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Rossi F, Duchaine C, Tignat-Perrier R, Joly M, Larose C, Dommergue A, Turgeon N, Veillette M, Sellegri K, Baray JL, Amato P. Temporal variations of antimicrobial resistance genes in aerosols: A one-year monitoring at the puy de Dôme summit (Central France). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169567. [PMID: 38145686 DOI: 10.1016/j.scitotenv.2023.169567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/27/2023]
Abstract
The recent characterization of antibiotic resistance genes (ARGs) in clouds evidenced that the atmosphere actively partakes in the global spreading of antibiotic resistance worldwide. Indeed, the outdoor atmosphere continuously receives large quantities of particles of biological origins, emitted from both anthropogenic or natural sources at the near Earth's surface. Nonetheless, our understanding of the composition of the atmospheric resistome, especially at mid-altitude (i.e. above 1000 m a.s.l.), remains largely limited. The atmosphere is vast and highly dynamic, so that the diversity and abundance of ARGs are expected to fluctuate both spatially and temporally. In this work, the abundance and diversity of ARGs were assessed in atmospheric aerosol samples collected weekly between July 2016 and August 2017 at the mountain site of puy de Dôme (1465 m a.s.l., central France). Our results evidence the presence of 33 different subtypes of ARGs in atmospheric aerosols, out of 34 assessed, whose total concentration fluctuated seasonally from 59 to 1.1 × 105 copies m-3 of air. These were heavily dominated by genes from the quinolone resistance family, notably the qepA gene encoding efflux pump mechanisms, which represented >95 % of total ARGs concentration. Its abundance positively correlated with that of bacteria affiliated with the genera Kineococcus, Neorhizobium, Devosia or Massilia, ubiquitous in soils. This, along with the high abundance of Sphingomonas species, points toward a large contribution of natural sources to the airborne ARGs. Nonetheless, the increased contribution of macrolide resistance (notably the erm35 gene) during winter suggests a sporadic diffusion of ARGs from human activities. Our observations depict the atmosphere as an important vector of ARGs from terrestrial sources. Therefore, monitoring ARGs in airborne microorganisms appears necessary to fully understand the dynamics of antimicrobial resistances in the environment and mitigate the threats they may represent.
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Affiliation(s)
- Florent Rossi
- Département de biochimie, de microbiologie et de bio-informatique, Faculté́ des sciences et de génie, Université́ Laval, Québec, Canada; Centre de recherche de l'institut de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Caroline Duchaine
- Département de biochimie, de microbiologie et de bio-informatique, Faculté́ des sciences et de génie, Université́ Laval, Québec, Canada; Centre de recherche de l'institut de cardiologie et de pneumologie de Québec, Québec, Canada; Canada Research Chair on Bioaerosols, Canada.
| | - Romie Tignat-Perrier
- Laboratoire Ampère, École Centrale de Lyon, CNRS, Université de Lyon, Ecully, France; Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, INRAE, Grenoble INP, Grenoble, France
| | - Muriel Joly
- Université Clermont Auvergne, CNRS, Institut de Chimie de Clermont-Ferrand, Clermont-Ferrand, France
| | - Catherine Larose
- Laboratoire Ampère, École Centrale de Lyon, CNRS, Université de Lyon, Ecully, France
| | - Aurélien Dommergue
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, INRAE, Grenoble INP, Grenoble, France
| | - Nathalie Turgeon
- Département de biochimie, de microbiologie et de bio-informatique, Faculté́ des sciences et de génie, Université́ Laval, Québec, Canada; Centre de recherche de l'institut de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Marc Veillette
- Département de biochimie, de microbiologie et de bio-informatique, Faculté́ des sciences et de génie, Université́ Laval, Québec, Canada; Centre de recherche de l'institut de cardiologie et de pneumologie de Québec, Québec, Canada
| | - Karine Sellegri
- Université Clermont Auvergne, CNRS, Laboratoire de Météorologie physique, UMR 6016, Clermont-Ferrand, France
| | - Jean-Luc Baray
- Université Clermont Auvergne, CNRS, Observatoire de physique du Globe de Clermont-Ferrand, UAR 833, Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Laboratoire de Météorologie physique, UMR 6016, Clermont-Ferrand, France
| | - Pierre Amato
- Université Clermont Auvergne, CNRS, Institut de Chimie de Clermont-Ferrand, Clermont-Ferrand, France
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Lappan R, Thakar J, Molares Moncayo L, Besser A, Bradley JA, Goordial J, Trembath-Reichert E, Greening C. The atmosphere: a transport medium or an active microbial ecosystem? THE ISME JOURNAL 2024; 18:wrae092. [PMID: 38804464 PMCID: PMC11214262 DOI: 10.1093/ismejo/wrae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- School of Earth, Atmosphere & Environment, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
| | - Jordan Thakar
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Laura Molares Moncayo
- School of Geography, Queen Mary University of London, London E1 4NS, United Kingdom
- Natural History Museum, London SW7 5BD, United Kingdom
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
| | - Alexi Besser
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, United States
| | - James A Bradley
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jacqueline Goordial
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | | | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
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Ray AE, Tribbia DZ, Cowan DA, Ferrari BC. Clearing the air: unraveling past and guiding future research in atmospheric chemosynthesis. Microbiol Mol Biol Rev 2023; 87:e0004823. [PMID: 37914532 PMCID: PMC10732025 DOI: 10.1128/mmbr.00048-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2023] Open
Abstract
SUMMARY Atmospheric chemosynthesis is a recently proposed form of chemoautotrophic microbial primary production. The proposed process relies on the oxidation of trace concentrations of hydrogen (≤530 ppbv), carbon monoxide (≤90 ppbv), and methane (≤1,870 ppbv) gases using high-affinity enzymes. Atmospheric hydrogen and carbon monoxide oxidation have been primarily linked to microbial growth in desert surface soils scarce in liquid water and organic nutrients, and low in photosynthetic communities. It is well established that the oxidation of trace hydrogen and carbon monoxide gases widely supports the persistence of microbial communities in a diminished metabolic state, with the former potentially providing a reliable source of metabolic water. Microbial atmospheric methane oxidation also occurs in oligotrophic desert soils and is widespread throughout copiotrophic environments, with established links to microbial growth. Despite these findings, the direct link between trace gas oxidation and carbon fixation remains disputable. Here, we review the supporting evidence, outlining major gaps in our understanding of this phenomenon, and propose approaches to validate atmospheric chemosynthesis as a primary production process. We also explore the implications of this minimalistic survival strategy in terms of nutrient cycling, climate change, aerobiology, and astrobiology.
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Affiliation(s)
- Angelique E. Ray
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Dana Z. Tribbia
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
| | - Don A. Cowan
- Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Belinda C. Ferrari
- School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, Australia
- Australian Centre for Astrobiology, UNSW Sydney, Sydney, Australia
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Casamayor EO, Cáliz J, Triadó-Margarit X, Pointing SB. Understanding atmospheric intercontinental dispersal of harmful microorganisms. Curr Opin Biotechnol 2023; 81:102945. [PMID: 37087840 DOI: 10.1016/j.copbio.2023.102945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/01/2023] [Accepted: 03/20/2023] [Indexed: 04/25/2023]
Abstract
The atmosphere is a major route for microbial intercontinental dispersal, including harmful microorganisms, antibiotic resistance genes, and allergens, with strong implications in ecosystem functioning and global health. Long-distance dispersal is facilitated by air movement at higher altitudes in the free troposphere and is affected by anthropogenic forcing, climate change, and by the general atmospheric circulation, mainly in the intertropical convergence zone. The survival of microorganisms during atmospheric transport and their remote invasive potential are fundamental questions, but data are scarce. Extreme atmospheric conditions represent a challenge to survival that requires specific adaptive strategies, and recovery of air samples from the high altitudes relevant to study harmful microorganisms can be challenging. In this paper, we highlight the scope of the problem, identify challenges and knowledge gaps, and offer a roadmap for improved understanding of intercontinental microbial dispersal and their outcomes. Greater understanding of long-distance dispersal requires research focus on local factors that affect emissions, coupled with conditions influencing transport and survival at high altitudes, and eventual deposition at sink locations.
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Affiliation(s)
- Emilio O Casamayor
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain.
| | - Joan Cáliz
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Xavier Triadó-Margarit
- Ecology of the Global Microbiome, Center for Advanced Studies of Blanes-CSIC, E-17300 Blanes, Spain
| | - Stephen B Pointing
- Yale-NUS College & Department of Biological Sciences, National University of Singapore, Singapore
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Basapathi Raghavendra J, Mathanlal T, Zorzano MP, Martin-Torres J. An Optimized Active Sampling Procedure for Aerobiological DNA Studies. SENSORS (BASEL, SWITZERLAND) 2023; 23:2836. [PMID: 36905039 PMCID: PMC10006969 DOI: 10.3390/s23052836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/02/2023] [Accepted: 03/03/2023] [Indexed: 06/18/2023]
Abstract
The Earth's atmosphere plays a critical role in transporting and dispersing biological aerosols. Nevertheless, the amount of microbial biomass in suspension in the air is so low that it is extremely difficult to monitor the changes over time in these communities. Real-time genomic studies can provide a sensitive and rapid method for monitoring changes in the composition of bioaerosols. However, the low abundance of deoxyribose nucleic acid (DNA) and proteins in the atmosphere, which is of the order of the contamination produced by operators and instruments, poses a challenge for the sampling process and the analyte extraction. In this study, we designed an optimized, portable, closed bioaerosol sampler based on membrane filters using commercial off-the-shelf components, demonstrating its end-to-end operation. This sampler can operate autonomously outdoors for a prolonged time, capturing ambient bioaerosols and avoiding user contamination. We first performed a comparative analysis in a controlled environment to select the optimal active membrane filter based on its ability to capture and extract DNA. We have designed a bioaerosol chamber for this purpose and tested three commercial DNA extraction kits. The bioaerosol sampler was tested outdoors in a representative environment and run for 24 h at 150 L/min. Our methodology suggests that a 0.22-µm polyether sulfone (PES) membrane filter can recover up to 4 ng of DNA in this period, sufficient for genomic applications. This system, along with the robust extraction protocol, can be automated for continuous environmental monitoring to gain insights into the time evolution of microbial communities within the air.
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Affiliation(s)
| | - Thasshwin Mathanlal
- Department of Planetary Sciences, School of Geosciences, University of Aberdeen, Aberdeen AB24 3UE, UK
| | - Maria-Paz Zorzano
- Centro de Astrobiología (CSIC-INTA), Torrejon de Ardoz, 28850 Madrid, Spain
| | - Javier Martin-Torres
- Department of Planetary Sciences, School of Geosciences, University of Aberdeen, Aberdeen AB24 3UE, UK
- Instituto Andaluz de Ciencias de la Tierra (CSIC-UGR), 18100 Granada, Spain
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Tholcke LC, Fang WH, Gornick BR, Schlechter JA. Investigating Particulate Production in The Operating Suite Following the Use of Waterless Alcohol Based Dry Scrub Versus Traditional Hand Washing and Drying with Commonly Used Surgical Towels: An Experimental Study. Am J Infect Control 2022; 51:551-556. [PMID: 35901994 DOI: 10.1016/j.ajic.2022.07.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 07/19/2022] [Accepted: 07/20/2022] [Indexed: 11/01/2022]
Abstract
BACKGROUND An often-overlooked item that could cause contamination in the operating suite are the towels used for hand drying following surgical scrub. The purpose of this current study was to determine if there was a difference in the particulate count from different hand drying methods following surgical hand preparation. METHODS Three simulated hand drying groups were established: disposable sterilized surgical towels, reusable sterilized surgical towels, and a waterless alcohol-based dry rub. Particle size measurements of 0.3 µm, 5.0 µm, and 10.0 µm were collected at time zero and repeated every minute for 5 minutes for a total of 10 trials each. RESULTS Both the reusable and disposable towels produced significantly more particle matter in all size groups compared to the alcohol scrub control group. A comparison analysis and ANOVA testing demonstrated that alcohol dry scrub produced significantly fewer particles compared to both the disposable blue towels (P<0.01) and the reusable green towels (P<0.01). Disposable towels produced significantly more particles in the 0.3 µm count compared to reusable towels (P<0.05). CONCLUSIONS An alcohol-based dry rub without using a towel yielded the lowest amount of particulate formation in this experimental model, while reusable surgical towels produced the highest number of particles. LEVEL OF EVIDENCE Level II Experimental Study.
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Affiliation(s)
- Loren C Tholcke
- Department of Orthopaedic Surgery, Children's Hospital of Orange County, Orange, CA; Department of Orthopaedic Surgery, Riverside University Health System Medical Center, Moreno Valley, CA.
| | - William H Fang
- Department of Translational Medicine, Western University of Health Sciences, CA.
| | - Bryn R Gornick
- Department of Orthopaedic Surgery, Children's Hospital of Orange County, Orange, CA.
| | - John A Schlechter
- Department of Orthopaedic Surgery, Children's Hospital of Orange County, Orange, CA; Department of Orthopaedic Surgery, Riverside University Health System Medical Center, Moreno Valley, CA.
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Jiang S, Sun B, Zhu R, Che C, Ma D, Wang R, Dai H. Airborne microbial community structure and potential pathogen identification across the PM size fractions and seasons in the urban atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 831:154665. [PMID: 35314242 DOI: 10.1016/j.scitotenv.2022.154665] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/14/2022] [Accepted: 03/14/2022] [Indexed: 06/14/2023]
Abstract
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 PM1.0, PM2.5, 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 PM1.0 were one to two orders of magnitude higher than those in PM2.5 and PM10 across seasons, but their α-diversity tended to increase from PM1.0 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.
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Affiliation(s)
- Shaoyi Jiang
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Bowen Sun
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Renbin Zhu
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China.
| | - Chenshuai Che
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
| | - Dawei Ma
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Runfang Wang
- State Grid Anhui Electric Power Research Institute, Hefei 230601, China
| | - Haitao Dai
- Institute of Polar Environment & Anhui Key Laboratory of Polar Environment and Global Change, School of Earth and Space Sciences, University of Science and Technology of China, Hefei 230026, China
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Munyaneza J, Jia Q, Qaraah FA, Hossain MF, Wu C, Zhen H, Xiu G. A review of atmospheric microplastics pollution: In-depth sighting of sources, analytical methods, physiognomies, transport and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 822:153339. [PMID: 35077799 DOI: 10.1016/j.scitotenv.2022.153339] [Citation(s) in RCA: 34] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 01/16/2022] [Accepted: 01/18/2022] [Indexed: 06/14/2023]
Abstract
Micro-sized plastics were first examined for atmospheric environment in 2016. From then on, they have been detected in both indoor and outdoor atmospheric samples, with indoor environments demonstrated as containing a big proportion of these particles. The sparse distribution of these particles, is attributed to their swift and long distance transportation that is mainly eased by their tiny size (1 μm to 5 mm) and low density. Due to ongoing limitation on detectable size, analysis methods together with a lack of standardized sampling and analytical procedures, few studies were conducted on airborne microplastics (MPs). Thus, the facts regarding the occurrence, global spatial distribution, fate, and threats to ecosystem and human health of airborne MPs, are still far from being fully clarified. This literature review is a broad depiction of a state of knowledge on atmospheric MPs. Within it, robust and concise information on the sources, inspection, transport, and threats pertaining to airborne MPs are presented. Particularly, the paper entails some information concerning traffic-generated MPs pollution, which has not been frequently discussed within previously published reports. In addition, this paper has widely unveiled sectors and aspects in need of further attention, with the gaps to be filled pinpointed.
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Affiliation(s)
- Janvier Munyaneza
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Qilong Jia
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Fahim A Qaraah
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Md Faysal Hossain
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Chengzi Wu
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Huajun Zhen
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Guangli Xiu
- Shanghai Environmental Protection Key Laboratory on Environmental Standard and Risk Management of Chemical Pollutants, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; State Environmental Protection Key Lab of Environmental Risk Assessment and Control on Chemical Processes, School of Resources & Environmental Engineering, East China University of Science and Technology, Shanghai 200237, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai 200092, China.
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Analysis of Environmental and Pathogenic Bacteria Attached to Aerosol Particles Size-Separated with a Metal Mesh Device. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19095773. [PMID: 35565166 PMCID: PMC9099785 DOI: 10.3390/ijerph19095773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 05/04/2022] [Accepted: 05/06/2022] [Indexed: 02/01/2023]
Abstract
Metal mesh devices (MMDs) are novel materials that enable the precise separation of particles by size. Structurally, MMDs consist of a periodic arrangement of square apertures of characteristic shapes and sizes on a thin nickel membrane. The present study describes the separation of aerosol particles using palm-top-size collection devices equipped with three types of MMDs differing in pore size. Aerosols were collected at a farm located in the suburbs of Nairobi, Kenya; aerosol particles were isolated, and pathogenic bacteria were identified in this microflora by next-generation sequencing analysis. The composition of the microflora in aerosol particles was found to depend on particle size. Gene fragments were obtained from the collected aerosols by PCR using primers specific for the genus Mycobacterium. This analysis showed that Mycobacterium obuense, a non-tuberculous species of mycobacteria that causes lung diseases, was present in these aerosols. These findings showed that application of this MMD analytical protocol to aerosol particles can facilitate the investigation of airborne pathogenic bacteria.
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10
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Mehmood T, Peng L. Polyethylene scaffold net and synthetic grass fragmentation: a source of microplastics in the atmosphere? JOURNAL OF HAZARDOUS MATERIALS 2022; 429:128391. [PMID: 35236024 DOI: 10.1016/j.jhazmat.2022.128391] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/19/2022] [Accepted: 01/27/2022] [Indexed: 05/12/2023]
Abstract
Microplastics (MPs) implications in the atmosphere are of current global concern. Currently, there is a growing interest regarding source appointment, fate, level of toxicity, and exposure intensity of ambient air MPs. Recent data suggest that polyethylene (PE) dominates ambient MPs in China's megacities. Albeit understanding of PE sources is limited and restricted to typical sources polluting terrestrial and marine environments. However, the air is a distinct environmental component and may have some separate pollution sources as well as the relative contribution of different sources could also contrast in different environments. Urbanization and fast construction activity resulting from increased economic growth in these places might be a potential source of ambient PE. Recently, the use of scaffold netting on construction sites and synthetic grass as land covering sheets has been on the rise. Generally, these PE items are often inferior and composed of recycled material, making them more prone to degradation. Also, because these items were continually exposed to open air, there is a considerable risk of fragmentation and atmospheric mixing. Therefore, unchecked and excessive usage of these materials can be risky. Here, PE's physical and chemical characteristics, transport and health risks in urban air are discussed here.
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Affiliation(s)
- Tariq Mehmood
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, PR China; College of Ecology and Environment, Hainan University, Haikou, Hainan Province, PR China 570228
| | - Licheng Peng
- Key Laboratory of Agro-Forestry Environmental Processes and Ecological Regulation of Hainan Province, PR China; College of Ecology and Environment, Hainan University, Haikou, Hainan Province, PR China 570228.
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11
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Diversity and Source of Airborne Microbial Communities at Differential Polluted Sites of Rome. ATMOSPHERE 2022. [DOI: 10.3390/atmos13020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Biogenic fraction of airborne PM10 which includes bacteria, viruses, fungi and pollens, has been proposed as one of the potential causes of the PM10 toxicity. The present study aimed to provide a comprehensive understanding of the microbial community variations associated to PM10, and their main local sources in the surrounding environment in three urban sites of Rome, characterized by differential pollution rate: green area, residential area and polluted area close to the traffic roads. We combined high-throughput amplicon sequencing of the bacterial 16S rRNA gene and the fungal internal transcribed spacer (ITS) region, with detailed chemical analysis of particulate matter sampled from air, paved road surfaces and leaf surfaces of Quercus ilex. Our results demonstrated that bacterial and fungal airborne communities were characterized by the highest alpha-diversity and grouped separately from epiphytic and road dust communities. The reconstruction of source-sink relationships revealed that the resuspension/deposition of road dust from traffic might contribute to the maximum magnitude of microbial exchanges. The relative abundance of extremotolerant microbes was found to be enhanced in epiphytic communities and was associated to a progressively increase of pollution levels as well as opportunistic human pathogenicity in fungal communities.
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12
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Tan H, Wong KY, Nyakuma BB, Kamar HM, Chong WT, Wong SL, Kang HS. Systematic study on the relationship between particulate matter and microbial counts in hospital operating rooms. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:6710-6721. [PMID: 34458973 PMCID: PMC8403507 DOI: 10.1007/s11356-021-16171-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 08/22/2021] [Indexed: 06/04/2023]
Abstract
In this study, a systematic procedure for establishing the relationship between particulate matter (PM) and microbial counts in four operating rooms (ORs) was developed. The ORs are located in a private hospital on the western coast of Peninsular Malaysia. The objective of developing the systematic procedure is to ensure that the correlation between the PMs and microbial counts are valid. Each of the procedures is conducted based on the ISO, IEST, and NEBB standards. The procedures involved verifying the operating parameters are air change rate, room differential pressure, relative humidity, and air temperature. Upon verifying that the OR parameters are in the recommended operating range, the measurements of the PMs and sampling of the microbes were conducted. The TSI 9510-02 particle counter was used to measure three different sizes of PMs: PM 0.5, PM 5, and PM 10. The MAS-100ECO air sampler was used to quantify the microbial counts. The present study confirms that PM 0.5 does not have an apparent positive correlation with the microbial count. However, the evident correlation of 7% and 15% were identified for both PM 5 and PM 10, respectively. Therefore, it is suggested that frequent monitoring of both PM 5 and PM 10 should be practised in an OR before each surgical procedure. This correlation approach could provide an instantaneous estimation of the microbial counts present in the OR.
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Affiliation(s)
- Huiyi Tan
- School of Chemical and Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Keng Yinn Wong
- School of Mechanical Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
- Process Systems Engineering Centre (PROSPECT), Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
| | - Bemgba Bevan Nyakuma
- Department of Chemistry, Faculty of Sciences, Benue State University, Makurdi, Benue State, P. M. B 102119, Nigeria
| | - Haslinda Mohamed Kamar
- School of Mechanical Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Wen Tong Chong
- Department of Mechanical Engineering, Faculty of Engineering, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Syie Luing Wong
- Dpto. Matemática Aplicada, Ciencia e Ingeniería de Materiales y Tecnología Electrónica, Universidad Rey Juan Carlos, C/ Tulipán s/n, Móstoles, Madrid, Spain
| | - Hooi Siang Kang
- School of Mechanical Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
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13
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Triadó-Margarit X, Cáliz J, Casamayor EO. A long-term atmospheric baseline for intercontinental exchange of airborne pathogens. ENVIRONMENT INTERNATIONAL 2022; 158:106916. [PMID: 34627012 DOI: 10.1016/j.envint.2021.106916] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/30/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
The atmosphere is a potential pathway for global-scale and long-range dispersal of viable microorganisms, promoting biological interconnections among the total environment. We aimed to provide relevant baseline information for long-range long-term intercontinental exchange of potentially infectious airborne microorganisms of major interest in environmental and health-related disciplines. We used an interannual survey (7-y) with wet depositions fortnightly collected above the boundary layer (free troposphere) at a remote high-elevation LTER (Long-Term-Ecological-Research) site, analyzed by 16S and 18S rRNA genes, and compared to a database of 475 well-known pathogens. We applied a conservative approach on close relatives of pathogenic species (>98% identity) standing their theoretical upper limit for atmospheric baseline relative abundances. We identified c. 2-3% of the total airborne microbiota as potential pathogens. Their most frequent environmental origins were soil, aquatic, and anthropogenic sources. Phytopathogens (mostly fungi) were the potential infectious agents most widely present. We uncovered consistent interannual dynamics with taxa foreseeable over time (i.e., predictable seasonal behavior) and under recurrent environmental scenarios (e.g., Saharan dust intrusions), respectively, being highly valuable microbial forensic environmental indicators. Up to 8 bacterial and 21 fungal genera consistently showed temporal abundances and recurrences unevenly distributed. Incidence of allergenic fungi was lower in summer, and significantly higher in spring. Close relatives to Coccidioides posadasii consistently showed higher signals (i.e., high specificity and high fidelity) in winter, whereas Cryptococcus neoformans had a significant signal in spring. Along Saharan dust intrusions, the bacterial phytopathogens Acidovorax avenae and Agrobacterium tumefaciens and the fungal phytopathogens Pseudozyma hubeiensis and Peniophora sp. consistently showed higher signals. Potential human pathogens showed low proportion, being mostly fungal allergens. Microorganisms related to obligated human, amphibian and fish pathogens were commonly found in winter. More studies in remote field sites above the boundary layer will unveil whether or not a similar trend is found globally.
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Affiliation(s)
- Xavier Triadó-Margarit
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Joan Cáliz
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain
| | - Emilio O Casamayor
- Integrative Freshwater Ecology Group & LTER-AT Research Group, Centre of Advanced Studies of Blanes-Spanish Council for Research CEAB-CSIC, Blanes E-17300, Spain.
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14
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Allen S, Allen D, Baladima F, Phoenix VR, Thomas JL, Le Roux G, Sonke JE. Evidence of free tropospheric and long-range transport of microplastic at Pic du Midi Observatory. Nat Commun 2021; 12:7242. [PMID: 34934062 PMCID: PMC8692471 DOI: 10.1038/s41467-021-27454-7] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Accepted: 11/05/2021] [Indexed: 11/16/2022] Open
Abstract
The emerging threat of atmospheric microplastic pollution has prompted researchers to study areas previously considered beyond the reach of plastic. Investigating the range of atmospheric microplastic transport is key to understanding the global extent of this problem. While atmospheric microplastics have been discovered in the planetary boundary layer, their occurrence in the free troposphere is relatively unexplored. Confronting this is important because their presence in the free troposphere would facilitate transport over greater distances and thus the potential to reach more distal and remote parts of the planet. Here we show evidence of 0.09-0.66 microplastics particles/m3 over 4 summer months from the Pic du Midi Observatory at 2877 meters above sea level. These results exhibit true free tropospheric transport of microplastic, and high altitude microplastic particles <50 µm (aerodynamic diameter). Analysis of air/particle history modelling shows intercontinental and trans-oceanic transport of microplastics illustrating the potential for global aerosol microplastic transport.
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Affiliation(s)
- S. Allen
- grid.11984.350000000121138138Centre for Water, Environment, Sustainability and Public Health (WESP), Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, G11XJ UK ,grid.508721.9Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, CNRS, Toulouse, France ,grid.6572.60000 0004 1936 7486School of Geography/Institute for Global Innovation, University of Birmingham, Birmingham, B15 2TT UK
| | - D. Allen
- grid.11984.350000000121138138Centre for Water, Environment, Sustainability and Public Health (WESP), Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, G11XJ UK ,grid.508721.9Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, CNRS, Toulouse, France
| | - F. Baladima
- grid.5676.20000000417654326Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, IGE, 38000 Grenoble, France
| | - V. R. Phoenix
- grid.11984.350000000121138138Centre for Water, Environment, Sustainability and Public Health (WESP), Department of Civil and Environmental Engineering, University of Strathclyde, Glasgow, G11XJ UK
| | - J. L. Thomas
- grid.5676.20000000417654326Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, IGE, 38000 Grenoble, France
| | - G. Le Roux
- grid.508721.9Laboratoire écologie fonctionnelle et environnement, Université de Toulouse, CNRS, Toulouse, France
| | - J. E. Sonke
- grid.15781.3a0000 0001 0723 035XGéosciences Environnement Toulouse, CNRS/IRD/Université Paul Sabatier, Toulouse, 3 France
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15
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Liao Z, Ji X, Ma Y, Lv B, Huang W, Zhu X, Fang M, Wang Q, Wang X, Dahlgren R, Shang X. Airborne microplastics in indoor and outdoor environments of a coastal city in Eastern China. JOURNAL OF HAZARDOUS MATERIALS 2021; 417:126007. [PMID: 33992007 DOI: 10.1016/j.jhazmat.2021.126007] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/22/2021] [Accepted: 04/28/2021] [Indexed: 05/09/2023]
Abstract
Microplastics (MPs) in marine and terrestrial environments have been intensively studied, but the dynamics of airborne MPs remains limited. Existing studies on atmospheric MPs are mostly derived from collection of atmospheric deposition, whereas direct measurements of airborne MPs are scarce. However, the abundance of airborne MPs is more relevant for evaluating human inhalation exposure risk. Herein, airborne MPs in indoor and outdoor environments from urban and rural areas of a coastal city in eastern China were investigated. MP concentrations (mean±SD) in indoor air (1583 ± 1180 n/m3) were an order of magnitude higher than outdoor air (189 ± 85 n/m3), and airborne MP concentrations in urban areas (224 ± 70 n/m3) were higher than rural areas (101 ± 47 n/m3). MPs smaller than 100 µm dominated airborne MPs, and the predominant shape of airborne MPs was fragments, as opposed to fibers. The larger MP size fractions contained a higher proportion of fibers, whereas the smaller size fractions were nearly exclusively composed of fragments. The health risk caused by ubiquitous airborne MPs should not be discounted as the maximum annual outdoor exposure of airborne MPs can reach 1 million/year, while indoor exposure may be even higher due to higher indoor airborne MP concentrations.
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Affiliation(s)
- Zhonglu Liao
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Xiaoliang Ji
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Yuan Ma
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Baoqiang Lv
- School of Life and Environmental Science, National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou 325035, China
| | - Wei Huang
- Laboratory of Marine Ecosystem and Biogeochemistry, Second Institute of Oceanography SOA, Hangzhou 310012, China
| | - Xuan Zhu
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Mingzhu Fang
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China
| | - Qi Wang
- School of Life and Environmental Science, National & Local Joint Engineering Research Center for Ecological Treatment Technology of Urban Water Pollution, Wenzhou University, Wenzhou 325035, China
| | - Xuedong Wang
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China.
| | - Randy Dahlgren
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China; Department of Land, Air and Water Resources, University of California Davis, CA 95616, USA
| | - Xu Shang
- Key Laboratory of Watershed Sciences and Health of Zhejiang Province, School of Public Health and Management, Wenzhou Medical University, Wenzhou 325035, China.
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16
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Akanyange SN, Lyu X, Zhao X, Li X, Zhang Y, Crittenden JC, Anning C, Chen T, Jiang T, Zhao H. Does microplastic really represent a threat? A review of the atmospheric contamination sources and potential impacts. THE SCIENCE OF THE TOTAL ENVIRONMENT 2021; 777:146020. [PMID: 33677289 DOI: 10.1016/j.scitotenv.2021.146020] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/14/2021] [Accepted: 02/16/2021] [Indexed: 06/12/2023]
Abstract
Microplastics (MPs) are regarded as one of the major atmospheric contaminants that have gained wide attention across the globe in the current dispensation. Airborne MPs have been collected in atmospheric fallouts, in indoor and outdoor air as well as along roadways and indoor dust. The most dominating constituent shapes and forms of identified airborne MPs are fibers and synthetic textiles, respectively. With the breathing mechanism as a spontaneous practice for survival, the inhalation of airborne MPs is an inevitable deal. The level of toxicity of MPs to organisms stems from its physiochemical speciation. The smaller size and almost weightless nature make it possible to suspend in the atmosphere and be inhaled and create potential health problems. Nonetheless, the data available concerning the presence of airborne MPs and its environmental and human health impacts is limited. In this review, we extensively discuss the rigorous and suitable methodologies adopted for the analysis of airborne MPs in previous studies. The characteristics and sources of airborne MPs, the potential health impacts on humans, and some mitigating measures have also been discussed thoroughly.
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Affiliation(s)
- Stephen Nyabire Akanyange
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Xianjun Lyu
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Xiaohan Zhao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Xue Li
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Yan Zhang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China.
| | - John C Crittenden
- School of Civil and Environmental Engineering, Georgia Institute of Technology, 828 W. Peachtree Street, Suite 320, Atlanta, GA 30332-0595, USA
| | - Cosmos Anning
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Tianpeng Chen
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Tianlin Jiang
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
| | - Huaqing Zhao
- College of Safety and Environmental Engineering, Shandong University of Science and Technology, Qingdao 266000, China
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17
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Milani C, Lugli GA, Fontana F, Mancabelli L, Alessandri G, Longhi G, Anzalone R, Viappiani A, Turroni F, van Sinderen D, Ventura M. METAnnotatorX2: a Comprehensive Tool for Deep and Shallow Metagenomic Data Set Analyses. mSystems 2021; 6:e0058321. [PMID: 34184911 PMCID: PMC8269244 DOI: 10.1128/msystems.00583-21] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 06/10/2021] [Indexed: 12/04/2022] Open
Abstract
The use of bioinformatic tools for read-based taxonomic and functional analyses of metagenomic data sets, including their assembly and management, is rather fragmentary due to the absence of an accepted gold standard. Moreover, most currently available software tools need input of millions of reads and rely on approximations in data analysis in order to reduce computing times. These issues result in suboptimal results in terms of accuracy, sensitivity, and specificity when used either for the reconstruction of taxonomic or functional profiles through read analysis or analysis of genomes reconstructed by metagenomic assembly. Moreover, the recent introduction of novel DNA sequencing technologies that generate long reads, such as Nanopore and PacBio, represent a valuable data resource that still suffers from a lack of dedicated tools to perform integrated hybrid analysis alongside short read data. In order to overcome these limitations, here we describe a comprehensive bioinformatic platform, METAnnotatorX2, aimed at providing an optimized user-friendly resource which maximizes output quality, while also allowing user-specific adaptation of the pipeline and straightforward integrated analysis of both short and long read data. To further improve performance quality and accuracy of taxonomic assignment of reads and contigs, custom preprocessed and taxonomically revised genomic databases for viruses, prokaryotes, and various eukaryotes were developed. The performance of METAnnotatorX2 was tested by analysis of artificial data sets encompassing viral, archaeal, bacterial, and eukaryotic (fungal) sequence reads that simulate different biological matrices. Moreover, real biological samples were employed to validate in silico results. IMPORTANCE We developed a novel tool, i.e., METAnnotatorX2, that includes a number of new advanced features for analysis of deep and shallow metagenomic data sets and is accompanied by (regularly updated) customized databases for archaea, bacteria, fungi, protists, and viruses. Both software and databases were developed so as to maximize sensitivity and specificity while including support for shallow metagenomic data sets. Through extensive tests performed on Illumina and Nanopore artificial data sets, we demonstrated the high performance of the software to not only extract taxonomic and functional information from sequence reads but also to assemble and process genomes from metagenomic data. The robustness of these functionalities was validated using "real-life" data sets obtained from Illumina and Nanopore sequencing of biological samples. Furthermore, the performance of METAnnotatorX2 was compared to other available software tools for analysis of shotgun metagenomics data.
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Affiliation(s)
- Christian Milani
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Gabriele Andrea Lugli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Federico Fontana
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | - Leonardo Mancabelli
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Alessandri
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
| | - Giulia Longhi
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- GenProbio srl, Parma, Italy
| | | | | | - Francesca Turroni
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
| | - Douwe van Sinderen
- APC Microbiome Ireland and School of Microbiology, Bioscience Institute, National University of Ireland, Cork, Ireland
| | - Marco Ventura
- Laboratory of Probiogenomics, Department of Chemistry, Life Sciences, and Environmental Sustainability, University of Parma, Parma, Italy
- Microbiome Research Hub, University of Parma, Parma, Italy
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18
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DeFlorio W, Liu S, White AR, Taylor TM, Cisneros-Zevallos L, Min Y, Scholar EMA. Recent developments in antimicrobial and antifouling coatings to reduce or prevent contamination and cross-contamination of food contact surfaces by bacteria. Compr Rev Food Sci Food Saf 2021; 20:3093-3134. [PMID: 33949079 DOI: 10.1111/1541-4337.12750] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/28/2021] [Accepted: 03/06/2021] [Indexed: 12/29/2022]
Abstract
Illness as the result of ingesting bacterially contaminated foodstuffs represents a significant annual loss of human quality of life and economic impact globally. Significant research investment has recently been made in developing new materials that can be used to construct food contacting tools and surfaces that might minimize the risk of cross-contamination of bacteria from one food item to another. This is done to mitigate the spread of bacterial contamination and resultant foodborne illness. Internet-based literature search tools such as Web of Science, Google Scholar, and Scopus were utilized to investigate publishing trends within the last 10 years related to the development of antimicrobial and antifouling surfaces with potential use in food processing applications. Technologies investigated were categorized into four major groups: antimicrobial agent-releasing coatings, contact-based antimicrobial coatings, superhydrophobic antifouling coatings, and repulsion-based antifouling coatings. The advantages for each group and technical challenges remaining before wide-scale implementation were compared. A diverse array of emerging antimicrobial and antifouling technologies were identified, designed to suit a wide range of food contact applications. Although each poses distinct and promising advantages, significant further research investment will likely be required to reliably produce effective materials economically and safely enough to equip large-scale operations such as farms, food processing facilities, and kitchens.
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Affiliation(s)
- William DeFlorio
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Shuhao Liu
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA
| | - Andrew R White
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | | | - Luis Cisneros-Zevallos
- Department of Nutrition and Food Science, Texas A&M University, College Station, Texas, USA.,Department of Horticultural Sciences, Texas A&M University, College Station, Texas, USA
| | - Younjin Min
- Department of Chemical and Environmental Engineering, University of California, Riverside, California, USA
| | - Ethan M A Scholar
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas, USA.,Department of Materials Science and Engineering, Texas A&M University, College Station, Texas, USA
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19
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Experimental parameters defining ultra-low biomass bioaerosol analysis. NPJ Biofilms Microbiomes 2021; 7:37. [PMID: 33863892 PMCID: PMC8052325 DOI: 10.1038/s41522-021-00209-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/19/2021] [Indexed: 02/02/2023] Open
Abstract
Investigation of the microbial ecology of terrestrial, aquatic and atmospheric ecosystems requires specific sampling and analytical technologies, owing to vastly different biomass densities typically encountered. In particular, the ultra-low biomass nature of air presents an inherent analytical challenge that is confounded by temporal fluctuations in community structure. Our ultra-low biomass pipeline advances the field of bioaerosol research by significantly reducing sampling times from days/weeks/months to minutes/hours, while maintaining the ability to perform species-level identification through direct metagenomic sequencing. The study further addresses all experimental factors contributing to analysis outcome, such as amassment, storage and extraction, as well as factors that impact on nucleic acid analysis. Quantity and quality of nucleic acid extracts from each optimisation step are evaluated using fluorometry, qPCR and sequencing. Both metagenomics and marker gene amplification-based (16S and ITS) sequencing are assessed with regard to their taxonomic resolution and inter-comparability. The pipeline is robust across a wide range of climatic settings, ranging from arctic to desert to tropical environments. Ultimately, the pipeline can be adapted to environmental settings, such as dust and surfaces, which also require ultra-low biomass analytics.
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20
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Stern RA, Mahmoudi N, Buckee CO, Schartup AT, Koutrakis P, Ferguson ST, Wolfson JM, Wofsy SC, Daube BC, Sunderland EM. The Microbiome of Size-Fractionated Airborne Particles from the Sahara Region. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:1487-1496. [PMID: 33474936 DOI: 10.1021/acs.est.0c06332] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Diverse airborne microbes affect human health and biodiversity, and the Sahara region of West Africa is a globally important source region for atmospheric dust. We collected size-fractionated (>10, 10-2.5, 2.5-1.0, 1.0-0.5, and <0.5 μm) atmospheric particles in Mali, West Africa and conducted the first cultivation-independent study of airborne microbes in this region using 16S rRNA gene sequencing. Abundant and diverse microbes were detected in all particle size fractions at levels higher than those previously hypothesized for desert regions. Average daily abundance was 1.94 × 105 16S rRNA copies/m3. Daily patterns in abundance for particles <0.5 μm differed significantly from other size fractions likely because they form mainly in the atmosphere and have limited surface resuspension. Particles >10 μm contained the greatest fraction of daily abundance (51-62%) and had significantly greater diversity than smaller particles. Greater bacterial abundance of particles >2.5 μm that are bigger than the average bacterium suggests that most airborne bacteria are present as aggregates or attached to particles rather than as free-floating cells. Particles >10 μm have very short atmospheric lifetimes and thus tend to have more localized origins. We confirmed the presence of several potential pathogens using polymerase chain reaction that are candidates for viability and strain testing in future studies. These species were detected on all particle sizes tested, including particles <2.5 μm that are expected to undergo long-range transport. Overall, our results suggest that the composition and sources of airborne microbes can be better discriminated by collecting size-fractionated samples.
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Affiliation(s)
- Rebecca A Stern
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Nagissa Mahmoudi
- Department of Earth and Planetary Sciences, McGill University, Montreal, Quebec H3A 0E8, Canada
| | - Caroline O Buckee
- Center for Communicable Disease Dynamics, Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Amina T Schartup
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
- Scripps Institution of Oceanography, La Jolla, California 92037, United States
| | - Petros Koutrakis
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Stephen T Ferguson
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Jack M Wolfson
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Steven C Wofsy
- Department of Earth and Planetary Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Bruce C Daube
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
| | - Elsie M Sunderland
- Harvard John A. Paulson School of Engineering and Applied Science, Harvard University, Cambridge, Massachusetts 02138, United States
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts 02115, United States
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21
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Palladino G, Morozzi P, Biagi E, Brattich E, Turroni S, Rampelli S, Tositti L, Candela M. Particulate matter emission sources and meteorological parameters combine to shape the airborne bacteria communities in the Ligurian coast, Italy. Sci Rep 2021; 11:175. [PMID: 33420408 PMCID: PMC7794459 DOI: 10.1038/s41598-020-80642-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/23/2020] [Indexed: 01/29/2023] Open
Abstract
Aim of the present study is to explore how the chemical composition of particulate matter (PM) and meteorological conditions combine in shaping the air microbiome in Savona (Italy), a medium-size, heavily inhabited urban settlement, hosting a wide range of industrial activities. In particular, the air microbiome and PM10 were monitored over six months in 2012. During that time, the air microbiome was highly dynamic, fluctuating between different compositional states, likely resulting from the aerosolization of different microbiomes emission sources. According to our findings, this dynamic process depends on the combination of local meteorological parameters and particle emission sources, which may affect the prevalent aerosolized microbiomes, thus representing further fundamental tools for source apportionment in a holistic approach encompassing chemical as well as microbiological pollution. In particular, we showed that, in the investigated area, industrial emissions and winds blowing from the inlands combine with an airborne microbiome which include faecal microbiomes components, suggesting multiple citizens' exposure to both chemicals and microorganisms of faecal origin, as related to landscape exploitation and population density. In conclusion, our findings support the need to include monitoring of the air microbiome compositional structure as a relevant factor for the final assessment of local air quality.
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Affiliation(s)
- Giorgia Palladino
- grid.6292.f0000 0004 1757 1758Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy ,Fano Marine Center (FMC), Viale Adriatico 1, 61032 Fano, Italy
| | - Pietro Morozzi
- grid.6292.f0000 0004 1757 1758Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Elena Biagi
- grid.6292.f0000 0004 1757 1758Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy ,Fano Marine Center (FMC), Viale Adriatico 1, 61032 Fano, Italy
| | - Erika Brattich
- grid.6292.f0000 0004 1757 1758Department of Physics and Astronomy, University of Bologna, Viale Berti Pichat 6/2, 40127 Bologna, Italy
| | - Silvia Turroni
- grid.6292.f0000 0004 1757 1758Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Simone Rampelli
- grid.6292.f0000 0004 1757 1758Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy
| | - Laura Tositti
- grid.6292.f0000 0004 1757 1758Department of Chemistry “Giacomo Ciamician”, University of Bologna, Via Selmi 2, 40126 Bologna, Italy
| | - Marco Candela
- grid.6292.f0000 0004 1757 1758Unit of Microbiome Science and Biotechnology, Department of Pharmacy and Biotechnology, University of Bologna, Via Belmeloro 6, 40126 Bologna, Italy ,Fano Marine Center (FMC), Viale Adriatico 1, 61032 Fano, Italy
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22
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Untangling Species-Level Composition of Complex Bacterial Communities through a Novel Metagenomic Approach. mSystems 2020; 5:5/4/e00404-20. [PMID: 32723792 PMCID: PMC7394355 DOI: 10.1128/msystems.00404-20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
16S small-subunit (SSU) rRNA gene-based bacterial profiling is the gold standard for cost-effective taxonomic reconstruction of complex bacterial populations down to the genus level. However, it has been proven ineffective in clinical and research settings requiring higher taxonomic resolution. We therefore developed a bacterial profiling method based on the internal transcribed spacer (ITS) region employing optimized primers and a comprehensive ITS database for accurate cataloguing of bacterial communities at (sub)species resolution. Performance of the microbial ITS profiling pipeline was tested through analysis of host-associated, food, and environmental matrices, while its efficacy in clinical settings was assessed through analysis of mucosal biopsy specimens of colorectal cancer, leading to the identification of putative novel biomarkers. The data collected indicate that the proposed pipeline represents a major step forward in cost-effective identification and screening of microbial biomarkers at (sub)species level, with relevant impact in research, industrial, and clinical settings.IMPORTANCE We developed a novel method for accurate cataloguing of bacterial communities at (sub)species level involving amplification of the internal transcribed spacer (ITS) region through optimized primers, followed by next-generation sequencing and taxonomic classification of amplicons by means of a comprehensive database of bacterial ITS sequences. Host-associated, food, and environmental matrices were employed to test the performance of the microbial ITS profiling pipeline. Moreover, mucosal biopsy samples from colorectal cancer patients were analyzed to demonstrate the scientific relevance of this profiling approach in a clinical setting through identification of putative novel biomarkers. The results indicate that the ITS-based profiling pipeline proposed here represents a key metagenomic tool with major relevance for research, industrial, and clinical settings.
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23
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Jaing C, Thissen J, Morrison M, Dillon MB, Waters SM, Graham GT, Be NA, Nicoll P, Verma S, Caro T, Smith DJ. Sierra Nevada sweep: metagenomic measurements of bioaerosols vertically distributed across the troposphere. Sci Rep 2020; 10:12399. [PMID: 32709938 PMCID: PMC7382458 DOI: 10.1038/s41598-020-69188-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 07/08/2020] [Indexed: 12/14/2022] Open
Abstract
To explore how airborne microbial patterns change with height above the Earth’s surface, we flew NASA’s C-20A aircraft on two consecutive days in June 2018 along identical flight paths over the US Sierra Nevada mountain range at four different altitudes ranging from 10,000 ft to 40,000 ft. Bioaerosols were analyzed by metagenomic DNA sequencing and traditional culturing methods to characterize the composition and diversity of atmospheric samples compared to experimental controls. The relative abundance of taxa changed significantly at each altitude sampled, and the diversity profile shifted across the two sampling days, revealing a regional atmospheric microbiome that is dynamically changing. The most proportionally abundant microbial genera were Mycobacterium and Achromobacter at 10,000 ft; Stenotrophomonas and Achromobacter at 20,000 ft; Delftia and Pseudoperonospora at 30,000 ft; and Alcaligenes and Penicillium at 40,000 ft. Culture-based detections also identified viable Bacillus zhangzhouensis, Bacillus pumilus, and Bacillus spp. in the upper troposphere. To estimate bioaerosol dispersal, we developed a human exposure likelihood model (7-day forecast) using general aerosol characteristics and measured meteorological conditions. By coupling metagenomics to a predictive atmospheric model, we aim to set the stage for field campaigns that monitor global bioaerosol emissions and impacts.
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Affiliation(s)
- Crystal Jaing
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA.
| | - James Thissen
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Michael Morrison
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Michael B Dillon
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Samantha M Waters
- Universities Space Research Association, Maryland, USA.,NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA, USA
| | | | - Nicholas A Be
- Physical & Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | | | - Sonali Verma
- Blue Marble Space Institute of Science, Space Bioscences Division, NASA Ames Research Center, Moffett Field, CA, USA
| | - Tristan Caro
- Department of Geological Sciences, University of Colorado, Boulder, CO, USA
| | - David J Smith
- NASA Ames Research Center, Space Biosciences Division, Moffett Field, CA, USA
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24
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Kabir E, Azzouz A, Raza N, Bhardwaj SK, Kim KH, Tabatabaei M, Kukkar D. Recent Advances in Monitoring, Sampling, and Sensing Techniques for Bioaerosols in the Atmosphere. ACS Sens 2020; 5:1254-1267. [PMID: 32227840 DOI: 10.1021/acssensors.9b02585] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Bioaerosols in the form of microscopic airborne particles pose pervasive risks to humans and livestock. As either fully active components (e.g., viruses, bacteria, and fungi) or as whole or part of inactive fragments, they are among the least investigated pollutants in nature. Their identification and quantification are essential to addressing related dangers and to establishing proper exposure thresholds. However, difficulties in the development (and selection) of detection techniques and an associated lack of standardized procedures make the sensing of bioaerosols challenging. Through a comprehensive literature search, this review examines the mechanisms of conventional and advanced bioaerosol detection methods. It also provides a roadmap for future research and development in the selection of suitable methodologies for bioaerosol detection. The development of sample collection and sensing technology make it possible for continuous and automated operation. However, intensive efforts should be put to overcome the limitations of current technology as most of the currently available options tend to suffer from lengthy sample acquisition times and/or nonspecificity of probe material.
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Affiliation(s)
- Ehsanul Kabir
- Department of Farm Power and Machinery, Bangladesh Agricultural University, Mymensingh 2202, Bangladesh
| | - Abdelmonaim Azzouz
- Department of Chemistry, Faculty of Science, University of Abdelmalek Essaadi, B.P. 2121, M’Hannech II, 93002 Tétouan, Morocco
| | - Nadeem Raza
- Government Emerson College, Bahauddin Zakariya University, Multan 60800, Pakistan
| | - Sanjeev Kumar Bhardwaj
- Center of Innovative and Applied Bioprocessing, (CIAB) [DBT, Govt. of India], Knowledge
City, Sector 81, Mohali, Punjab 140306, India
| | - Ki-Hyun Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Korea
| | - Meisam Tabatabaei
- Microbial Biotechnology Department, Agricultural Biotechnology Institute of Iran, Agricultural Research, Education, and Extension Organization (AREEO), 31535-1897 Karaj, Iran
| | - Deepak Kukkar
- Department of Civil and Environmental Engineering, Hanyang University, 222 Wangsimni-Ro, Seoul 04763, Korea
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25
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Els N, Greilinger M, Reisecker M, Tignat-Perrier R, Baumann-Stanzer K, Kasper-Giebl A, Sattler B, Larose C. Comparison of Bacterial and Fungal Composition and Their Chemical Interaction in Free Tropospheric Air and Snow Over an Entire Winter Season at Mount Sonnblick, Austria. Front Microbiol 2020; 11:980. [PMID: 32508790 PMCID: PMC7251065 DOI: 10.3389/fmicb.2020.00980] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2020] [Accepted: 04/23/2020] [Indexed: 11/24/2022] Open
Abstract
We investigated the interactions of air and snow over one entire winter accumulation period as well as the importance of chemical markers in a pristine free-tropospheric environment to explain variation in a microbiological dataset. To overcome the limitations of short term bioaerosol sampling, we sampled the atmosphere continuously onto quartzfiber air filters using a DIGITEL high volume PM10 sampler. The bacterial and fungal communities, sequenced using Illumina MiSeq, as well as the chemical components of the atmosphere were compared to those of a late season snow profile. Results reveal strong dynamics in the composition of bacterial and fungal communities in air and snow. In fall the two compartments were similar, suggesting a strong interaction between them. The overlap diminished as the season progressed due to an evolution within the snowpack throughout winter and spring. Certain bacterial and fungal genera were only detected in air samples, which implies that a distinct air microbiome might exist. These organisms are likely not incorporated in clouds and thus not precipitated or scavenged in snow. Although snow appears to be seeded by the atmosphere, both air and snow showed differing bacterial and fungal communities and chemical composition. Season and alpha diversity were major drivers for microbial variability in snow and air, and only a few chemical markers were identified as important in explaining microbial diversity. Air microbial community variation was more related to chemical markers than snow microbial composition. For air microbial communities Cl–, TC/OC, SO42–, Mg2+, and Fe/Al, all compounds related to dust or anthropogenic activities, were identified as related to bacterial variability while dust related Ca2+ was significant in snow. The only common driver for snow and air was SO42–, a tracer for anthropogenic sources. The occurrence of chemical compounds was coupled with boundary layer injections in the free troposphere (FT). Boundary layer injections also caused the observed variations in community composition and chemistry between the two compartments. Long-term monitoring is required for a more valid insight in post-depositional selection in snow.
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Affiliation(s)
- Nora Els
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Marion Greilinger
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria.,Zentralanstalt für Meteorologie und Geodynamik (ZAMG), Vienna, Austria
| | - Michael Reisecker
- Avalanche Warning Service Tyrol, Department of Civil Protection, Federal State Government of Tyrol, Innsbruck, Austria
| | - Romie Tignat-Perrier
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
| | | | - Anne Kasper-Giebl
- Institute of Chemical Technologies and Analytics, Vienna University of Technology, Vienna, Austria
| | - Birgit Sattler
- Institute of Ecology, University of Innsbruck, Innsbruck, Austria
| | - Catherine Larose
- Environmental Microbial Genomics Group, Laboratoire Ampère, École Centrale de Lyon, Écully, France
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26
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Tignat-Perrier R, Dommergue A, Thollot A, Magand O, Amato P, Joly M, Sellegri K, Vogel TM, Larose C. Seasonal shift in airborne microbial communities. THE SCIENCE OF THE TOTAL ENVIRONMENT 2020; 716:137129. [PMID: 32044476 DOI: 10.1016/j.scitotenv.2020.137129] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 01/29/2020] [Accepted: 02/03/2020] [Indexed: 05/23/2023]
Abstract
Microorganisms are ubiquitous in the atmosphere. Global investigations on the geographical and temporal distribution of airborne microbial communities are critical for identifying the sources and the factors shaping airborne communities. At mid-latitude sites, a seasonal shift in both the concentration and diversity of airborne microbial communities has been systematically observed in the planetary boundary layer. While the factors suspected of affecting this seasonal change were hypothesized (e.g., changes in the surface conditions, meteorological parameters and global air circulation), our understanding on how these factors influence the temporal variation of airborne microbial communities, especially at the microbial taxon level, remains limited. Here, we investigated the distribution of both airborne bacterial and fungal communities on a weekly basis over more than one year at the mid-latitude and continental site of puy de Dôme (France; +1465 m altitude above sea level). The seasonal shift in microbial community structure was likely correlated to the seasonal changes in the characteristics of puy de Dôme's landscape (croplands and natural vegetation). The airborne microbial taxa that were the most affected by seasonal changes trended differently throughout the seasons in relation with their trophic mode. In addition, the windy and variable local meteorological conditions found at puy de Dôme were likely responsible for the intraseasonal variability observed in the composition of airborne microbial communities.
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Affiliation(s)
- Romie Tignat-Perrier
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France; Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France.
| | - Aurélien Dommergue
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Alban Thollot
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Olivier Magand
- Institut des Géosciences de l'Environnement, Université Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Muriel Joly
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Karine Sellegri
- Institut de Chimie de Clermont-Ferrand, CNRS UMR 6096 Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
| | - Catherine Larose
- Environmental Microbial Genomics, CNRS UMR 5005 Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Écully, France
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27
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Bøifot KO, Gohli J, Moen LV, Dybwad M. Performance evaluation of a new custom, multi-component DNA isolation method optimized for use in shotgun metagenomic sequencing-based aerosol microbiome research. ENVIRONMENTAL MICROBIOME 2020; 15:1. [PMID: 33902731 PMCID: PMC8067373 DOI: 10.1186/s40793-019-0349-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Accepted: 12/03/2019] [Indexed: 05/08/2023]
Abstract
BACKGROUND Aerosol microbiome research advances our understanding of bioaerosols, including how airborne microorganisms affect our health and surrounding environment. Traditional microbiological/molecular methods are commonly used to study bioaerosols, but do not allow for generic, unbiased microbiome profiling. Recent studies have adopted shotgun metagenomic sequencing (SMS) to address this issue. However, SMS requires relatively large DNA inputs, which are challenging when studying low biomass air environments, and puts high requirements on air sampling, sample processing and DNA isolation protocols. Previous SMS studies have consequently adopted various mitigation strategies, including long-duration sampling, sample pooling, and whole genome amplification, each associated with some inherent drawbacks/limitations. RESULTS Here, we demonstrate a new custom, multi-component DNA isolation method optimized for SMS-based aerosol microbiome research. The method achieves improved DNA yields from filter-collected air samples by isolating DNA from the entire filter extract, and ensures a more comprehensive microbiome representation by combining chemical, enzymatic and mechanical lysis. Benchmarking against two state-of-the-art DNA isolation methods was performed with a mock microbial community and real-world air samples. All methods demonstrated similar performance regarding DNA yield and community representation with the mock community. However, with subway samples, the new method obtained drastically improved DNA yields, while SMS revealed that the new method reported higher diversity. The new method involves intermediate filter extract separation into a pellet and supernatant fraction. Using subway samples, we demonstrate that supernatant inclusion results in improved DNA yields. Furthermore, SMS of pellet and supernatant fractions revealed overall similar taxonomic composition but also identified differences that could bias the microbiome profile, emphasizing the importance of processing the entire filter extract. CONCLUSIONS By demonstrating and benchmarking a new DNA isolation method optimized for SMS-based aerosol microbiome research with both a mock microbial community and real-world air samples, this study contributes to improved selection, harmonization, and standardization of DNA isolation methods. Our findings highlight the importance of ensuring end-to-end sample integrity and using methods with well-defined performance characteristics. Taken together, the demonstrated performance characteristics suggest the new method could be used to improve the quality of SMS-based aerosol microbiome research in low biomass air environments.
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Affiliation(s)
- Kari Oline Bøifot
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK
| | - Jostein Gohli
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Line Victoria Moen
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway
| | - Marius Dybwad
- Norwegian Defence Research Establishment, P.O. Box 25, NO-2027, Kjeller, Norway.
- Department of Analytics, Environmental & Forensic Sciences, King's College London, 150 Stamford Street, London, SE1 9NH, UK.
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28
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Tignat-Perrier R, Dommergue A, Thollot A, Keuschnig C, Magand O, Vogel TM, Larose C. Global airborne microbial communities controlled by surrounding landscapes and wind conditions. Sci Rep 2019; 9:14441. [PMID: 31595018 PMCID: PMC6783533 DOI: 10.1038/s41598-019-51073-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/23/2019] [Indexed: 11/21/2022] Open
Abstract
The atmosphere is an important route for transporting and disseminating microorganisms over short and long distances. Understanding how microorganisms are distributed in the atmosphere is critical due to their role in public health, meteorology and atmospheric chemistry. In order to determine the dominant processes that structure airborne microbial communities, we investigated the diversity and abundance of both bacteria and fungi from the PM10 particle size (particulate matter of 10 micrometers or less in diameter) as well as particulate matter chemistry and local meteorological characteristics over time at nine different meteorological stations around the world. The bacterial genera Bacillus and Sphingomonas as well as the fungal species Pseudotaeniolina globaosa and Cladophialophora proteae were the most abundant taxa of the dataset, although their relative abundances varied greatly based on sampling site. Bacterial and fungal concentration was the highest at the high-altitude and semi-arid plateau of Namco (China; 3.56 × 106 ± 3.01 × 106 cells/m3) and at the high-altitude and vegetated mountain peak Storm-Peak (Colorado, USA; 8.78 × 104 ± 6.49 × 104 cells/m3), respectively. Surrounding ecosystems, especially within a 50 km perimeter of our sampling stations, were the main contributors to the composition of airborne microbial communities. Temporal stability in the composition of airborne microbial communities was mainly explained by the diversity and evenness of the surrounding landscapes and the wind direction variability over time. Airborne microbial communities appear to be the result of large inputs from nearby sources with possible low and diluted inputs from distant sources.
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Affiliation(s)
- Romie Tignat-Perrier
- Institut des Géosciences de l'Environnement, Univ Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France. .,Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France.
| | - Aurélien Dommergue
- Institut des Géosciences de l'Environnement, Univ Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Alban Thollot
- Institut des Géosciences de l'Environnement, Univ Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Christoph Keuschnig
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
| | - Olivier Magand
- Institut des Géosciences de l'Environnement, Univ Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Timothy M Vogel
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
| | - Catherine Larose
- Environmental Microbial Genomics, Laboratoire Ampère, Ecole Centrale de Lyon, Université de Lyon, Ecully, France
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