Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France).

The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.

Evidence of nitrate-based nighttime atmospheric nucleation driven by marine microorganisms in the South Pacific.

Our understanding of ocean-cloud interactions and their effect on climate lacks insight into a key pathway: do biogenic marine emissions form new particles in the open ocean atmosphere? Using measurements collected in ship-borne air-sea interface tanks deployed in the Southwestern Pacific Ocean, we identified new particle formation (NPF) during nighttime that was related to plankton community composition. We show that nitrate ions are the only species for which abundance could support NPF rates in our semicontrolled experiments. Nitrate ions also prevailed in the natural pristine marine atmosphere and were elevated under higher sub-10 nm particle concentrations. We hypothesize that these nucleation events were fueled by complex, short-term biogeochemical cycling involving the microbial loop. These findings suggest a new perspective with a previously unidentified role of nitrate of marine biogeochemical origin in aerosol nucleation.

Evaluation of the Sources, Precursors, and Processing of Aerosols at a High-Altitude Tropical Site.

This work presents the results from a set of aerosol- and gas-phase measurements collected during the BIO-MAÏDO field campaign in Réunion between March 8 and April 5, 2019. Several offline and online sampling devices were installed at the Maïdo Observatory (MO), a remote high-altitude site in the Southern Hemisphere, allowing the physical and chemical characterization of atmospheric aerosols and gases. The evaluation of short-lived gas-phase measurements allows us to conclude that air masses sampled during this period contained little or no anthropogenic influence. The dominance of sulfate and organic species in the submicron fraction of the aerosol is similar to that measured at other coastal sites. Carboxylic acids on PM10 showed a significant contribution of oxalic acid, a typical tracer of aqueous processed air masses, increasing at the end of the campaign. This result agrees with the positive matrix factorization analysis of the submicron organic aerosol, where more oxidized organic aerosols (MOOAs) dominated the organic aerosol with an increasing contribution toward the end of the campaign. Using a combination of air mass trajectories (model predictions), it was possible to assess the impact of aqueous phase processing on the formation of secondary organic aerosols (SOAs). Our results show how specific chemical signatures and physical properties of air masses, possibly affected by cloud processing, can be identified at Réunion. These changes in properties are represented by a shift in aerosol size distribution to large diameters and an increased contribution of secondary sulfate and organic aerosols after cloud processing.

Surface ocean microbiota determine cloud precursors.

One pathway by which the oceans influence climate is via the emission of sea spray that may subsequently influence cloud properties. Sea spray emissions are known to be dependent on atmospheric and oceanic physicochemical parameters, but the potential role of ocean biology on sea spray fluxes remains poorly characterized. Here we show a consistent significant relationship between seawater nanophytoplankton cell abundances and sea-spray derived Cloud Condensation Nuclei (CCN) number fluxes, generated using water from three different oceanic regions. This sensitivity of CCN number fluxes to ocean biology is currently unaccounted for in climate models yet our measurements indicate that it influences fluxes by more than one order of magnitude over the range of phytoplankton investigated.

A biogenic secondary organic aerosol source of cirrus ice nucleating particles.

Atmospheric ice nucleating particles (INPs) influence global climate by altering cloud formation, lifetime, and precipitation efficiency. The role of secondary organic aerosol (SOA) material as a source of INPs in the ambient atmosphere has not been well defined. Here, we demonstrate the potential for biogenic SOA to activate as depositional INPs in the upper troposphere by combining field measurements with laboratory experiments. Ambient INPs were measured in a remote mountaintop location at -46 °C and an ice supersaturation of 30% with concentrations ranging from 0.1 to 70 L-1. Concentrations of depositional INPs were positively correlated with the mass fractions and loadings of isoprene-derived secondary organic aerosols. Compositional analysis of ice residuals showed that ambient particles with isoprene-derived SOA material can act as depositional ice nuclei. Laboratory experiments further demonstrated the ability of isoprene-derived SOA to nucleate ice under a range of atmospheric conditions. We further show that ambient concentrations of isoprene-derived SOA can be competitive with other INP sources. This demonstrates that isoprene and potentially other biogenically-derived SOA materials could influence cirrus formation and properties.

Seasonal shift in airborne microbial communities.

Microorganisms are ubiquitous in the atmosphere. Global investigations on the geographical and temporal distribution of airborne microbial communities are critical for identifying the sources and the factors shaping airborne communities. At mid-latitude sites, a seasonal shift in both the concentration and diversity of airborne microbial communities has been systematically observed in the planetary boundary layer. While the factors suspected of affecting this seasonal change were hypothesized (e.g., changes in the surface conditions, meteorological parameters and global air circulation), our understanding on how these factors influence the temporal variation of airborne microbial communities, especially at the microbial taxon level, remains limited. Here, we investigated the distribution of both airborne bacterial and fungal communities on a weekly basis over more than one year at the mid-latitude and continental site of puy de Dôme (France; +1465 m altitude above sea level). The seasonal shift in microbial community structure was likely correlated to the seasonal changes in the characteristics of puy de Dôme's landscape (croplands and natural vegetation). The airborne microbial taxa that were the most affected by seasonal changes trended differently throughout the seasons in relation with their trophic mode. In addition, the windy and variable local meteorological conditions found at puy de Dôme were likely responsible for the intraseasonal variability observed in the composition of airborne microbial communities.

Methods to Investigate the Global Atmospheric Microbiome.

The interplay between microbes and atmospheric physical and chemical conditions is an open field of research that can only be fully addressed using multidisciplinary approaches. The lack of coordinated efforts to gather data at representative temporal and spatial scales limits aerobiology to help understand large scale patterns of global microbial biodiversity and its causal relationships with the environmental context. This paper presents the sampling strategy and analytical protocols developed in order to integrate different fields of research such as microbiology, -omics biology, atmospheric chemistry, physics and meteorology to characterize atmospheric microbial life. These include control of chemical and microbial contaminations from sampling to analysis and identification of experimental procedures for characterizing airborne microbial biodiversity and its functioning from the atmospheric samples collected at remote sites from low cell density environments. We used high-volume sampling strategy to address both chemical and microbial composition of the atmosphere, because it can help overcome low aerosol and microbial cell concentrations. To account for contaminations, exposed and unexposed control filters were processed along with the samples. We present a method that allows for the extraction of chemical and biological data from the same quartz filters. We tested different sampling times, extraction kits and methods to optimize DNA yield from filters. Based on our results, we recommend supplementary sterilization steps to reduce filter contamination induced by handling and transport. These include manipulation under laminar flow hoods and UV sterilization. In terms of DNA extraction, we recommend a vortex step and a heating step to reduce binding to the quartz fibers of the filters. These steps have led to a 10-fold increase in DNA yield, allowing for downstream omics analysis of air samples. Based on our results, our method can be integrated into pre-existing long-term monitoring field protocols for the atmosphere both in terms of atmospheric chemistry and biology. We recommend using standardized air volumes and to develop standard operating protocols for field users to better control the operational quality.

Corrigendum: Collocated observations of cloud condensation nuclei, particle size distributions, and chemical composition.

This corrects the article DOI: 10.1038/sdata.2017.3.

Collocated observations of cloud condensation nuclei, particle size distributions, and chemical composition.

Cloud condensation nuclei (CCN) number concentrations alongside with submicrometer particle number size distributions and particle chemical composition have been measured at atmospheric observatories of the Aerosols, Clouds, and Trace gases Research InfraStructure (ACTRIS) as well as other international sites over multiple years. Here, harmonized data records from 11 observatories are summarized, spanning 98,677 instrument hours for CCN data, 157,880 for particle number size distributions, and 70,817 for chemical composition data. The observatories represent nine different environments, e.g., Arctic, Atlantic, Pacific and Mediterranean maritime, boreal forest, or high alpine atmospheric conditions. This is a unique collection of aerosol particle properties most relevant for studying aerosol-cloud interactions which constitute the largest uncertainty in anthropogenic radiative forcing of the climate. The dataset is appropriate for comprehensive aerosol characterization (e.g., closure studies of CCN), model-measurement intercomparison and satellite retrieval method evaluation, among others. Data have been acquired and processed following international recommendations for quality assurance and have undergone multiple stages of quality assessment.

LIDAR developments at Clermont-Ferrand--France for atmospheric observation.

We present a Rayleigh-Mie-Raman LIDAR system in operation at Clermont-Ferrand (France) since 2008. The system provides continuous vertical tropospheric profiles of aerosols, cirrus optical properties and water vapour mixing ratio. Located in proximity to the high altitude Puy de Dôme station, labelled as the GAW global station PUY since August 2014, it is a useful tool to describe the boundary layer dynamics and hence interpret in situ measurements. This LIDAR has been upgraded with specific hardware/software developments and laboratory calibrations in order to improve the quality of the profiles, calibrate the depolarization ratio, and increase the automation of operation. As a result, we provide a climatological water vapour profile analysis for the 2009-2013 period, showing an annual cycle with a winter minimum and a summer maximum, consistent with in-situ observations at the PUY station. An overview of a preliminary climatology of cirrus clouds frequency shows that in 2014, more than 30% of days present cirrus events. Finally, the backscatter coefficient profile observed on 27 September 2014 shows the capacity of the system to detect cirrus clouds at 13 km altitude, in presence of aerosols below the 5 km altitude.

Observations of nucleation of new particles in a volcanic plume.

Volcanic eruptions caused major weather and climatic changes on timescales ranging from hours to centuries in the past. Volcanic particles are injected in the atmosphere both as primary particles rapidly deposited due to their large sizes on time scales of minutes to a few weeks in the troposphere, and secondary particles mainly derived from the oxidation of sulfur dioxide. These particles are responsible for the atmospheric cooling observed at both regional and global scales following large volcanic eruptions. However, large condensational sinks due to preexisting particles within the plume, and unknown nucleation mechanisms under these circumstances make the assumption of new secondary particle formation still uncertain because the phenomenon has never been observed in a volcanic plume. In this work, we report the first observation of nucleation and new secondary particle formation events in a volcanic plume. These measurements were performed at the puy de Dôme atmospheric research station in central France during the Eyjafjallajokull volcano eruption in Spring 2010. We show that the nucleation is indeed linked to exceptionally high concentrations of sulfuric acid and present an unusual high particle formation rate. In addition we demonstrate that the binary H(2)SO(4) - H(2)O nucleation scheme, as it is usually considered in modeling studies, underestimates by 7 to 8 orders of magnitude the observed particle formation rate and, therefore, should not be applied in tropospheric conditions. These results may help to revisit all past simulations of the impact of volcanic eruptions on climate.

High frequency new particle formation in the Himalayas.

Rising air pollution levels in South Asia will have worldwide environmental consequences. Transport of pollutants from the densely populated regions of India, Pakistan, China, and Nepal to the Himalayas may lead to substantial radiative forcing in South Asia with potential effects on the monsoon circulation and, hence, on regional climate and hydrological cycles, as well as to dramatic impacts on glacier retreat. An improved description of particulate sources is needed to constrain the simulation of future regional climate changes. Here, the first evidence of very frequent new particle formation events occurring up to high altitudes is presented. A 16-month record of aerosol size distribution from the Nepal Climate Observatory at Pyramid (Nepal, 5,079 m above sea level), the highest atmospheric research station, is shown. Aerosol concentrations are driven by intense ultrafine particle events occurring on >35% of the days at the interface between clean tropospheric air and the more polluted air rising from the valleys. During a pilot study, we observed a significant increase of ion cluster concentrations with the onset of new particle formation events. The ion clusters rapidly grew to a 10-nm size within a few hours, confirming, thus, that in situ nucleation takes place up to high altitudes. The initiation of the new particle events coincides with the shift from free tropospheric downslope winds to thermal upslope winds from the valley in the morning hours. The new particle formation events represent a very significant additional source of particles possibly injected into the free troposphere by thermal winds.