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The formation of ice particles in Earth's atmosphere strongly influences the dynamics and optical properties of clouds and their impacts on the climate system. Ice formation in clouds is often triggered heterogeneously by ice-nucleating particles (INPs) that represent a very low number of particles in the atmosphere. To date, many sources of INPs, such as mineral and soil dust, have been investigated and identified in the low and mid latitudes. Although less is known about the sources of ice nucleation at high latitudes, efforts have been made to identify the sources of INPs in the Arctic and boreal environments. In this study, we investigate the INP emission potential from high-latitude boreal forests in the mixed-phase cloud regime. We introduce the HyICE-2018 measurement campaign conducted in the boreal forest of Hyytiala, Finland, between February and June 2018. The campaign utilized the infrastructure of the Station for Measuring Ecosystem-Atmosphere Relations (SMEAR) II, with additional INP instruments, including the Portable Ice Nucleation Chamber I and II (PINC and PINCii), the SPectrometer for Ice Nuclei (SPIN), the Portable Ice Nucleation Experiment (PINE), the Ice Nucleation SpEctrometer of the Karlsruhe Institute of Technology (INSEKT) and the Microlitre Nucleation by Immersed Particle Instrument (mu L-NIPI), used to quantify the INP concentrations and sources in the boreal environment. In this contribution, we describe the measurement infrastructure and operating procedures during HyICE-2018, and we report results from specific time periods where INP instruments were run in parallel for inter-comparison purposes. Our results show that the suite of instruments deployed during HyICE-2018 reports consistent results and therefore lays the foundation for forthcoming results to be considered holistically. In addition, we compare measured INP concentrations to INP parameterizations, and we observe good agreement with the Tobo et al. (2013) parameterization developed from measurements conducted in a ponderosa pine forest ecosystem in Colorado, USA., Atmospheric Chemistry and Physics, 22 (8), ISSN:1680-7375, ISSN:1680-7367

Surrogate viruses theoretically provide an opportunity to study the viral spread in an indoor environment, a highly needed understanding during the pandemic, in a safe manner to humans and the environment. However, the safety of surrogate viruses for humans as an aerosol at concentrations has not been established. In this study, Phi6 surrogate was aerosolized at concentration (Particulate matter(2.5): similar to 1018 mu g m(-3)) in the studied indoor space. Participants were closely followed for any symptoms. We measured the bacterial endotoxin concentration the virus solution used for aerosolization as well as the concentration in the room air containing the aerosolized viruses. In addition, we measured how the bacterial endotoxin concentration the sample was affected by different traditional virus purification procedures. Despite the puri-fication, bacterial endotoxin concentration of the Phi6 was high (350 EU/ml in solution used aerosols) with both (two) purification protocols. Bacterial endotoxins were also detected aerosolized form, but below the occupational exposure limit of 90 EU/m(3). Despite these concerns, no symptoms were observed in exposed humans when they were using personal protective equipment. In the future, purification protocols should be developed to reduce associated terial endotoxin levels in enveloped bacterial virus specimens to ensure even safer research use surrogate viruses.

Objective COVID-19 spreads through aerosols produced in coughing, talking, exhalation, and also in some surgical procedures. Use of CO2 laser in laryngeal surgery has been observed to generate aerosols, however, other techniques, such cold dissection and microdebrider, have not been sufficiently investigated. We aimed to assess whether aerosol generation occurs during laryngeal operations and the effect of different instruments on aerosol production. Methods We measured particle concentration generated during surgeries with an Optical Particle Sizer. Cough data collected from volunteers and aerosol concentration of an empty operating room served as references. Aerosol concentrations when using different techniques and equipment were compared with references as well as with each other. Results Thirteen laryngological surgeries were evaluated. The highest total aerosol concentrations were observed when using CO2 laser and these were significantly higher than the concentrations when using microdebrider or cold dissection (p p p p p = 0.146, p = 0.753). In comparing all three techniques, microdebrider produced the least aerosol particles. Conclusions Microdebrider and cold dissection can be regarded as aerosol-generating relative to background reference concentrations, but they should not be considered as high-risk aerosol-generating procedures, as the concentrations are low and do not exceed those of coughing. A step-down algorithm from CO2 laser to cold instruments and microdebrider is recommended to lower the risk of airborne infections among medical staff.

A new bubble-generating glass chamber with an extensive set of aerosol production experiments is presented. Compared to the experiments described in the literature since the ground-setting works of Edward C.​​​​​​​ Monahan et al. in 1980s, the current setup is among the medium-sized installations allowing for accurate control of the air discharge, water temperature, and salinity. The size and material of the chamber offer a variety of applications due to its portability, measurement setup adjustability, and sterilization option. The experiments have been conducted in a cylindrical bubbling tank of 10 L volume that was filled by ∼ 30 %–40 % with water of controlled salt content and temperature and covered with a hermetic lid. The chamber was used to study the characteristics of aerosols produced by bursting bubbles under different conditions. In line with previous findings, the sea spray aerosol production was shown to depend linearly on the surface area covered by the bubbles, which in turn is a near-linear function of the air discharge through the water. Observed dependencies of the aerosol size spectra and particle fluxes on water salinity and temperature, being qualitatively comparable with the previous experiments, substantially refined the existing parameterizations. In particular, the bubble size was practically independent from the air discharge through the water body, except in the case of very small flows. Also, the dependence of aerosol spectrum and amount on salinity was much weaker than suggested in some previous experiments. The temperature dependence, to the contrary, was significant and consistent, with a transition in the spectrum shape at ∼ 10 ∘C. Theoretical analysis based on the basic conservation laws supported the main results of the experiments but also highlighted the need for a better understanding of the aerosol production from a cold water surface.

SARS- CoV- 2 has been detected both in air and on surfaces, but questions remain about the patient-specific and environmental factors affecting virus transmission. Additionally, more detailed information on viral sampling of the air is needed. This prospective cohort study (N= 56) presents results from 258 air and 252 surface samples from the surroundings of 23 hospitalized and eight home- treated COVID-19 index patients between July 2020 and March 2021 and compares the results between the measured environments and patient factors. Additionally, epidemiological and experimental investigations were performed. The proportions of qRT- PCR- positiveair (10.7% hospital/17.6% homes) and surface samples (8.8%/12.9%) showed statisti-cal similarity in hospital and homes. Significant SARS- CoV- 2 air contamination was observed in a large (655.25 m3) mechanically ventilated (1.67 air changes per hour, 32.4– 421 L/s/patient) patient hall even with only two patients present. All positive air samples were obtained in the absence of aerosol- generating procedures. In four cases, positive environmental samples were detected after the patients had devel-oped a neutralizing IgG response. SARS- CoV- 2 RNA was detected in the following particle sizes: 0.65– 4.7 μm , 7. 0– 12.0 μm, >10μm, and

Meat and bone meal (MBM), as slaughterhouse waste, is a potential biostimulating agent, but its efficiency and reliability in composting are largely unknown. To access the MBM application to the composting process of asparagus straw rice, we followed the composting process for 60 days in 220-L composters and another 180 days in 20-L buckets in treatments applied with MBM or urea. The microbial succession was investigated by high-throughput sequencing. Compared with urea treatments, MBM addition stabilized pH and extended the thermophilic phase for 7 days. The germination index of MBM treatments was 24.76% higher than that of urea treatments. MBM also promoted higher microbial diversity and shifted community compositions. Organic matter and pH were the most significant factors that influence the bacterial and fungal community structure. At the genus level, MBM enriched relative abundances of organic matter-degrading bacteria (Alterococcus) and lignocellulose-degrading fungi (Trichoderma), as well as lignocellulolytic enzyme activities. Notably, MBM addition decreased sum abundances of plant pathogenic fungi of Phaeoacremonium, Acremonium, and Geosmithia from 17.27 to 0.11%. This study demonstrated the potential of MBM as an effective additive in asparagus straw composting, thus providing insights into the development of new industrial aerobic fermentation.

Publisher Copyright: © 2022 Meat and Bone Meal (MBM) and β-cyclodextrin were added to a soil sample co-contaminated by hydrocarbons (diesel fraction C10-C21 and lubricant oil fraction C22-C40) and heavy metals to promote soil remediation. The pilot study was conducted in the laboratory, maintaining optimal conditions (i.e., temperature, pH, water content, soil aeration) to facilitate hydrocarbon biodegradation. Two different experimental tests were prepared: one for the analysis of hydrocarbons in soil, the other to monitor the dynamics of some elements of interest. For the first test, the two hydrocarbon fractions in the soil were quantified separately by GC-FID, following the ISO 16703:2004(E) standard protocol. Sampling and analysis were done every two weeks, for three consecutive months. For the second test (dynamics of certain elements in the soil), soil and leachate samples were analyzed by ICP-MS after appropriate pretreatment steps.

We report an experimental infection of American mink with SARS-CoV-2 Omicron variant and show that mink remain positive for viral RNA for days, experience clinical signs and histopathologic changes, and transmit the virus to uninfected recipients. Preparedness is crucial to avoid spread among mink and spillover to human populations.

This study compared electrokinetic (EK) remediation with and without interval power breaking in the removal of total and plant available cadmium (Cd) in the soil. Two laboratory experiments, i.e. EK remediation with interval power breaking (24-12 h power-on-off cycles) and conventional EK remediation (continuous power supply) with the same accumulated time (192 h) of power supply were conducted to remove soil Cd. After the EK remediation by interval power breaking, the total Cd removal efficiency in the soil rose to 38%, in comparison to 28% by the conventional EK remediation. As for the plant available Cd, the removal efficiency was enhanced from 52% to 63%. Additionally, the electric current during the EK remediation and electric conductivity after the EK remediation were higher in the soil treated by interval power breaking, which indicated an enhanced desorption and/or migration of charged species. It further meant that the higher removal efficiency of soil Cd by interval power breaking could be related to the enhanced desorption and/or migration of Cd species. This study indicated that both conventional EK remediation and EK remediation with interval power breaking were effective methods to remove soil Cd but EK remediation with interval power breaking was more efficient.

Intubation, laryngoscopy, and extubation are considered highly aerosol-generating procedures, and additional safety protocols are used during COVID-19 pandemic in these procedures. However, previous studies are mainly experimental and have neither analyzed staff exposure to aerosol generation in the real-life operating room environment nor compared the exposure to aerosol concentrations generated during normal patient care. To assess operational staff exposure to potentially infectious particle generation during general anesthesia, we measured particle concentration and size distribution with patients undergoing surgery with Optical Particle Sizer.A single-center observative multidisciplinary clinical study in Helsinki University Hospital with 39 adult patients who underwent general anesthesia with tracheal intubation. Mean particle concentrations during different anesthesia procedures were statistically compared with cough control data collected from 37 volunteers to assess the differences in particle generation.This study measured 25 preoxygenations, 30 mask ventilations, 28 intubations, and 24 extubations. The highest total aerosol concentration of 1153 particles (p)/cm³ was observed during mask ventilation. Preoxygenations, mask ventilations, and extubations as well as uncomplicated intubations generated mean aerosol concentrations statistically comparable to coughing. It is noteworthy that difficult intubation generated significantly fewer aerosols than either uncomplicated intubation (p = .007) or coughing (p = 0.006).Anesthesia induction generates mainly small (1 µm) aerosol particles. Based on our results, general anesthesia procedures are not highly aerosol-generating compared with coughing. Thus, their definition as high-risk aerosol-generating procedures should be re-evaluated due to comparable exposures during normal patient care.The list of aerosol-generating procedures guides the use of protective equipments in hospitals. Intubation is listed as a high-risk aerosol-generating procedure, however, aerosol generation has not been measured thoroughly. We measured aerosol generation during general anesthesia. None of the general anesthesia procedures generated statistically more aerosols than coughing and thus should not be considered as higher risk compared to normal respiratory activities.

A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.

COVID-19 has highlighted the need for indoor risk-reduction strategies. Our aim is to provide information about the virus dispersion and attempts to reduce the infection risk. Indoor transmission was studied simulating a dining situation in a restaurant. Aerosolized Phi6 viruses were detected with several methods. The aerosol dispersion was modeled by using the Large-Eddy Simulation (LES) technique. Three risk-reduction strategies were studied: (1) augmenting ventilation with air purifiers, (2) spatial partitioning with dividers, and (3) combination of 1 and 2. In all simulations infectious viruses were detected throughout the space proving the existence long-distance aerosol transmission indoors. Experimental cumulative virus numbers and LES dispersion results were qualitatively similar. The LES results were further utilized to derive the evolution of infection probability. Air purifiers augmenting the effective ventilation rate by 65% reduced the spatially averaged infection probability by 30%-32%. This relative reduction manifests with approximately 15 min lag as aerosol dispersion only gradually reaches the purifier units. Both viral findings and LES results confirm that spatial partitioning has a negligible effect on the mean infection-probability indoors, but may affect the local levels adversely. Exploitation of high-resolution LES jointly with microbiological measurements enables an informative interpretation of the experimental results and facilitates a more complete risk assessment.

Background: Suspected aerosol-generating dental instruments may cause risks for operators by transmitting pathogens, such as the SARS-CoV-2 virus. The aim of our study was to measure aerosol generation in various dental procedures in clinical settings. Methods: The study population comprised of 84 patients who underwent 253 different dental procedures measured with Optical Particle Sizer in a dental office setting. Aerosol particles from 0.3 to 10 μm in diameter were measured. Dental procedures included oral examinations (N ¼ 52), restorative procedures with air turbine handpiece (N ¼ 8), high-speed (N ¼ 6) and low-speed (N ¼ 30) handpieces, ultrasonic scaling (N ¼ 31), periodontal treatment using hand instruments (N ¼ 60), endodontic treatment (N ¼ 12), intraoral radiographs (N ¼ 24), and dental local anesthesia (N ¼ 31). Results: Air turbine handpieces significantly elevated 5 μm median (p ¼ 0.023), maximum (p ¼ 0.013) particle number concentrations,> 5 μm particle mass concentrations (p ¼ 0.021) and maximum total particle mass concentrations (p ¼ 0.022). High-speed dental handpieces elevated aerosol concentration levels compared to the levels produced during oral examination. Conclusions: Air turbine handpieces produced the highest levels of

In order to effectively predict the formation of ice in clouds we need to know which subsets of aerosol particles are effective at nucleating ice, how they are distributed and where they are from. A large proportion of ice-nucleating particles (INPs) in many locations are likely of biological origin, and some INPs are extremely small, being just tens of nanometres in size. The identity and sources of such INPs are not well characterized. Here, we show that several different types of virus particles can nucleate ice, with up to about 1 in 20 million virus particles able to nucleate ice at −20 ∘C. In terms of the impact on cloud glaciation, the ice-nucleating ability (the fraction which are ice nucleation active as a function of temperature) taken together with typical virus particle concentrations in the atmosphere leads to the conclusion that virus particles make a minor contribution to the atmospheric ice-nucleating particle population in the terrestrial-influenced atmosphere. However, they cannot be ruled out as being important in the remote marine atmosphere. It is striking that virus particles have an ice-nucleating activity, and further work should be done to explore other types of viruses for both their ice-nucleating potential and to understand the mechanism by which viruses nucleate ice.

Lipid membrane fusion is an essential function in many biological processes. Detailed mechanisms of membrane fusion and the protein structures involved have been mainly studied in eukaryotic systems, whereas very little is known about membrane fusion in prokaryotes. Haloarchaeal pleomorphic viruses (HRPVs) have a membrane envelope decorated with spikes that are presumed to be responsible for host attachment and membrane fusion. Here we determine atomic structures of the ectodomains of the 57-kDa spike protein VP5 from two related HRPVs revealing a previously unreported V-shaped fold. By Volta phase plate cryo-electron tomography we show that VP5 is monomeric on the viral surface, and we establish the orientation of the molecules with respect to the viral membrane. We also show that the viral membrane fuses with the host cytoplasmic membrane in a process mediated by VP5. This sheds light on protein structures involved in prokaryotic membrane fusion., Lipid membrane fusion is an essential function in many biological processes but little is known about membrane fusion in prokaryotes. The authors here study how haloarchaeal pleomorphic viruses (HRPVs) infect archaeal hosts. The structure-function analysis of the spike proteins shed light on prokaryotic membrane fusion.

Microalgal cultivation in aquaculture wastewater (AWW) from recirculating aquaculture systems (RAS) is an approach for combined production of valuable algal biomass and AWW treatment. The growth, nutrient uptake, fatty acid (FA) profile, and tocopherol content of mixed algal cultures of Euglena gracilis with Selenastrum grown in AWWs from pikeperch (Sander lucioperca) and catfish (Clarias anguillaris) RAS were studied. The highest algal biomass (1.5gL(-1)), lipid (84.9mgL(-1)), and tocopherol (877.2gL(-1)) yields were achieved in sludge-amended pike perch AWW. Nutrient removal rates in experiments were 98.9-99.5 and 98.4-99.8% for NH4-N and PO4-P, and 75.4-89.2% and 84.3-95.7% for TN and TP, respectively, whereas the COD was reduced by 45.8-67.6%. Biomass EPA and DHA content met, while ARA and tocopherol content exceeded the requirements for fish feed. Algal cultivation in AWWs is a promising alternative for AWW treatment while providing a replacement for fish oil in feed.

Simple Summary Environmental changes of habitat shaped the sable (Carnivora Mustelidae Martes zibellina) gut microbial community structure and altered the functions of gut microbiota, showing that the wild sable gut microbial community diversity was resilient and responded to environment change. Elevated habitat is a pivotal factor for wild sable survival and reproduction, and the adaptability is in part enabled through their gut microbial communities. Our observations show that despite having been forced to migrate from low altitudes to high altitudes because of anthropogenic habitat encroachment, wild sables showed robustness in adapting to harsh conditions. Additionally, we propose that the crucial factor enabling wild sables to survive in changeable environments was their gut microbial communities. It is widely understood that harsh conditions, such as high altitude and low temperature environments, have an adverse effect on wild fauna survival. However, our results suggested that increasing altitude can enhance some functions in wild sable gut microbial communities. In recent decades, wild sable (Carnivora Mustelidae Martes zibellina) habitats, which are often natural forests, have been squeezed by anthropogenic disturbances such as clear-cutting, tilling and grazing. Sables tend to live in sloped areas with relatively harsh conditions. Here, we determine effects of environmental factors on wild sable gut microbial communities between high and low altitude habitats using Illumina Miseq sequencing of bacterial 16S rRNA genes. Our results showed that despite wild sable gut microbial community diversity being resilient to many environmental factors, community composition was sensitive to altitude. Wild sable gut microbial communities were dominated by Firmicutes (relative abundance 38.23%), followed by Actinobacteria (30.29%), and Proteobacteria (28.15%). Altitude was negatively correlated with the abundance of Firmicutes, suggesting sable likely consume more vegetarian food in lower habitats where plant diversity, temperature and vegetation coverage were greater. In addition, our functional genes prediction and qPCR results demonstrated that energy/fat processing microorganisms and functional genes are enriched with increasing altitude, which likely enhanced metabolic functions and supported wild sables to survive in elevated habitats. Overall, our results improve the knowledge of the ecological impact of habitat change, providing insights into wild animal protection at the mountain area with hash climate conditions.

The brackish Baltic Sea is under diesel oil pollution risk due to heavy ship traffic. The situation is exasperated by densely distributed marinas and a vigorous although seasonal recreational boating. The seasonality and physical environmental variations hamper the monitoring of microbial communities in response to diesel oil spills. Hence, an 8-week simulation experiment was established in metal basins (containing 265 L sea water and 18 kg quartz sand or natural shore sand as the littoral sediment) to study the effect of accidental diesel oil spills on microbial communities. Our results demonstrated that microbial communities in the surface water responded to diesel oil contamination, whereas those in the littoral sediment did not, indicating that diesel oil degradation mainly happened in the water. Diesel oil decreased the abundance of bacteria and fungi, but increased bacterial diversity in the water. Time was the predominant driver of microbial succession, attributable to the adaption strategies of microbes. Bacteria were more sensitive to diesel oil contamination than fungi and archaea. Diesel oil increased relative abundances of bacterial phyla, Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Flavobacteriia and Cytophagia, and fungal phylum Ascomycota in the surface water. Overall, this study improves the understanding of the immediate ecological impact of accidental diesel oil contamination, providing insights into risk management at the coastal area.

We provide research findings on the physics of aerosol dispersion relevant to the hypothesized aerosol transmission of SARS-CoV-2. We utilize physics-based modeling at different levels of complexity, and literature on coronaviruses, to investigate the possibility of airborne transmission. The previous literature, our 0D-3D simulations by various physics-based models, and theoretical calculations, indicate that the typical size range of speech and cough originated droplets (d < 20microns) allows lingering in the air for O(1h) so that they could be inhaled. Consistent with the previous literature, numerical evidence on the rapid drying process of even large droplets, up to sizes O(100microns), into droplet nuclei/aerosols is provided. Based on the literature and the public media sources, we provide evidence that the infected individuals could have been exposed to aerosols/droplet nuclei by inhaling them in significant numbers e.g. O(100). By 3D computational fluid dynamics (CFD) simulations, we give examples on the transport and dilution of aerosols (d, Preprint, 58 pages, 15 figures

An efficient chromatography-based virus purification method has been developed and validated for the nonpathogenic infectious virus PRD1. Compared to the conventional method that consists of relatively time-consuming and labour-intensive precipitation and density gradient ultracentrifugation steps, the method developed here is performed in a single flow using tandem-coupled anion exchange and size exclusion chromatography (AIEX-SEC) columns. This inline approach helps to minimize the loss of virus in the process and streamlines time consumption, since no physical transfer of the sample is required between purification steps. In the development process, sample feed composition, dynamic binding capacity and elution conditions for the AIEX resin as well as different exclusion limits for SEC resins were optimized to achieve maximal yield of pure infectious viruses. Utilizing this new approach, a high-quality virus sample was produced from a lysate feed in 320 min with a total yield of 13 mg purified particles per litre of cell lysate, constituting a 3.5-fold yield increase as compared to the conventional method, without compromising the high specific infectivity of the product (6 x 1012 to 7 x 10(12) pfu/mg of protein). The yield of infectious viruses of the lysate feed was 54%. The easy scalability of chromatography-based methods provide a direct route to industrial usage without any significant changes needed to be made to the purification regime. This is especially interesting as the method has high potential to be used for purification of various viruses and nanoparticles, including adenovirus.

Gut microbes play an essential role in the development and functioning of the human immune system. A disturbed gut microbiota composition is often associated with a number of health disorders including immune-mediated diseases. Differences in host characteristics such as ethnicity, living habit and diet have been used to explain differences in the gut microbiota composition in inter-continental comparison studies. As our previous studies imply that daily skin contact with organic gardening materials modify gut microflora, here we investigated the association between living environment and gut microbiota in a homogenous western population along an urban-rural gradient. We obtained stool samples from 48 native elderly Finns in province Hame in August and November 2015 and identified the bacterial phylotypes using 16S rRNA Illumina MiSeq sequencing. We assumed that yard vegetation and land cover classes surrounding homes explain the stool bacterial community in generalized linear mixed models. Diverse yard vegetation was associated with a reduced abundance of Clostridium sensu stricto and an increased abundance of Faecalibacterium and Prevotellaceae. The abundance of Bacteroides was positively and strongly associated with the built environment. Exclusion of animal owners did not alter the main associations. These results suggest that diverse vegetation around homes is associated with health-related changes in gut microbiota composition. Manipulation of the garden diversity, possibly jointly with urban planning, is a promising candidate for future intervention studies that aim to maintain gut homeostasis. (C) 2020 The Authors. Published by Elsevier B.V.

Fenton’s reaction-based chemical oxidation is in principle a method that can be utilized for all organic fuel residues thus making it a potential all-purpose, multi-contaminant, in situ application for cases in which storage and distribution of different types of fuels have resulted in contamination of soil or groundwater. Since peroxide breakdown reactions are also expected to lead to a physical transport of the target compound, this secondary physical removal, or rebound concentrations related to it, is prone to be affected by the chemical properties of the target compound. Also, since soil conditions are seldom optimal for Fenton’s reaction, the balance between chemical oxidation and transport may vary. In this study, it was found that, with a high enough hydrogen peroxide concentration (5 M), methyl tert-butyl ether–spiked groundwater could be treated even under suboptimal conditions for chemical mineralization. In these cases, volatilization was not only contributing to the total removal but also leading to rebound effects similar to those associated with air sparging techniques. Likewise for diesel, temporal transport from soil to the aqueous phase was found to lead to false positives that outweighed the actual remediation effect through chemical mineralization.

The protection of the viral genome during extracellular transport is an absolute requirement for virus survival and replication. In addition to the almost universal proteinaceous capsids, certain viruses add a membrane layer that encloses their double-stranded (ds) DNA genome within the protein shell. Using the membrane-containing enterobacterial virus PRD1 as a prototype, and a combination of nanoindentation assays by atomic force microscopy and finite element modelling, we show that PRD1 provides a greater stability against mechanical stress than that achieved by the majority of dsDNA icosahedral viruses that lack a membrane. We propose that the combination of a stiff and brittle proteinaceous shell coupled with a soft and compliant membrane vesicle yields a tough composite nanomaterial well-suited to protect the viral DNA during extracellular transport., We thank MINECO for the Severo Ochoa Excellence Accreditation to the CIC bioGUNE (SEV-2016-0644) and the University of Helsinki and Academy of Finland (grant 1306833) for the support to Biomolecular Complex Purification (Biocomplex), part of Instruct-FI, used in this study. This research was supported by Bruker – Spain (to S. A. and N. G. A. A.), by the Academy of Finland (Academy Professor funding grants 283072 and 255342 to D. H. B.), by the European Research Council (starting grant FP7-ERC-2012-StG-306435 to R. P. R.), and by the Spanish Ministry of Economy and Competitiveness (MINECO/FEDER; MAT2014-54867-R to R. P. R.; MAT2015-63704-P to G. A. S.; BFU2015-64541-R to N. G. A. A.).

Soil contamination with diesel oil is frequent and methods to improve remediation of diesel oil contaminated soils are urgently needed. The aim of the current study was to assess the potential of meat and bone meal (MBM) as a biostimulation agent to enhance diesel oil degradation in contaminated soils collected from southern Finland. MBM (2 % w/w) increased oil degradation in soils when compared to natural attenuation. The increase was comparable to soils treated with a traditional fertilizer (urea). Soil pH increased rapidly in urea treated soil but remained at the level of natural attenuation in MBM treated soil, suggesting that in large-scale experiments MBM treated soils avoid the usual negative impact of urea on soil pH and ultimately microbial degradation. These results indicate that MBM addition enhances diesel oil degradation, and that MBM speeds up ex situ bioremediation of oil contaminated soils.

International audience; The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.

Many of the largest known viruses belong to the PRD1-adeno structural lineage characterised by conserved pseudo-hexameric capsomers composed of three copies of a single major capsid protein (MCP). Here, by high-resolution cryo-EM analysis, we show that a class of archaeal viruses possess hetero-hexameric MCPs which mimic the PRD1-adeno lineage trimer. These hetero-hexamers are built from heterodimers and utilise a jigsaw-puzzle system of pegs and holes, and underlying minor capsid proteins, to assemble the capsid laterally from the 5-fold vertices. At these vertices proteins engage inwards with the internal membrane vesicle whilst 2-fold symmetric horn-like structures protrude outwards. The horns are assembled from repeated globular domains attached to a central spine, presumably facilitating multimeric attachment to the cell receptor. Such viruses may represent precursors of the main PRD1-adeno lineage, similarly engaging cell-receptors via 5-fold spikes and using minor proteins to define particle size., Here, the authors present the cryo-EM structure of the archaeal virus SH1 at 3.8 Å resolution and show how the major capsid proteins assemble into hetero-hexamers, providing insights into the assembly process of this and related PRD1-adeno lineage viruses.

Nitrogen limitation is considered a good strategy for enhancement of algal lipid production while conversely N repletion has been shown to result in biomass rich in proteins. In this study, the influence of long-term N limitation onEuglena gracilisfatty acid (FA), protein, chlorophylla, and carotenoid concentrations was studied in N limited cultures. Biomass composition was analyzed from three-time points from N starved late stationary phase cultures, exposed to three different initial N concentrations in the growth medium. Total lipid content increased under N limitation in ageing cultures, but the low N content and prolonged cultivation time resulted in the formation of a high proportion of saturated FAs. Furthermore, growth as well as the production of proteins, chlorophyllaand carotenoids were enhanced in higher N concentrations and metabolism of these cellular components stayed stable during the stationary growth phase. Our findings showed that a higher N availability and a shorter cultivation time is a good strategy for efficientE. gracilisbiomass production, regardless of whether the produced biomass is intended for maximal recovery of polyunsaturated FAs, proteins, or photosynthetic pigments. Additionally, we showed an increase of neoxanthin, β-carotene, and diadinoxanthin as a response to higher N availability.

The vertical double β-barrel major capsid protein (MCP) fold, fingerprint of the PRD1-adeno viral lineage, is widespread in many viruses infecting organisms across the three domains of life. The discovery of PRD1-like viruses with two MCPs challenged the known assembly principles. Here, we present the cryo-electron microscopy (cryo-EM) structures of the archaeal, halophilic, internal membrane-containing Haloarcula californiae icosahedral virus 1 (HCIV-1) and Haloarcula hispanica icosahedral virus 2 (HHIV-2) at 3.7 and 3.8 Å resolution, respectively. Our structures reveal proteins located beneath the morphologically distinct two- and three-tower capsomers and homopentameric membrane proteins at the vertices that orchestrate the positioning of pre-formed vertical single β-barrel MCP heterodimers. The cryo-EM based structures together with the proteomics data provide insights into the assembly mechanism of this type of viruses and into those with membrane-less double β-barrel MCPs., Here, the authors present the cryo-EM structures of two archaeal, halophilic, internal membrane-containing icosahedral viruses at 3.7 and 3.8 Å resolution, providing insights into the assembly process of these and related PRD1-adeno lineage viruses.

Viruses are a significant threat to both human health and the economy, and there is an urgent need for novel anti-viral drugs and vaccines. High-resolution viral structures inform our understanding of the virosphere, and inspire novel therapies. Here we present a method of obtaining such structural information that avoids potentially disruptive handling, by collecting diffraction data from intact infected cells. We identify a suitable combination of cell type and virus to accumulate particles in the cells, establish a suitable time point where most cells contain virus condensates and use electron microscopy to demonstrate that these are ordered crystalline arrays of empty capsids. We then use an X-ray free electron laser to provide extremely bright illumination of sub-micron intracellular condensates of bacteriophage phiX174 inside living Escherichia coli at room temperature. We have been able to collect low resolution diffraction data. Despite the limited resolution and completeness of these initial data, due to a far from optimal experimental setup, we have used novel methodology to determine a putative space group, unit cell dimensions, particle packing and likely maturation state of the particles.

Certain pleomorphic archaeal viruses are highly infectious even at saturated salt. These viruses belong to the genus Betapleolipovirus of the recently described archaeal virus family Pleolipoviridae. Pleolipoviruses comprise single-stranded or double-stranded, circular or linear DNA genomes that share countless homologues among various archaeal genetic elements. Here we describe a new extremely halophilic betapleolipovirus, Halorubrum pleomorphic virus 9 (HRPV9), which has an integrase gene. We also identified new genes encoding minor pleolipoviral structural proteins. The studies on HRPV9 enhance our knowledge on pleolipoviruses, especially their reciprocal relatedness and relation to certain archaeal plasmids, proviruses and membrane vesicles. (C) 2018 The Authors. Published by Elsevier Masson SAS on behalf of Institut Pasteur.

Basic and applied virus research requires specimens that are purified to high homogeneity. Thus, there is much interest in the efficient production and purification of viruses and their subassemblies. Advances in the production steps have shifted the bottle neck of the process to the purification. Nonetheless, the development of purification techniques for different viruses is challenging due to the complex biological nature of the infected cell cultures as well as the biophysical and -chemical differences in the virus particles. We used bacteriophage phi 6 as a model virus in our attempts to provide a new purification method for enveloped viruses. We compared asymmetrical flow field-flow fractionation (AF4)-based virus purification method to the well-established ultracentrifugation-based purification of phi 6. In addition, binding of phi 6 virions to monolithic anion exchange columns was tested to evaluate their applicability in concentrating the AF4 purified specimens. Our results show that AF4 enables one-hour purification of infectious enveloped viruses with specific infectivity of similar to 1 x 10(13) PFU/mg of protein and similar to 65-95% yields. Obtained purity was comparable with that obtained using ultracentrifugation, but the yields from AF4 purification were 2-3-fold higher. Importantly, high quality virus preparations could be obtained directly from crude cell lysates. Furthermore, when used in combination with inline light scattering detectors, AF4 purification could be coupled to simultaneous quality control of obtained virus specimen.

Phage Cr39582 was induced by mitomycin C from Pseudoalteromonas sp. strain Cr6751, isolated from a marine invertebrate gut. Pseudoalteromonas phage Cr39582 has 85% pairwise nucleotide identity with phage PM2 but lacks sequence homology in the spike protein. This report supports previous bioinformatic identification of corticoviral sequences within aquatic bacterial genomes.

Extremely halophilic Archaea are the only known hosts for pleolipoviruses which are pleomorphic non-lytic viruses resembling cellular membrane vesicles. Recently, pleolipoviruses have been acknowledged by the International Committee on Taxonomy of Viruses (ICTV) as the first virus family that contains related viruses with different DNA genomes. Genomic diversity of pleolipoviruses includes single-stranded and double-stranded DNA molecules and their combinations as linear or circular molecules. To date, only eight viruses belong to the family Pleolipoviridae. In order to obtain more information about the diversity of pleolipoviruses, further isolates are needed. Here we describe the characterization of a new halophilic virus isolate, Haloarcula hispanica pleomorphic virus 4 (HHPV4). All pleolipoviruses and related proviruses contain a conserved core of approximately five genes designating this virus family, but the sequence similarity among different isolates is low. We demonstrate that over half of HHPV4 genome is identical to the genome of pleomorphic virus HHPV3. The genomic regions encoding known virion components are identical between the two viruses, but HHPV4 includes unique genetic elements, e.g., a putative integrase gene. The co-evolution of these two viruses demonstrates the presence of high recombination frequency in halophilic microbiota and can provide new insights considering links between viruses, membrane vesicles, and plasmids.

Viruses are recognized as important actors in ocean ecology and biogeochemical cycles, but many details are not yet understood. We participated in a winter expedition to the Weddell Sea, Antarctica, to isolate viruses and to measure virus-like particle abundance (flow cytometry) in sea ice. We isolated 59 bacterial strains and the first four Antarctic sea-ice viruses known (PANV1, PANV2, OANV1 and OANV2), which grow in bacterial hosts belonging to the typical sea-ice genera Paraglaciecola and Octadecabacter. The viruses were specific for bacteria at the strain level, although OANV1 was able to infect strains from two different classes. Both PANV1 and PANV2 infected 11/15 isolated Paraglaciecola strains that had almost identical 16S rRNA gene sequences, but the plating efficiencies differed among the strains, whereas OANV1 infected 3/7 Octadecabacter and 1/15 Paraglaciecola strains and OANV2 1/7 Octadecabacter strains. All the phages were cold-active and able to infect their original host at 0 degrees C and 4 degrees C, but not at higher temperatures. The results showed that virus-host interactions can be very complex and that the viral community can also be dynamic in the winter-sea ice.

Viruses come in various shapes and sizes, and a number of viruses originate from extremities, e.g. high salinity or elevated temperature. One challenge for studying extreme viruses is to find efficient purification conditions where viruses maintain their infectivity. Asymmetrical flow field-flow fractionation (AF4) is a gentle native chromatography-like technique for size-based separation. It does not have solid stationary phase and the mobile phase composition is readily adjustable according to the sample needs. Due to the high separation power of specimens up to 50 A mu m, AF4 is suitable for virus purification. Here, we applied AF4 for extremophilic viruses representing four morphotypes: lemon-shaped, tailed and tailless icosahedral, as well as pleomorphic enveloped. AF4 was applied to input samples of different purity: crude supernatants of infected cultures, polyethylene glycol-precipitated viruses and viruses purified by ultracentrifugation. All four virus morphotypes were successfully purified by AF4. AF4 purification of culture supernatants or polyethylene glycol-precipitated viruses yielded high recoveries, and the purities were comparable to those obtained by the multistep ultracentrifugation purification methods. In addition, we also demonstrate that AF4 is a rapid monitoring tool for virus production in slowly growing host cells living in extreme conditions.

Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha-and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.