Impacts of Saharan Dust Intrusions on Bacterial Communities of the Low Troposphere

Toward an integrative framework for microbial community coalescence

Community coalescence is defined as the mixing of intact ecological communities. From river confluences to fecal microbiota transplantation, community coalescence constitutes a common ecological occurrence affecting natural and engineered microbial systems. In this opinion article, we propose an integrative framework for microbial community coalescence to guide advances in our understanding of this important - yet underexplored - ecological phenomenon. We start by aligning community coalescence with the unified framework of biological invasion and enumerate commonalities and idiosyncrasies between these two analogous processes. Then, we discuss how organismal interactions and cohesive establishment affect coalescence outcomes with direct implications for community functioning. Last, we propose the use of ecological null modeling to study the interplay of ecological processes structuring community reassembly following coalescence.

Microbial composition of Saharan dust plumes deposited as red rain in Granada (Southern Spain)

During durst storms, also biological material is transported from arid areas such as the Sahara Desert. In the present work, rain samples containing significant amounts of mineral dust have been collected in Granada during different red rain episodes. Biological features (bacteria, biofilm, pollen grain and fungal spore) as well as size-particle distribution and mineralogical composition were studied by SEM. Nanobacteria were observed for the first time in red rain samples. A preliminary metabarcoding analysis was performed on three red rain samples. Here, Bacillota made up 18 % and Pseudomonadota 23 % of the whole prokaryotic community. The fungal community was characterized by a high abundance of Ascomycota and, dependent on the origin, the presence of Chytridiomycota. By means of 16S rRNA sequencing, 18 cultivable microorganisms were identified. In general, members of the phyla Pseudomonadota and Bacillota made up the majority of taxa. Some species, such as Peribacillus frigoritolerans and Bacillus halotolerans were isolated during three different red rain episodes. Generally, red rain carries a wide variety of microorganisms, being their ecosystem and health effects largely unknown.

Respirable Metals, Bacteria, and Fungi during a Saharan-Sahelian Dust Event in Houston, Texas

Although airborne bacteria and fungi can impact human, animal, plant, and ecosystem health, very few studies have investigated the possible impact of their long-range transport in the context of more commonly measured aerosol species, especially those present in an urban environment. We report first-of-kind simultaneous measurements of the elemental and microbial composition of North American respirable airborne particulate matter concurrent with a Saharan-Sahelian dust episode. Comprehensive taxonomic and phylogenetic profiles of microbial communities obtained by 16S/18S/ITS rDNA sequencing identified hundreds of bacteria and fungi, including several cataloged in the World Health Organization's lists of global priority human pathogens along with numerous other animal and plant pathogens and (poly)extremophiles. While elemental analysis sensitively tracked long-range transported Saharan dust and its mixing with locally emitted aerosols, microbial diversity, phylogeny, composition, and abundance did not well correlate with the apportioned African dust mass. Bacterial/fungal diversity, phylogenetic signal, and community turnover were strongly correlated to apportioned sources (especially vehicular emissions and construction activities) and elemental composition (especially calcium). Bacterial communities were substantially more dissimilar from each other across sampling days than were fungal communities. Generalized dissimilarity modeling revealed that daily compositional turnover in both communities was linked to calcium concentrations and aerosols from local vehicles and Saharan dust. Because African dust is known to impact large areas in northern South America, the Caribbean Basin, and the southern United States, the microbiological impacts of such long-range transport should be assessed in these regions.

Bacterial molecular machinery in the Martian cryosphere conditions

The exploration of Mars is one of the main objectives of space missions since the red planet is considered to be, or was in the past, potentially habitable. Although the surface of Mars is now dry and arid, abundant research suggests that water covered Mars billions of years ago. Recently, the existence of liquid water in subglacial lakes has been postulated below the South pole of Mars. Until now, experiments have been carried out on the survival of microorganisms in Martian surface conditions, but it remains unknown how their adaptation mechanisms would be in the Martian cryosphere. In this work, two bacterial species (Bacillus subtilis and Curtobacterium flacumfaciens) were subjected to a simulated Martian environment during 24 h using a planetary chamber. Afterward, the molecular machinery of both species was studied to investigate how they had been modified. Proteomes, the entire set of proteins expressed by each bacterium under Earth (named standard) conditions and Martian conditions, were compared using proteomic techniques. To establish this evaluation, both the expression levels of each protein, and the variation in their distribution within the different functional categories were considered. The results showed that these bacterial species followed a different strategy. The Bacillus subtilis resistance approach consisted of improving its stress response, membrane bioenergetics, degradation of biomolecules; and to a lesser extent, increasing its mobility and the formation of biofilms or resistance endospores. On the contrary, enduring strategy of Curtobacterium flacumfaciens comprised of strengthening the cell envelope, trying to protect cells from the extracellular environment. These results are especially important due to their implications for planetary protection, missions to Mars and sample return since contamination by microorganisms would invalidate the results of these investigations.

Perspectives on Sampling and New Generation Sequencing Methods for Low-Biomass Bioaerosols in Atmospheric Environments

Bioaerosols play essential roles in the atmospheric environment and can affect human health. With a few exceptions (e.g., farm or rainforest environments), bioaerosol samples from wide-ranging environments typically have a low biomass, including bioaerosols from indoor environments (e.g., residential homes, offices, or hospitals), outdoor environments (e.g., urban or rural air). Some specialized environments (e.g., clean rooms, the Earth's upper atmosphere, or the international space station) have an ultra-low-biomass. This review discusses the primary sources of bioaerosols and influencing factors, the recent advances in air sampling techniques and the new generation sequencing (NGS) methods used for the characterization of low-biomass bioaerosol communities, and challenges in terms of the bias introduced by different air samplers when samples are subjected to NGS analysis with a focus on ultra-low biomass. High-volume filter-based or liquid-based air samplers compatible with NGS analysis are required to improve the bioaerosol detection limits for microorganisms. A thorough understanding of the performance and outcomes of bioaerosol sampling using NGS methods and a robust protocol for aerosol sample treatment for NGS analysis are needed. Advances in NGS techniques and bioinformatic tools will contribute toward the precise high-throughput identification of the taxonomic profiles of bioaerosol communities and the determination of their functional and ecological attributes in the atmospheric environment. In particular, long-read amplicon sequencing, viability PCR, and meta-transcriptomics are promising techniques for discriminating and detecting pathogenic microorganisms that may be active and infectious in bioaerosols and, therefore, pose a threat to human health.

Supplementary Information

The online version contains supplementary material available at 10.1007/s41745-023-00380-x.

Overview of PM2.5 and health outcomes: Focusing on components, sources, and pollutant mixture co-exposure

PM_2.5 varies in source and composition over time and space as a complicated mixture. Consequently, the health effects caused by PM_2.5 varies significantly over time and generally exhibit significant regional variations. According to numerous studies, a notable relationship exists between PM_2.5 and the occurrence of many diseases, such as respiratory, cardiovascular, and nervous system diseases, as well as cancer. Therefore, a comprehensive understanding of the effect of PM_2.5 on human health is critical. The toxic effects of various PM_2.5 components, as well as the overall toxicity of PM_2.5 are discussed in this review to provide a foundation for precise PM_2.5 emission control. Furthermore, this review summarizes the synergistic effect of PM_2.5 and other pollutants, which can be used to draft effective policies.

Aircraft surveys for air eDNA: probing biodiversity in the sky

Air is a medium for dispersal of environmental DNA (eDNA) carried in bioaerosols, yet the atmosphere is mostly unexplored as a source of genetic material encompassing all domains of life. In this study, we designed and deployed a robust, sterilizable hardware system for airborne nucleic acid capture featuring active filtration of a quantifiable, controllable volume of air and a high-integrity chamber to protect the sample from loss or contamination. We used our hardware system on an aircraft across multiple height transects over major aerosolization sources to collect air eDNA, coupled with high-throughput amplicon sequencing using multiple DNA metabarcoding markers targeting bacteria, plants, and vertebrates to test the hypothesis of large-scale genetic presence of these bioaerosols throughout the planetary boundary layer in the lower troposphere. Here, we demonstrate that the multi-taxa DNA assemblages inventoried up to 2,500 m using our airplane-mounted hardware system are reflective of major aerosolization sources in the survey area and show previously unreported airborne species detections (i.e., Allium sativum L). We also pioneer an aerial survey flight grid standardized for atmospheric sampling of genetic material and aeroallergens using a light aircraft and limited resources. Our results show that air eDNA from terrestrial bacteria, plants, and vertebrates is detectable up to high altitude using our airborne air sampler and demonstrate the usefulness of light aircraft in monitoring campaigns. However, our work also underscores the need for improved marker choices and reference databases for species in the air column, particularly eukaryotes. Taken together, our findings reveal strong connectivity or mixing of terrestrial-associated eDNA from ground level aerosolization sources and the atmosphere, and we recommend that parameters and indices considering lifting action, atmospheric instability, and potential for convection be incorporated in future surveys for air eDNA. Overall, this work establishes a foundation for light aircraft campaigns to comprehensively and economically inventory bioaerosol emissions and impacts at scale, enabling transformative future opportunities in airborne DNA technology.

Comparison of Atmospheric and Lithospheric Culturable Bacterial Communities from Two Dissimilar Active Volcanic Sites, Surtsey Island and Fimmvörðuháls Mountain in Iceland

Surface microbes are aerosolized into the atmosphere by wind and events such as dust storms and volcanic eruptions. Before they reach their deposition site, they experience stressful atmospheric conditions which preclude the successful dispersal of a large fraction of cells. In this study, our objectives were to assess and compare the atmospheric and lithospheric bacterial cultivable diversity of two geographically different Icelandic volcanic sites: the island Surtsey and the Fimmvörðuháls mountain, to predict the origin of the culturable microbes from these sites, and to select airborne candidates for further investigation. Using a combination of MALDI Biotyper analysis and partial 16S rRNA gene sequencing, a total of 1162 strains were identified, belonging to 72 species affiliated to 40 genera with potentially 26 new species. The most prevalent phyla identified were Proteobacteria and Actinobacteria. Statistical analysis showed significant differences between atmospheric and lithospheric microbial communities, with distinct communities in Surtsey’s air. By combining the air mass back trajectories and the analysis of the closest representative species of our isolates, we concluded that 85% of our isolates came from the surrounding environments and only 15% from long distances. The taxonomic proportions of the isolates were reflected by the site’s nature and location.

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

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

Effect of Indian monsoon on the glacial airborne bacteria over the Tibetan Plateau

The glacier of the Tibetan Plateau (TP) is influenced by the Indian monsoon and continental westerlies. Wind flow can carry a variety of bacteria and disperse across the TP. Once these bacteria are colonized to the glacier surface, they could affect the biogeochemical cycle of the glacial ecosystems. However, very few studies have focused on the relationships between these airborne bacteria and atmospheric circulation over glaciers of the TP. Here we studied the diversity, taxonomic composition, and community structure of airborne bacteria on six TP glaciers using 16S rRNA gene sequencing. The results revealed an increase in the airborne bacterial diversity over the glaciers under the effect of the Indian monsoon. Airborne bacteria were dominated by Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria, while relative abundances of Bacteroidetes and Firmicutes were significantly higher under the influence of the Indian monsoon in the southern and central of the TP, respectively. Moreover, significantly different airborne bacterial community structures were observed over glaciers under the influence of the Indian monsoon, which could be explained by the increased community stochasticity. In addition, the Indian monsoon increases the diversity and relative abundance of potential pathogens, which includes the most notorious bacteria such as Pseudomonas fluorescens, Staphylococcus aureus, and Clostridium butyricum. Our results revealed for the first time that atmospheric circulation influences the composition of airborne bacteria over the glaciers on the TP, this may provide critical insights into the distinct microbial community structure and function in glaciers across the TP.

Assessment of the association between dust storms and COVID-19 infection rate in southwest Iran

This study assesses a plausible correlation between a dust intrusion episode and a daily increase in COVID-19 cases. A surge in COVID-19 cases was observed a few days after a Middle East Dust (MED) event that peaked on 25^th April 2020 in southwest Iran. To investigate potential causal factors for the spike in number of cases, cross-correlations between daily combined aerosol optical depths (AODs) and confirmed cases were computed for Khuzestan, Iran. Additionally, atmospheric stability data time series were assessed by covering before, during, and after dust intrusion, producing four statistically clustered distinct city groups. Groups 1 and 2 had different peak lag times of 10 and 4-5 days, respectively. Since there were statistically significant associations between AOD levels and confirmed cases in both groups, dust incursion may have increased population susceptibility to COVID-19 disease. Group 3 was utilized as a control group with neither a significant level of dust incursion during the episodic period nor any significant associations. Group 4 cities, which experienced high dust incursion levels, showed no significant correlation with confirmed case count increases. Random Forest Analysis assessed the influence of wind speed and AOD, showing relative importance of 0.31 and 0.23 on the daily increase percent of confirmed cases, respectively. This study may serve as a reference for better understanding and predicting factors affecting COVID-19 transmission and diffusion routes, focusing on the role of MED intrusions.

Socio-Environmental Determinants and Human Health Exposures in Arid and Semi-Arid Zones of Iran-Narrative Review

Lifestyle is different in arid and semi-arid zones. However, where people are born and live have a lasting influence on their social and environmental exposure. This review focuses on the, various dimensions of environmental health imbalance inequality especially in significant environmental sources such as (ie, air, water, soil) among provinces that creates a big health gap in the center, East and the Southeast of Iran. Thus, the population of the arid and semi-arid zones of Iran is facing respiratory, cardiovascular, cancer and infection diseases linked to environmental problems such as chemical and microbial pollution due to air pollution and unsafe water sources, respectively. The prevalence of certain types of cancer such as skin, stomach, bladder, prostate and colorectal cancer together with some respiratory and cardiovascular diseases in arid and semiarid zones such as Kerman, Yazd, etc., has been reported in comparison with other provinces frequently. These impacts have effects on multiple levels of health security in those zones. Based on these concerns, we propose key questions that should guide research in the context of the socio environmental science to support science-based management actions in Iran and other similar semi-arid areas worldwide.

Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM2.5 by African dust incursions to the Mediterranean atmosphere

PM_2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM_2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.

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.

Characterization of long-range transported bioaerosols in the Central Mediterranean

Airborne bacteria were characterized over a 2-y period via high-throughput massive sequencing of 16S rRNA gene in aerosol samples collected at a background mountain European Monitoring and Evaluation Programme (EMEP) Network site (Monte Martano, Italy) located in the Central Mediterranean area. The air mass origin of nineteen samples was identified by air mass modelling and a detailed chemical analysis was performed. Four main origins (Saharan, North-western, North-eastern, and Regional) were identified, and distinct microbial communities were associated with these air masses. Samples featured a great bacterial diversity with Protobacteria being the most abundant phylum, and Sphingomonas followed by Acidovorax, Acinetobacter and Stenotrophomonas the most abundant genera of the dataset. Bacterial genera including potential human and animal pathogens were more abundant in European and in Regional samples compared to Saharan samples; this stressed the relevance of anthropic impact on bacterial populations transported by air masses that cross densely populated areas. The principal aerosol chemical characteristics and the airborne bacterial communities were correlated by cluster analysis, similarity tests and non-metric multidimensional scaling analysis, explaining most of the variability observed. However, the strong correlation between bacterial community structure and air mass origin hampered the possibility to disentangle the effects of variations in bacterial populations and in dust provenance on variations in chemical variables.