AirDNA sampler: An efficient and simple device enabling high-yield, high-quality airborne environment DNA for metagenomic applications

Environmental DNA (eDNA) collection techniques across diverse ecosystems: a mini-review of promising new tools for eDNA metabarcoding

Environmental DNA (eDNA) analysis has significantly transformed the way biodiversity assessment and monitoring are conducted in many environments. This review study synthesizes findings from multiple studies to provide a comprehensive overview of eDNA collection strategies in diverse settings. The review examines the techniques used for sampling eDNA in water, air, soil, sediment, and coral reef ecosystems. Water filtration, sediment sampling, and passive sampling devices are commonly used methods for collecting eDNA in aquatic environments. These techniques provide non-invasive ways to identify and track aquatic organisms, offering vital information about the interactions within the community and the global distribution of species. Similarly, the use of airborne eDNA sampling techniques is becoming increasingly promising for evaluating biodiversity on land, although there is room for improvement. Soil eDNA extraction techniques involve the use of soil coring to collect samples, followed by DNA extraction from these samples, and the application of metabarcoding methods. These techniques allow for thorough investigations of biodiversity in the soil. Specialized techniques for collecting eDNA are required for coral reef ecosystems due to their intricate habitat structure and fluctuating water conditions. The importance of choosing appropriate techniques for eDNA collection based on ecosystem parameters and research objectives is emphasized by comparative analysis. This mini-review consolidates knowledge from a selected body of recent studies and serves as a helpful resource for scholars and practitioners involved in biodiversity monitoring and conservation across diverse ecosystems.

Efficiency of the Coriolis µ Air Sampling Device for Fungal Contamination Analysis of Indoor Air: A Case Study

Molds are frequent indoor contaminants, where they can colonize many materials. The subsequent aerosolization of fungal spores from moldy surfaces can strongly impact indoor air quality and the health of occupants. The investigation of fungal contamination of habitations is a key point in evaluating sanitary risks and understanding the relationship that may exist between the fungal presence on surfaces and air contamination. However, to date there is no "gold standard" of sampling indoor air for such investigations. Among various air sampling methods, impingement can be used for capturing fungal spores, as it enables real-time sampling and preserves analytical follow-up. Its efficiency varies depending on several factors, such as spore hydrophobicity, sampling conditions, etc. Sampling devices may also impact the results, with recovery rates sometimes lower than filtration-based methods. The Coriolis µ air sampler, an impingement-based device, utilizes centrifugal force to concentrate airborne particles into a liquid medium, offering flexibility for molecular analysis. Several studies have used this device for air sampling, demonstrating its application in detecting pollen, fungal spores, bacteria, and viruses, but it is most often used in laboratory conditions. The present case study, conducted in a moldy house, aims to investigate the efficiency of this device in sampling fungal spores for DNA analysis in indoor environments. The results obtained suggest that the use of this device requires an optimized methodology to enhance its efficiency and reliability in bioaerosol research.

Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant

Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.

Interplay of xenobiotic-degrading and antibiotic-resistant microorganisms among the microbiome found in the air, handrail, and floor of the subway station

Investigating the quality of the subway environment, especially regarding antibiotic resistance genes (ARGs) and xenobiotics, conveys ecological and health impacts. In this study, compositions and relations of microorganisms harboring ARGs and xenobiotic degradation and metabolism genes (XDGs) in the Sukhumvit subway station (MRT-SKV) in Bangkok was assessed by analyzing the taxonomic and genetic diversity of the microbiome in the air and on the surfaces of floor and handrail. The major bacteria in the MRT-SKV (including Moraxella, which was abundant in the bioaerosol and handrail samples, and Staphylococcus, which was abundant in the bioaerosol samples) were found to contain both ARGs and XDGs. The co-abundance correlation network revealed notable relationships among bacteria harboring antibiotic resistance genes (ARGs) and xenobiotic degradation genes (XDGs). Significant associations were observed between ARGs linked to glycopeptide and fluoroquinolone resistance and genes associated with benzoate, styrene, and atrazine degradation pathways, as well as between ARGs related to cephamycin, cephalosporin, and MLS resistance and XDGs associated with the cytochrome P450-dependent drug metabolism pathway. These correlations suggested that selective pressure exerted by certain xenobiotics and antibiotics can simultaneously affect both ARGs and XDGs in the environment and should favor correlations and co-survival among ARG- and XDG-containing bacteria in the environments. The correlations may occur via shared mechanisms of resistance to both xenobiotics and antibiotics. Finally, different correlation pairs were seen in different niches (air, handrail, floor) of the subway environment or different geolocations. Thus, the relationship between ARG and XDG pairs most likely depends on the unique characteristics of the niches and on the prominent types of xenobiotics and antibiotics in the subway environment. The results indicated that interactions and connections between microbial communities can impact how they function. These microorganisms can have profound effects on accumulation of xenobiotics and ARGs in the MRT-SKV.