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

PLoS ONE, Journal Year: 2023, Volume and Issue: 18(6), P. e0287567 - e0287567

Published: June 29, 2023

Analyzing temporal and spatial distributions of airborne particles biological origins is vital for the assessment monitoring air quality, especially with regard to public health, environmental ecology, atmospheric chemistry. However, analysis frequently impeded by low levels biomass in air, metagenomic DNA explore diversity composition living organisms their components air. To obtain sufficient amounts from bioaerosols, researchers usually need a long sampling time an expensive high-volume sampler. This work shows utilization device containing economical, portable ventilation fan combination customized multi-sheet filter holders effectively high yields genomic relatively short time. The device, named 'AirDNA' sampler, performed better than other commercial samplers, including MD8 Airport Coriolis compact samplers. Using AirDNA average yield 40.49 ng (12.47-23.24 at 95% CI) was obtained only 1 hour 0.85 probability obtaining ≥10 DNA. system suitable quantity quality be further used amplicon metabarcoding sequencing 16S, 18S, cytochrome c oxidase I (COI) regions, indicating that it can detect various prokaryotes eukaryotes. Our results showed effectiveness our apparatus simple setup affordable devices short-term or long-term spatiotemporal analysis. technique well suited built environments, bioaerosols health purposes fine-scale studies.

Language: Английский

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Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges

FEMS Microbiology Ecology, Journal Year: 2023, Volume and Issue: 99(10)

Published: Sept. 4, 2023

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range metabolic capabilities, microorganisms are affected with consequences on host organisms functioning environment. They also play key roles in fate pollutants through degradation, transformation, transfer organic or inorganic compounds. Thus, they crucial for development nature-based solutions to reduce bio-based environmental risk assessment chemicals. At intersection between microbial ecology, toxicology, biogeochemistry, ecotoxicology a fast-expanding research area aiming decipher interactions microorganisms. This perspective paper gives an overview identified Ecotoxicomic network within emerging One Health framework light ongoing interest biological approaches remediation current state art ecology. We highlight prevailing knowledge gaps pitfalls exploring complex among environment context chemical pinpoint areas where future efforts needed.

Language: Английский

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Bacterial Community Composition and Diversity of Soils from Different Geographical Locations in the Northeastern USA

Microbiology Research, Journal Year: 2025, Volume and Issue: 16(2), P. 47 - 47

Published: Feb. 14, 2025

Soil is the most dynamic matrix in environment and where biogeochemical cycles take place through activities of microorganisms such as bacteria. A 16S rRNA sequence analysis seven different soil samples from geographical locations northeastern part United States America was conducted order to determine bacterial community composition diversity whether distance affects composition. Microbial DNA extracted each sample next generation sequencing performed. Overall, predominant phyla with high relative abundance were found be members Pseudomonadota, Actinomycetota, Acidobacteriota, Chloroflexota, Bacteroidota which comprised core microbiome all 7 soils analyzed. At level, top four bacteria belonged Rhizobiales, Actinomycetales, Gaiellales, Solirubrobacterales. Bacterial identification at genus level predominantly unclassified an average 58%. However, when possible, abundant genera detected Bradyrhizobium Rhodoplanes. Surface states New York, Maryland, Delaware showed lowest compared suburban state Jersey. Similarity between communities decreased increasing distance, indicating dispersal limitations some colonize habitats types show others did not. samples, deterministic factors land management possible vehicle emissions probably affected assemblage communities. Stochastic processes might have determined biogeographical distribution influencing structure diversity.

Language: Английский

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Microbial genomics and genome sequencing approaches

Elsevier eBooks, Journal Year: 2025, Volume and Issue: unknown, P. 3 - 20

Published: Jan. 1, 2025

Language: Английский

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Molecular tools for environmental monitoring: A review of metabarcoding studies applied to a strategic Italian Peninsula, the Apulian region

Journal of Ecology and the Natural Environment, Journal Year: 2025, Volume and Issue: 17(1), P. 1 - 12

Published: Jan. 31, 2025

Language: Английский

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Consequences of Domestication on Gut Microbiome: A Comparative Analysis Between Wild Boars and Domestic Pigs

Animals, Journal Year: 2025, Volume and Issue: 15(5), P. 747 - 747

Published: March 5, 2025

The gut microbiota plays a vital role in the physiological functions and health of animals. Domestic pigs (Sus scrofa domesticus) wild boars scrofa), which share common ancestor, present unique model for exploring evolutionary changes due to domestication. Comparing these two groups provides opportunity identify microorganisms that may have been lost or altered during This study employed 16S rRNA sequencing compare compositions domestic boars, analyzing 69 fecal samples from both groups. Our results indicate significant differences taxonomic profiles between Specifically, genera Bifidobacterium Lactobacillus, were found higher abundance boars. In contrast, exhibited decreased variety potentially health-enhancing bacteria, likely factors such as simplified diets antibiotic use. Functional gene analysis revealed pathways related carbohydrate metabolism, lipid immune response, environmental adaptability more enriched These findings demonstrate composition underscoring impact domestication on microbial diversity. Further research is necessary explore potential transferring beneficial microbes populations.

Language: Английский

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Evaluation of soil fungal communities using the ITS2 sublocus and 18S gene primers under different amplification methods

Fungal ecology, Journal Year: 2025, Volume and Issue: 76, P. 101425 - 101425

Published: April 10, 2025

Language: Английский

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Fungal Microbiota in Peritoneal Dialysis Effluent Related Peritonitis Patients by Amplicon Sequencing of Internal Transcribed Spacer based on Oxford Nanopore Technologies

Fungal Biology, Journal Year: 2025, Volume and Issue: unknown, P. 101587 - 101587

Published: April 1, 2025

Language: Английский

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Dynamic Changes in Prokaryotic and Eukaryotic Communities and Networks in Minimally Managed Cabbage-Cultivated Field Soils

Genes, Journal Year: 2025, Volume and Issue: 16(5), P. 482 - 482

Published: April 24, 2025

Background/Objectives: Taxonomic profiling of soil microbial communities is useful for assessing and monitoring the biological status agricultural land. In this study, we aimed to investigate changes in taxonomic structure organisms minimally managed fields. Methods: We used DNA metabarcoding both terrestrial prokaryotes eukaryotes cabbage-cultivated uncultivated sites a field central Japan from February August 2021. Analyses relative abundances prokaryotic eukaryotic sequence variants (SVs) their β-diversities, subsequent redundancy analysis (RDA) clarified dynamic during cultivation. further investigated fungi-, protist-, animal-derived SVs, abundant SVs each phylum, as well co-occurrence networks top 150 SVs. Results: The results revealed that fractions predatory or parasitic protists animals increased, whereas those fungi earthworm Enchytraeus spp. decreased. derived diatoms, Ciliophora, class Vampyrellidae (Cercozoa), mites increased subsequently decreased period. These findings suggest fed on bacteria autotrophic (such diatoms) propagated spring, followed by propagation parasitism host eukaryotes. also changed, especially markedly changed April May, May June–August, supporting observations mentioned above. Conclusions: indicate sequential fields with minimal practices could be sustainable natural farming.

Language: Английский

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A case study of environmental pollution by pathogenic bacteria and metal(oid)s at Soran Landfill Site, Erbil, Iraqi Kurdistan Region

Environmental Monitoring and Assessment, Journal Year: 2023, Volume and Issue: 195(7)

Published: June 7, 2023

Environmental pollution is a serious issue all around the world, especially when it caused by metal(oid)s and pathogenic microorganisms. This study reports here for first time on contamination of soil water with bacteria directly resulting from Soran Landfill Site. landfill level 2 solid waste disposal site that lacks leachate collection infrastructure. The potentially an environmental public hazard content significantly dangerous microorganisms through release into nearby river. levels As, Cd, Co, Cr, Cu, Mn, Mo, Pb, Zn, Ni obtained inductively coupled plasma mass spectrometer in soil, stream mud, samples. Five indices are used to assess potential risks. According indices, Cd Pb significant, whereas Zn moderate. A total 32 isolates were defined liquid samples: 18, 9, 5, respectively. Moreover, 16 s rRNA analysis suggested belong three enteric bacterial phyla Proteobacteria, Actinobacteria, Firmicutes. closest GenBank matches 16S rDNA sequences indicated presence genera: Pseudomonas, Bacillus, Lysinibacillus, Exiguobacterium, Trichococcus, Providencia, Enterococcus, Macrococcus, Serratia, Salinicoccus, Proteus, Rhodococcus, Brevibacterium, Shigella, Micrococcus, Morganella, Corynebacterium, Escherichia, Acinetobacter. identity percentage was mostly between 95%-100%. results this show microbiological geochemical soils, surface ground harmful toxic originating specifically which subsequently incorporated surrounding environment, creating thus considerable health risk.

Language: Английский

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