Taxon-specific aerosolization of bacteria and viruses in an experimental ocean-atmosphere mesocosm

Contribution of Large Marine Aerosols in Phytoplankton Dispersal

Sea-spray aerosol (SSA) plays a crucial role in climate processes by influencing radiative forcing, cloud formation, and precipitation. While SSA particles with diameters between 0.1 and 10 μm are commonly studied, larger aerosols (>20 μm) have been observed over terrestrial and oceanic regions but are generally overlooked. Large bioaerosols can be formed by pollen, fungal spores, and cell debris. However, the abundance, dynamics, and composition of large marine aerosols remain poorly understood. This study observed wave and atmospheric conditions driving aerosol production, the resulting SSA abundance, and sizes (up to 90 μm), and collected collocated SSA samples for microscopy analysis during a two-month time period. SSA above 20 μm were frequently observed, containing a diverse range of intact phytoplankton cells, including small flagellates (2 μm), to diatoms, and colonial cells (above 40 μm). The abundance of small flagellates suggests that sea-to-air transfer may be an important, yet overlooked, dispersal mechanism for these groups. To the best of our knowledge, this is the first evidence of direct airborne observation (rather than deposition) of large intact phytoplankton cells. These findings highlight the ubiquity of large marine aerosols and their capacity to carry intact phytoplankton cells.

CyanoHABs and CAPs: assessing community-based monitoring of PM2.5 with regional sources of pollution in rural, northeastern North Carolina

Underserved rural communities in northeastern North Carolina (NC), surrounding the Albemarle Sound, have faced degraded environmental quality from various sources of air and water pollution. However, access to local air quality data is regionally scarce due to a lack of state-run monitoring stations, which has motivated local community science efforts. In January 2022, we co-developed a community-led study to investigate the relationship between fine particulate matter (PM2.5) and sources of regional air pollution, with a specific focus on previously identified emissions from cyanobacterial harmful algal blooms (CyanoHABs). Using low-cost PurpleAir air quality sensors to quantify PM2.5 mass, satellite-derived indicators of CyanoHABs, and other publicly available atmospheric and meteorological data, we assessed environmental drivers of PM2.5 mass in the airshed of the Albemarle Sound estuary during 2022-2023. We found that bias-corrected PurpleAir PM2.5 mass concentrations aligned with composite data from the three nearest federal reference equivalent measurements within 1 μg m-3 on average, and that the temporal variation in PM2.5 was most closely associated with changes in criteria air pollutants. Ultimately, satellite-based indicators of CyanoHABs (Microcystis spp. equivalent cell counts and bloom spatial extent) were not strongly associated with ambient/episodic increases in PurpleAir PM2.5 mass during our study period. For the first time, we provide local PM2.5 measurements to rural communities in northeastern NC with an assessment of environmental drivers of PM2.5 pollution events. Additional compositional analyses of PM2.5 are warranted to further inform respiratory risk assessments for this region of NC. Despite the lack of correlation between CyanoHABs and PM2.5 observed, this work serves to inform future studies that seek to employ widely available and low-cost approaches to monitor both CyanoHAB aerosol emissions and general air quality in rural coastal regions at high spatial and temporal resolutions.

A comprehensive characterisation of natural aerosol sources in the high Arctic during the onset of sea ice melt

The interactions between aerosols and clouds are still one of the largest sources of uncertainty in quantifying anthropogenic radiative forcing. To reduce this uncertainty, we must first determine the baseline natural aerosol loading for different environments. In the pristine and hardly accessible polar regions, the exact nature of local aerosol sources remains poorly understood. It is unclear how oceans, including sea ice, control the aerosol budget, influence cloud formation, and determine the cloud phase. One critical question relates to the abundance and characteristics of biological aerosol particles that are important for the formation and microphysical properties of Arctic mixed-phase clouds. Within this work, we conducted a comprehensive analysis of various potential local sources of natural aerosols in the high Arctic over the pack ice during the ARTofMELT expedition in May-June 2023. Samples of snow, sea ice, seawater, and the sea surface microlayer (SML) were analysed for their microphysical, chemical, and fluorescent properties immediately after collection. Accompanied analyses of ice nucleating properties and biological cell quantification were performed at a later stage. We found that increased biological activity in seawater and the SML during the late Arctic spring led to higher emissions of fluorescent primary biological aerosol particles (fPBAPs) and other highly fluorescent particles (OHFPs, here organic-coated sea salt particles). Surprisingly, the concentrations of ice nucleating particles (INPs) in the corresponding liquid samples did not follow this trend. Gradients in OHFPs, fPBAPs, and black carbon indicated an anthropogenic pollution signal in surface samples especially in snow but also in the top layer of the sea ice core and SML samples. Salinity did not affect the aerosolisation of fPBAPs or sample ice nucleating activity. Compared to seawater, INP and fPBAP concentrations were enriched in sea ice samples. All samples showed distinct differences in their biological, chemical, and physical properties, which can be used in future work for an improved source apportionment of natural Arctic aerosol to reduce uncertainties associated with their representation in models and impacts on Arctic mixed-phase clouds.

Dust storm-driven dispersal of potential pathogens and antibiotic resistance genes in the Eastern Mediterranean

The atmosphere hosts a microbiome that connects distant ecosystems yet remains relatively unexplored. In this study, we tested the hypothesis that dust storms enhance the spread of pathogenic microorganisms and whether these microorganisms carry antibiotic resistance and virulence-related genes in the Eastern Mediterranean. We collected air samples during a seasonal transition period, capturing data from 13 dusty days originating from Middle Eastern sources, including the Saharan Desert, Iraq, Iran, and Saudi Arabia, and 32 clear days, with temperatures ranging from 16.5 to 27.1 °C. Using metagenomic analysis, we identified several facultative pathogens like Klebsiella pneumoniae, Stenotrophomonas maltophilia, and Aspergillus fumigatus, which are linked to human respiratory diseases, and others like Zymoseptoria tritici, Fusarium poae, and Puccinia striiformis, which are harmful to wheat. The abundance of these pathogens increased during dust storms and with rising temperatures. Although we did not find strong evidence that these species harbored antibiotic resistance or virulence-related genes, which could be linked to their pathogenic potential, dust storms transported up to 125 times more total antibiotic resistance genes, as measured by RPKM abundance, compared to clear conditions. These levels during dust storms far exceeded those found in other ecosystems. While further research is needed to determine whether dust storms and temperature variations pose an immediate threat to public health and the environment, our findings underscore the importance of continuous monitoring of atmospheric microbiomes. This surveillance is crucial for assessing potential risks to human health and ecosystem stability, particularly in the face of accelerating global climate change.

Selective transmission of airborne bacterial communities from the ocean to the atmosphere over the Northern Pacific Ocean

This study simultaneously measured the taxonomic diversity of bacterial communities in both seawater and PM2.5 aerosol samples collected from the Northern Pacific Ocean during a cruise covering 7724 km between 37°N 126°E and 58°N 179°E. The relative abundance of Proteobacteria, Cyanobacteria, and Firmicutes were found to be more prevalent in aerosol samples (39 ± 16 %, 5.1 ± 1.9 %, and 3.2 ± 1.7 %, respectively) than in seawater samples (26 ± 9 %, 3.8 ± 1.7 %, and 0.02 ± 0.09 %, respectively). The preferential aerosolization of bacterial communities such as Proteobacteria and Firmicutes was likely to be accompanied by a terrestrial origin and high hydrophobicity. Cyanobacteria could undergo increased aerosolization, possibly because of their smaller size in the significantly higher salinity open ocean (32.8 ± 0.14 PSU) compared to those in lower salinity coastal areas (31.3 ± 1.4 PSU). The results of this study indicated that bacterial properties substantially affect their transfer from the ocean to the atmosphere, possibly influencing climate change and public health.

Antibiotic resistance and resistome risks of inhalable bioaerosols at aeration tank of a full-scale wastewater treatment plant

Antibiotic resistome could be aerosolized under wastewater aeration processes, however, their seasonal variation, mobility, hosts, aerosolization behavior, and risk, are largely unknown. Herein, the antibiotic resistant pollution associated with fine particulate matter (PM2.5) from the actual aeration tank (AerT), was analyzed using metagenomic assembly. The antibiotic resistance of AerT-PM2.5 was characterized by significant seasonality. Antibiotic resistance genes (ARGs) in AerT-PM2.5, exhibited higher enrichment and mobility and were harbored more by pathogens than those in upwind-PM2.5, regardless of sampling season. Mobile ARGs were mainly flanked by transposase. Totally, 18 pathogenic antibiotic-resistant bacteria (PARB) carried more than one ARG, including 9 PARB with multiple ARG types. Although wastewater exerted a dominant source contribution for the airborne ARGs (47.31-55.56 %) and PARB (46.18-64.32 %), aeration endowed differential aerosolization capacity for various ARGs and PARB from wastewater. Airborne antibiotic resistome was mainly determined by bacterial community and indirectly influenced by meteorological conditions (i.e., relative humidity). Higher PM2.5-borne resistome risk was observed in AerT than upwind, and the most serious resistome risk of AerT-PM2.5 was found in winter. This study emphasizes the importance of wastewater aeration processes in emission of airborne antibiotic resistome and offers referenced information for mitigating air pollution in wastewater treatment plants.

The dynamics and assembly patterns of airborne pathogen communities in the municipal food waste treatment system and its risk implications

While municipal solid waste (MSW) provides an ideal habitat for pathogen propagation, the dynamics and assembly of airborne pathogen communities in these environments remain largely unknown. Here, we combined amplicon and metagenomics with spatiotemporal sampling to study inhalable particulate matter-carried potential pathogenic bacteria at full-scale food waste treatment plants (FWTPs), alongside comparisons to urban air in the area. The results showed that pathogenic bacteria constituted a notable portion (64.5 % ± 20.6 %, n = 75) of the total bacterial communities in FWTPs-impacted air, with species and relative abundance 2-4 times higher than that of urban air, and contributed over 50 % of pathogens to the outdoor air. Airborne pathogen community structures were highly shaped by sampling sites (i.e. treatment units), but conserved across seasons (summer vs. winter) and particle sizes (PM2.5vs. PM10). Notably, Acinetobacter johnsonii-dominated pathogens (i.e. biofilm-related species) presented high levels of aerosolization and consistently occupied the upper-representative niches in all neutral models, highlighting their persistent exposure risk. Furthermore, pathogen community assembly was strongly driven by stochastic processes (58.8 %-96.8 %), while environmental variables explained only limited variations (3.4 %-28.7 %). In particular, the relative importance of stochastic processes clearly increased along an outdoor-to-indoor gradient (84.9 %-96.5 % vs. 71.3 %-76 %), which might be related to indoor anthropogenic activities that weaken microbial network stability and environmental filtering effects. This work enhances our knowledge of the dynamic behaviors and risk of airborne pathogen communities in MSW disposal and underscores the role of FWTPs in disseminating airborne pathogens.

Midseason drying increases soil dissolved organic carbon and rice yield via soil cbbL bacteria

An understanding of how irrigation regimes affect autotrophic microorganisms is essential, as this has direct implications for the soil organic carbon (SOC) content, rice yield and the sustainable agricultural practices. Here, the effects of three irrigation regimes on autotrophic microorganisms, soil active organic carbon fractions, and rice yield were explored. The irrigation regimes were: 1) rainfed (RF), 2) midseason drying (MD), and 3) continuous flooding (CF). The SOC, microbial biomass carbon (MBC), MBC/SOC ratio, dissolved organic carbon (DOC), DOC/SOC ratio, the cbbL (the cbbL gene encodes the large subunit of ribulose-1, 5-bisphosphate carboxylase) bacterial alpha diversity and community composition, and rice yield were assessed under each regime. The highest MBC content (646 mg kg-1 in the early season and 1007 mg kg-1 in the late season) and MBC/SOC ratio (3% in the early season and 5% in the late season) were observed under the RF regime. The soil DOC content and DOC/SOC ratio were the highest in the MD regime, followed by the CF regime. The lowest values were observed under the RF regime, with greater differences observed in the late season. Soil cbbL bacterial alpha diversity was the highest in the MD regime and the lowest in the CF regime. The irrigation regimes altered the composition of the cbbL microbial community, with Burkholderiales and Corynebacteriales exhibiting the highest relative abundances in the MD regime. In the late season, the rice yield in the MD regime was 53% and 14% greater than the RF and CF regimes, respectively. A partial-least-squares path model showed that the optimal regime (MD regime) increased the alpha diversity of the soil cbbL bacteria and the relative abundances of several probiotic microorganisms. This, in turn, increased soil DOC content and its contribution to SOC, eventually increasing the rice yield. These findings clarified the effects of different water management strategies on autotrophic microorganisms, organic carbon, and rice yield, providing guidance for implementing suitable water management practices to enhance soil fertility and rice yield.

Airborne antibiotic resistome from sludge dewatering systems: Mobility, pathogen accessibility, cross-media migration propensity, impacting factors, and risks

Bioaerosol contamination was considered as a potential health threat in sludge dewatering systems (SDSs), while emission and risk of airborne antibiotic resistome remain largely unclear. Herein, seasonal investigations of fine particulate matter (PM2.5) were conducted using metagenomics-based methods within and around different SDSs, together with an analysis of sewage sludge. Featured with evident seasonality, antibiotic resistance genes (ARGs) in SDS-PM2.5 also possessed greater accumulation, transfer, and pathogen accessibility than those in ambient air PM2.5. Mobile ARGs in SDS-PM2.5 mainly encoded resistance to tetracycline, and most were flanked by integrase. Some pathogenic antibiotic resistant bacteria (PARB), including Enterobacter asburiae, Escherichia coli, Enterococcus faecium, and Staphylococcus aureus, also carried mobile genetic elements in SDS-PM2.5. Dewatering behavior actuated > 50.56% of ARG subtypes and > 42.86% of PARB in sewage sludge to aerosolize into air. Relative humidity, temperature, and PM2.5 concentration collectively drove the evolution of bacterial community and indirectly promoted the antibiotic resistance of SDS-PM2.5. SDS-PM2.5 posed more serious resistome risks than sewage sludge and ambient air PM2.5, and the highest levels were discovered in winter. These findings underline the role of dewatering behavior in facilitating resistome's aerosolization, and the need to mitigate this potential air pollution.

Surface microlayer-mediated virome dissemination in the Central Arctic

BACKGROUND

Aquatic viruses act as key players in shaping microbial communities. In polar environments, they face significant challenges such as limited host availability and harsh conditions. However, due to the restricted accessibility of these ecosystems, our understanding of viral diversity, abundance, adaptations, and host interactions remains limited.

RESULTS

To fill this knowledge gap, we studied viruses from atmosphere-close aquatic ecosystems in the Central Arctic and Northern Greenland. Aquatic samples for virus-host analysis were collected from ~60 cm depth and the submillimeter surface microlayer (SML) during the Synoptic Arctic Survey 2021 on icebreaker Oden in the Arctic summer. Water was sampled from a melt pond and open water before undergoing size-fractioned filtration, followed by genome-resolved metagenomic and cultivation investigations. The prokaryotic diversity in the melt pond was considerably lower compared to that of open water. The melt pond was dominated by a Flavobacterium sp. and Aquiluna sp., the latter having a relatively small genome size of 1.2 Mb and the metabolic potential to generate ATP using the phosphate acetyltransferase-acetate kinase pathway. Viral diversity on the host fraction (0.2-5 µm) of the melt pond was strikingly limited compared to that of open water. From the 1154 viral operational taxonomic units (vOTUs), of which two-thirds were predicted bacteriophages, 17.2% encoded for auxiliary metabolic genes (AMGs) with metabolic functions. Some AMGs like glycerol-3-phosphate cytidylyltransferase and ice-binding like proteins might serve to provide cryoprotection for the host. Prophages were often associated with SML genomes, and two active prophages of new viral genera from the Arctic SML strain Leeuwenhoekiella aequorea Arc30 were induced. We found evidence that vOTU abundance in the SML compared to that of ~60 cm depth was more positively correlated with the distribution of a vOTU across five different Arctic stations.

CONCLUSIONS

The results indicate that viruses employ elaborate strategies to endure in extreme, host-limited environments. Moreover, our observations suggest that the immediate air-sea interface serves as a platform for viral distribution in the Central Arctic. Video Abstract.

Emission Characteristics of Aerosols Generated during the Micro-Nano Bubble Aeration Process in Wastewater

Micro-nano bubble (MNB) aeration is an emerging technology that considerably enhances the aeration efficiency of wastewater. This study evaluates, for the first time, aerosolization at the water-air interface during MNB aeration. Our results show that the concentration of culturable mixed microorganisms (i.e., bacteria, fungi, and intestinal bacteria) in the in situ MNB generation (MNBs-G) phase is 2170 CFU/m3, 1.38 and 1.58-fold higher than those in medium-bubble aeration (MBA; 1568 CFU/m3) and small-bubble aeration (SBA; 1376 CFU/m3) aerosols, respectively. Conversely, the concentration of culturable mixed microorganisms in the MNB persistent dissolved oxygen (MNBs-O) phase is only 914 CFU/m3. Microbiological analysis shows a lower abundance of bacterial pathogens in MNBs-G (34.12%) and MNBs-O (34.02%) phases than in MBA (39.63%) and SBA (38.87%) aerosols. Acinetobacter is prevalent in MNBs-G (14.76%) and MNBs-O (8.22%) aerosols, whereas Bacillus and Arcobacter are prevalent in MBA (23.96%) and SBA (6.92%) aerosols, respectively. The total concentrations of chemicals [i.e., total organic carbon, water-soluble ions, and metal(loid)s] in aerosols formed via MNB aeration (205.98-373.74 μg/m3) are lower than those in MBA and SBA (398.69-594.92 μg/m3). Compared to MBA and SBA, the MNBs-G phase exhibits higher emissions of 12 elements in aerosols (i.e., NO3-, NO2-, Ca2+, Na+, K+, Mg2+, Zn, Cd, Fe, Mn, As, and Cr), whereas the MNBs-O phase generally shows lower emissions. These findings highlight the potential of optimized MNB aeration technology in considerably mitigating aerosol emissions and thereby advancing environmental sustainability in wastewater treatment.

Interfacial Enrichment of Lauric Acid Assisted by Long-Chain Fatty Acids, Acidity and Salinity at Sea Spray Aerosol Surfaces

Surfactant monolayers at sea spray aerosol (SSA) surfaces regulate various atmospheric processes including gas transfer, cloud interactions, and radiative properties. Most experimental studies of SSA employ a simplified surfactant mixture of long-chain fatty acids (LCFAs) as a proxy for the sea surface microlayer or SSA surface. However, medium-chain fatty acids (MCFAs) make up nearly 30% of the FA fraction in nascent SSA. Given that LCFA monolayers are easily disrupted upon the introduction of chemical heterogeneity (such as mixed chain lengths), simple FA proxies are unlikely to represent realistic SSA interfaces. Integrating experimental and computational techniques, we characterize the impact that partially soluble MCFAs have on the properties of atmospherically relevant LCFA mixtures. We explore the extent to which the MCFA lauric acid (LA) is surface stabilized by varying acidity, salinity, and monolayer composition. We also discuss the impacts of pH on LCFA-assisted LA retention, where the presence of LCFAs may shift the surface-adsorption equilibria of laurate─the conjugate base─toward higher surface activities. Molecular dynamic simulations suggest a mechanism for the enhanced surface retention of laurate. We conclude that increased FA heterogeneity at SSA surfaces promotes surface activity of soluble FA species, altering monolayer phase behavior and impacting climate-relevant atmospheric processes.

Unveiling the microbial realm with VEBA 2.0: a modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible software suite that bridges the gap between genomics and biotechnological solutions.

The impact of bioaerosol trajectories on microbial community assembly and physicochemical dynamics in the atmosphere

This study explored the assembly mechanisms and physicochemical dynamics of microbial communities within atmospheric bioaerosols, focusing on the influence of different aerial trajectories. Over two years, samples near Seoul were classified into 'North', 'Southwest', and 'Others' categories based on their aerial trajectories. Physicochemical analysis of the PM2.5 particles revealed distinct ion compositions for each cluster, reflecting diverse environmental influences. Microbial community analysis revealed that shared dominant bacterial phyla were present in all clusters. However, distinct taxonomic profiles and biomarkers were also evident, such as coastal bacteria in the 'Southwest' cluster correlating with wind speed, and arid soil-originated bacteria in the 'North' cluster correlating with cations. These findings demonstrate that biomarkers in each cluster are representative of the distinct environments associated with their aerial trajectories. Notably, cluster 'Southwest' the highest microbial diversity and a strong alignment with the neutral community model, suggesting a large influence of passive dispersal from marine environments. Contrarily, 'North' and 'Others' were more influenced by niche-dependent factors. This study highlights the complex interplay between environmental factors and microbial dynamics in bioaerosols and provides important insights for environmental monitoring and public health risk assessment.

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.

Unveiling the Microbial Realm with VEBA 2.0: A modular bioinformatics suite for end-to-end genome-resolved prokaryotic, (micro)eukaryotic, and viral multi-omics from either short- or long-read sequencing

The microbiome is a complex community of microorganisms, encompassing prokaryotic (bacterial and archaeal), eukaryotic, and viral entities. This microbial ensemble plays a pivotal role in influencing the health and productivity of diverse ecosystems while shaping the web of life. However, many software suites developed to study microbiomes analyze only the prokaryotic community and provide limited to no support for viruses and microeukaryotes. Previously, we introduced the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite to address this critical gap in microbiome research by extending genome-resolved analysis beyond prokaryotes to encompass the understudied realms of eukaryotes and viruses. Here we present VEBA 2.0 with key updates including a comprehensive clustered microeukaryotic protein database, rapid genome/protein-level clustering, bioprospecting, non-coding/organelle gene modeling, genome-resolved taxonomic/pathway profiling, long-read support, and containerization. We demonstrate VEBA's versatile application through the analysis of diverse case studies including marine water, Siberian permafrost, and white-tailed deer lung tissues with the latter showcasing how to identify integrated viruses. VEBA represents a crucial advancement in microbiome research, offering a powerful and accessible platform that bridges the gap between genomics and biotechnological solutions.

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.

Impact of airborne algicidal bacteria on marine phytoplankton blooms

Ocean microbes are involved in global processes such as nutrient and carbon cycling. Recent studies indicated diverse modes of algal-bacterial interactions, including mutualism and pathogenicity, which have a substantial impact on ecology and oceanic carbon sequestration, and hence, on climate. However, the airborne dispersal and pathogenicity of bacteria in the marine ecosystem remained elusive. Here, we isolated an airborne algicidal bacterium, Roseovarius nubinhibens, emitted to the atmosphere as primary marine aerosol (referred also as sea spray aerosols) and collected above a coccolithophore bloom in the North Atlantic Ocean. The aerosolized bacteria retained infective properties and induced lysis of Gephyrocapsa huxleyi cultures.This suggests that the transport of marine bacteria through the atmosphere can effectively spread infection agents over vast oceanic regions, highlighting its significance in regulating the cell fate in algal blooms.

Bubble manipulates the release of viral aerosols in aeration

Bubble bursting is a common phenomenon in many industrial and natural processes, plays an important role in mediating mass transfer across the water-air interface. But the interplay between bubbles and pathogens remains unclear and the mechanisms of virus aerosolization by the bubble properties have not been well studied. The main objective of this study was to evaluate the water-to-air transfer of viruses by bubbles of different sizes. Unlike the dominant view of smaller bubbles less bioaerosols, it was found that the smaller bubbles could generate significantly more viral aerosols regardless of the virus species (Phi6, MS2, PhiX174, and T7), when the Sauter mean bubble diameters were between 0.56 and 1.65 mm under constant aeration flow rate. The mechanism studies denied the possibilities of more aerosols or better dispersion of viruses in the aerosols generated by the smaller bubbles. However, deeper bubbling could transfer more viruses to the air for MS2, PhiX174, and T7. Their concentrations in aerosols were linearly related to the bubbling depth for these non-enveloped viruses, which demonstrates the bubble-scavenging effect as a main mechanism except for the enveloped virus Phi6. Whereas, unlike these three non-enveloped viruses, Phi6 could survive relatively better in the aerosols generated from the smaller bubbles, though the enhancement of aerosolization by the smaller bubbles was much larger than the improvement of survival. Other mechanisms still remain unknown for this enveloped virus. This study suggests that the attempt of decreasing the bubble size in aeration tank of the wastewater treatment plant might significantly increase the solubility of oxygen as well as the risk of viral aerosols.

Pathogenic Bacteria Are the Primary Determinants Shaping PM2.5-Borne Resistomes in the Municipal Food Waste Treatment System

Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM2.5-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM2.5 (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM2.5 (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; p < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM2.5 exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM2.5 (1.46 ± 0.21 copies/16S rRNA gene, N = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that Acinetobacter johnsonii-dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO42-) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM2.5-borne resistant pathogens was about 5-11 times higher than those in urban PM2.5, and could be more severe than hospital PM2.5 in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.

Marine viruses disperse bidirectionally along the natural water cycle

Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.

Microbiome Interconnectedness throughout Environments with Major Consequences for Healthy People and a Healthy Planet

Microbiomes have highly important roles for ecosystem functioning and carry out key functions that support planetary health, including nutrient cycling, climate regulation, and water filtration. Microbiomes are also intimately associated with complex multicellular organisms such as humans, other animals, plants, and insects and perform crucial roles for the health of their hosts. Although we are starting to understand that microbiomes in different systems are interconnected, there is still a poor understanding of microbiome transfer and connectivity. In this review we show how microbiomes are connected within and transferred between different habitats and discuss the functional consequences of these connections. Microbiome transfer occurs between and within abiotic (e.g., air, soil, and water) and biotic environments, and can either be mediated through different vectors (e.g., insects or food) or direct interactions. Such transfer processes may also include the transmission of pathogens or antibiotic resistance genes. However, here, we highlight the fact that microbiome transmission can have positive effects on planetary and human health, where transmitted microorganisms potentially providing novel functions may be important for the adaptation of ecosystems.

Evaporation-induced hydrodynamics control plasmid transfer during surface-associated microbial growth

Droplet evaporation is a general process in unsaturated environments that results in micro-scale hydrodynamic flows which in turn determine the spatial distributions of microbial cells across surfaces. These spatial distributions can have significant effects on the development and functioning of surface-associated microbial communities, with consequences for important processes such as the spread of plasmids. Here, we experimentally quantified how evaporation-induced hydrodynamic processes modulate the initial deposition patterns of microbial cells (via the coffee ring effect and Marangoni convection) and how these patterns control the spread of an antibiotic resistance-encoding plasmid during surface-associated growth. We found that plasmid spread is a function of the initial density of cells deposited along the droplet periphery, which is a manifestation of the coffee ring effect. Using an individual-based model, we systematically linked how the different initial cell deposition patterns caused by the relative strengths of the coffee ring effect and Marangoni convection determine the extent of plasmid transfer during surface-associated growth. Our study demonstrates that evaporation-induced hydrodynamic processes that are common in nature can alter crucial ecological properties of surface-associated microbial communities and control the proliferation of plasmids, with consequences on the spread of antibiotic resistance and other plasmid-encoded traits.

Effect of odor treatment systems on bioaerosol microbial concentration and diversity from wastewater treatment plants

Biofiltration, activated carbon and chemical scrubbing are technologies used for odor control in wastewater treatment plants. These systems may also influence the airborne microbial load in treated air. The study objectives were to 1) evaluate the capacity of three odor control system technologies to reduce the airborne concentration of total bacteria, Legionella, L. pneumophila, non-tuberculous mycobacteria (NTM) and Cladosporium in winter and summer seasons and 2) to describe the microbial ecology of the biofiltration system and evaluate its impact on treated air microbial diversity. A reduction of the total bacterial concentration up to 25 times was observed after odor treatment. Quantification by qPCR revealed the presence of Legionella spp. in all air samples ranging between 26 and 1140 GC/m³, while L. pneumophila was not detected except for three samples below the limit of quantification. A significant increase of up to 25-fold of Legionella spp. was noticed at the outlet of two of the three treatment systems. NTM were ubiquitously detected before air treatment (up to 2500 GC/m³) and were significantly reduced by all 3 systems (up to 13-fold). Cladosporium was measured at low concentrations for each system (< 190 GC/m³), with 68 % of the air samples below the limit of detection. Biodiversity results revealed that biofiltration system is an active process that adapts to air pollutants over time. Legionella spp. were detected in significant abundance in the air once treated in winter (up to 27 %). Nevertheless, the abundance of protozoan hosts is low and does not explain the multiplication of Legionella spp. The season remains the most influential factor shaping biodiversity. In summer only, air biofiltration caused a significant enrichment of the biodiversity. Although odor control technologies are not designed for bacterial mitigation, findings from this study suggest their potential to reduce the abundance of some genera harboring pathogenic species.

The aeromicrobiome: the selective and dynamic outer-layer of the Earth's microbiome

The atmosphere is an integral component of the Earth's microbiome. Abundance, viability, and diversity of microorganisms circulating in the air are determined by various factors including environmental physical variables and intrinsic and biological properties of microbes, all ranging over large scales. The aeromicrobiome is thus poorly understood and difficult to predict due to the high heterogeneity of the airborne microorganisms and their properties, spatially and temporally. The atmosphere acts as a highly selective dispersion means on large scales for microbial cells, exposing them to a multitude of physical and chemical atmospheric processes. We provide here a brief critical review of the current knowledge and propose future research directions aiming at improving our comprehension of the atmosphere as a biome.

Micro- and nanoplastics transfer from seawater to the atmosphere through aerosolization under controlled laboratory conditions

Sea spray has been suggested to enable the transfer of micro- and nanoplastics (MNPs) from the ocean to the atmosphere, but only a few studies support the role of sea spray aerosols (SSAs) as a source of airborne particles. We demonstrated that MNPs are aerosolized during wave action, via SSAs, under controlled laboratory conditions. We used a mini-Marine-Aerosol-Reference-Tank (miniMART), a device that mimics naturally occurring physical mechanisms producing SSAs, and assessed the aerosolization of fluorescent polystyrene beads (0.5-10 μm), in artificial seawater. The SSAs contained up to 18,809 particles/mL of aerosols for 0.5 μm beads, with an enrichment factor of 19-fold, and 1977 particles/mL of aerosols for 10 μm beads with a 2-fold enrichment factor. Our study demonstrates that the use of the miniMART is essential to assess MNPs aerosolization in a standardized way, supporting the hypothesis which states that MNPs in the surface of the ocean may be transferred to the atmosphere.

Virus infection of phytoplankton increases average molar mass and reduces hygroscopicity of aerosolized organic matter

Viral infection of phytoplankton is a pervasive mechanism of cell death and bloom termination, which leads to the production of dissolved and colloidal organic matter that can be aerosolized into the atmosphere. Earth-observing satellites can track the growth and death of phytoplankton blooms on weekly time scales but the impact of viral infection on the cloud forming potential of associated aerosols is largely unknown. Here, we determine the influence of viral-derived organic matter, purified viruses, and marine hydrogels on the cloud condensation nuclei activity of their aerosolized solutions, compared to organic exudates from healthy phytoplankton. Dissolved organic material derived from exponentially growing and infected cells of well-characterized eukaryotic phytoplankton host-virus systems, including viruses from diatoms, coccolithophores and chlorophytes, was concentrated, desalted, and nebulized to form aerosol particles composed of primarily of organic matter. Aerosols from infected phytoplankton cultures resulted in an increase in critical activation diameter and average molar mass in three out of five combinations evaluated, along with a decrease in organic kappa (hygroscopicity) compared to healthy cultures and seawater controls. The infected samples also displayed evidence of increased surface tension depression at realistic cloud water vapor supersaturations. Amending the samples with xanthan gum to simulate marine hydrogels increased variability in organic kappa and surface tension in aerosols with high organic to salt ratios. Our findings suggest that the pulses of increased dissolved organic matter associated with viral infection in surface waters may increase the molar mass of dissolved organic compounds relative to surface waters occupied by healthy phytoplankton or low phytoplankton biomass.

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.

Bacterial and Chemical Evidence of Coastal Water Pollution from the Tijuana River in Sea Spray Aerosol

Roughly half of the human population lives near the coast, and coastal water pollution (CWP) is widespread. Coastal waters along Tijuana, Mexico, and Imperial Beach (IB), USA, are frequently polluted by millions of gallons of untreated sewage and stormwater runoff. Entering coastal waters causes over 100 million global annual illnesses, but CWP has the potential to reach many more people on land via transfer in sea spray aerosol (SSA). Using 16S rRNA gene amplicon sequencing, we found sewage-associated bacteria in the polluted Tijuana River flowing into coastal waters and returning to land in marine aerosol. Tentative chemical identification from non-targeted tandem mass spectrometry identified anthropogenic compounds as chemical indicators of aerosolized CWP, but they were ubiquitous and present at highest concentrations in continental aerosol. Bacteria were better tracers of airborne CWP, and 40 tracer bacteria comprised up to 76% of the bacteria community in IB air. These findings confirm that CWP transfers in SSA and exposes many people along the coast. Climate change may exacerbate CWP with more extreme storms, and our findings call for minimizing CWP and investigating the health effects of airborne exposure.

Exhaled Breath Aerosol Shedding of Highly Transmissible Versus Prior Severe Acute Respiratory Syndrome Coronavirus 2 Variants

BACKGROUND

Aerosol inhalation is recognized as the dominant mode of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission. Three highly transmissible lineages evolved during the pandemic. One hypothesis to explain increased transmissibility is that natural selection favors variants with higher rates of viral aerosol shedding. However, the extent of aerosol shedding of successive SARS-CoV-2 variants is unknown. We aimed to measure the infectivity and rate of SARS-CoV-2 shedding into exhaled breath aerosol (EBA) by individuals during the Delta and Omicron waves and compared those rates with those of prior SARS-CoV-2 variants from our previously published work.

METHODS

Individuals with coronavirus disease 2019 (COVID-19) (n = 93; 32 vaccinated and 20 boosted) were recruited to give samples, including 30-minute breath samples into a Gesundheit-II EBA sampler. Samples were quantified for viral RNA using reverse-transcription polymerase chain reaction and cultured for virus.

RESULTS

Alpha (n = 4), Delta (n = 3), and Omicron (n = 29) cases shed significantly more viral RNA copies into EBAs than cases infected with ancestral strains and variants not associated with increased transmissibility (n = 57). All Delta and Omicron cases were fully vaccinated and most Omicron cases were boosted. We cultured virus from the EBA of 1 boosted and 3 fully vaccinated cases.

CONCLUSIONS

Alpha, Delta, and Omicron independently evolved high viral aerosol shedding phenotypes, demonstrating convergent evolution. Vaccinated and boosted cases can shed infectious SARS-CoV-2 via EBA. These findings support a dominant role of infectious aerosols in transmission of SARS-CoV-2. Monitoring aerosol shedding from new variants and emerging pathogens can be an important component of future threat assessments and guide interventions to prevent transmission.

Fog-Induced Alteration in Airborne Microbial Community: a Study over Central Indo-Gangetic Plain in India

Fog supports an increase in airborne microbial loading by providing water with nutrients and protecting it from harmful incoming solar radiation. To improve our present understanding of fog-induced alteration in an atmospheric microbial community, a study was conducted during 1 to 14 January 2021 for continuous investigation of airborne bacteria over a rural site, Arthauli (25.95°N, 85.10°E), in central Indo-Gangetic Plain (IGP) in India. An increase of 36% ± 0.4% in airborne bacterial loading was noticed under fog versus prefog conditions, and a decrease of 48% ± 0.4% was noticed under the postfog condition. Airborne bacterial loading had a strong correlation with RH (R2 = 0.56; P < 0.05), temperature (R2 = -0.55, P < 0.05), and wind speed (R2 = -0.52, P < 0.05). Unique types of bacteria, representing about 29% of the whole community, were detected only under foggy conditions, likely by a continuous supply of nutrients and water from a cold, calm, and humid atmosphere. As a result, no significant diurnal variation of bacterial loading was noticed on a foggy day, with a higher daily mean concentration of about (8.4 ± 1.7) × 105 cells · m-3 than that on a typical winter day [(6.3 ± 3.8) × 105 cells · m-3]. A typical winter day experienced about a 60% decrease in bacterial loading in the afternoon in comparison to that in the morning. A 3-day back-trajectory analysis suggests a slow movement of airmass along with the wind blowing from west to central IGP. Fog pauses wind movement, which reduces continuous transportation of urban sources while increasing airborne bacteria from local sources. The abundances of Gp6 (14.8% ± 8.6%), Anaeromyxobacter (7.1% ± 2.8%), and Gp7 (6.8 ± 2.6%) have been observed to increase due to occurrences of fog over central IGP. IMPORTANCE Fog was investigated in the present study as a cause of alteration in the airborne microbial community. Occurrences of fog were responsible for an increase in airborne microbial loading (36%) over central IGP in India due to the easy availability of nutrients and water in the air and dimming of harmful solar radiation. More than 90% of unique bacteria were detected under fog (64%) and postfog (28%) conditions. A few bacteria, like Gp18 (0.5% ± 0.3%), Alicyclobacillus (0.5% ± 0.1%), Sinomonas (0.4% ± 0.2%), and Phenylobacterium (0.4% ± 0.2%), were detected only under foggy conditions. A strong correlation between meteorological parameters and bacterial loading was found in the current research work. The present study provides additional support toward a new direction in interdisciplinary science for the detailed investigations of the effects of meteorological conditions on airborne bacteria and their implications for society.

Assembly and Capsid Expansion Mechanism of Bacteriophage P22 Revealed by High-Resolution Cryo-EM Structures

The formation of many double-stranded DNA viruses, such as herpesviruses and bacteriophages, begins with the scaffolding-protein-mediated assembly of the procapsid. Subsequently, the procapsid undergoes extensive structural rearrangement and expansion to become the mature capsid. Bacteriophage P22 is an established model system used to study virus maturation. Here, we report the cryo-electron microscopy structures of procapsid, empty procapsid, empty mature capsid, and mature capsid of phage P22 at resolutions of 2.6 Å, 3.9 Å, 2.8 Å, and 3.0 Å, respectively. The structure of the procapsid allowed us to build an accurate model of the coat protein gp5 and the C-terminal region of the scaffolding protein gp8. In addition, interactions among the gp5 subunits responsible for procapsid assembly and stabilization were identified. Two C-terminal α-helices of gp8 were observed to interact with the coat protein in the procapsid. The amino acid interactions between gp5 and gp8 in the procapsid were consistent with the results of previous biochemical studies involving mutant proteins. Our structures reveal hydrogen bonds and salt bridges between the gp5 subunits in the procapsid and the conformational changes of the gp5 domains involved in the closure of the local sixfold opening and a thinner capsid shell during capsid maturation.

Lipid Biogeochemistry and Modern Lipidomic Techniques

Lipids are structurally diverse biomolecules that serve multiple roles in cells. As such, they are used as biomarkers in the modern ocean and as paleoproxies to explore the geological past. Here, I review lipid geochemistry, biosynthesis, and compartmentalization; the varied uses of lipids as biomarkers; and the evolution of analytical techniques used to measure and characterize lipids. Advancements in high-resolution accurate-mass mass spectrometry have revolutionized the lipidomic and metabolomic fields, both of which are quickly being integrated into marine meta-omic studies. Lipidomics allows us to analyze tens of thousands of features, providing an open analytical window and the ability to quantify unknown compounds that can be structurally elucidated later. However, lipidome annotation is not a trivial matter and represents one of the biggest challenges for oceanographers, owing in part to the lack of marine lipids in current in silico databases and data repositories. A case study reveals the gaps in our knowledge and open opportunities to answer fundamental questions about molecular-level control of chemical reactions and global-scale patterns in the lipidscape.

Harmful cyanobacterial aerosolization dynamics in the airshed of a eutrophic estuary

In addition to obvious negative effects on water quality in eutrophic aquatic ecosystems, recent work suggests that cyanobacterial harmful algal blooms (CHABs) also impact air quality via emissions carrying cyanobacterial cells and cyanotoxins. However, the environmental controls on CHAB-derived aerosol and its potential public health impacts remain largely unknown. Accordingly, the aims of this study were to 1) investigate the occurrence of microcystins (MC) and putatively toxic cyanobacterial communities in particulate matter ≤ 2.5 μm in diameter (PM_2.5), 2) elucidate environmental conditions promoting their aerosolization, and 3) identify associations between CHABs and PM_2.5 concentrations in the airshed of the Chowan River-Albemarle Sound, an oligohaline, eutrophic estuary in eastern North Carolina, USA. In summer 2020, during peak CHAB season, continuous PM_2.5 samples and interval water samples were collected at two distinctive sites for targeted analyses of cyanobacterial community composition and MC concentration. Supporting air and water quality measurements were made in parallel to contextualize findings and permit statistical analyses of environmental factors driving changes in CHAB-derived aerosol. MC concentrations were low throughout the study, but a CHAB dominated by Dolichospermum occurred from late June to early August. Several aquatic CHAB genera recovered from Chowan River surface water were identified in PM_2.5 during multiple time points, including Anabaena, Aphanizomenon, Dolichospermum, Microcystis, and Pseudanabaena. Cyanobacterial enrichment in PM_2.5 was indistinctive between subspecies, but at one site during the early bloom, we observed the simultaneous enrichment of several cyanobacterial genera in PM_2.5. In association with the CHAB, the median PM_2.5 mass concentration increased to 8.97 μg m^-3 (IQR = 5.15), significantly above the non-bloom background of 5.35 μg m^-3 (IQR = 3.70) (W = 1835, p < 0.001). Results underscore the need for highly resolved temporal measurements to conclusively investigate the role that CHABs play in regional air quality and respiratory health risk.

Bubbles spray aerosols: Certitudes and mysteries

Ocean spray aerosol formed by bubble bursting are at the core of a broad range of atmospheric processes: they are efficient cloud condensation nuclei and carry a variety of chemical, biological, and biomass material from the surface of the ocean to the atmosphere. The origin and composition of these aerosols is sensibly controlled by the detailed fluid mechanics of bubble bursting. This perspective summarizes our present-day knowledge on how bursting bubbles at the surface of a liquid pool contribute to its fragmentation, namely to the formation of droplets stripped from the pool, and associated mechanisms. In particular, we describe bounds and yields for each distinct mechanism, and the way they are sensitive to the bubble production and environmental conditions. We also underline the consequences of each mechanism on some of the many air-sea interactions phenomena identified to date. Attention is specifically payed at delimiting the known from the unknown and the certitudes from the speculations.

VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes

BACKGROUND

With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

RESULTS

In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

CONCLUSIONS

The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.

Airborne microbial community structure and potential pathogen identification across the PM size fractions and seasons in the urban atmosphere

As a vital component of airborne bioaerosols, bacteria and fungi seriously endanger human health as pathogens and allergens. However, comprehensive effects of environmental variables on airborne microbial community structures remain poorly understood across the PM sizes and seasons. We collected atmospheric PM_1.0, PM_2.5, and PM₁₀ samples in Hefei, a typical rapidly-developing city in East China, across three seasons, and performed a comprehensive analysis of airborne microbial community structures using qPCR and high-throughput sequencing. Overall the bacterial and fungal abundances in PM_1.0 were one to two orders of magnitude higher than those in PM_2.5 and PM₁₀ across seasons, but their α-diversity tended to increase from PM_1.0 to PM₁₀. The bacterial gene abundances showed a strong positive correlation (P < 0.05) with atmospheric SO₂ and NO₂ concentrations and air quality index. The bacterial gene abundances were significantly higher (P = 0.001) than fungi, and the bacterial diversity showed stronger seasonality. The PM sizes influenced distribution patterns for airborne microbial communities within the same season. Source-tracking analysis indicated that soils, plants, human and animal feces represented important sources of airborne bacteria with a total relative abundance of more than 60% in summer, but total abundance from the unidentified sources surpassed in fall and winter. Total 10 potential bacterial and 12 potential fungal pathogens were identified at the species level with the highest relative abundances in summer, and their abundances increased with the PM sizes. Together, our results indicated that a complex set of environmental factors, including water-soluble ions in PM, changes in air pollutant levels and meteorological conditions, and shifts in the relative importance of available microbial sources, acted to control the seasonal compositions of microbial communities in the urban atmosphere.

Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica

Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.

Factors controlling the transfer of biogenic organic species from seawater to sea spray aerosol

Ocean waves transfer sea spray aerosol (SSA) to the atmosphere, and these SSA particles can be enriched in organic matter relative to salts compared to seawater ratios. A fundamental understanding of the factors controlling the transfer of biogenic organic matter from the ocean to the atmosphere remains elusive. Field studies that focus on understanding the connection between organic species in seawater and SSA are complicated by the numerous processes and sources affecting the composition of aerosols in the marine environment. Here, an isolated ocean-atmosphere system enables direct measurements of the sea-air transfer of different classes of biogenic organic matter over the course of two phytoplankton blooms. By measuring excitation-emission matrices of bulk seawater, the sea surface microlayer, and SSA, we investigate time series of the transfer of fluorescent species including chlorophyll-a, protein-like substances, and humic-like substances. Herein, we show the emergence of different molecular classes in SSA at specific times over the course of a phytoplankton bloom, suggesting that SSA chemical composition changes over time in response to changing ocean biological conditions. We compare the temporal behaviors for the transfer of each component, and discuss the factors contributing to differences in transfer between phases.

Submicron drops from flapping bursting bubbles

Bubble bursting aerosols play a critical role in forming clouds, scattering sunlight, and transporting pathogens from water to the air. Most of them are produced from the fragmentation of bubble cap film. They usually have a diameter below 1 μm. However, their physical production mechanism has remained unknown. In this work, we discovered that these drops are probably generated from flapping bubble cap film (like a flapping flag). It explains the mysterious relation between bubble size and number of drops produced per bubble, providing a fundamental framework for understanding the production flux of bubble bursting aerosols, such as sea spray aerosol, and substance transfer through the air–water interface during drop ejection.

Tiny water drops produced from bubble bursting play a critical role in forming clouds, scattering sunlight, and transporting pathogens from water to the air. Bubbles burst by nucleating a hole at their cap foot and may produce jets or film drops. The latter originate from the fragmentation of liquid ligaments formed by the centripetal destabilization of the opening hole rim. They constitute a major fraction of the aerosols produced from bubbles with cap radius of curvature (R) > ∼0.4 × capillary length (a). However, our present understanding of the corresponding mechanisms does not explain the production of most submicron film drops, which represent the main number fraction of sea spray aerosols. In this study, we report observations showing that bursting bubbles with R < ∼0.4a are actually mainly responsible for submicron film drop production, through a mechanism involving the flapping shear instability of the cap with the outer environment. With this proposed pathway, the complex relations between bubble size and number of drops produced per bubble can be better explained, providing a fundamental framework for understanding the production flux of aerosols and the transfer of substances mediated by bubble bursting through the air–water interface and the sensitivity of the process to the nature of the environment.

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.

Bioactive Natural Products in Actinobacteria Isolated in Rainwater From Storm Clouds Transported by Western Winds in Spain

Actinobacteria are the main producers of bioactive natural products essential for human health. Although their diversity in the atmosphere remains largely unexplored, using a multidisciplinary approach, we studied here 27 antibiotic producing Actinobacteria strains, isolated from 13 different precipitation events at three locations in Northern and Southern Spain. Rain samples were collected throughout 2013-2016, from events with prevailing Western winds. NOAA HYSPLIT meteorological analyses were used to estimate the sources and trajectories of the air-mass that caused the rainfall events. Five-day backward air masses trajectories of the diverse events reveals a main oceanic source from the North Atlantic Ocean, and in some events long range transport from the Pacific and the Arctic Oceans; terrestrial sources from continental North America and Western Europe were also estimated. Different strains were isolated depending on the precipitation event and the latitude of the sampling site. Taxonomic identification by 16S rRNA sequencing and phylogenetic analysis revealed these strains to belong to two Actinobacteria genera. Most of the isolates belong to the genus Streptomyces, thus increasing the number of species of this genus isolated from the atmosphere. Furthermore, five strains belonging to the rare Actinobacterial genus Nocardiopsis were isolated in some events. These results reinforce our previous Streptomyces atmospheric dispersion model, which we extend herein to the genus Nocardiopsis. Production of bioactive secondary metabolites was analyzed by LC-UV-MS. Comparative analyses of Streptomyces and Nocardiopsis metabolites with natural product databases led to the identification of multiple, chemically diverse, compounds. Among bioactive natural products identified 55% are antibiotics, both antibacterial and antifungal, and 23% have antitumor or cytotoxic properties; also compounds with antiparasitic, anti-inflammatory, immunosuppressive, antiviral, insecticidal, neuroprotective, anti-arthritic activities were found. Our findings suggest that over time, through samples collected from different precipitation events, and space, in different sampling places, we can have access to a great diversity of Actinobacteria producing an extraordinary reservoir of bioactive natural products, from remote and very distant origins, thus highlighting the atmosphere as a contrasted source for the discovery of novel compounds of relevance in medicine and biotechnology.

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.

The emergency discharge of sewage to the Bay of Gdańsk as a source of bacterial enrichment in coastal air

The purpose of this research was to study the presence of potential pathogenic bacteria in the seawater and air in five coastal towns (Hel, Puck, Gdynia, Sopot, Gdańsk-Brzeźno) as well as the enrichment of bacteria from the seawater into the coastal air after an emergency discharge of sewage into the Bay of Gdańsk. A total of 594 samples of air and seawater were collected in the coastal zone between spring and summer (between 2014 and 2018). Air samples were collected using the impact method with a SAS Super ISO 100. The multivariate analysis, conducted using contingency tables, showed a statistically significant variation between the concentration of coliforms, psychrophilic and mesophilic bacteria in the seawater microlayer and air in 2018, after an emergency discharge of sewage into the Bay of Gdańsk, compared to 2014-2017. Moreover, we detected a marine aerosol enrichment in psychrophilic, mesophilic bacteria, coliforms and Escherichia coli. We also showed a statistically significant relationship between the total concentration of bacteria and humidity, air temperature, speed and wind direction. This increased concentration of bacteria in the seawater and coastal air, and the high factor of air enrichment with bacteria maybe associated with the emergency discharge of wastewater into the Bay of Gdańsk. Therefore, it is suggested that in the event of a malfunction of a sewage treatment plant, as well as after floods or sudden rainfall, the public should be informed about the sanitary and epidemiological status of the coastal waters and be recommended to limit their use of coastal leisure areas.

Higher Number of Yeast-like Fungi in the Air in 2018 after an Emergency Discharge of Raw Sewage to the Gulf of Gdańsk—Use of Contingency Tables

This study aimed to investigate the differences between the number of yeast-like fungi and molds in the coastal air of five coastal towns of the Gulf of Gdańsk in 2014–2017 vs. 2018, which saw an emergency discharge of sewage. In 2014–2017, a total of 62 duplicate samples were collected in the coastal towns of Hel, Puck, Gdynia, Sopot, and Gdańsk-Brzeźno. In 2018, after the emergency disposal of raw sewage, 26 air samples were collected. A Pearson chi-squared test of independence showed that during 2018 in Hel and Sopot, the mean number of molds and yeast-like fungi was higher than in 2014–2017. The result was significantly positive, p ≤ 2.22 × 10−16. The analysis of the General Asymptotic Symmetry Test showed that in Puck and Gdańsk-Brzeźno, the average number of Aspergillus sp. mold fungi was higher in 2018 after an emergency discharge of sewage into the Gulf of Gdańsk compared to the period 2014–2017. The result was not statistically significant. In addition, the average number of Penicillium sp. molds in 2018 in Gdańsk-Brzeźno was higher than in 2014–2017, but statistically insignificant (p = 0.9593). In 2018, the average number of Cladosporium sp. molds in Sopot was higher, but also statistically insignificant (p = 0.2114) compared to 2014–2017. Our results indicate that the study of the number of yeast-like fungi in the air may indicate coastal areas that may be particularly at risk of bacterial or mycological pathogens, e.g., after an emergency discharge of raw sewage.

Characteristics of size-segregated aerosols emitted from an aerobic moving bed biofilm reactor at a full-scale wastewater treatment plant

Aerosol emissions from wastewater treatment plants (WWTPs) have been associated with health reverberation but studies about characteristics of size-segregated aerosol particulate matter (PM) are scarce. In this study, the measurement of particulate number size distribution in the range of < 10 µm, and the collection of PM_10-2.5, PM_2.5-1.0 and PM_1.0, were conducted from an aerobic moving bed biofilm reactor (MBBR) at a full-scale WWTP. MBBR aerosols showed a unimodal number size distribution, with the majority of particles (>94%) in the ultrafine size range (<100 nm). For toxic metal(loid)s or potential pathogens, significant differences were found within MBBR aerosols (PM_10-2.5, PM_2.5-1.0, and PM_1.0), and also between MBBR aerosols and wastewater. Both wastewater and ambient air had important source contributions for MBBR aerosols. The compositions of toxic metal(loid)s in PM_1.0, and the populations of potential bacterial or fungal pathogens in PM_10-2.5 and PM_2.5-1.0, were dominated by that from wastewater. Compared to PM_10-2.5 and PM_2.5-1.0, PM_1.0 had the highest aerosolization potential for the toxic metal(loid)s of As, Cd, Co, Cr, Li, Mn, Ni, U, and Zn, and the genera of Acinetobacter, Pseudomonas and Fusarium. Due to the size-segregated specialty, targeted measures should be employed to reduce the health risks. CAPSULE: The compositions of toxic metal(loid)s in PM_1.0, and the populations of potential pathogens in PM_10-2.5 and PM_2.5-1.0, were dominated by that from wastewater.

Unraveling interfacial properties of organic-coated marine aerosol with lipase incorporation

Marine aerosols are believed to have an organic surface coating on which fatty acids act as an important component due to their high surface activity. In addition, various kinds of enzyme species are abundantly found in seawater, some of which have been identified to exist in marine aerosols. Herein, from the perspective of marine aerosol interface simulation, we investigate the effect of Burkholderia cepacia lipase on the surface properties of stearic acid (SA) monolayer at the air-water interface by using surface-sensitive techniques of Langmuir trough and Infrared reflection-absorption spectroscopy (IRRAS). Our findings indicate that the stearic acid film undergoes a significant expansion, especially when the lipase concentration is 500 nM, because of the incorporation of lipase as observed from the surface pressure-area (π-A) isotherms. IRRAS spectra also show reduced intensities and ordering in the methylene stretching vibration region of stearic acid as a result of low surface density and disordered packing as the enzyme concentration increases. In particular, when the concentration of lipase is 500 nM, the lowest I_as/I_s values are shown on both pure water subphase and artificial seawater subphase, indicating more gauche conformations for SA. Furthermore, SA films with lipase incorporation were also studied at three different pH of subphase environment, considering the decrease of pH caused by the reaction with acidic gases during the aerosol aging process. The results reflect a more pronounced expansion of SA monolayer in acidic environment at pH 2.5, suggesting that hydrophobic interaction plays an important role in the disorder of the SA monolayer. In view of the coexistence of fatty acids and enzymes in the marine environment, this study provides a further understanding of the surface organization and behavior of organic-coated marine aerosols and deepen the knowledge of lipid-enzyme interfacial interactions occurring in the atmosphere.

Habitat heterogeneity induced by pyrogenic organic matter in wildfire-perturbed soils mediates bacterial community assembly processes

Although pyrogenic organic matter (PyOM) generated during wildfires plays a critical role in post-fire ecosystem recovery, the specific mechanisms by which PyOM controls soil microbial community assembly after wildfire perturbation remain largely uncharacterized. Herein we characterized the effect of PyOM on soil bacterial communities at two independent wildfire-perturbed forest sites. We observed that α-diversity of bacterial communities was the highest in wildfire-perturbed soils and that bacterial communities gradually changed along a sequence of unburnt soil → burnt soil → PyOM. The microbial communities reconstructed from unburnt soil and PyOM resembled the real bacterial communities in wildfire-perturbed soils in their α-diversity and community structure. Bacterial specialists in PyOM and soils clustered in phylogenetic coherent lineages with intra-lineage pH-niche conservatism and inter-lineage pH-niche divergence. Our results suggest that PyOM mediates bacterial community assembly in wildfire-perturbed soils by a combination of environmental selection and dispersal of phylogenetic coherent specialists with habitat preference in the heterogeneous microhabitats of burnt soils with distinct PyOM patches.

Airborne transmission pathway for coastal water pollution

Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.

Growth phase-dependent surface properties of Legionella pneumophila and their role in adhesion to stainless steel coated QCM-D sensors

Legionella pneumophila cell surface hydrophobicity and charge are important determinants of their mobility and persistence in engineered water systems (EWS). These surface properties may differ depending on the growth phase of L. pneumophila resulting in variable adhesion and persistence within EWS. We describe the growth-dependent variations in L. pneumophila cell surface hydrophobicity and surface charge using the microbial adhesion to hydrocarbon assay and microelectrophoresis, respectively, and their role in cell adhesion to stainless steel using a quartz crystal microbalance with dissipation (QCM-D) monitoring instrument. We observed a steady increase in L. pneumophila hydrophobicity during their lifecycle in culture media. Cell surfaces of stationary phase L. pneumophila were significantly more hydrophobic than their lag and midexponential counterparts. No significant changes in L. pneumophila cell surface charge were noted. Morphology of L. pneumophila remained relatively constant throughout their lifecycle. In the QCM-D study, lag and exponential phase L. pneumophila weakly adhered to stainless steel surfaces resulting in viscoelastic layers. In contrast, stationary phase bacteria were tightly and irreversibly bound to the surfaces, forming rigid layers. Our results suggest that the stationary phase of L. pneumophila would highly favour their adhesion to plumbing surfaces and persistence in EWS.