposed to three BAC concentrations.Other genes related tomembrane fatty acid metabolism and redox metabolic reactions also showed an altered expression.
Our findings indicate that the response of A. hydrophila INISA09 to BAC primarily occurs at the envelop level, which is the primary target of BAC. Our study elucidates the mechanisms of antimicrobial susceptibility in aquatic environments against a widely used disinfectant and will help better understand howbacteria can adapt to biocide pollution. To our knowledge, this is the first study addressing the resistance to BAC in an environmental A. hydrophila isolate. We propose that this bacterial species could also serve as a new model to study antimicrobial pollution in aquatic environments.
Climate change is becoming one of the greatest challenges facing our society, particularly due to the continued use of fossil fuels. The steadily increasing demand for energy and the continuously growing world population will further intensify these challenges. The development of renewable energies is therefore of central importance. The 2020 EU Energy Roadmap aims to increase the share of renewable energies (gross energy consumption) to 55% by 2050.
Hydrogen (H2) has the highest potential to become the primary renewable energy source. It is envisioned that by 2050 up to 24% of the total energy demand of Europe is to be ensured by H2. However, a decisive disadvantage of the climate friendly alternatives is the massive containment demand, which needs to be highly secure, cost efficient and easily extractable.
Underground geological formations (UGF) represent a seemingly optimal alternative to meet the rapidly increasing storage demand. In this context, many studies are currently underway to determine the feasibility and risks of UGF. However, little or no consideration is being given to microbiology. Therefore, in this Research Topic we will focus on achieving a greater understanding of the impact microorganisms exert on UGF, with a particular emphasis on interdisciplinary studies.
As many subsurface microbial communities can use H2 as an electron donor, production of seemingly undesirable metabolic byproducts, such as hydrogen sulfide, methane, and acids, are also to be expected. However, the rate of the H2 conversion by the microorganisms, how their metabolic activities impact the UGF on a short-term and long-term scale, the extent of damages microorganisms exert on the infrastructure, or potential use of microorganisms to enhance UGF are just a few questions that require urgent research to assess the role of microorganisms in this new anthropogenic use of the subsurface environment. These and many questions can be addressed in this article collection. In particular, understanding microbial community changes and activity rates will help assess operational and environmental risks, develop mitigation strategies and provide new insights on life under extreme conditions (i.e., pressure, salinity).
In this Research Topic, the editorial team particularly welcomes Original Research, Hypothesis and Theory, Method, and Review manuscripts that deal with the latest advances in microbiology in formations that are planned or currently prepared for hydrogen storage, from both fundamental and practical points of view. The ultimate objective is to promote a deeper understanding into the sustainability of UGF and generate interdisciplinary research involving microbiologists, reservoir engineers, geologists, chemists, physicists.
The topics of interest include, but are not limited to:
• Microbial diversity in different underground hydrogen storage sites or formations currently being considered for hydrogen storage
• Mechanism and impact of microbial growth under high H2 pressure
• Potential role of microorganisms in the short-term and long-term storage of hydrogen
• Potential influences of microorganisms on the hydrogen storage infrastructure systems, e.g., microbiologically influenced corrosion, biofilm growth
• Hydrogen-solid-microorganism interactions, including the influence of microbial growth on UGF geological parameters
• Mechanism and modelling of microbial impact on hydrogen storage
UGF relevant for this Research Topic include porous media, salt caverns, deep aquifers, hard rock caverns and depleted oil/gas reservoirs.
We present how mesoporosity can be engineered in transition metal phosphate (TMPs) materials in a template-free manner. The method involves the transformation of a precursor metal phosphate phase, called M-struvite (NH4MPO4·6H2O, M = Mg2+, Ni2+, Co2+, NixCo1−x2+). It relies on the thermal decomposition of crystalline M-struvite precursors to an amorphous and simultaneously mesoporous phase, which forms during degassing of NH3 and H2O. The temporal evolution of mesoporous frameworks and the response of the metal coordination environment were followed by in situ and ex situ scattering and diffraction, as well as X-ray spectroscopy. Despite sharing the same precursor struvite structure, different amorphous and mesoporous structures were obtained depending on the involved transition metal. We highlight the systematic differences in absolute surface area, pore shape, pore size, and phase transitions depending on the metal cation present in the analogous M-struvites. The amorphous structures of thermally decomposed Mg-, Ni- and NixCo1−x-struvites exhibit high surface areas and pore volumes (240 m2 g−1 and 0.32 cm−3 g−1 for Mg and 90 m2 g−1 and 0.13 cm−3 g−1 for Ni). We propose that the low-cost, environmentally friendly M-struvites could be obtained as recycling products from industrial and agricultural wastewaters. These waste products could be then upcycled into mesoporous TMPs through a simple thermal treatment for further application, for instance in (electro)catalysis.