Airborne bacteria confirm the pristine nature of the Southern Ocean boundary layer

Aerosol sources and transport paths co-control the atmospheric bacterial diversity over the coastal East China Sea

Airborne bacteria along with chemical composition of aerosols were investigated during five sampling seasons at an offshore island of the East China Sea. Bacterial diversity was the lowest in spring, the highest in winter, and similar between the autumns of 2019 and 2020, suggesting remarkably seasonal variation but little interannual change. Geodermatophilus (Actinobacteria) was the indicator genus of mineral dust (MD) showed higher proportion in spring than in other seasons. Mastigocladopsis_PCC-10914 (Cyanobacteria) as the indicator of sea salt (SS) demonstrated the highest percentages in both autumns, when the air masses mainly passed over the ocean prior to the sampling site. The higher proportions of soil-derived genera Rubellimicrobium and Craurococcus (both Proteobacteria) and extremophile Chroococcidiopsis_SAG_2023 (Cyanobacteria) were found in summer and winter, respectively. Our study explores the linkage between aerosol source and transport path and bacterial composition, which has implication to understanding of land-sea transmission of bacterial taxa.

Evolution and adaptation of terrestrial plant-associated Plantibacter species into remote marine environments

Microbes are thought to be distributed and circulated around the world, but the connection between marine and terrestrial microbiomes remains largely unknown. We use Plantibacter, a representative genus associated with plants, as our research model to investigate the global distribution and adaptation of plant-related bacteria in plant-free environments, particularly in the remote Southern Ocean and the deep Atlantic Ocean. The marine isolates and their plant-associated relatives shared over 98% whole-genome average nucleotide identity (ANI), indicating recent divergence and ongoing speciation from plant-related niches to marine environments. Comparative genomics revealed that the marine strains acquired new genes via horizontal gene transfer from non-Plantibacter species and refined existing genes through positive selection to improve adaptation to new habitats. Meanwhile, marine strains retained the ability to interact with plants, such as modifying root system architecture and promoting germination. Furthermore, Plantibacter species were found to be widely distributed in marine environments, revealing an unrecognized phenomenon that plant-associated microbiomes have colonized the ocean, which could serve as a reservoir for plant growth-promoting microbes. This study demonstrates the presence of an active reservoir of terrestrial plant growth-promoting bacteria in remote marine systems and advances our understanding of the microbial connections between plant-associated and plant-free environments at the genome level.

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

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

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.

East Asian monsoon manipulates the richness and taxonomic composition of airborne bacteria over China coastal area

Airborne bacteria may have significant impacts on aerosol properties, public health and ecosystem depending on their taxonomic composition and transport. This study investigated the seasonal and spatial variations of bacterial composition and richness over the east coast of China and the roles of East Asian monsoon played through synchronous sampling and 16S rRNA sequencing analysis of airborne bacteria at Huaniao island of the East China Sea (ECS) and the urban and rural sites of Shanghai. Airborne bacteria showed higher richness over the land sites than Huaniao island with the highest values found in the urban and rural springs associated with the growing plants. For the island, the maximal richness occurred in winter as the result of prevailing terrestrial winds controlled by East Asian winter monsoon. Proteobacteria, Actinobacteria and Cyanobacteria were found to be top three phyla, together accounting for 75 % of total airborne bacteria. Radiation-resistant Deinococcus, Methylobacterium belonging to Rhizobiales (related to vegetation) and Mastigocladopsis_PCC_10914 originating from marine ecosystem were indicator genera for urban, rural and island sites, respectively. The Bray-Curits dissimilarity of taxonomic composition between the island and two land sites was the lowest in winter with the representative genera over island also typically from the soil. Our results reveal that seasonal change of monsoon wind directions evidently affects the richness and taxonomic composition of airborne bacteria in China coastal area. Particularly, prevailing terrestrial winds lead to the dominance of land-derived bacteria over the coastal ECS which may have a potential impact on marine ecosystem.

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.

Persistence and Potential Atmospheric Ramifications of Ice-Nucleating Particles Released from Thawing Permafrost

Permafrost underlies approximately a quarter of the Northern Hemisphere and is changing amidst a warming climate. Thawed permafrost can enter water bodies through top-down thaw, thermokarst erosion, and slumping. Recent work revealed that permafrost contains ice-nucleating particles (INPs) with concentrations comparable to midlatitude topsoil. These INPs may impact the surface energy budget of the Arctic by affecting mixed-phase clouds, if emitted into the atmosphere. In two 3-4-week experiments, we placed 30,000- and 1000-year-old ice-rich silt permafrost in a tank with artificial freshwater and monitored aerosol INP emissions and water INP concentrations as the water's salinity and temperature were varied to mimic aging and transport of thawed material into seawater. We also tracked aerosol and water INP composition through thermal treatments and peroxide digestions and bacterial community composition with DNA sequencing. We found that the older permafrost produced the highest and most stable airborne INP concentrations, with levels comparable to desert dust when normalized to particle surface area. Both samples showed that the transfer of INPs to air persisted during simulated transport to the ocean, demonstrating a potential to influence the Arctic INP budget. This suggests an urgent need for quantifying permafrost INP sources and airborne emission mechanisms in climate models.

Dissecting giant hailstones: A glimpse into the troposphere with its diverse bacterial communities and fibrous microplastics

The formation of giant hailstones is a rare weather event that has devastating consequences in inhabited areas. This hazard has been occurring more frequently and with greater size of hailstones in recent years, and thus needs to be better understood. While the generally accepted mechanism is thought to be a process similar to the formation of smaller hailstones but with exceptional duration and stronger updrafts, recent evidence suggests that biotic and abiotic factors also influence the growth of these unusually large ice chunks. In this study, we improved these findings by determining the distribution of a wide variety of these factors throughout the hail volume and expanding the search to include new particles that are common in the environment and are of anthropogenic origin. We melted the concentric layers of several giant hailstones that fell to the ground over a small region in Slovenia in 2019. The samples, up to 13 cm in diameter, were analyzed for biotic and abiotic constituents that could have influenced their formation. Using 16S rRNA-based metagenomics approaches, we identified a highly diverse bacterial community, and by using scanning electron microscopy and Raman spectroscopy, we found natural and synthetic fibers concentrated in the cores of the giant hailstones. For the first time, we were able to detect the existence of microplastic fibers in giant hailstones and determine the changes in the distribution of sand within the volume of the samples. Our results suggest that changes in the composition of hail layers and their great diversity are important factors that should be considered in research. It also appears that anthropogenic microfiber pollutants were a significant factor in the formation of the giant hailstones analyzed in this study.

Aerobiology over the Southern Ocean - Implications for bacterial colonization of Antarctica

Parts of the Antarctic are experiencing dramatic ecosystem change due to rapid and record warming, which may weaken biogeographic boundaries and modify dispersal barriers, increasing the risk of biological invasions. In this study, we collected air samples from 100 locations around the Southern Ocean to analyze bacterial biodiversity in the circumpolar air around the Antarctic continent, as understanding dispersal processes is paramount to assessing the risks of microbiological invasions. We also compared the Southern Ocean air bacterial biodiversity to non-polar ecosystems to identify the potential origin of these Southern Ocean air microorganisms. The bacterial diversity in the air had both local and global origins and presented low richness overall but high heterogeneity, compatible with a scenario whereby samples are composed of a suite of different species in very low relative abundances. Only 4% of Amplicon Sequence Variants (ASVs) were identified in both polar and non-polar air masses, suggesting that the polar air mass over the Southern Ocean can act as a selective dispersal filter. Furthermore, both microbial diversity and community structure both varied significantly with meteorological data, suggesting that regional bacterial biodiversity could be sensitive to changes in weather conditions, potentially altering the existing pattern of microbial deposition in the Antarctic.

Microbial ecology of the Southern Ocean

The Southern Ocean (SO) distributes climate signals and nutrients worldwide, playing a pivotal role in global carbon sequestration. Microbial communities are essential mediators of primary productivity and carbon sequestration, yet we lack a comprehensive understanding of microbial diversity and functionality in the SO. Here, we examine contemporary studies in this unique polar system, focusing on prokaryotic communities and their relationships with other trophic levels (i.e. phytoplankton and viruses). Strong seasonal variations and the characteristic features of this ocean are directly linked to community composition and ecosystem functions. Specifically, we discuss characteristics of SO microbial communities and emphasise differences from the Arctic Ocean microbiome. We highlight the importance of abundant bacteria in recycling photosynthetically derived organic matter. These heterotrophs appear to control carbon flux to higher trophic levels when light and iron availability favour primary production in spring and summer. Conversely, during winter, evidence suggests that chemolithoautotrophs contribute to prokaryotic production in Antarctic waters. We conclude by reviewing the effects of climate change on marine microbiota in the SO.

Black carbon footprint of human presence in Antarctica

Black carbon (BC) from fossil fuel and biomass combustion darkens the snow and makes it melt sooner. The BC footprint of research activities and tourism in Antarctica has likely increased as human presence in the continent has surged in recent decades. Here, we report on measurements of the BC concentration in snow samples from 28 sites across a transect of about 2,000 km from the northern tip of Antarctica (62°S) to the southern Ellsworth Mountains (79°S). Our surveys show that BC content in snow surrounding research facilities and popular shore tourist-landing sites is considerably above background levels measured elsewhere in the continent. The resulting radiative forcing is accelerating snow melting and shrinking the snowpack on BC-impacted areas on the Antarctic Peninsula and associated archipelagos by up to 23 mm water equivalent (w.e.) every summer.

Earth, Wind, Fire, and Pollution: Aerosol Nutrient Sources and Impacts on Ocean Biogeochemistry

A key Earth system science question is the role of atmospheric deposition in supplying vital nutrients to the phytoplankton that form the base of marine food webs. Industrial and vehicular pollution, wildfires, volcanoes, biogenic debris, and desert dust all carry nutrients within their plumes throughout the globe. In remote ocean ecosystems, aerosol deposition represents an essential new source of nutrients for primary production. The large spatiotemporal variability in aerosols from myriad sources combined with the differential responses of marine biota to changing fluxes makes it crucially important to understand where, when, and how much nutrients from the atmosphere enter marine ecosystems. This review brings together existing literature, experimental evidence of impacts, and new atmospheric nutrient observations that can be compared with atmospheric and ocean biogeochemistry modeling. We evaluate the contribution and spatiotemporal variability of nutrient-bearing aerosols from desert dust, wildfire, volcanic, and anthropogenic sources, including the organic component, deposition fluxes, and oceanic impacts.

OUP accepted manuscript

The atmosphere connects habitats across multiple spatial scales via airborne dispersal of microbial cells, propagules and biomolecules. Atmospheric microorganisms have been implicated in a variety of biochemical and biophysical transformations. Here, we review ecological aspects of airborne microorganisms with respect to their dispersal, activity and contribution to climatic processes. Latest studies utilizing metagenomic approaches demonstrate that airborne microbial communities exhibit pronounced biogeography, driven by a combination of biotic and abiotic factors. We quantify distributions and fluxes of microbial cells between surface habitats and the atmosphere and place special emphasis on long-range pathogen dispersal. Recent advances have established that these processes may be relevant for macroecological outcomes in terrestrial and marine habitats. We evaluate the potential biological transformation of atmospheric volatile organic compounds and other substrates by airborne microorganisms and discuss clouds as hotspots of microbial metabolic activity in the atmosphere. Furthermore, we emphasize the role of microorganisms as ice nucleating particles and their relevance for the water cycle via formation of clouds and precipitation. Finally, potential impacts of anthropogenic forcing on the natural atmospheric microbiota via emission of particulate matter, greenhouse gases and microorganisms are discussed.

The decay of airborne bacteria and fungi in a constant temperature and humidity test chamber

Despite substantial research to profile the microbial characteristics in the atmosphere, the changing metabolism underpinning microbial successional dynamics remains ambiguous. Herein, we applied qPCR, high-throughput sequencing of the genes encoding 16S and ITS rRNA to render the bacterial/fungal dynamics of ambient PM_2.5 filters maintained at constant conditions of temperature (20 ± 2 °C) and humidity (50 ± 5%). The incubation experiments which lasted for 50 days aim to simulate a metabolic process of microbe in two types PM_2.5 (polluted and non-polluted). The results show that microbial community species in polluted PM_2.5 had faster decay rates, more bacterial diversity and less fungal community compared to the non-polluted ones. For bacteria, the proportion of anaerobic species is higher than aerobic ones, and their performance of contain mobile elements, form-biofilms, and pathogenic risks declined rapidly as times went by. Whereas for fungi, saprotroph species occupied about 70% of the population, resulting in a specified peak of abundance due to the adequacy nutrients supplied by the apoptosis cells. Combining the classified microbial species, we found stable community structure and the volatile ones related to the various metabolic survival strategies during different time. Without the input of peripheral environment, the health risks of airborne microbe descend to a healthy level after 20 days, implying their biologic effectiveness was about 20 days no matter the air is polluted or not. This study provided new insights into the different metabolic survival of airborne microorganisms in ideal and stable conditions.

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.

Local meteorological conditions, shape and desiccation influence dispersal capabilities for airborne microorganisms

The atmosphere plays an important role in the dispersal of microorganisms, as well as in the connectivity of most of the planet's ecosystems. In recent decades, interest in microbial diversity and dispersion in the atmosphere has increased due to its importance in various fields. However, there are few studies on the abundance of airborne microorganisms and the factors, such as meteorology, that affect their distribution. Likewise, the physical-mathematical models attempting to reproduce their possible origins also require integrating some biological features. We collected airborne microorganisms under different meteorological conditions at a sampling station over a 12-day period to expand the knowledge about abundance of airborne microorganisms, their relationship with atmospheric conditions and their possible origins with a biological perspective. Total abundance and size distribution of microorganisms were measured in all samples using epifluorescence techniques. Their possible origins were estimated using refined mathematical simulation models of the air masses back-trajectories considering dry deposition. Our results showed microbial abundance values similar to those found in temperate regions over land surface. In our contribution we report a clear relationship between the abundance and, considered as a whole, local meteorological conditions. Despite most of the captured particles were small spherical microorganisms (diameter < 20 μm), large filamentous microorganisms, surprisingly up to 400 μm, were also found. We demonstrate the possibility that these large microorganisms can have their origin at long distances, showing thus probability of remarkable long dispersal, without ruling out a nearby origin, when their equivalent spherical diameter (ESD) and drying capacity are considered.

Sources, Occurrence and Characteristics of Fluorescent Biological Aerosol Particles Measured Over the Pristine Southern Ocean

In this study, we investigate the occurrence of primary biological aerosol particles (PBAP) over all sectors of the Southern Ocean (SO) based on a 90-day data set collected during the Antarctic Circumnavigation Expedition (ACE) in austral summer 2016-2017. Super-micrometer PBAP (1-16 µm diameter) were measured by a wide band integrated bioaerosol sensor (WIBS-4). Low (3σ) and high (9σ) fluorescence thresholds are used to obtain statistics on fluorescent and hyper-fluorescent PBAP, respectively. Our focus is on data obtained over the pristine ocean, that is, more than 200 km away from land. The results indicate that (hyper-)fluorescent PBAP are correlated to atmospheric variables associated with sea spray aerosol (SSA) particles (wind speed, total super-micrometer aerosol number concentration, chloride and sodium concentrations). This suggests that a main source of PBAP over the SO is SSA. The median percentage contribution of fluorescent and hyper-fluorescent PBAP to super-micrometer SSA was 1.6% and 0.13%, respectively. We demonstrate that the fraction of (hyper-)fluorescent PBAP to total super-micrometer particles positively correlates with concentrations of bacteria and several taxa of pythoplankton measured in seawater, indicating that marine biota concentrations modulate the PBAP source flux. We investigate the fluorescent properties of (hyper-)fluorescent PBAP for several events that occurred near land masses. We find that the fluorescence signal characteristics of particles near land is much more variable than over the pristine ocean. We conclude that the source and concentration of fluorescent PBAP over the open ocean is similar across all sampled sectors of the SO.

Overview of biological ice nucleating particles in the atmosphere

Biological particles in the Earth's atmosphere are a distinctive category of ice nucleating particles (INPs) due to their capability of facilitating ice crystal formation in clouds at relatively warm temperatures. Field observations and model simulations have shown that biological INPs affect cloud and precipitation formation and regulate regional or even global climate, although there are considerable uncertainties in modeling and large gaps between observed and model simulated contribution of biological particles to atmospheric INPs. This paper overviews the latest researches about biological INPs in the atmosphere. Firstly, we describe the primary ice nucleation mechanisms, and measurements and model simulations of atmospheric biological INPs. Secondly, we summarize the ice nucleating properties of biological INPs from diverse sources such as soils or dust, vegetation (e.g., leaves and pollen grains), sea spray, and fresh waters, and controlling factors of biological INPs in the atmosphere. Then we review the abundance and distribution of atmospheric biological INPs in diverse ecosystems. Finally, we discuss the open questions in further studies on atmospheric biological INPs, including the requirements for developing novel detection techniques and simulation models, as well as the comprehensive investigation of characteristics and influencing factors of atmospheric biological INPs.