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Pigment-producing microorganisms are prevalent on glacier surfaces, decreasing the snow and ice albedo. This impacts the absorption of solar radiation and accelerates rates of glacier surface melting. Studying the glacier surface ecosystem is important to understand the effects of anthropogenic climate change, and to further our knowledge of how glacier-dwelling organisms and their evolution impact downstream ecosystems. Recent studies have revealed links between habitat type, seasonality, physicochemical characteristics and the microbial composition of the supraglacial environment. However, these studies are limited in number, time points and locations. Thus, global drivers of supraglacial microbial community composition remain unknown. To fill this gap, we used data produced by our team over the last five years, as well as gathered from public repositories, to investigate the prokaryotic and eukaryotic composition of supraglacial environments worldwide.We used 18S and 16S rRNA gene amplicon sequencing to study the microbial composition and diversity of more than eight hundred surface snow, ice and cryoconite samples from glaciers and snowfields all over the world, including Arctic, Antarctic and temperate glaciers. Results reveal a worldwide core microbiome specific to this environment, composed of generalist, freshwater and cold-adapted taxa. Distance-decay and latitudinal patterns can be identified, but key factors in determining microbial community diversity and composition rest on local to regional biogeographical scales. Habitat biology shows different responses to biogeographical drivers, likely influenced by their structure: cryoconite communities present a higher distance-decay and location specialization than snow and ice communities. In addition, communities of prokaryotes are less location-specific than those of eukaryotes. This study highlights the need for further investigation into the drivers of microbial dissemination onto glaciers and their response to local biogeography.

International audience; Bioaerosols have impacts on atmospheric processes, as well as ecosystem and human health. Common bioaerosol collection methods include impaction, liquid impingement, filtration, and electrostatic precipitation. These methods are used by active samplers that require an air mover and power, but this requirement can also represent a major constraint in field studies. Alternatively, passive samplers do not require power and can operate for long times. In this study, the Rutgers Electrostatic Passive Sampler (REPS), which captures particles by electrostatic attraction and gravitational settling, was deployed at the summit of puy de Dôme (1465 m a.s.l., France) alongside an active PM10 sampler (~1000 L min-1) collecting aerosols on a quartz fiber filter. The diversity of the airborne bacteria captured by both samplers across six weekly sampling periods was examined by 16S rRNA gene amplicon sequencing. The dominant phyla observed by both samplers were similar and included Firmicutes, Proteobacteria, and Actinobacteriota. Overall, 12 to 63% of the total bacterial richness at the genus level was shared between the two samplers, depending upon a paired sample, i.e., sampling week. The PM10 sampler and REPS detected the same dominant genera, including Lysinibacillus and Sphingomonas, although their relative abundances for each paired sampler varied. The observed bacterial richness and diversity, as estimated through Shannon's and Simpson's indexes, were significantly greater in REPS samples compared to the PM10 samples. The results suggest that REPS could be used for simple and convenient sampling of bioaerosols, especially in remote areas and other locations with limited power access.

Glacier and ice sheet surfaces host diverse communities of microorganisms whose activity (or inactivity) influences biogeochemical cycles and ice melting. Supraglacial microbes endure various environmental extremes including resource scarcity, frequent temperature fluctuations above and below the freezing point of water, and high UV irradiance during summer followed by months of total darkness during winter. One strategy that enables microbial life to persist through environmental extremes is dormancy, which despite being prevalent among microbial communities in natural settings, has not been directly measured and quantified in glacier surface ecosystems. Here, we use a combination of metabarcoding and metatranscriptomic analyses, as well as cell-specific activity (BONCAT) incubations to assess the diversity and activity of microbial communities from glacial surfaces in Iceland and Greenland. We also present a new ecological model for glacier microorganisms and simulate physiological state-changes in the glacial microbial community under idealized (i) freezing, (ii) thawing, and (iii) freeze-thaw conditions. We show that a high proportion (>50%) of bacterial cells are translationally active in-situ on snow and ice surfaces, with Actinomycetota, Pseudomonadota, and Planctomycetota dominating the total and active community compositions, and that glacier microorganisms, even when frozen, could resume translational activity within 24 h after thawing. Our data suggest that glacial microorganisms respond rapidly to dynamic and changing conditions typical of their natural environment. We deduce that the biology and biogeochemistry of glacier surfaces are shaped by processes occurring over short (i.e., daily) timescales, and thus are susceptible to change following the expected alterations to the melt-regime of glaciers driven by climate change. A better understanding of the activity of microorganisms on glacier surfaces is critical in addressing the growing concern of climate change in Polar regions, as well as for their use as analogues to life in potentially habitable icy worlds.

Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.

In Arctic regions, thawing permafrost soils are projected to release 50 to 250 Gt of carbon by 2100. This data is mostly derived from carbon-rich wetlands, although 71% of this carbon pool is stored in faster-thawing mineral soils, where ecosystems close to the outer boundaries of permafrost regions are especially vulnerable. Although extensive data exists from currently thawing sites and short-term thawing experiments, investigations of the long-term changes following final thaw and co-occurring drainage are scarce. Here we show ecosystem changes at two comparable tussock tundra sites with distinct permafrost thaw histories, representing 15 and 25 years of natural drainage, that resulted in a 10-fold decrease in CH4 emissions (3.2 ± 2.2 vs. 0.3 ± 0.4 mg C-CH4 m−2 day−1), while CO2 emissions were comparable. These data extend the time perspective from earlier studies based on short-term experimental drainage. The overall microbial community structures did not differ significantly between sites, although the drier top soils at the most advanced site led to a loss of methanogens and their syntrophic partners in surface layers while the abundance of methanotrophs remained unchanged. The resulting deeper aeration zones likely increased CH4 oxidation due to the longer residence time of CH4 in the oxidation zone, while the observed loss of aerenchyma plants reduced CH4 diffusion from deeper soil layers directly to the atmosphere. Our findings highlight the importance of including hydrological, vegetation and microbial specific responses when studying long-term effects of climate change on CH4 emissions and underscores the need for data from different soil types and thaw histories.

1AbstractWe introduce a homemade pipeline allowing to improve the quality of the metagenomic annotations carried out when using shallow depth metagenomic datasets. The main motivation being to be able to quantify more precisely, with greater certainty, the genes involved in bacterial interactions. The limitation in our experimental design is that we use a sequencing technique with a low throughput (miSeq) compared to the metagenomic standard (hiSeq) because we carry out a fairly large sampling (almost a hundred samples) in time series. This methodological constraint from our study means that the assembly of the sequences is not very exhaustive (less than 50% of the sequences manage to be assembled). In this chapter, we will therefore present a new pipeline designed to specifically deal with such kind of data. We used co-assembly and a sequence annotation strategy in order to recover the sequences that could not be mapped on the assembled contigs. In addition, in order to avoid adding too much noise, when rescuing reads, we have built an algorithm to define a threshold of e-value based on the noise of the sequence annotation learned from sequences mapped in the assembly.We have selected several recent tools known to be effective for assembling, mapping and annotating these data. In addition, this pipeline was also built in order to be very user-friendly in terms of installation. In this idea of reproducibility, accessibility and transparency, we have designed an installation script to allow each user to install each tool required for the pipeline in a simple and reproducible way. Regarding the performances of this pipeline, we were able to show that the expected error rate (False discovery rate) for the annotation was close to 5%. Finally, we also used an actual dataset from a bioremediation site and showed that the representability of the samples seemed much better when we used our pipeline than when we used a classic metagenome assembly strategy.

Would you believe us if we told you that, when you breathe in, you inhale thousands of microorganisms with every breath. Although this might sound scary, be assured that they are safe for your health. These airborne microorganisms, too small to see with the naked eye, consist of many different species. Who are they? Where do they come from? What do they do in the air? These are some of the questions that we answer in this article, although many questions about airborne microorganisms remain to be explored.

Microbial analysis at the micro scale of soil is essential to the overall understanding of microbial organization and interactions, and necessary for a better understanding of soil ecosystem functioning. While bacterial communities have been extensively described, little is known about the organization of fungal communities as well as functional potentials at scales relevant to microbial interactions. Fungal and bacterial communities and changes in nitrogen cycling potentials in the pristine Rothamsted Park Grass soil (bulk soil) as well as in its particle size sub-fractions (PSFs; > 250 μm, 250-63 μm, 63-20 μm, 20-2 μm, < 2 μm and supernatant) were studied. The potential for nitrogen reduction was found elevated in bigger aggregates. The relative abundance of Basidiomycota deceased with decreasing particle size, Ascomycota showed an increase and Mucoromycota became more prominent in particles less than 20 μm.Bacterial community structures changed below 20 μm at the scale where microbes operate. Strikingly, only members of two bacterial and one fungal phyla (Proteobacteria, Bacteroidota and Ascomycota, respectively) were washed-off the soil during fractionation and accumulated in the supernatant fraction where most of the detected bacterial genera (e.g., Pseudomonas, Massilia, Mucilaginibacter, Edaphobaculum, Duganella, Janthinobacterium and Variovorax) were previously associated with exopolysaccharide production and biofilm formation.Overall, the applied method shows potential to study soil microbial communities at micro scales which might be useful in studies focusing on the role of specific fungal taxa in soil structure formation as well as research on how and by whom biofilm-like structures are distributed and organized in soil.ImportanceIntensive exploitation of soils has led to increasing environmental concerns such as pollution, erosion, emission of greenhouse gases and, in general, the weakening of its ecosystem services that are mainly regulated by microbial activity. Microbial activity and metabolism drive the formation of soil aggregates, ranging in size from a few micrometres to several millimetres. Understanding biological mechanisms related to aggregate size classes can provide insight into large-scale processes, but most research has focused on macroaggregates. Here, we investigated the microbial community and its functional changes at these smaller scales that are clearly more relevant for assessing microbial activity. We demonstrated that fungal communities are more sensitive to bigger size classes than bacteria, suggesting their dominant role in soil structure formation and turnover. We also identified preferential niches for reductive processes within the nitrogen cycle and a selection of specific taxa by analysing the water used for the wet-fractionation approach.

Simple Summary This interdisciplinary study, conducted by experts in evolutionary biology, ecology, ecosystem studies, arts, medicine, forensic analyses, agriculture, law, and philosophy of science describe how microbiome studies are convergently affecting the concepts and practices of diverse fields and practices, that now consider microbiomes within their legitimate scope. Consequently, it describes what seems to be an ongoing pluridisciplinary epistemic revolution, with the potential to fundamentally change how we understand the world through an ecologization of pre-existing concepts, a greater focus on interactions, the use of multi-scalar interaction networks as explanatory frameworks, the reconceptualization of the usual definitions of individuals, and a de-anthropocentrification of our perception of phenomena. Abstract Many separate fields and practices nowadays consider microbes as part of their legitimate focus. Therefore, microbiome studies may act as unexpected unifying forces across very different disciplines. Here, we summarize how microbiomes appear as novel major biological players, offer new artistic frontiers, new uses from medicine to laws, and inspire novel ontologies. We identify several convergent emerging themes across ecosystem studies, microbial and evolutionary ecology, arts, medicine, forensic analyses, law and philosophy of science, as well as some outstanding issues raised by microbiome studies across these disciplines and practices. An ‘epistemic revolution induced by microbiome studies’ seems to be ongoing, characterized by four features: (i) an ecologization of pre-existing concepts within disciplines, (ii) a growing interest in systemic analyses of the investigated or represented phenomena and a greater focus on interactions as their root causes, (iii) the intent to use openly multi-scalar interaction networks as an explanatory framework to investigate phenomena to acknowledge the causal effects of microbiomes, (iv) a reconceptualization of the usual definitions of which individuals are worth considering as an explanans or as an explanandum by a given field, which result in a fifth strong trend, namely (v) a de-anthropocentrification of our perception of the world.

Light-absorbing carbonaceous aerosols emitted by biomass or fossil fuel combustion can contribute to amplify Arctic climate warming by lowering the albedo of snow. The Svalbard archipelago, being near to Europe and Russia, is particularly affected by these pollutants, and improved knowledge of their distribution in snow is needed to assess their impact. Here we present and synthesize new data obtained on Svalbard between 2007 and 2018, comprising 324 measurements of elemental (EC) and organic carbon (OC) in snow from 49 sites. We used these data, combined with meteorological and aerosol data and snowpack modelling, to investigate the variability of EC and OC deposition in Svalbard snow across latitude, longitude, elevation and time. Overall, EC concentrations (CsnowEC) ranged from −1, while OC concentrations (CsnowOC) ranged from −1, with the highest values observed near Ny-Ålesund. Calculated snowpack loadings (LsnowEC, LsnowOC) in April 2016 were 0.1 to 16.2 mg m−2 and 1.7 to 320.1 mg m−2, respectively. The median CsnowEC and LsnowEC in the late 2015‒16 winter snowpack on glaciers were close to or lower than those found in earlier (2007–09), comparable surveys. Both LsnowEC and LsnowOCC increased exponentially with elevation and snow accumulation, with dry deposition likely playing a minor role. Estimated area-averaged snowpack loads across Svalbard were 1.8 mg EC m−2 and 71.5 mg OC m−2 in April 2016. An ~ 11-year long dataset of spring surface snow measurements from central Brøgger Peninsula was used to quantify the interannual variability of EC and OC deposition in snow. On average, CsnowEC and CsnowOC at Ny-Ålesund (50 m a.s.l.) were 3 and 7 times higher, respectively, than on the nearby Austre Brøggerbreen glacier (456 m a.s.l.), and the median EC/OC in Ny-Ålesund was 6 times higher, pointing to some local EC emission from Ny-Ålesund. While no long-term trends between 2011 and 2018 were found, CsnowEC and CsnowOC showed synchronous variations at Ny-Ålesund and Austre Brøggerbreen. Comparing CsnowEC at Austre Brøggerbreen with aerosol data from Zeppelin Observatory, we found that snowfall washout ratios between 10 and 300 predict a range of CsnowEC in agreement with that measured in surface snow. Together, results from this study and comparable surveys confirm the existence of a longitudinal gradient in EC deposition across the Arctic and sub-Arctic, with the lowest CsnowEC found in the western Arctic (Alaska, Yukon) and central Greenland, and the highest in northwestern Russia and Siberia.

Primary biological aerosol particles and microorganisms are ubiquitous in the atmosphere. Investigations of airborne chemical markers and microbial communities are critical for identifying sources, transport and transformation processes of aerosols. One potential major source of airborne chemical compounds and microbial communities (e.g. L- and D-amino acids, Flavobacteria) could be related to phytoplankton blooms that occur during the spring season in Arctic fjord systems. Here, we conducted a field study in a polar environment to investigate the occurrence in coarse and fine particles of water-soluble compounds (major ions, carboxylic acids and free L- and D-amino acids) and airborne bacterial communities in aerosol samples. The sampling was conducted with a 6 day sampling frequency at the Gruvebadet observatory, close to Ny-Alesund (Svalbard Islands). Glycine, D-amino acids and C4- organic acids increased during the exponential phase of a marine bloom that occurred in Kongsfjorden and started to drop at the beginning of the main-bloom phase. On the other hand, Polaribacter together with free L-amino acids overlapped with the Chlorophyll a peak and the subsequent decline, and thus might constitute a useful marker for the main-bloom phase.

The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 10

The Svalbard archipelago, between 74° and 81° N, is ∼60 % covered by glaciers and located at the Arctic sea ice edge. The region experiences rapid variations in atmospheric flow during the snow season (from late September to May) and can be affected by air advected both from lower and higher latitudes, which likely impact the chemical composition of snowfall. While long-term changes in Svalbard snow chemistry have been documented in ice cores drilled from two high-elevation glaciers, the spatial variability of the snowpack composition across Svalbard is comparatively poorly understood. Here, we report the results of the most comprehensive seasonal snow chemistry survey to date, carried out in April 2016 across 22 sites on 7 glaciers across the archipelago. At each glacier, three snow pits were sampled along altitudinal profiles and the collected samples were analysed for major ions (Ca2+, K+, Na+, Mg2+, NH+4, SO42−, Br−, Cl− and NO3−) and stable water isotopes (δ18O, δ2H). The main aims were to investigate the natural and anthropogenic processes influencing the snowpack and to better understand the influence of atmospheric aerosol transport and deposition patterns on the snow chemical composition. The snow deposited in the southern region of Svalbard was characterized by the highest total ionic loads, mainly attributed to sea salt particles. Both NO3− and NH4+ in the seasonal snowpack reflected secondary aerosol formation and post-depositional changes, resulting in very different spatial deposition patterns: NO3− had its highest loading in northwestern Spitsbergen, and NH4+ in the southwest. The Br− enrichment in snow was highest in northeastern glacier sites closest to areas of extensive sea ice coverage. Spatial correlation patterns between Na+ and δ18O suggest that the influence of long-range transport of aerosols on snow chemistry is proportionally greater above 600–700 m a.s.l.

International audience; Alpine soils are warming strongly, leading to profound alterations in carbon cycling and greenhouse gas budgets, mediated via the soil microbiome. To explore microbial responses to global warming, we incubated eight alpine soils between 4 and 35 °C and linked the temperature dependency of bacterial growth with alterations in community structures and the identification of temperature sensitive taxa. The temperature optimum for bacterial growth was between 27 and 30 °C and was higher in soils from warmer environments. This temperature framing the upper limit of naturally occurring temperatures was a tipping point above which the temperature range for growth shifted towards higher temperatures together with pronounced changes in community structures and diversity based on both 16S rRNA gene and transcript sequencing. For instance, at the highest temperature, we observed a strong increase in OTUs affiliated with Burkholderia-Paraburkholderia, Phenylobacterium, Pseudolabrys, Edaphobacter and Sphingomonas. Dominance at high temperature was explained by a priori adaptation to high temperature, high growth potential as well as stress resistance. At the highest temperature, we moreover observed an overall increase in copiotrophic properties in the community along with high growth rates. Further, temperature effects on community structures depended on the long-term climatic legacy of the soils. These findings contribute to extrapolating from single to multiple sites across a large range of conditions.

International audience; Fungal denitrification is claimed to produce non‐negligible amounts of N2O in soils, but few tested species have shown significant activity. We hypothesized that denitrifying fungi would be found among those with assimilatory nitrate reductase, and tested 20 such batch cultures for their respiratory metabolism, including two positive controls, Fusarium oxysporum and Fusarium lichenicola, throughout the transition from oxic to anoxic conditions in media supplemented with urn:x-wiley:14622912:media:emi14980:emi14980-math-0001. Enzymatic reduction of urn:x-wiley:14622912:media:emi14980:emi14980-math-0002 (NIR) and NO (NOR) was assessed by correcting measured NO‐ and N2O‐kinetics for abiotic NO‐ and N2O‐production (sterile controls). Significant anaerobic respiration was only confirmed for the positive controls and for two of three Fusarium solani cultures. The NO kinetics in six cultures showed NIR but not NOR activity, observed through the accumulation of NO. Others had NOR but not NIR activity, thus reducing abiotically produced NO to N2O. The presence of candidate genes (nirK and p450nor) was confirmed in the positive controls, but not in some of the NO or N2O accumulating cultures. Based on our results, we conclude that only the Fusarium cultures were able to sustain anaerobic respiration and produced low amounts of N2O as a response to an abiotic NO production from the medium.

We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphere continuously onto quartzfiber air filters using a DIGITEL high volume PM10 sampler. The bacterial and fungal communities, sequenced using Illumina MiSeq, as well as the chemical components of the atmosphere were compared to those of a late season snow profile. Results reveal strong dynamics in the composition of bacterial and fungal communities in air and snow. In fall the two compartments were similar, suggesting a strong interaction between them. The overlap diminished as the season progressed due to an evolution within the snowpack throughout winter and spring. Certain bacterial and fungal genera were only detected in air samples, which implies that a distinct air microbiome might exist. These organisms are likely not incorporated in clouds and thus not precipitated or scavenged in snow. Although snow appears to be seeded by the atmosphere, both air and snow showed differing bacterial and fungal communities and chemical composition. Season and alpha diversity were major drivers for microbial variability in snow and air, and only a few chemical markers were identified as important in explaining microbial diversity. Air microbial community variation was more related to chemical markers than snow microbial composition. For air microbial communities Cl–, TC/OC, SO42–, Mg2+, and Fe/Al, all compounds related to dust or anthropogenic activities, were identified as related to bacterial variability while dust related Ca2+was significant in snow. The only common driver for snow and air was SO42–, a tracer for anthropogenic sources. The occurrence of chemical compounds was coupled with boundary layer injections in the free troposphere (FT). Boundary layer injections also caused the observed variations in community composition and chemistry between the two compartments. Long-term monitoring is required for a more valid insight in post-depositional selection in snow.

Microbes active in extremely cold environments are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold-specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of twenty snow samples collected during early and late spring in Svalbard, Norway using our computational read-based microbiome function annotation tool, mi-faser. Our results revealed a more diverse microbiome functional capacity and activity in the early compared to in the late spring samples. The dissimilarity between the metagenomes and metatranscriptomes of the same samples was also significantly higher in the early spring. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant organisms, while late spring samples reflect a new community that is metabolically active. We additionally showed that the abundance of the sequencing reads mapping to the fatty acid synthesis-related microbial pathways was significantly positively correlated with organic acid levels, in both our late spring metagenomes and metatranscriptomes. Moreover, the geraniol degradation pathway and the styrene degradation pathway read abundances correlated and inversely correlated, respectively, with the organic acid levels. These results suggest a possible nutrient switch. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures.

Microbes active in extreme cold are not as well explored as those of other extreme environments. Studies have revealed a substantial microbial diversity and identified cold‐specific microbiome molecular functions. We analyzed the metagenomes and metatranscriptomes of 20 snow samples collected in early and late spring in Svalbard, Norway using mi‐faser, our read‐based computational microbiome function annotation tool. Our results reveal a more diverse microbiome functional capacity and activity in the early‐ vs. late‐spring samples. We also find that functional dissimilarity between the same‐sample metagenomes and metatranscriptomes is significantly higher in early than late spring samples. These findings suggest that early spring samples may contain a larger fraction of DNA of dormant (or dead) organisms, while late spring samples reflect a new, metabolically active community. We further show that the abundance of sequencing reads mapping to the fatty acid synthesis‐related microbial pathways in late spring metagenomes and metatranscriptomes is significantly correlated with the organic acid levels measured in these samples. Similarly, the organic acid levels correlate with the pathway read abundances of geraniol degradation and inversely correlate with those of styrene degradation, suggesting a possible nutrient change. Our study thus highlights the activity of microbial degradation pathways of complex organic compounds previously unreported at low temperatures., Computational analysis of metagenomic and metatranscriptomic data from snow samples collected at different springtimes in Svalbard, Norway suggests that a new microbial community is metabolically active in the late spring, while early spring samples likely overwhelmingly carry genomic residue from prior seasons. Furthermore, the correlation between the sequencing‐based, computationally determined metabolic pathways, and the experimentally measured organic acid concentration highlights active microbial degradation of complex organic compounds previously unreported at low temperatures.

Microorganisms are ubiquitous in the atmosphere, and some airborne microbial cells were shown to be particularly resistant to atmospheric physical and chemical conditions (e.g., ultraviolet – UV – radiation, desiccation and the presence of radicals). In addition to surviving, some cultivable microorganisms of airborne origin were shown to be able to grow on atmospheric chemicals in laboratory experiments. Metagenomic investigations have been used to identify specific signatures of microbial functional potential in different ecosystems. We conducted a comparative metagenomic study on the overall microbial functional potential and specific metabolic and stress-related microbial functions of atmospheric microorganisms in order to determine whether airborne microbial communities possess an atmosphere-specific functional potential signature as compared to other ecosystems (i.e., soil, sediment, snow, feces, surface seawater etc.). In the absence of a specific atmospheric signature, the atmospheric samples collected at nine sites around the world were similar to their underlying ecosystems. In addition, atmospheric samples were characterized by a relatively high proportion of fungi. The higher proportion of sequences annotated as genes involved in stress-related functions (i.e., functions related to the response to desiccation, UV radiation, oxidative stress etc.) resulted in part from the high concentrations of fungi that might resist and survive atmospheric physical stress better than bacteria.

International audience; 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.

Primary biological aerosols are transported over large distances, are traveling in various media such as dry air masses, clouds or fog, and eventually deposited with dry deposition, especially for larger particles, or precipitation like rain, hail or snow. To investigate relative abundance and diversity of airborne bacterial and fungal communities, samples have been collected with a liquid impinger (Coriolis μ) from the top of Mount Sonnblick (3106 m asl, Austrian Alps) from the respective sources under a temporal aspect over four seasons over the year to include all climatic conditions. Bacterial and fungal samples (16S rRNA and ITS) were sequenced using Illumina MiSeq paired-end sequencing, investigated for relative abundance by qPCR(16S rRNA and 18S rRNA) and ice nucleation activity. Results show that there is no stable free tropospheric air microbial community and air mass origin was different for the four sampling periods which exerted influence on the microbial composition of the atmosphere although a core microbiome could be identified consisting of 61 bacterial OTUs and eight fungal genera. Differentiation between seasons was stronger pronounced in air than in precipitation, with rain being most different and variable of precipitation types, indicating distinct forces driving microbial fate in the air. Microorganisms precipitated with snow, hail or rain or being transported by clouds differ in their species composition from free tropospheric air masses and do not mirror the air community structure. They were more diverse, distinct in composition, 16S:18S ratio and abundance from free-floating PBA. Hence, snow or cloud samples are not suitable proxies for free tropospheric air microbiome composition, since separation processes in aerosolization, transport and scavenging occur. The microbial composition of arriving precipitation or clouds represents only a part of the microbial air composition communities of the cumulative sources of origin. Relative abundance and composition of ice nucleation-active bacteria showed a higher share of relative % reads of known ice nucleation-active bacteria present in all wet phases compared to air. Results propose a separation of IN-active reads with higher shares occurring in precipitation. This study presents the first comparison of free tropospheric bacterial and fungal abundance and diversity in time

Chernobyl and Fukushima were subjected to radionuclide (RN) contamination that has led to environmental problems. In order to explore the ability of microorganisms to survive in these environments, we used a combined 16S rRNA and metagenomic approach to describe the prokaryotic community structure and metabolic potential over a gradient of RN concentrations (137Cs 1680–0.4 and 90Sr 209.1–1.9 kBq kg−1) in soil samples. The taxonomic results showed that samples with low 137Cs content (37.8–0.4 kBq kg−1) from Fukushima and Chernobyl clustered together. In order to determine the effect of soil chemical parameters such as organic carbon (OC), Cesium-137 (137Cs) and Strontium-90 (90Sr) on the functional potential of microbial communities, multiple predictor model analysis using piecewiseSEM was carried out on Chernobyl soil metagenomes. The model identified 46 genes that were correlated to these parameters of which most have previously been described as mechanisms used by microorganisms under stress conditions. This study provides a baseline taxonomic and metagenomic dataset for Fukushima and Chernobyl, respectively, including physical and chemical characteristics. Our results pave the way for evaluating the possible RN selective pressure that might contribute to shaping microbial community structure and their functions in contaminated soils.