The aerobiome uncovered: Multi-marker metabarcoding reveals potential drivers of turn-over in the full microbial community in the air

Swine farming shifted the gut antibiotic resistome of local people

Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.

Investigating the inoculum dynamics of Cladosporium on the surface of raspberry fruits and in the air

Raspberry production is under threat from the emerging fungal pathogenic genus Cladosporium. We used amplicon-sequencing, coupled with qPCR, to investigate how fruit age, fruit location within a polytunnel, polytunnel location and sampling date affected the fruit epiphytic microbiome. Fruit age was the most important factor impacting the fungal microbiome, followed by sampling date and polytunnel location. In contrast, polytunnel location and fruit age were important factors impacting the bacterial microbiome composition, followed by the sampling date. The within-tunnel location had a small significant effect on the fungal microbiome and no effect on the bacterial microbiome. As fruit ripened, fungal diversity increased and the bacterial diversity decreased. Cladosporium was the most abundant fungus of the fruit epiphytic microbiome, accounting for nearly 44% of all fungal sequences. Rotorod air samplers were used to study how the concentration of airborne Cladosporium inoculum (quantified by qPCR) varied between location (inside and outside the polytunnel) and time (daytime vs. nighttime). Quantified Cladosporium DNA was significantly higher during the day than the night and inside the polytunnel than the outside. This study demonstrated the dynamic nature of epiphytic raspberry fruit microbiomes and airborne Cladosporium inoculum within polytunnels, which will impact disease risks on raspberry fruit.

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.

Decrypting seasonal patterns of key pollen taxa in cool temperate Australia: A multi-barcode metabarcoding analysis

Pollen allergies pose a considerable global public health concern. Allergy risk can vary significantly within plant families, yet some key pollen allergens can only be identified to family level by current optical methods. Pollen information with greater taxonomic resolution is therefore required to best support allergy prevention and self-management. We used environmental DNA (eDNA) metabarcoding to deepen taxonomic insights into the seasonal composition of airborne pollen in cool temperate Australia, a region with high rates of allergic respiratory disease. In Hobart, Tasmania, we collected routine weekly air samples from December 2018 until October 2020 and sequenced the internal transcribed spacer 2 (ITS2) and chloroplastic tRNA-Leucine tRNA-Phenylalanine intergenic spacer (trnL-trnF) regions in order to address the following questions: a) What is the genus-level diversity of known and potential aeroallergens in Hobart, in particular, in the families Poaceae, Cupressaceae and Myrtaceae? b) How do the atmospheric concentrations of these taxa change over time, and c) Does trnL-trnF enhance resolution of biodiversity when used in addition to ITS2? Our results suggest that individuals in the region are exposed to temperate grasses including Poa and Bromus in the peak grass pollen season, however low levels of exposure to the subtropical grass Cynodon may occur in autumn and winter. Within Cupressaceae, both metabarcodes showed that exposure is predominantly to pollen from the introduced genera Cupressus and Juniperus. Only ITS2 detected the native genus, Callitris. Both metabarcodes detected Eucalyptus as the major Myrtaceae genus, with trnL-trnF exhibiting primer bias for this family. These findings help refine our understanding of allergy triggers in Tasmania and highlight the utility of multiple metabarcodes in aerobiome studies.

Airborne environmental DNA captures terrestrial vertebrate diversity in nature

The current biodiversity and climate crises highlight the need for efficient tools to monitor terrestrial ecosystems. Here, we provide evidence for the use of airborne eDNA analyses as a novel method for detecting terrestrial vertebrate communities in nature. Metabarcoding of 143 airborne eDNA samples collected during 3 days in a mixed forest in Denmark yielded 64 bird, mammal, fish and amphibian taxa, of which the detected 57 'wild' taxa represent over a quarter of the around 210 terrestrial vertebrates that occur in the overall area. We provide evidence for the spatial movement and temporal patterns of airborne eDNA and for the influence of weather conditions on vertebrate detections. This study demonstrates airborne eDNA for high-resolution biomonitoring of vertebrates in terrestrial systems and elucidates its potential to guide global nature management and conservation efforts in the ongoing biodiversity crisis.

Distinct responses of airborne abundant and rare microbial communities to atmospheric changes associated with Chinese New Year

Airborne microorganisms, including pathogens, would change with surrounding environments and become issues of global concern due to their threats to human health. Microbial communities typically contain a few abundant but many rare species. However, how the airborne abundant and rare microbial communities respond to environmental changes is still unclear, especially at hour scale. Here, we used a sequencing approach based on bacterial 16S rRNA genes and fungal ITS2 regions to investigate the high time-resolved dynamics of airborne bacteria and fungi and to explore the responses of abundant and rare microbes to the atmospheric changes. Our results showed that air pollutants and microbial communities were significantly affected by human activities related to the Chinese New Year (CNY). Before CNY, significant hour-scale changes in both abundant and rare subcommunities were observed, while only abundant bacterial subcommunity changed with hour time series during CNY. Air pollutants and meteorological parameters explained 61.5%-74.2% variations of abundant community but only 13.3%-21.6% variations of rare communities. These results suggested that abundant species were more sensitive to environmental changes than rare taxa. Stochastic processes predominated in the assembly of abundant communities, but deterministic processes determined the assembly of rare communities. Potential bacterial pathogens during CNY were the highest, suggesting an increased health risk of airborne microbes during CNY. Overall, our findings highlighted the "holiday effect" of CNY on airborne microbes and expanded the current understanding of the ecological mechanisms and health risks of microbes in a changing atmosphere.

The aerobiome-health axis: a paradigm shift in bioaerosol thinking

Historically, a primary aim of bioaerosol research has been to understand and prevent 'unhealthy' human exposures to pathogens and allergens. However, there has been a recent paradigm shift in thinking about bioaerosols. Exposure to a diverse aerobiome - the microbiome of the air - is now considered necessary to be healthy.

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.

Airborne bacterial community and antibiotic resistome in the swine farming environment: Metagenomic insights into livestock relevance, pathogen hosts and public risks

Globally extensive use of antibiotics has accelerated antimicrobial resistance (AMR) in the environment. As one of the biggest antibiotic consumers, livestock farms are hotspots in AMR prevalence, especially those in the atmosphere can transmit over long distances and pose inhalation risks to the public. Here, we collected total suspended particulates in swine farms and ambient air of an intensive swine farming area. Bacterial communities and antibiotic resistomes were analyzed using amplicon and metagenomic sequencing approaches. AMR risks and inhalation exposure to potential human-pathogenic antibiotic-resistant bacteria (HPARB) were subsequently estimated with comparison to the reported hospital samples. The results show that swine farms shaped the airborne bacterial community by increasing abundances, reducing diversities and shifting compositions. Swine feces contributed 77% of bacteria to swine farm air, and about 35% to ambient air. Airborne antibiotic resistomes in swine farms mainly conferred resistance to tetracyclines, aminoglycosides and lincosamides, and over 48% were originated from swine feces. Distinct to the hospital air, Firmicutes were dominant bacteria in swine farming environments with conditional pathogens including Clostridium, Streptococcus and Aerococcus being major hosts of antibiotic resistance genes (ARGs). Therein, genomes of S. alactolyticus carrying (transposase/recombinase-associated) ARGs and virulence factor genes were retrieved from the metagenomes of all swine feces and swine farm air samples, but they were not detected in any hospital air samples. This suggests the indication of S. alactolyticus in swine farming environments with potential hazards to human health. Swine farm air faced higher AMR risks than hospital air and swine feces. The inhalation intake of HPARB by a swine farm worker was about three orders of magnitude higher than a person who works in the hospital. Consequently, this study depicted atmospheric transmission of bacteria and antibiotic resistomes from swine feces to the environment.

Transforming terrestrial biodiversity surveys using airborne eDNA

Studies show that land-living animals, plants, fungi, and bacteria leave DNA traces in the air. These results imply that sequencing of bioaerosols might be a powerful tool for simultaneous surveys of terrestrial biodiversity across lifeforms, but in parallel, it highlights the need to carefully control for possible contaminants.

Interactive effects of global change drivers as determinants of the link between soil biodiversity and ecosystem functioning

Biodiversity, both aboveground and belowground, is negatively affected by global changes such as drought or warming. This loss of biodiversity impacts Earth's ecosystems, as there is a positive relationship between biodiversity and ecosystem functioning (BEF). Even though soils host a large fraction of biodiversity that underlies major ecosystem functions, studies exploring the relationship between soil biodiversity and ecosystem functioning (sBEF) as influenced by global change drivers (GCDs) remain scarce. Here we highlight the need to decipher sBEF relationships under the effect of interactive GCDs that are intimately connected in a changing world. We first state that sBEF relationships depend on the type of function (e.g., C cycling or decomposition) and biodiversity facet (e.g., abundance, species richness, or biomass) considered. Then, we shed light on the impact of single and interactive GCDs on soil biodiversity and sBEF and show that results from scarce studies studying interactive effects range from antagonistic to additive to synergistic when two individual GCDs cooccur. This indicates the need for studies quantitatively accounting for the impacts of interactive GCDs on sBEF relationships. Finally, we provide guidelines for optimized methodological and experimental approaches to study sBEF in a changing world that will provide more valuable information on the real impact of (interactive) GCDs on sBEF. Together, we highlight the need to decipher the sBEF relationship in soils to better understand soil functioning under ongoing global changes, as changes in sBEF are of immediate importance for ecosystem functioning.

Observed electric charge of insect swarms and their contribution to atmospheric electricity

The atmosphere hosts multiple sources of electric charge that influence critical processes such as the aggregation of droplets and the removal of dust and aerosols. This is evident in the variability of the atmospheric electric field. Whereas these electric fields are known to respond to physical and geological processes, the effect of biotic sources of charge has not hitherto been considered. Here, we combine theoretical and empirical evidence to demonstrate that honeybee swarms directly contribute to atmospheric electricity, in proportion to the swarm density. We provide a quantitative assessment of this finding, by comparing the electrical contribution of various swarming insect species with common abiotic sources of charge. This reveals that the charge contribution of some insect swarms will be comparable with that of meteorologically induced variations. The observed transport of charge by insects therefore demonstrates an unexplored role of biogenic space charge for physical and ecological processes in the atmosphere.

Fungal exposome, human health, and unmet needs: A 2022 update with special focus on allergy

Humans inhale, ingest, and touch thousands of fungi each day. The ubiquity and diversity of the fungal kingdom, reflected by its complex taxonomy, are in sharp contrast with our scarce knowledge about its distribution, pathogenic effects, and effective interventions at the environmental and individual levels. Here, we present an overview of salient features of fungi as permanent players of the human exposome and key determinants of human health, through the lens of fungal allergy and other fungal hypersensitivity reactions. Improved understanding of the fungal exposome sheds new light on the epidemiology of fungal-related hypersensitivity diseases, their immunological substratum, the currently available methods, and biomarkers for environmental and medical fungi. Unmet needs are described and potential approaches are highlighted as perspectives.

Environmental DNA Metabarcoding: A Novel Contrivance for Documenting Terrestrial Biodiversity

Simple Summary

The innovative concept of environmental DNA has found its foot in aquatic ecosystems but remains an unexplored area of research concerning terrestrial ecosystems. When making management choices, it is important to understand the rate of eDNA degradation, the persistence of DNA in terrestrial habitats, and the variables affecting eDNA detectability for a target species. Therefore an attempt has been made to provide comprehensive information regarding the exertion of eDNA in terrestrial ecosystems from 2012 to 2022. The information provided will assist ecologists, researchers and decision-makers in developing a holistic understanding of environmental DNA and its applicability as a biodiversity monitoring contrivance.

Abstract

The dearth of cardinal data on species presence, dispersion, abundance, and habitat prerequisites, besides the threats impeded by escalating human pressure has enormously affected biodiversity conservation. The innovative concept of eDNA, has been introduced as a way of overcoming many of the difficulties of rigorous conventional investigations, and is hence becoming a prominent and novel method for assessing biodiversity. Recently the demand for eDNA in ecology and conservation has expanded exceedingly, despite the lack of coordinated development in appreciation of its strengths and limitations. Therefore it is pertinent and indispensable to evaluate the extent and significance of eDNA-based investigations in terrestrial habitats and to classify and recognize the critical considerations that need to be accounted before using such an approach. Presented here is a brief review to summarize the prospects and constraints of utilizing eDNA in terrestrial ecosystems, which has not been explored and exploited in greater depth and detail in such ecosystems. Given these obstacles, we focused primarily on compiling the most current research findings from journals accessible in eDNA analysis that discuss terrestrial ecosystems (2012–2022). In the current evaluation, we also review advancements and limitations related to the eDNA technique.

Elevational Gradients Impose Dispersal Limitation on Streptomyces

Dispersal governs microbial biogeography, but the rates and mechanisms of dispersal remain poorly characterized for most microbial taxa. Dispersal limitation is driven by limits on dissemination and establishment, respectively. Elevation gradients create striking patterns of biogeography because they produce steep environmental gradients at small spatial scales, and these gradients offer a powerful tool to examine mechanisms of dispersal limitation. We focus on Streptomyces, a bacterial genus common to soil, by using a taxon-specific phylogenetic marker, the RNA polymerase-encoding rpoB gene. By targeting Streptomyces, we assess dispersal limitation at finer phylogenetic resolution than is possible using whole community analyses. We characterized Streptomyces diversity at local spatial scales (100 to 3,000 m) in two temperate forest sites located in the Adirondacks region of New York State: Woods Lake (<100 m elevation change), and Whiteface Mountain (>1,000 m elevation change). Beta diversity varied considerably at both locations, indicative of dispersal limitation acting at local spatial scales, but beta diversity was significantly higher at Whiteface Mountain. Beta diversity varied across elevation at Whiteface Mountain, being lowest at the mountain’s base. We show that Streptomyces taxa exhibit elevational preferences, and these preferences are phylogenetically conserved. These results indicate that habitat preferences influence Streptomyces biogeography and suggest that barriers to establishment structure Streptomyces communities at higher elevations. These data illustrate that Streptomyces biogeography is governed by dispersal limitation resulting from a complex mixture of stochastic and deterministic processes.

Particulate Matter in Swine Barns: A Comprehensive Review

Particulate matter (PM) represents an air quality management challenge for confined swine production systems. Due to the limited space and ventilation rate, PM can reach relatively high concentrations in swine barns. PM in swine barns possesses different physical, chemical, and biological characteristics than that in the atmosphere and other indoor environments. As a result, it exerts different environmental and health effects and creates some unique challenges regarding PM measurement and mitigation. Numerous research efforts have been made, generating massive data and information. However, relevant review reports are sporadic. This study aims to provide an updated comprehensive review of swine barn PM, focusing on publications since 1990. It covers various topics including PM characteristics, sources, measurement methods, and in-barn mitigation technologies. As PM in swine barns is primarily of biological origins, bioaerosols are reviewed in great detail. Relevant topics include bacterial/fungal counts, viruses, microbial community composition, antibiotic-resistant bacteria, antibiotic resistance genes, endotoxins, and (1→3)-β-D-glucans. For each topic, existing knowledge is summarized and discussed and knowledge gaps are identified. Overall, PM in swine barns is complicated in chemical and biological composition and highly variable in mass concentrations, size, and microbial abundance. Feed, feces, and skins constitute the major PM sources. Regarding in-barn PM mitigation, four technologies (oil/water sprinkling, ionization, alternation of feed and feeders, and recirculating air filtration) are dominant. However, none of them have been widely used in commercial barns. A collective discussion of major knowledge gaps and future research needs is offered at the end of the report.

Contrasting effects of soil microbial interactions on growth-defence relationships between early- and mid-successional plant communities

Plants allocate resources to processes related to growth and enemy defence. Simultaneously, they interact with complex soil microbiomes that also affect plant performance. While the influence of individual microbial groups on single plants is increasingly studied, effects of microbial interactions on growth, defence and growth-defence relationships remain unknown, especially at the plant community level. We investigated how three microbial groups (bacteria, fungi, protists), alone and in full-factorial combinations, affect plant performance and potential growth-defence relationships by measuring phenolics composition in early- and mid-successional grass and forb communities in a glasshouse experiment. Microbial groups did not affect plant growth and only fungi increased defence compounds in early- and mid-successional forbs, while grasses were not affected. Shoot biomass-defence relationships were negatively correlated in most microbial treatments in early-successional forbs, but positively in several microbial treatments in mid-successional forbs. The growth-defence relationship was generally negative in early-successional but not in mid-successional grasses. The presence of different microbiomes commonly removed the observed growth-defence relationships. We conclude that soil microorganisms and their interactions can shift growth-defence relationships differentially for plant functional groups and the relationships vary between successional stages. Microbial interaction-induced growth-defence shifts might therefore underlie distinct plant strategies and fitness.

Metabarcoding insights into the diet and trophic diversity of six declining farmland birds

Knowledge of feeding ecology of declining species, such as farmland birds, is essential to address their conservation requirements, especially when their habitats are suffering important reductions of trophic resources. In this study, we apply a metabarcoding approach to describe the diet composition of six of the most significant farmland birds inhabiting European cereal pseudo-steppes: little bustard, great bustard, pin-tailed sandgrouse, black-bellied sandgrouse, red-legged partridge, and common quail. We further studied seasonal diet variations (autumn to spring) in all species but the common quail, whose diet was studied during spring and summer. We show that study species´ diets mostly consisted of plants, although in the case of little bustard and great bustard arthropods are also highly relevant. Among arthropods, we found high proportions of thrips, arachnids, and springtails, which were previously unreported in their diet, and some taxa that could be used as antiparasitic food. Moreover, we report that little bustard's diet is the least rich of that of all studied species, and that diet of all these species is less diverse in winter than in autumn and spring. Diet composition of these declining species supports the importance of natural and semi-natural vegetation and landscape mosaics that can provide a wide variety of arthropods, plants, and seeds all year-round.

Highly comparable metabarcoding results from MGI-Tech and Illumina sequencing platforms

With the developments in DNA nanoball sequencing technologies and the emergence of new platforms, there is an increasing interest in their performance in comparison with the widely used sequencing-by-synthesis methods. Here, we test the consistency of metabarcoding results from DNBSEQ-G400RS (DNA nanoball sequencing platform by MGI-Tech) and NovaSeq 6000 (sequencing-by-synthesis platform by Illumina) platforms using technical replicates of DNA libraries that consist of COI gene amplicons from 120 soil DNA samples. By subjecting raw sequencing data from both platforms to a uniform bioinformatics processing, we found that the proportion of high-quality reads passing through the filtering steps was similar in both datasets. Per-sample operational taxonomic unit (OTU) and amplicon sequence variant (ASV) richness patterns were highly correlated, but sequencing data from DNBSEQ-G400RS harbored a higher number of OTUs. This may be related to the lower dominance of most common OTUs in DNBSEQ data set (thus revealing higher richness by detecting rare taxa) and/or to a lower effective read quality leading to generation of spurious OTUs. However, there was no statistical difference in the ASV and post-clustered ASV richness between platforms, suggesting that additional denoising step in the ASV workflow had effectively removed the 'noisy' reads. Both OTU-based and ASV-based composition were strongly correlated between the sequencing platforms, with essentially interchangeable results. Therefore, we conclude that DNBSEQ-G400RS and NovaSeq 6000 are both equally efficient high-throughput sequencing platforms to be utilized in studies aiming to apply the metabarcoding approach, but the main benefit of the former is related to lower sequencing cost.

Air-dispersed aquatic microorganisms show establishment and growth preferences in different freshwater colonisation habitats

We attempted to mimic aeolian ecosystems to examine how filters posed by regional characteristics can influence the establishment and growth of airborne microcolonisers of a common air source. Using a natural single source of aerosols we applied a combined microscopy and high-throughput sequencing approach to examine the diversity, settling and growth potential of air-dispersed microbes in water containers representing newly formed aquatic colonisation habitats of different trophic states and salinity. Heterotrophic microeukaryotes were favoured as initial settlers when nutrients were low, while autotrophs rapidly proliferated in the high-nutrient containers, possibly due to favourable germinating conditions for their preferred mode of dispersal with resting spores. Following settling of colonisers, we investigated two contrasting hypotheses: if the different water colonisation habitats harboured the same microbial communities after establishment and growth periods, this would point towards a selection of best-fit cosmopolitan colonisers, regardless of habitat-specific characteristics. Alternatively, community dissimilarities after the growth period would suggest a selection of settlers due to bottom-up controls combined with priority effects. Both analyses suggested that the structure of the microbial communities in the different colonisation habitats were driven by nutrient content and salinity, showing clustering to similar bottom-up forces and dissimilarities in significantly different colonisation habitats.