Microorganisms isolated from the water phase of tropospheric clouds at the Puy de Dôme: major groups and growth abilities at low temperatures

Stochastic microbial dispersal drives local extinction and global diversity

Airborne dispersal of microorganisms is a ubiquitous migration mechanism, allowing otherwise independent microbial habitats to interact via biomass exchange. Here, we study the ecological implications of such advective transport using a simple spatial model for bacteria-phage interactions: the population dynamics at each habitat are described by classical Lotka-Volterra equations; however, species populations are taken as integer, that is, a discrete, positive extinction threshold exists. Spatially, species can spread from habitat to habitat by stochastic airborne dispersal. In any given habitat, the spatial biomass exchange causes incessant population density oscillations, which, as a consequence, occasionally drive species to extinction. The balance between local extinction events and dispersal-induced migration allows species to persist globally, even though diversity would be depleted by competitive exclusion, locally. The disruptive effect of biomass dispersal thus acts to increase microbial diversity, allowing system-scale coexistence of multiple species that would not coexist locally.

Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors

In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.

Aeromicrobiology: A global review of the cycling and relationships of bioaerosols with the atmosphere

Airborne microorganisms and biological matter (bioaerosols) play a key role in global biogeochemical cycling, human and crop health trends, and climate patterns. Their presence in the atmosphere is controlled by three main stages: emission, transport, and deposition. Aerial survival rates of bioaerosols are increased through adaptations such as ultra-violet radiation and desiccation resistance or association with particulate matter. Current research into modern concerns such as climate change, global gene transfer, and pathogenicity often neglects to consider atmospheric involvement. This comprehensive review outlines the transpiring of bioaerosols across taxa in the atmosphere, with significant focus on their interactions with environmental elements including abiotic factors (e.g., atmospheric composition, water cycle, and pollution) and events (e.g., dust storms, hurricanes, and wildfires). The aim of this review is to increase understanding and shed light on needed research regarding the interplay between global atmospheric phenomena and the aeromicrobiome. The abundantly documented bacteria and fungi are discussed in context of their cycling and human health impacts. Gaps in knowledge regarding airborne viral community, the challenges and importance of studying their composition, concentrations and survival in the air are addressed, along with understudied plant pathogenic oomycetes, and archaea cycling. Key methodologies in sampling, collection, and processing are described to provide an up-to-date picture of ameliorations in the field. We propose optimization to microbiological methods, commonly used in soil and water analysis, that adjust them to the context of aerobiology, along with other directions towards novel and necessary advancements. This review offers new perspectives into aeromicrobiology and calls for advancements in global-scale bioremediation, insights into ecology, climate change impacts, and pathogenicity transmittance.

Contribution of soil bacteria to the atmosphere across biomes

The dispersion of microorganisms through the atmosphere is a continual and essential process that underpins biogeography and ecosystem development and function. Despite the ubiquity of atmospheric microorganisms globally, specific knowledge of the determinants of atmospheric microbial diversity at any given location remains unresolved. Here we describe bacterial diversity in the atmospheric boundary layer and underlying soil at twelve globally distributed locations encompassing all major biomes, and characterise the contribution of local and distant soils to the observed atmospheric community. Across biomes the diversity of bacteria in the atmosphere was negatively correlated with mean annual precipitation but positively correlated to mean annual temperature. We identified distinct non-randomly assembled atmosphere and soil communities from each location, and some broad trends persisted across biomes including the enrichment of desiccation and UV tolerant taxa in the atmospheric community. Source tracking revealed that local soils were more influential than distant soil sources in determining observed diversity in the atmosphere, with more emissive semi-arid and arid biomes contributing most to signatures from distant soil. Our findings highlight complexities in the atmospheric microbiota that are relevant to understanding regional and global ecosystem connectivity.

Metabolically active bacteria detected with click chemistry in low organic matter rainwater

Rain contains encapsulated bacteria that can be transported over vast distances during relatively short periods of time. However, the ecological significance of bacteria in "precontact" rainwater-rainwater prior to contact with non-atmospheric surfaces-remains relatively undefined given the methodological challenges of studying low-abundance microbes in a natural assemblage. Here, we implement single-cell "click" chemistry in a novel application to detect the protein synthesis of bacteria in precontact rainwater samples as a measure of metabolic activity. Using epifluorescence microscopy, we find approximately 103-104 bacteria cells mL-1 with up to 7.2% of the observed cells actively synthesizing protein. Additionally, our measurement of less than 30 μM total organic carbon in the samples show that some rainwater bacteria can metabolize substrates in very low organic matter conditions, comparable to extremophiles in the deep ocean. Overall, our results raise new questions for the field of rainwater microbiology and may help inform efforts to develop quantitative microbial risk assessments for the appropriate use of harvested rainwater.

Desert dust intrusions and their incidence on airborne biological content. Review and case study in the Iberian Peninsula

Desert dust intrusions cause the transport of airborne particulate matter from natural sources, with important consequences for climate regulation, biodiversity, ecosystem functioning and dynamics, human health, and socio-economic activities. Some effects of desert intrusions are reinforced or aggravated by the bioaerosol content of the air during these episodes. The influence of desert intrusions on airborne bioaerosol content has been very little studied from a scientific point of view. In this study, a systematic review of scientific literature during 1970-2021 was carried out following the standard protocol Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA). After this literature review, only 6% of the articles on airborne transport from desert areas published in the last 50 years are in some way associated with airborne pollen, and of these, only a small proportion focus on the study of pollen-related parameters. The Iberian Peninsula is affected by Saharan intrusions due to its proximity to the African continent and is seeing an increasing trend the number of intrusion events. There is a close relationship among the conditions favouring the occurrence of intrusion episodes, the transport of particulate matter, and the transport of bioaerosols such as pollen grains, spores, or bacteria. The lack of linearity in this relationship and the different seasonal patterns in the occurrence of intrusion events and the pollen season of most plants hinders the study of the correspondence between both phenomena. It is therefore important to analyse the proportion of pollen that comes from regional sources and the proportion that travels over long distances, and the atmospheric conditions that cause greater pollen emission during dust episodes. Current advances in aerobiological techniques make it possible to identify bioaerosols such as pollen and spores that serve as indicators of long-distance transport from remote areas belonging to other bioclimatic and biogeographical units. A greater incidence of desert intrusion episodes may pose a challenge for both traditional systems and for the calibration and correct validation of automatic aerobiological monitoring methods.

Influence of strong iron-binding ligands on cloud water oxidant capacity

Iron (Fe) plays a dual role in atmospheric chemistry: it is involved in chemical and photochemical reactivity and serves as a micronutrient for microorganisms that have recently been shown to produce strong organic ligands. These ligands control the reactivity, mobility, solubility and speciation of Fe, which have a potential impact on Fe bioavailability and cloud water oxidant capacity. In this work, the concentrations of Fe-binding ligands and the conditional stability constants were experimentally measured for the first time by Competitive Ligand Exchange-Adsorptive Cathodic Stripping Voltammetry (CLE-ACSV) technique in cloud water samples collected at puy de Dôme (France). The conditional stability constants, which indicate the strength of the Fe-ligand complexes, are higher than those considered until now in cloud chemistry (mainly Fe-oxalate). To understand the effect of Fe complexation on cloud water reactivity, we used the CLEPS cloud chemistry model. According to the model results, we found that Fe complexation impacts the hydroxyl radical formation rate: contrary to our expectations, Fe complexation by natural organic ligands led to an increase in hydroxyl radical production. These findings have important impacts on cloud chemistry and the global iron cycle.

In situ bio/chemical characterization of Venus cloud particles using Life-signature Detection Microscope for Venus (Venus LDM)

Much of the information about the size and shape of aerosols forming haze and the cloud layer of Venus is obtained from indirect inferences from nephelometers on probes and from analysis of the variation of polarization with the phase angle and the glory feature from images of Venus. Microscopic imaging of Venus' aerosols has been advocated recently. Direct measurements from a fluorescence microscope can provide information on the morphology, density, and biochemical characteristics of the particles; thus, the fluorescence microscope is attractive for the in situ particle characterization of Venus' cloud layer. Fluorescence imaging of Venus' cloud particles presents several challenges due to the sulfuric acid composition and the corrosive effects. In this article, we identify the challenges and describe our approach to overcoming them for a fluorescence microscope based on an in situ bio/chemical and physical characterization instrument for use in the clouds of Venus from a suitable aerial platform. We report that a pH adjustment using alkali was effective for obtaining fluorescence images, and that fluorescence attenuation was observed after the adjustment, even when the acidophile suspension in the concentrated sulfuric acid was used as a sample.

Climatic and landscape changes as drivers of environmental feedback that influence rainfall frequency in the United States

Previous studies have identified regions where the occurrence of rainfall significantly increases or decreases the probability for subsequent rainfall over periods that range from a few days to several weeks. These observable phenomena are termed "rainfall feedback" (RF). To better understand the land-atmosphere interactions involved in RF, the behavior of RF patterns was analyzed using data from 1849 to 2016 at ~3000 sites in the contiguous United States. We also considered changes in major land-use types and applied a geographically weighted regression model technique for analyzing the predictors of RF. This approach identified non-linear and spatially non-stationary relationships between RF, climate, land use, and land type. RF patterns in certain regions of the United States are predictable by modeling variables associated with climate, season, and land use. The model outputs also demonstrate the extent to which the effect of precipitation, temperature, and land use on RF depend on season and location. Specifically, major changes were observed for land use associated with agriculture in the western United States, which had negative and positive influences on RF in summer and winter, respectively. In contrast, developed land in the eastern United States correlated with positive RF values in summer but with negative ones in winter. We discuss how changes in climate and land use would be expected to affect land-atmosphere interactions, as well as the possible role that physical mechanisms and rain-enhanced bioaerosol emissions may play in the spatiotemporal changes observed for historical patterns of rainfall frequency in the United States.

Ocean Aerobiology

Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO₂. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼10⁴ years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.

Rainfalls sprinkle cloud bacterial diversity while scavenging biomass

Bacteria circulate in the atmosphere, through clouds and precipitation to surface ecosystems. Here, we conducted a coordinated study of bacteria assemblages in clouds and precipitation at two sites distant of ∼800 m in elevation in a rural vegetated area around puy de Dôme Mountain, France, and analysed them in regard to meteorological, chemical and air masses' history data. In both clouds and precipitation, bacteria generally associated with vegetation or soil dominated. Elevated ATP-to-cell ratio in clouds compared with precipitation suggested a higher proportion of viable cells and/or specific biological processes. The increase of bacterial cell concentration from clouds to precipitation indicated strong below-cloud scavenging. Using ions as tracers, we derive that 0.2 to 25.5% of the 1.1 × 107 to 6.6 × 108 bacteria cell/m2/h1 deposited with precipitation originated from the source clouds. Yet, the relative species richness decreased with the proportion of inputs from clouds, pointing them as sources of distant microbial diversity. Biodiversity profiles, thus, differed between clouds and precipitation in relation with distant/local influencing sources, and potentially with bacterial phenotypic traits. Notably Undibacterium, Bacillus and Staphylococcus were more represented in clouds, while epiphytic bacteria such as Massilia, Sphingomonas, Rhodococcus and Pseudomonas were enriched in precipitation.

Venus, an Astrobiology Target

We present a case for the exploration of Venus as an astrobiology target-(1) investigations focused on the likelihood that liquid water existed on the surface in the past, leading to the potential for the origin and evolution of life, (2) investigations into the potential for habitable zones within Venus' present-day clouds and Venus-like exo atmospheres, (3) theoretical investigations into how active aerobiology may impact the radiative energy balance of Venus' clouds and Venus-like atmospheres, and (4) application of these investigative approaches toward better understanding the atmospheric dynamics and habitability of exoplanets. The proximity of Venus to Earth, guidance for exoplanet habitability investigations, and access to the potential cloud habitable layer and surface for prolonged in situ extended measurements together make the planet a very attractive target for near term astrobiological exploration.

Characterization of the Aerobic Anoxygenic Phototrophic Bacterium Sphingomonas sp. AAP5

An aerobic, yellow-pigmented, bacteriochlorophyll a-producing strain, designated AAP5 (=DSM 111157=CCUG 74776), was isolated from the alpine lake Gossenköllesee located in the Tyrolean Alps, Austria. Here, we report its description and polyphasic characterization. Phylogenetic analysis of the 16S rRNA gene showed that strain AAP5 belongs to the bacterial genus Sphingomonas and has the highest pairwise 16S rRNA gene sequence similarity with Sphingomonas glacialis (98.3%), Sphingomonas psychrolutea (96.8%), and Sphingomonas melonis (96.5%). Its genomic DNA G + C content is 65.9%. Further, in silico DNA-DNA hybridization and calculation of the average nucleotide identity speaks for the close phylogenetic relationship of AAP5 and Sphingomonas glacialis. The high percentage (76.2%) of shared orthologous gene clusters between strain AAP5 and Sphingomonas paucimobilis NCTC 11030^T, the type species of the genus, supports the classification of the two strains into the same genus. Strain AAP5 was found to contain C_18:1ω7c (64.6%) as a predominant fatty acid (>10%) and the polar lipid profile contained phosphatidylglycerol, diphosphatidylglycerol, phosphatidylethanolamine, sphingoglycolipid, six unidentified glycolipids, one unidentified phospholipid, and two unidentified lipids. The main respiratory quinone was ubiquinone-10. Strain AAP5 is a facultative photoheterotroph containing type-2 photosynthetic reaction centers and, in addition, contains a xathorhodopsin gene. No CO₂-fixation pathways were found.

Falling bacterial communities from the atmosphere

BACKGROUND

Bacteria emitted into the atmosphere eventually settle to the pedosphere via sedimentation (dry deposition) or precipitation (wet deposition), constituting a part of the global cycling of substances on Earth, including the water cycle. In this study, we aim to investigate the taxonomic compositions and flux densities of bacterial deposition, for which little is known regarding the relative contributions of each mode of atmospheric deposition, the taxonomic structures and memberships, and the aerodynamic properties in the atmosphere.

RESULTS

Precipitation was found to dominate atmospheric bacterial deposition, contributing to 95% of the total flux density at our sampling site in Korea, while bacterial communities in precipitation were significantly different from those in sedimentation, in terms of both their structures and memberships. Large aerodynamic diameters of atmospheric bacteria were observed, with an annual mean of 8.84 μm, which appears to be related to their large sedimentation velocities, with an annual mean of 1.72 cm s^- 1 for all bacterial taxa combined. The observed mean sedimentation velocity for atmospheric bacteria was larger than the previously reported mean sedimentation velocities for fungi and plants.

CONCLUSIONS

Large aerodynamic diameters of atmospheric bacteria, which are likely due to the aggregation and/or attachment to other larger particles, are thought to contribute to large sedimentation velocities, high efficiencies as cloud nuclei, and large amounts of precipitation of atmospheric bacteria. Moreover, the different microbiotas between precipitation and sedimentation might indicate specific bacterial involvement and/or selective bacterial growth in clouds. Overall, our findings add novel insight into how bacteria participate in atmospheric processes and material circulations, including hydrological circulation, on Earth.

Differential colonization of microbial communities inhabiting Lede stone in the urban and rural environment

Air pollution is one of the main actors of stone deterioration. It influences not only the material itself but also prokaryotes colonizing rocks. Prokaryotes can affect rock substrates and biological colonization will most likely become relatively more important during the course of the 21st century. Therefore, it is necessary to understand the effects of air pollution on biological colonization and on the impact of this colonization on rock weathering. For this reason, we studied the prokaryotic community of Lede stone from two deteriorated monuments in Belgium: one in the urban and one in the rural environment. This research conducts 16S rRNA gene Next Generation Sequencing combined with an isolation campaign. It revealed diverse and complex prokaryotic communities with more specialized bacteria present in the urban environment, while archaea were barely detected. Some genera could cause biodeterioration but the isolates did not produce a significant amount of acid. Soluble salts analysis revealed an important effect of salts on the prokaryotic community. Colour measurements at least indicate that a main effect of prokaryotes might be on the aesthetics: In the countryside prokaryotic communities seemed to discolour Lede stone, while pollution most likely blackened building stones in the urban environment.

Community Structure and Influencing Factors of Airborne Microbial Aerosols over Three Chinese Cities with Contrasting Social-Economic Levels

As an important part of atmospheric aerosol, airborne bacteria have major impacts on human health. However, variations of airborne community structure due to human-induced activities and their possible impact on human health have not been well understood. In this study, we sampled atmospheric microbial aerosols in three Chinese cities (Shanghai, Xiamen, and Zhangzhou) with contrasting social-economic levels and analyzed the bacterial composition using high-throughput sequencing methods. A high similarity of the predominant phyla was observed in three cities but the relative abundances were quite different. At the genus level, the most dominant genus in Shanghai and Xiamen was Deinococcus while the most dominant genus in Zhangzhou was Clostridium. The different characteristics of airborne bacterial in the three cities above may be ascribed to the environmental variables affected by human over-activities such as the vehicle exhausts and coal-burning emissions in Shanghai, the tourist aggregation and construction works in Xiamen, the extensive uses of chemical fertilizers, and agricultural activities in Zhangzhou. The variation of the bacterial community and the pathogenic bacteria detected in three cities would have a potential threat to human health.

Microbial mercury methylation in the cryosphere: Progress and prospects

Mercury (Hg) is one of the most toxic heavy metals, and its cycle is mainly controlled by oxidation-reduction reactions carried out by photochemical or microbial process under suitable conditions. The deposition and accumulation of methylmercury (MeHg) in various ecosystems, including the cryospheric components such as snow, meltwater, glaciers, and ice sheet, and subsequently in the food chain pose serious health concerns for living beings. Unlike the abundance of knowledge about the processes of MeHg production over land and oceans, little is known about the sources and production/degradation rate of MeHg in cryosphere systems. In addition, processes controlling the concentration of Hg and MeHg in the cryosphere remains poorly understood, and filling this scientific gap has been challenging. Therefore, it is essential to study and review the deposition and accumulation by biological, physical, and chemical mechanisms involved in Hg methylation in the cryosphere. This review attempts to address knowledge gaps in understanding processes, especially biotic and abiotic, applicable for Hg methylation in the cryosphere. First, we focus on the variability in Hg concentration and mechanisms of Hg methylation, including physical, chemical, microbial, and biological processes, and transportation in the cryosphere. Then, we elaborate on the mechanism of redox reactions and biotic and abiotic factors controlling Hg methylation and biogeochemistry of Hg in the cryosphere. We also present possible mechanisms of Hg methylation with an emphasis on microbial transformation and molecular function to understand variability in Hg concentration in the cryosphere. Recent advancements in the genetic and physicochemical mechanisms of Hg methylation are also presented. Finally, we summarize and propose a method to study the unsolved issues of Hg methylation in the cryosphere.

Metabolic modulations of Pseudomonas graminis in response to H2O2 in cloud water

In cloud water, microorganisms are exposed to very strong stresses especially related to the presence of reactive oxygen species including H₂O₂ and radicals, which are the driving force of cloud chemistry. In order to understand how the bacterium Pseudomonas graminis isolated from cloud water respond to this oxidative stress, it was incubated in microcosms containing a synthetic solution of cloud water in the presence or in the absence of H₂O₂. P. graminis metabolome was examined by LC-MS and NMR after 50 min and after 24 hours of incubation. After 50 min, the cells were metabolizing H₂O₂ while this compound was still present in the medium, and it was completely biodegraded after 24 hours. Cells exposed to H₂O₂ had a distinct metabolome as compared to unexposed cells, revealing modulations of certain metabolic pathways in response to oxidative stress. These data indicated that the regulations observed mainly involved carbohydrate, glutathione, energy, lipid, peptides and amino-acids metabolisms. When cells had detoxified H₂O₂ from the medium, their metabolome was not distinguishable anymore from unexposed cells, highlighting the capacity of resilience of this bacterium. This work illustrates the interactions existing between the cloud microbial metabolome and cloud chemistry.

Survival and ice nucleation activity of Pseudomonas syringae strains exposed to simulated high-altitude atmospheric conditions

Pseudomonas syringae produces highly efficient biological ice nuclei (IN) that were proposed to influence precipitation by freezing water in clouds. This bacterium may be capable of dispersing through the atmosphere, having been reported in rain, snow, and cloud water samples. This study assesses its survival and maintenance of IN activity under stressing conditions present at high altitudes, such as UV radiation within clouds. Strains of the pathovars syringae and garcae were compared to Escherichia coli. While UV-C effectively inactivated these cells, the Pseudomonas were much more tolerant to UV-B. The P. syringae strains were also more resistant to radiation from a solar simulator, composed of UV-A and UV-B, while only one of them suffered a decline in IN activity at −5 °C after long exposures. Desiccation at different relative humidity values also affected the IN, but some activity at −5 °C was always maintained. The pathovar garcae tended to be more resistant than the pathovar syringae, particularly to desiccation, though its IN were found to be generally more sensitive. Compared to E. coli, the P. syringae strains appear to be better adapted to survival under conditions present at high altitudes and in clouds.

Size distribution of bioaerosols from biomass burning emissions: Characteristics of bacterial and fungal communities in submicron (PM1.0) and fine (PM2.5) particles

The North China Plain is the agricultural heartland in China. High PM_2.5 levels and elevated chemical pollutants have been observed during crop harvest seasons due to open biomass burning. Biomass burning in the wheat-harvest season may significantly deteriorate the regional air quality. The harmful ingredients in smoke particles also have severe implications for toxicity and health effects. Previous studies have illustrated the potential role of bioaerosols as ice-nuclei and cloud condensation nuclei and highlighted their influence on biochemical cycles and human health effects. In a monthly field observation campaign of biomass burning conducted at the summit of Mount Tai in July 2015, we reported the composition, potential role, size distribution of microorganisms in particulate matters PM_1.0, PM_2.5, and estimated their contribution to particles. The wide-range particle spectrometer suggested that the predominant particles were distributed in submicron particles (PM_1.0), which resulted in a similar community structure for bacteria and fungi in PM_1.0 and PM_2.5. Among bacteria, the predominant Pseudomonas accounted for 18.06% and 21.29% in PM_1.0 and PM_2.5, respectively. Alternaria covered up to 69.01% and 72.76% of the fungal community in PM_1.0 and PM_2.5, respectively. A disparity between bacterial communities was identified by the abundance of rare species, such as Bacilli being higher in PM_1.0 (2.4%) than in PM_2.5 (1.8%), and Defluviicoccus being higher in PM_2.5 (2.5%) than in PM_1.0 (0.5%), which may be related to cell size and cell growth patterns. Quantitative PCR revealed that microbial cell numbers in PM_2.5 were higher than in PM_1.0, and that the bacterial cell number was about an order of magnitude greater than the fungal cell number. However, the mass concentration and contribution of fungi to particulate matter was much higher than that of bacteria, suggesting the underestimated role of fungi in atmospheric aerosols. Airborne microorganisms in alpine areas remained less characterized. The findings presented here illustrated the potentially important impacts on air quality and bioaerosol pollution by biomass burning, which provides an essential reference for understanding the transmission and health effects of bioaerosols.

Living at the Extremes: Extremophiles and the Limits of Life in a Planetary Context

Prokaryotic life has dominated most of the evolutionary history of our planet, evolving to occupy virtually all available environmental niches. Extremophiles, especially those thriving under multiple extremes, represent a key area of research for multiple disciplines, spanning from the study of adaptations to harsh conditions, to the biogeochemical cycling of elements. Extremophile research also has implications for origin of life studies and the search for life on other planetary and celestial bodies. In this article, we will review the current state of knowledge for the biospace in which life operates on Earth and will discuss it in a planetary context, highlighting knowledge gaps and areas of opportunity.

Modeling and Statistical Optimization of Culture Conditions for Improvement of Antifungal Compounds Production by Streptomyces albidoflavus S19 Strain of Wastewater Origin

BACKGROUND

The actinomycetes strains isolated from unexplored ecosystems are a promising alternative for the biosynthesis of novel antimicrobial compounds. Depending on the interesting antifungal activity of the studied strain S19, the statistical method seems to be an effective tool for optimizing the production of anticandidal molecules.

INTRODUCTION

This study was conducted in order to optimize the culture parameters (medium nutrients concentrations and initial pH value) affecting the production of antifungal metabolites from S. albidoflavus strain S19 (obtained from wastewater collected in Bejaia region, Algeria) using Response Surface Metho-dology (RSM). The best conditions for anti-Candida albicans compounds biosynthesis were determined.

METHODS AND RESULTS

The antimicrobial producer strain S. albidoflavus S19 was identified on the basis of morphological, chemicals characters and physiological characteristics along with 16S rRNA gene se-quencing analysis.Response Surface Methodology by Central Composite Design (CCD) was employed to improve the anti-C. albicans agents production through the optimization of medium parameters. The highest antifungal ac-tivity was obtained by using a mixture of 2g l-1 starch, 4g l-1 yeast extract, 2g l-1 peptone at pH 11.

CONCLUSION

The strain S19 isolated from wastewater showed a significant anti-C. albicans activity and this study revealed the effectiveness of RSM and CCD for increasing bioactive compounds production, rising the diameter of inhibition zones from 13 to 34 mm.

Aeolian dispersal of bacteria in southwest Greenland: their sources, abundance, diversity and physiological states

The Arctic is undergoing dramatic climatic changes that cause profound transformations in its terrestrial ecosystems and consequently in the microbial communities that inhabit them. The assembly of these communities is affected by aeolian deposition. However, the abundance, diversity, sources and activity of airborne microorganisms in the Arctic are poorly understood. We studied bacteria in the atmosphere over southwest Greenland and found that the diversity of bacterial communities correlated positively with air temperature and negatively with relative humidity. The communities consisted of 1.3×103 ± 1.0×103 cells m-3, which were aerosolized from local terrestrial environments or transported from marine, glaciated and terrestrial surfaces over long distances. On average, airborne bacterial cells displayed a high activity potential, reflected in the high 16S rRNA copy number (590 ± 300 rRNA cell-1), that correlated positively with water vapor pressure. We observed that bacterial clades differed in their activity potential. For instance, a high activity potential was seen for Rubrobacteridae and Clostridiales, while a low activity potential was observed for Proteobacteria. Of those bacterial families that harbor ice-nucleation active species, which are known to facilitate freezing and may thus be involved in cloud and rain formation, cells with a high activity potential were rare in air, but were enriched in rain.

Draft Genome Sequence of the UV-Resistant Antarctic Bacterium Sphingomonas sp. Strain UV9

We report the draft genome sequence of the Antarctic UV-resistant bacterium Sphingomonas sp. strain UV9. The strain has a genome size of 4.25 Mb, a 65.62% GC content, and 3,879 protein-coding sequences.

We report the draft genome sequence of the Antarctic UV-resistant bacterium Sphingomonas sp. strain UV9. The strain has a genome size of 4.25 Mb, a 65.62% GC content, and 3,879 protein-coding sequences. Among others, genes encoding the resolving of the DNA damage produced by the UV irradiation were identified.

Profile of inhalable bacteria in PM2.5 at Mt. Tai, China: Abundance, community, and influence of air mass trajectories

Bacteria are ubiquitous in the near-surface atmosphere where they constitute an important component of aerosols with the potential to affect climate change, ecosystems, atmospheric process and human health. Limitation in tracking bacterial diversity accurately has thus far prevented the knowledge of airborne bacteria and their pathogenic properties. We performed a comprehensive assessment of bacterial abundance and diverse community in PM_2.5 collected at Mt. Tai, via high-throughput sequencing and real-time PCR. The samples exhibited a high microbial biodiversity and complex chemical composition. The dominating populations were gram-negative bacteria including Burkholderia, Delftia, Bradyrhizobium, and Methylobacterium. The PM mass concentration, chemical composition, bacterial concentration and community structure varied under the influence of different air-mass trajectories. The highest mass concentration of PM_2.5 (61 μg m^-3) and major chemical components were recorded during periods when marine southeasterly air masses were dominant. The local terrestrial air masses from Shandong peninsula and its adjacent areas harbored highest bacterial concentration loading (602 cells m^-3) and more potential pathogens at the site. In contrast, samples influenced by the long-distance air flow from Siberia and Outer Mongolia were found to have a highest richness and diversity as an average, which was also marked by the increase of dust-associated bacteria (Brevibacillus and Staphylococcus). The primary research may serve as an important reference for the environmental microbiologist, health workers, and city planners.

The biology of fog: results from coastal Maine and Namib Desert reveal common drivers of fog microbial composition

Fog supplies water and nutrients to systems ranging from coastal forests to inland deserts. Fog droplets can also contain bacterial and fungal aerosols, but our understanding of fog biology is limited. Using metagenomic tools and culturing, we provide a unique look at fungal and bacterial communities in fog at two fog-dominated sites: coastal Maine (USA) and the Namib Desert (Namibia). Microbial communities in the fog at both sites were diverse, distinct from clear aerosols, and influenced by both soil and marine sources. Fog from both sites contained Actinobacteria and Firmicutes, commonly soil- and air-associated phyla, but also contained bacterial taxa associated with marine environments including Cyanobacteria, Oceanospirillales, Novosphingobium, Pseudoalteromonas, and Bradyrhizobiaceae. Marine influence on fog communities was greatest near the coast, but still evident in Namib fogs 50 km inland. In both systems, differences between pre- and post-fog aerosol communities suggest that fog events can significantly alter microbial aerosol diversity and composition. Fog is likely to enhance viability of transported microbes and facilitate their deposition, making fog biology ecologically important in fog-dominated environments. Fog may introduce novel species to terrestrial ecosystems, including human and plant pathogens, warranting further work on the drivers of this important and underrecognized aerobiological transfer between marine and terrestrial systems.

Effect of Aerosolization and Drying on the Viability of Pseudomonas syringae Cells

Airborne dispersal of microorganisms influences their biogeography, gene flow, atmospheric processes, human health and transmission of pathogens that affect humans, plants and animals. The extent of their impact depends essentially on cell-survival rates during the process of aerosolization. A central factor for cell-survival is water availability prior to and upon aerosolization. Also, the ability of cells to successfully cope with stress induced by drying determines their chances of survival. In this study, we used the ice-nucleation active, plant pathogenic Pseudomonas syringae strain R10.79 as a model organism to investigate the effect of drying on cell survival. Two forms of drying were simulated: drying of cells in small droplets aerosolized from a wet environment by bubble bursting and drying of cells in large droplets deposited on a surface. For drying of cells both in aerosol and surface droplets, the relative humidity (RH) was varied in the range between 10 and 90%. The fraction of surviving cells was determined by live/dead staining followed by flow cytometry. We also evaluated the effect of salt concentration in the water droplets on the survival of drying cells by varying the ionic strength between 0 and 700 mM using NaCl and sea salt. For both aerosol and surface drying, cell survival increased with decreasing RH (p < 0.01), and for surface drying, survival was correlated with increasing salt concentration (p < 0.001). Imaging cells with TEM showed shrunk cytoplasm and cell wall damage for a large fraction of aerosolized cells. Ultimately, we observed a 10-fold higher fraction of surviving cells when dried as aerosol compared to when dried on a surface. We conclude that the conditions, under which cells dry, significantly affect their survival and thus their success to spread through the atmosphere and colonize new environments as well as their ability to affect atmospheric processes.

Striking Similarities Between Botrytis cinerea From Non-agricultural and From Agricultural Habitats

Investigations into life history of microorganisms that cause plant diseases have been limited mostly to contexts where they are in interaction with plants, and with cropped or otherwise managed vegetation. Therefore, knowledge about the diversity of plant pathogens, about potential reservoirs of inoculum and about the processes that contribute to their survival and adaptation is limited to these contexts. The agro-centric perspective of plant pathogen life histories is incoherent with respect to the capacity of many of them to persist as saprophytes on various substrates. In this context we have investigated the ubiquity of the broad host range necrotrophic fungus Botrytis cinerea, outside of agricultural settings and have determined if the populations in these natural habitats can be distinguished phenotypically and phylogenetically from populations isolated from diseased crops. Over a period of 5 years, we isolated B. cinerea from 235 samples of various substrates collected in France including rainfall, snowpack, river, and lake water, epilithic biofilms in mountain streams, leaf litter and plant debris, rock surfaces, bird feathers and healthy wild plants from outside of agricultural fields. All substrates except rock surfaces harbored B. cinerea leading us to establish a collection of purified strains that were compared to B. cinerea from diseased tomato, grapes and various other crops in France. Phylogenetic comparisons of 321 strains from crop plants and 100 strains from environmental substrates based on sequences of 9 microsatellite markers revealed that strains from crops and the environment could not be distinguished. Furthermore, the genetic diversity of strains outside of agriculture was just as broad as within agriculture. In tests to determine the aggressiveness of strains on tomato stems, the mean disease severity caused by strains from environmental substrates was statistically identical to the severity of disease caused by strains from tomato, but was significantly greater than the severity caused by strains from grape or other crops. Our results suggest that highly diverse populations of this plant pathogen persist outside of agriculture in association with substrates other than plants and that this part of their life history is compatible with its capacity to maintain its potential as plant pathogen.

First evaluation of the effect of microorganisms on steady state hydroxyl radical concentrations in atmospheric waters

Clouds are complex multiphasic media where efficient chemical reactions take place and where microorganisms have been found to be metabolically active. Hydroxyl radical is the main oxidant in cloud water, and more generally in the atmosphere, during the day and drives the cloud oxidative capacity. However, only one measurement of the steady state hydroxyl radical concentrations in cloud water has been reported so far. Cloud chemistry models are used to estimate the hydroxyl radical concentrations with values ranging from 10^-12 to 10^-15 M that are surely overestimated due to a lack of knowledge about the speciation of the organic matter acting as a sink for hydroxyl radicals. The aim of this work is to quantify the concentration of hydroxyl radicals at steady state in rain and cloud waters and to measure the impact of native microflora on this concentration. First, the non-toxicity of terephthalic acid as probe is controlled before the analysis in real atmospheric water samples. Higher concentrations of hydroxyl radicals are found in cloud waters than in rain waters, with a mean value "1.6 ± 1.5" × 10^-16 M and "7.2 ± 5.0" × 10^-16 M for rain and cloud waters respectively and no real impact of microorganisms was observed. This method allows the measurement of steady state hydroxyl radical levels at very low concentrations (down to 10^-17 M) and it is biocompatible, fast and easy to handle. It is a useful tool, complementary to other methods, to give a better overview of atmospheric water oxidant capacity.

Survival of Extremophilic Yeasts in the Stratospheric Environment during Balloon Flights and in Laboratory Simulations

The high-altitude atmosphere is a harsh environment with extremely low temperatures, low pressure, and high UV irradiation. For this reason, it has been proposed as an analogue for Mars, presenting deleterious factors similar to those on the surface of that planet. We evaluated the survival of extremophilic UV-resistant yeasts isolated from a high-elevation area in the Atacama Desert under stratospheric conditions. As biological controls, intrinsically resistant Bacillus subtilis spores were used. Experiments were performed in two independent stratospheric balloon flights and with an environmental simulation chamber. The three following different conditions were evaluated: (i) desiccation, (ii) desiccation plus exposure to stratospheric low pressure and temperature, and (3) desiccation plus exposure to the full stratospheric environment (UV, low pressure, and temperature). Two strains, Naganishia (Cryptococcus) friedmannii 16LV2 and Exophiala sp. strain 15LV1, survived full exposures to the stratosphere in larger numbers than did B. subtilis spores. Holtermanniella watticus (also known as Holtermanniella wattica) 16LV1, however, suffered a substantial loss in viability upon desiccation and did not survive the stratospheric UV exposure. The remarkable resilience of N. friedmannii and Exophiala sp. 15LV1 under the extreme Mars-like conditions of the stratosphere confirms its potential as a eukaryotic model for astrobiology. Additionally, our results with N. friedmannii strengthen the recent hypothesis that yeasts belonging to the Naganishia genus are fit for aerial dispersion, which might account for the observed abundance of this species in high-elevation soils.IMPORTANCE Studies of eukaryotic microorganisms under conditions of astrobiological relevance, as well as the aerial dispersion potential of extremophilic yeasts, are still lacking in the literature compared to works with bacteria. Using stratospheric balloon flights and a simulation chamber, we demonstrate that yeasts isolated from an extreme environment are capable of surviving all stressors found in the stratosphere, including intense UV irradiation, scoring an even higher survival than B. subtilis spores. Notably, the yeast N. friedmannii, which displayed one of the highest tolerances to the stratospheric environment in the experiments, was recently proposed to be adapted to airborne transportation, although such a hypothesis had not yet been tested. Our results strengthen such an assumption and can help explain the observed distribution and ecology of this particular yeast species.

Regional fresh snowfall microbiology and chemistry are driven by geography in storm-tracked events, Colorado, USA

Snowfall is a global phenomenon highly integrated with hydrology and ecology. Forays into studying bioaerosols and their dependence on aeolian movement are largely constrained to either precipitation-independent analyses or in silico models. Though snowpack and glacial microbiological studies have been conducted, little is known about the biological component of meteoric snow. Through culture-independent phylogenetic and geochemical analyses, we show that the geographical location at which snow precipitates determines snowfall’s geochemical and microbiological composition. Storm-tracking, furthermore, can be used as a valuable environmental indicator to trace down what factors are influencing bioaerosols. We estimate annual aeolian snowfall deposits of up to ∼10 kg of bacterial/archaeal biomass per hectare along our study area of the eastern Front Range in Colorado. The dominant kinds of microbiota captured in an analysis of seven snow events at two different locations, one urban, one rural, across the winter of 2016/2017 included phyla Proteobacteria, Bacteroidetes, Firmicutes, and Acidobacteria, though a multitude of different kinds of organisms were found in both. Taxonomically, Bacteroidetes were more abundant in Golden (urban plain) snow while Proteobacteria were more common in Sunshine (rural mountain) samples. Chemically, Golden snowfall was positively correlated with some metals and anions. The work also hints at better informing the “everything is everywhere” hypotheses of the microbial world and that atmospheric transport of microbiota is not only common, but is capable of disseminating vast amounts of microbiota of different physiologies and genetics that then affect ecosystems globally. Snowfall, we conclude, is a significant repository of microbiological material with strong implications for both ecosystem genetic flux and general bio-aerosol theory.

Clean Low-Biomass Procedures and Their Application to Ancient Ice Core Microorganisms

Microorganisms in glacier ice provide tens to hundreds of thousands of years archive for a changing climate and microbial responses to it. Analyzing ancient ice is impeded by technical issues, including limited ice, low biomass, and contamination. While many approaches have been evaluated and advanced to remove contaminants on ice core surfaces, few studies leverage modern sequencing to establish in silico decontamination protocols for glacier ice. Here we sought to apply such “clean” sampling techniques with in silico decontamination approaches used elsewhere to investigate microorganisms archived in ice at ∼41 (D41, ∼20,000 years) and ∼49 m (D49, ∼30,000 years) depth in an ice core (GS3) from the summit of the Guliya ice cap in the northwestern Tibetan Plateau. Four “background” controls were established – a co-processed sterile water artificial ice core, two air samples collected from the ice processing laboratories, and a blank, sterile water sample – and used to assess contaminant microbial diversity and abundances. Amplicon sequencing revealed 29 microbial genera in these controls, but quantitative PCR showed that the controls contained about 50–100-times less 16S DNA than the glacial ice samples. As in prior work, we interpreted these low-abundance taxa in controls as “contaminants” and proportionally removed them in silico from the GS3 ice amplicon data. Because of the low biomass in the controls, we also compared prokaryotic 16S DNA amplicons from pre-amplified (by re-conditioning PCR) and standard amplicon sequencing, and found the resulting microbial profiles to be repeatable and nearly identical. Ecologically, the contaminant-controlled ice microbial profiles revealed significantly different microorganisms across the two depths in the GS3 ice core, which is consistent with changing climate, as reported for other glacier ice samples. Many GS3 ice core genera, including Methylobacterium, Sphingomonas, Flavobacterium, Janthinobacterium, Polaromonas, and Rhodobacter, were also abundant in previously studied ice cores, which suggests wide distribution across glacier environments. Together these findings help further establish “clean” procedures for studying low-biomass ice microbial communities and contribute to a baseline understanding of microorganisms archived in glacier ice.

Atmospheric Precipitations, Hailstone and Rainwater, as a Novel Source of Streptomyces Producing Bioactive Natural Products

A cultivation-dependent approach revealed that highly diverse populations of Streptomyces were present in atmospheric precipitations from a hailstorm event sampled in February 2016 in the Cantabrian Sea coast, North of Spain. A total of 29 bioactive Streptomyces strains isolated from small samples of hailstone and rainwater, collected from this hailstorm event, were studied here. Taxonomic identification by 16S rRNA sequencing revealed more than 20 different Streptomyces species, with their closest homologs displaying mainly oceanic but also terrestrial origins. Backward trajectory analysis revealed that the air-mass sources of the hailstorm event, with North Western winds, were originated in the Arctic Ocean (West Greenland and North Iceland) and Canada (Labrador), depending on the altitude. After traveling across the North Atlantic Ocean during 4 days the air mass reached Europe and precipitated as hailstone and rain water at the sampling place in Spain. The finding of Streptomyces species able to survive and disperse through the atmosphere increases our knowledge of the biogeography of genus Streptomyces on Earth, and reinforces our previous dispersion model, suggesting a generalized feature for the genus which could have been essential in his evolution. This unique atmospheric-derived Streptomyces collection was screened for production of bioactive secondary metabolites. Analyses of isolates ethyl acetate extracts by LC-UV-MS and further database comparison revealed an extraordinary diversity of bioactive natural products. One hundred molecules were identified, mostly displaying contrasted antibiotic and antitumor/cytotoxic activities, but also antiparasitic, antiviral, anti-inflammatory, neuroprotector, and insecticide properties. More interestingly, 38 molecules not identified in natural products databases might represent new natural products. Our results revealed for the first time an extraordinary diversity of Streptomyces species in the atmosphere able to produce an extraordinary repertoire of bioactive molecules, thus providing a very promising source for the discovery of novel pharmaceutical natural products.

Coping with Environmental Eukaryotes; Identification of Pseudomonas syringae Genes during the Interaction with Alternative Hosts or Predators

Understanding the molecular mechanisms underpinning the ecological success of plant pathogens is critical to develop strategies for controlling diseases and protecting crops. Recent observations have shown that plant pathogenic bacteria, particularly Pseudomonas, exist in a range of natural environments away from their natural plant host e.g., water courses, soil, non-host plants. This exposes them to a variety of eukaryotic predators such as nematodes, insects and amoebae present in the environment. Nematodes and amoeba in particular are bacterial predators while insect herbivores may act as indirect predators, ingesting bacteria on plant tissue. We therefore postulated that bacteria are probably under selective pressure to avoid or survive predation and have therefore developed appropriate coping mechanisms. We tested the hypothesis that plant pathogenic Pseudomonas syringae are able to cope with predation pressure and found that three pathovars show weak, but significant resistance or toxicity. To identify the gene systems that contribute to resistance or toxicity we applied a heterologous screening technique, called Rapid Virulence Annotation (RVA), for anti-predation and toxicity mechanisms. Three cosmid libraries for P. syringae pv. aesculi, pv. tomato and pv. phaseolicola, of approximately 2000 cosmids each, were screened in the susceptible/non-toxic bacterium Escherichia coli against nematode, amoebae and an insect. A number of potential conserved and unique genes were identified which included genes encoding haemolysins, biofilm formation, motility and adhesion. These data provide the first multi-pathovar comparative insight to how plant pathogens cope with different predation pressures and infection of an insect gut and provide a foundation for further study into the function of selected genes and their role in ecological success.

A review on airborne microorganisms in particulate matters: Composition, characteristics and influence factors

Airborne microorganisms (AM), vital components of particulate matters (PM), are widespread in the atmosphere. Since some AM have pathogenicity, they can lead to a wide range of diseases in human and other organisms, meanwhile, some AM act as cloud condensation nuclei and ice nuclei which let them can affect the climate. The inherent characteristics of AM play critical roles in many aspects which, in turn, can decide microbial traits. The uncertain factors bring various influences on AM, which make it difficult to elaborate effect trends as whole. Because of the potential roles of AM in environment and potent effects of factors on AM, detailed knowledge of them is of primary significance. This review highlights the issues of composition and characteristics of AM with size-distribution, species diversity, variation and so on, and summarizes the main factors which affect airborne microbial features. This general information is a knowledge base for further thorough researches of AM and relevant aspects. Besides, current knowledge gaps and new perspectives are offered to roundly understand the impacts and application of AM in nature and human health.

Metabolomic study of the response to cold shock in a strain of Pseudomonas syringae isolated from cloud water

INTRODUCTION

Active microorganisms have been recently discovered in clouds, thus demonstrating the capacity of microorganisms to exist in harsh environments, including exposure to UV and oxidants, osmotic and cold shocks, etc. It is important to understand how microorganisms respond to and survive such stresses at the metabolic level.

OBJECTIVES

The objective of this work is to assess metabolome modulation in a strain of Pseudomonas syringae isolated from cloud water and facing temperature downshift from 17 to 5 °C by identifying key molecules and pathways of the response/adaptation to cold shock.

METHODS

Bacterial extracts from suspensions of cells grown at 17 °C and further incubated in microcosms at 5 and 17 °C to mimic cloud conditions were analysed by combining LC-MS and NMR; the results were evaluated in comparison to similar suspensions kept at constant temperature. The differences in the metabolome profiles were deciphered using multivariate statistics (PLS-DA).

RESULTS

Key cold shock biomarkers were observed, including cryoprotectants (trehalose, glucose, glycerol, carnitine, glutamate), antioxidants (glutathione and carnitine) and their precursors, alkaloids (bellendine and slaframine) and metabolites involved in energy metabolism (ATP, carbohydrates). Furthermore, new short peptides (nine dipeptides and a tetrapeptide) were found that have no known function.

CONCLUSIONS

This study shows that in response to cold temperatures, Pseudomonas syringae PDD-32b-74 demonstrates numerous metabolism modifications to counteract the impacts of low temperatures.

Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium

Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C₁ growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production. Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.

Active microorganisms thrive among extremely diverse communities in cloud water

Clouds are key components in Earth’s functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain’s meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members. Communities consisted of ~10³−10⁴ bacteria and archaea mL^-1 and ~10²−10³ eukaryote cells mL^-1. They appeared extremely rich, with more than 28 000 distinct species detected in bacteria and 2 600 in eukaryotes. Proteobacteria and Bacteroidetes largely dominated in bacteria, while eukaryotes were essentially distributed among Fungi, Stramenopiles and Alveolata. Within these complex communities, the active members of cloud microbiota were identified as Alpha- (Sphingomonadales, Rhodospirillales and Rhizobiales), Beta- (Burkholderiales) and Gamma-Proteobacteria (Pseudomonadales). These groups of bacteria usually classified as epiphytic are probably the best candidates for interfering with abiotic chemical processes in clouds, and the most prone to successful aerial dispersion.

A Naganishia in high places: functioning populations or dormant cells from the atmosphere?

Here, we review the current state of knowledge concerning high-elevation members of the extremophilic Cryptococcus albidus clade (now classified as the genus Naganishia). These fungi dominate eukaryotic microbial communities across the highest elevation, soil-like material (tephra) on volcanoes such as Llullaillaco, Socompa, and Saírecabur in the Atacama region of Chile, Argentina, and Bolivia. Recent studies indicate that Naganishia species are among the most resistant organisms to UV radiation, and a strain of N. friedmannii from Volcán Llullaillaco is the first organism that is known to grow during the extreme, diurnal freeze-thaw cycles that occur on a continuous basis at elevations above 6000 m.a.s.l. in the Atacama region. These and other extremophilic traits discussed in this review may serve a dual purpose of allowing Naganishia species to survive long-distance transport through the atmosphere and to survive the extreme conditions found at high elevations. Current evidence indicates that there are frequent dispersal events between high-elevation volcanoes of Atacama region and the Dry Valleys of Antarctica via "Rossby Wave" merging of the polar and sub-tropical jet streams. This dispersal hypothesis needs further verification, as does the hypothesis that Naganishia species are flexible "opportunitrophs" that can grow during rare periods of water (from melting snow) and nutrient availability (from Aeolian inputs) in one of the most extreme terrestrial habitats on Earth.

Draft Genome Sequence of Pseudomonas graminis PDD-13b-3, a Model Strain Isolated from Cloud Water

The whole genome of Pseudomonas graminis PDD-13b-3, a strain of bacteria isolated from cloud water, was sequenced. This showed that this microorganism is equipped with genes that could potentially be involved in its survival in the atmosphere and clouds: those for oxidative stress and carbon starvation responses, DNA repair, and iron uptake.

Survival and electrotransformation of Pseudomonas syringae strains under simulated cloud-like conditions

To diversify their genetic material, and thereby allow adaptation to environmental disturbances and colonization of new ecological niches, bacteria use various evolutionary processes, including the acquisition of new genetic material by horizontal transfer mechanisms such as conjugation, transduction and transformation. Electrotransformation mediated by lightning-related electrical phenomena may constitute an additional gene-transfer mechanism occurring in nature. The presence in clouds of bacteria such as Pseudomonas syringae capable of forming ice nuclei that lead to precipitation, and that are likely to be involved in triggering lightning, led us to postulate that natural electrotransformation in clouds may contribute to the adaptive potential of these bacteria. Here, we quantify the survival rate of 10 P. syringae strains in liquid and icy media under such electrical pulses and their capacity to acquire exogenous DNA. In comparison to two other bacteria (Pseudomonas sp. N3 and Escherichia coli TOP10), P. syringae CC0094 appears to be best adapted for survival and for genetic electrotransformation under these conditions, which suggests that this bacterium would be able to survive and to get a boost in its adaptive potential while being transported in clouds and falling back to Earth with precipitation from storms.

Microorganisms and heavy metals associated with atmospheric deposition in a congested urban environment of a developing country: Sri Lanka

The presence of bacteria and heavy metals in atmospheric deposition were investigated in Kandy, Sri Lanka, which is a typical city in the developing world with significant traffic congestion. Atmospheric deposition samples were analyzed for Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb which are heavy metals common to urban environments. Al and Fe were found in high concentrations due to the presence of natural sources, but may also be re-suspended by vehicular traffic. Relatively high concentrations of toxic metals such as Cr and Pb in dissolved form were also found. High Zn loads can be attributed to vehicular emissions and the wide use of Zn coated roofing materials. The metal loads in wet deposition showed higher concentrations compared to dry deposition. The metal concentrations among the different sampling sites significantly differ from each other depending on the traffic conditions. Industrial activities are not significant in Kandy City. Consequently, the traffic exerts high influence on heavy metal loadings. As part of the bacterial investigations, nine species of culturable bacteria, namely; Sphingomonas sp., Pseudomonas aeruginosa, Pseudomonas monteilii, Klebsiella pneumonia, Ochrobactrum intermedium, Leclercia adecarboxylata, Exiguobacterium sp., Bacillus pumilus and Kocuria kristinae, which are opportunistic pathogens, were identified. This is the first time Pseudomonas monteilii and Ochrobactrum intermedium has been reported from a country in Asia. The culturable fraction constituted ~0.01 to 10%. Pigmented bacteria and endospore forming bacteria were copious in the atmospheric depositions due to their capability to withstand harsh environmental conditions. The presence of pathogenic bacteria and heavy metals creates potential human and ecosystem health risk.

Investigation of diverse bacteria in cloud water at Mt. Tai, China

Bacteria are abundant in atmospheric water phase with the potential to influence atmospheric processes and human health, yet relatively little information is known about the bacterial characteristics at high altitudes. Here we investigated the bacterial community by high throughput sequencing in 24 cloud water samples collected from September 26 to October 31, at the summit of Mt. Tai (36°15' N, 117°06' E, 1534m a.s.l) in China. Diverse bacterial population were identified and the gram-negative bacteria contributed the majority of total bacteria including Proteobacteria (81.6%) and Bacteroidetes (3.9%), followed by gram-positive bacteria Firmicutes (7.1%) and Actinobacteria (2.3%). These gram-negative taxa mainly inhabited in leaf-surface and cold environments. Meanwhile bacteria involved in the cloud condensation nuclei and ice nuclei formation were observed such as Sphingomonas (6.7%), Pseudomonas (4.1%), and Bacillus (1.1%). In addition, Sphingmonas was more active than that in daytime and participated in the cloud chemistry process. Meanwhile O₃ and SO₂ critically contributed to the variation of bacterial community. It is the first report on the bacterial community structure of cloud water over Asian area. Our results can serve as an important reference for environmental scientists, and biologists.

Evidence for a missing source of efficient ice nuclei

It has been known for several decades that some bioaerosols, such as ice-nucleation-active (INA) bacteria, especially Pseudomonas syringae strains, may play a critical potential role in the formation of clouds and precipitation. We investigated bacterial and fungal ice nuclei (IN) in rainwater samples collected from the Hulunber temperate grasslands in North China. The median freezing temperatures (T₅₀) for three years’ worth of unprocessed rain samples were greater than −10 °C based on immersion freezing testing. The heat and filtration treatments inactivated 7–54% and 2–89%, respectively, of the IN activity at temperatures warmer than −10 °C. We also determined the composition of the microbial community. The majority of observed Pseudomonas strains were distantly related to the verified ice-nucleating Pseudomonas strains, as revealed by phylogenetic analysis. Here, we show that there are submicron INA particles <220 nm in rainwater that are not identifiable as the known species of high-INA bacteria and fungi and there may be a new potential type of efficient submicroscale or nanoscale ice nucleator in the regional rainwater samplers. Our results suggest the need for a reinterpretation of the source of high-INA material in the formation of precipitation and contribute to the search for new methods of weather modification.

Applicability of LIVE/DEAD BacLight stain with glutaraldehyde fixation for the measurement of bacterial abundance and viability in rainwater

Rainwater contains substantial bacteria and rain is an efficient pathway for the dissemination of bacteria from the atmosphere to land and water surfaces. However, quantitative information on rainwater bacteria is very limited due to the lack of a reliable method. In this study, the epifluorescence microscopy enumeration with the LIVE/DEAD BacLight Bacterial Viability Kit stain was verified to quantify the abundance of viable and non-viable bacterial cells in rainwater, with the 4',6-diamidino-2-phenylindole (DAPI) stain for the reference of total cell counts. Results showed that the total counts of bacterial cells by LIVE/DEAD BacLight staining were consistent with those by DAPI staining, and the average detection efficiency was (109±29)%. The ratio of cell count with glutaraldehyde fixation to that without fixation was (106±5)% on average. The bacterial concentration in negative control was usually an order of magnitude lower than that in rainwater samples. However, in case of small precipitation, the abundance in negative control could be more than that in rainwater samples. These results indicate that the enumeration with LIVE/DEAD BacLight bacterial viability assay coupled with glutaraldehyde fixation and careful negative control investigation is an approach applicable to the measurement of the concentration and viability of bacterial cells in rainwater.

Siderophores in Cloud Waters and Potential Impact on Atmospheric Chemistry: Production by Microorganisms Isolated at the Puy de Dôme Station

A total of 450 bacteria and yeast strains isolated from cloud waters sampled at the puy de Dôme station in France (1465 m) were screened for their ability to produce siderophores. To achieve this, a high-throughput method in 96-well plates was adapted from the CAS (chrome azurol S) method. Notably, 42% of the isolates were siderophore producers. This production was examined according to the phyla of the tested strains and the type of chelating functional groups (i.e., hydroxamate, catechol, and mixed type). The most active bacteria in the clouds belong to the γ-Proteobacteria class, among which the Pseudomonas genus is the most frequently encountered. γ-Proteobacteria are produced in the majority of mixed function siderophores, such as pyoverdines, which bear a photoactive group. Finally, siderophore production was shown to vary with the origin of the air masses. The organic speciation of iron remains largely unknown in warm clouds. Our results suggest that siderophores could partly chelate Fe(III) in cloud waters and thus potentially impact the chemistry of the atmospheric aqueous phase.

Longitudinal Metagenomic Analysis of Hospital Air Identifies Clinically Relevant Microbes

We describe the sampling of sixty-three uncultured hospital air samples collected over a six-month period and analysis using shotgun metagenomic sequencing. Our primary goals were to determine the longitudinal metagenomic variability of this environment, identify and characterize genomes of potential pathogens and determine whether they are atypical to the hospital airborne metagenome. Air samples were collected from eight locations which included patient wards, the main lobby and outside. The resulting DNA libraries produced 972 million sequences representing 51 gigabases. Hierarchical clustering of samples by the most abundant 50 microbial orders generated three major nodes which primarily clustered by type of location. Because the indoor locations were longitudinally consistent, episodic relative increases in microbial genomic signatures related to the opportunistic pathogens Aspergillus, Penicillium and Stenotrophomonas were identified as outliers at specific locations. Further analysis of microbial reads specific for Stenotrophomonas maltophilia indicated homology to a sequenced multi-drug resistant clinical strain and we observed broad sequence coverage of resistance genes. We demonstrate that a shotgun metagenomic sequencing approach can be used to characterize the resistance determinants of pathogen genomes that are uncharacteristic for an otherwise consistent hospital air microbial metagenomic profile.

Molecular Evidence for Metabolically Active Bacteria in the Atmosphere

Bacterial metabolisms are responsible for critical chemical transformations in nearly all environments, including oceans, freshwater, and soil. Despite the ubiquity of bacteria in the atmosphere, little is known about the metabolic functioning of atmospheric bacterial communities. To gain a better understanding of the metabolism of bacterial communities in the atmosphere, we used a combined empirical and model-based approach to investigate the structure and composition of potentially active bacterial communities in air sampled at a high elevation research station. We found that the composition of the putatively active bacterial community (assayed via rRNA) differed significantly from the total bacterial community (assayed via rDNA). Rare taxa in the total (rDNA) community were disproportionately active relative to abundant taxa, and members of the order Rhodospirillales had the highest potential for activity. We developed theory to explore the effects of random sampling from the rRNA and rDNA communities on observed differences between the communities. We found that random sampling, particularly in cases where active taxa are rare in the rDNA community, will give rise to observed differences in community composition including the occurrence of “phantom taxa”, taxa which are detected in the rRNA community but not the rDNA community. We show that the use of comparative rRNA/rDNA techniques can reveal the structure and composition of the metabolically active portion of bacterial communities. Our observations suggest that metabolically active bacteria exist in the atmosphere and that these communities may be involved in the cycling of organic compounds in the atmosphere.

Investigation of the Interplanetary Transfer of Microbes in the Tanpopo Mission at the Exposed Facility of the International Space Station

The Tanpopo mission will address fundamental questions on the origin of terrestrial life. The main goal is to test the panspermia hypothesis. Panspermia is a long-standing hypothesis suggesting the interplanetary transport of microbes. Another goal is to test the possible origin of organic compounds carried from space by micrometeorites before the terrestrial origin of life. To investigate the panspermia hypothesis and the possible space origin of organic compounds, we performed space experiments at the Exposed Facility (EF) of the Japanese Experiment Module (JEM) of the International Space Station (ISS). The mission was named Tanpopo, which in Japanese means dandelion. We capture any orbiting microparticles, such as micrometeorites, space debris, and terrestrial particles carrying microbes as bioaerosols, by using blocks of silica aerogel. We also test the survival of microbial species and organic compounds in the space environment for up to 3 years. The goal of this review is to introduce an overview of the Tanpopo mission with particular emphasis on the investigation of the interplanetary transfer of microbes. The Exposed Experiment Handrail Attachment Mechanism with aluminum Capture Panels (CPs) and Exposure Panels (EPs) was exposed on the EF-JEM on May 26, 2015. The first CPs and EPs will be returned to the ground in mid-2016. Possible escape of terrestrial microbes from Earth to space will be evaluated by investigating the upper limit of terrestrial microbes by the capture experiment. Possible mechanisms for transfer of microbes over the stratosphere and an investigation of the effect of the microbial cell-aggregate size on survivability in space will also be discussed.

KEY WORDS

Panspermia-Astrobiology-Low-Earth orbit. Astrobiology 16, 363-376.