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Zhang Y, O'Loughlin EJ, Park SY, Kwon MJ. Effects of Fe(III) (hydr)oxide mineralogy on the development of microbial communities originating from soil, surface water, groundwater, and aerosols. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 905:166993. [PMID: 37717756 DOI: 10.1016/j.scitotenv.2023.166993] [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: 07/03/2023] [Revised: 09/09/2023] [Accepted: 09/09/2023] [Indexed: 09/19/2023]
Abstract
Microbial Fe(III) reduction is a key component of the iron cycle in natural environments. However, the susceptibility of Fe(III) (hydr)oxides to microbial reduction varies depending on the mineral's crystallinity, and the type of Fe(III) (hydr)oxide in turn will affect the composition of the microbial community. We created microcosm reactors with microbial communities from four different sources (soil, surface water, groundwater, and aerosols), three Fe(III) (hydr)oxides (lepidocrocite, goethite, and hematite) as electron acceptors, and acetate as an electron donor to investigate the shaping effect of Fe(III) mineral type on the development of microbial communities. During a 10-month incubation, changes in microbial community composition, Fe(III) reduction, and acetate utilization were monitored. Overall, there was greater reduction of lepidocrocite than of goethite and hematite, and the development of microbial communities originating from the same source diverged when supplied with different Fe(III) (hydr)oxides. Furthermore, each Fe(III) mineral was associated with unique taxa that emerged from different sources. This study illustrates the taxonomic diversity of Fe(III)-reducing microbes from a broad range of natural environments.
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Affiliation(s)
- Yidan Zhang
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Edward J O'Loughlin
- Biosciences Division, Argonne National Laboratory, Lemont, IL 60439, United States
| | - Su-Young Park
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea
| | - Man Jae Kwon
- Department of Earth and Environmental Sciences, Korea University, Seoul 02841, South Korea.
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2
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Khatiebi S, Kiprotich K, Onyando Z, Wekesa C, Chi CN, Mulambalah C, Okoth P. Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3724531. [PMID: 37521121 PMCID: PMC10382247 DOI: 10.1155/2023/3724531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.
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Affiliation(s)
- Sandra Khatiebi
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Kelvin Kiprotich
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Zedekiah Onyando
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Clabe Wekesa
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, University of Uppsala, P.O. Box 582, 75123 Uppsala, Sweden
| | - Chrispinus Mulambalah
- Department of Medical Microbiology & Parasitology, School of Medicine, Moi University, P.O. Box 4606, 30100 Eldoret, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
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Styles JN, Egorov AI, Griffin SM, Klein J, Scott JW, Sams EA, Hudgens E, Mugford C, Stewart JR, Lu K, Jaspers I, Keely SP, Brinkman NE, Arnold JW, Wade TJ. Greener residential environment is associated with increased bacterial diversity in outdoor ambient air. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 880:163266. [PMID: 37028654 DOI: 10.1016/j.scitotenv.2023.163266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 05/27/2023]
Abstract
In urban areas, exposure to greenspace has been found to be beneficial to human health. The biodiversity hypothesis proposed that exposure to diverse ambient microbes in greener areas may be one pathway leading to health benefits such as improved immune system functioning, reduced systemic inflammation, and ultimately reduced morbidity and mortality. Previous studies observed differences in ambient outdoor bacterial diversity between areas of high and low vegetated land cover but didn't focus on residential environments which are important to human health. This research examined the relationship between vegetated land and tree cover near residence and outdoor ambient air bacterial diversity and composition. We used a filter and pump system to collect ambient bacteria samples outside residences in the Raleigh-Durham-Chapel Hill metropolitan area and identified bacteria by 16S rRNA amplicon sequencing. Geospatial quantification of total vegetated land or tree cover was conducted within 500 m of each residence. Shannon's diversity index and weighted UniFrac distances were calculated to measure α (within-sample) and β (between-sample) diversity, respectively. Linear regression for α-diversity and permutational analysis of variance (PERMANOVA) for β-diversity were used to model relationships between vegetated land and tree cover and bacterial diversity. Data analysis included 73 ambient air samples collected near 69 residences. Analysis of β-diversity demonstrated differences in ambient air microbiome composition between areas of high and low vegetated land (p = 0.03) and tree cover (p = 0.07). These relationships remained consistent among quintiles of vegetated land (p = 0.03) and tree cover (p = 0.008) and continuous measures of vegetated land (p = 0.03) and tree cover (p = 0.03). Increased vegetated land and tree cover were also associated with increased ambient microbiome α-diversity (p = 0.06 and p = 0.03, respectively). To our knowledge, this is the first study to demonstrate associations between vegetated land and tree cover and the ambient air microbiome's diversity and composition in the residential ecosystem.
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Affiliation(s)
- Jennifer N Styles
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA; Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA; Department of Pediatrics, Division of Allergy and Immunology, Chapel Hill, NC, USA.
| | - Andrey I Egorov
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA
| | - Shannon M Griffin
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Cincinnati, OH, USA
| | - Jo Klein
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA; North Carolina State University Libraries, Raleigh, NC, USA
| | - J W Scott
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA
| | - Elizabeth A Sams
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA
| | - Edward Hudgens
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA
| | - Chris Mugford
- United States Public Health Service Commissioned Corps, Research Triangle Park, NC, USA; The Agency for Toxic Substances and Disease Registry, Boston, MA, USA
| | - Jill R Stewart
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Kun Lu
- Department of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Ilona Jaspers
- Curriculum in Toxicology and Environmental Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Center for Environmental Medicine, Asthma, and Lung Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Pediatrics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott P Keely
- United States Environmental Protection Agency, Center for Environmental Measurement and Monitoring, Office of Research and Development, Cincinnati, OH, USA
| | - Nichole E Brinkman
- United States Environmental Protection Agency, Center for Environmental Solutions and Emergency Response, Office of Research and Development, Cincinnati, OH, USA
| | - Jason W Arnold
- Division of Gastroenterology and Hepatology, Department of Medicine, Microbiome Core Facility, Center for Gastrointestinal Biology and Disease, School of Medicine, University of North Carolina, Chapel Hill, NC, USA; Department of Molecular Genetics and Microbiology, Duke Microbiome Center, Duke University, Durham, NC, USA
| | - Timothy J Wade
- United States Environmental Protection Agency, Center for Public Health and Environmental Assessment, Office of Research and Development, Research Triangle Park, NC, USA
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Ginn O, Lowry S, Brown J. A systematic review of enteric pathogens and antibiotic resistance genes in outdoor urban aerosols. ENVIRONMENTAL RESEARCH 2022; 212:113097. [PMID: 35339466 DOI: 10.1016/j.envres.2022.113097] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/10/2022] [Accepted: 03/06/2022] [Indexed: 06/14/2023]
Abstract
Aerosol transport of enteric microbiota including fecal pathogens and antimicrobial resistance genes (ARGs) has been documented in a range of settings but remains poorly understood outside indoor environments. We conducted a systematic review of the peer-reviewed literature to summarize evidence on specific enteric microbiota including enteric pathogens and ARGs that have been measured in aerosol samples in urban settings where the risks of outdoor exposure and antibiotic resistance (AR) spread may be highest. Following PRISMA guidelines, we conducted a key word search for articles published within the years 1990-2020 using relevant data sources. Two authors independently conducted the keyword searches of databases and conducted primary and secondary screenings before merging results. To be included, studies contained extractable data on enteric microbes and AR in outdoor aerosols regardless of source confirmation and reported on qualitative, quantitative, or viability data on enteric microbes or AR. Qualitative analyses and metric summaries revealed that enteric microbes and AR have been consistently reported in outdoor aerosols, generally via relative abundance measures, though gaps remain preventing full understanding of the role of the aeromicrobiological pathway in the fate and transport of enteric associated outdoor aerosols. We identified remaining gaps in the evidence base including a need for broad characterization of enteric pathogens in bioaerosols beyond bacterial genera, a need for greater sampling in locations of high enteric disease risk, and a need for quantitative estimation of microbial and nucleic acid densities that may be applied to fate and transport models and in quantitative microbial risk assessment.
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Affiliation(s)
- Olivia Ginn
- Department of Civil & Environmental Engineering & Earth Science, University of Notre Dame, Notre Dame, IN, 46556, USA.
| | - Sarah Lowry
- Department of Civil and Environmental Engineering, Stanford University, Stanford, CA, United States
| | - Joe Brown
- Deparment of Environmental Sciences and Engineering, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, 27599, United States.
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5
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Airborne Prokaryotic, Fungal and Eukaryotic Communities of an Urban Environment in the UK. ATMOSPHERE 2022. [DOI: 10.3390/atmos13081212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Bioaerosols often contain human pathogens and allergens affecting public health. However, relatively little attention has been given to bioaerosols compared with non-biological aerosols. In this study, we aimed to identify bioaerosol compositions in Manchester, UK by applying high throughput sequencing methods and to find potential sources. Samples were collected at Manchester Air Quality Super Site at the Firs Environmental Research Station in November 2019 and in February 2020. Total DNA has been extracted and sequenced targeting the 16S rRNA gene of prokaryotes, ITS region of fungal DNA and 18S rRNA gene of eukaryotes. We found marine environment-associated bacteria and archaea were relatively more abundant in the February 2020 samples compared with the November 2019 samples, consistent with the North West marine origin based on wind back-trajectory analysis. In contrast, an OTU belonging to Methylobacterium, which includes many species resistant to heavy metals, was relatively more abundant in November 2019 when there were higher metal concentrations. Fungal taxa that fruit all year were relatively more abundant in the February 2020 samples while autumn fruiting species generally had higher relative abundance in the November 2019 samples. There were higher relative abundances of land plants and algae in the February 2020 samples based on 18S rRNA gene sequencing. One of the OTUs belonging to the coniferous yew genus Taxus was more abundant in the February 2020 samples agreeing with the usual pollen season of yews in the UK which is from mid-January until late April. The result from this study suggests a potential application of bioaerosol profiling for tracing the source of atmospheric particles.
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6
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Urban Aerobiome and Effects on Human Health: A Systematic Review and Missing Evidence. ATMOSPHERE 2022. [DOI: 10.3390/atmos13071148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Urban air pollutants are a major public health concern and include biological matters which composes about 25% of the atmospheric aerosol particles. Airborne microorganisms were traditionally characterized by culture-based methods recognizing just 1.5–15.3% of the total bacterial diversity that was evaluable by genome signature in the air environment (aerobiome). Despite the large number of exposed people, urban aerobiomes are still weakly described even if recently advanced literature has been published. This paper aims to systematically review the state of knowledge on the urban aerobiome and human health effects. A total of 24 papers that used next generation sequencing (NGS) techniques for characterization and comprised a seasonal analysis have been included. A core of Proteobacteria, Actinobacteria, Firmicutes, and Bacteroides and various factors that influenced the community structure were detected. Heterogenic methods and results were reported, for both sampling and aerobiome diversity analysis, highlighting the necessity of in-depth and homogenized assessment thus reducing the risk of bias. The aerobiome can include threats for human health, such as pathogens and resistome spreading; however, its diversity seems to be protective for human health and reduced by high levels of air pollution. Evidence of the urban aerobiome effects on human health need to be filled up quickly for urban public health purposes.
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7
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Anthony MA, Crowther TW, van der Linde S, Suz LM, Bidartondo MI, Cox F, Schaub M, Rautio P, Ferretti M, Vesterdal L, De Vos B, Dettwiler M, Eickenscheidt N, Schmitz A, Meesenburg H, Andreae H, Jacob F, Dietrich HP, Waldner P, Gessler A, Frey B, Schramm O, van den Bulk P, Hensen A, Averill C. Forest tree growth is linked to mycorrhizal fungal composition and function across Europe. THE ISME JOURNAL 2022; 16:1327-1336. [PMID: 35001085 PMCID: PMC9038731 DOI: 10.1038/s41396-021-01159-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Revised: 11/10/2021] [Accepted: 11/17/2021] [Indexed: 11/08/2022]
Abstract
Most trees form symbioses with ectomycorrhizal fungi (EMF) which influence access to growth-limiting soil resources. Mesocosm experiments repeatedly show that EMF species differentially affect plant development, yet whether these effects ripple up to influence the growth of entire forests remains unknown. Here we tested the effects of EMF composition and functional genes relative to variation in well-known drivers of tree growth by combining paired molecular EMF surveys with high-resolution forest inventory data across 15 European countries. We show that EMF composition was linked to a three-fold difference in tree growth rate even when controlling for the primary abiotic drivers of tree growth. Fast tree growth was associated with EMF communities harboring high inorganic but low organic nitrogen acquisition gene proportions and EMF which form contact versus medium-distance fringe exploration types. These findings suggest that EMF composition is a strong bio-indicator of underlying drivers of tree growth and/or that variation of forest EMF communities causes differences in tree growth. While it may be too early to assign causality or directionality, our study is one of the first to link fine-scale variation within a key component of the forest microbiome to ecosystem functioning at a continental scale.
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Affiliation(s)
- Mark A Anthony
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland.
| | - Thomas W Crowther
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Sietse van der Linde
- Netherlands Food and Consumer Product Safety Authority, National Reference Centre, Wageningen, The Netherlands
| | | | - Martin I Bidartondo
- Royal Botanic Gardens, Kew, TW9 3DS, UK
- Department of Life Sciences, Imperial College London, Ascot, SL5 7PY, UK
| | - Filipa Cox
- Department of Earth and Environmental Sciences, The University of Manchester, Manchester, M13 9PT, UK
| | - Marcus Schaub
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pasi Rautio
- Natural Resources Institute Finland, Rovaniemi, Finland
| | - Marco Ferretti
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Lars Vesterdal
- Department of Geosciences and Natural Resource Management, University of Copenhagen, DK-1958, Frederiksberg C, Denmark
| | - Bruno De Vos
- Environment & Climate Unit, Research Institute for Nature and Forest, Geraardsbergen, Belgium
| | - Mike Dettwiler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
| | - Nadine Eickenscheidt
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, 45657, Recklinghausen, Germany
| | - Andreas Schmitz
- State Agency for Nature, Environment and Consumer Protection of North Rhine-Westphalia, 45657, Recklinghausen, Germany
- Thuenen Institut of Forest Ecosystems, 16225, Eberswalde, Germany
| | | | | | - Frank Jacob
- Sachsenforst State Forest, 01796, Pirna OT Graupa, Germany
| | | | - Peter Waldner
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Arthur Gessler
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Beat Frey
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Oliver Schramm
- Swiss Federal Institute for Forest, Snow and Landscape Research WSL, Birmensdorf, Switzerland
| | - Pim van den Bulk
- The Netherlands Organization for Applied Scientific Research at Petten, 1755LE, Petten, The Netherlands
| | - Arjan Hensen
- The Netherlands Organization for Applied Scientific Research at Petten, 1755LE, Petten, The Netherlands
| | - Colin Averill
- Department of Environmental Systems Science, ETH Zürich, Zürich, Switzerland
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8
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Yan X, Ma J, Chen X, Lei M, Li T, Han Y. Characteristics of airborne bacterial communities and antibiotic resistance genes under different air quality levels. ENVIRONMENT INTERNATIONAL 2022; 161:107127. [PMID: 35180669 DOI: 10.1016/j.envint.2022.107127] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 01/05/2022] [Accepted: 01/29/2022] [Indexed: 06/14/2023]
Abstract
Pathogenic bacteria and antibiotic resistance genes (ARGs) in bioaerosols are major threats to human health. In this study, the microbial community structure and ARG distribution characteristics of airborne bacteria in total suspended particulates (TSP) and PM2.5 were investigated under different air quality levels in Xinxiang, Central China. The results revealed that with the deterioration of air quality, the concentrations of airborne bacteria in both TSP and PM2.5 decreased; however, the relative amounts of pathogenic bacteria increased. The predominant genera in pathogenic bacteria of Bacillus, Sphingomonas, Corynebacterium, Rhodococcus, and Staphylococcus were identified in both TSP and PM2.5. Although the airborne bacteria concentrations and absolute abundances of ARGs in TSP were higher than those in PM2.5 under identical air quality conditions, the bacterial community structure and relative amounts of pathogenic bacteria were similar. In addition, the relationship between environmental factors of ions, metal elements, and meteorological parameters and the community structures of airborne bacteria and pathogenic bacteria were also analyzed. The effects of soluble ions and metal elements on several dominant genera of total bacteria and pathogenic bacteria differed, probably due to the strong tolerance of pathogenic bacteria to harsh atmospheric environments Different subtypes of ARGs showed various distribution characteristics with variations in air quality. The deterioration of air quality can inhibit the dissemination of ARGs, as the minimum values of all ARGs and class 1 integrase intI1 were observed under Severely Polluted conditions. This study provides a comprehensive understanding of the effect of air pollution levels on the airborne bacteria community composition and ARG distribution.
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Affiliation(s)
- Xu Yan
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China.
| | - Jiahui Ma
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Xinqing Chen
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Miao Lei
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Tianning Li
- School of Environment, Key Laboratory for Yellow River and Huai River Water Environment and Pollution Control, Ministry of Education, Henan Key Laboratory for Environmental Pollution Control, Henan Normal University, Xinxiang 453007, China
| | - Yunping Han
- Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
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9
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Robinson JM, Redvers N, Camargo A, Bosch CA, Breed MF, Brenner LA, Carney MA, Chauhan A, Dasari M, Dietz LG, Friedman M, Grieneisen L, Hoisington AJ, Horve PF, Hunter A, Jech S, Jorgensen A, Lowry CA, Man I, Mhuireach G, Navarro-Pérez E, Ritchie EG, Stewart JD, Watkins H, Weinstein P, Ishaq SL. Twenty Important Research Questions in Microbial Exposure and Social Equity. mSystems 2022; 7:e0124021. [PMID: 35089060 PMCID: PMC8725600 DOI: 10.1128/msystems.01240-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Social and political policy, human activities, and environmental change affect the ways in which microbial communities assemble and interact with people. These factors determine how different social groups are exposed to beneficial and/or harmful microorganisms, meaning microbial exposure has an important socioecological justice context. Therefore, greater consideration of microbial exposure and social equity in research, planning, and policy is imperative. Here, we identify 20 research questions considered fundamentally important to promoting equitable exposure to beneficial microorganisms, along with safeguarding resilient societies and ecosystems. The 20 research questions we identified span seven broad themes, including the following: (i) sociocultural interactions; (ii) Indigenous community health and well-being; (iii) humans, urban ecosystems, and environmental processes; (iv) human psychology and mental health; (v) microbiomes and infectious diseases; (vi) human health and food security; and (vii) microbiome-related planning, policy, and outreach. Our goal was to summarize this growing field and to stimulate impactful research avenues while providing focus for funders and policymakers.
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Affiliation(s)
- Jake M. Robinson
- University of Sheffield, Department of Landscape Architecture, Sheffield, United Kingdom
| | - Nicole Redvers
- Department of Family & Community Medicine, University of North Dakota School of Medicine & Health Sciences, Grand Forks, North Dakota, USA
| | | | - Christina A. Bosch
- Department of Literacy, Early, Bilingual and Special Education, Kremen School of Education and Human Development, California State University, Fresno, California, USA
| | - Martin F. Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, Australia
| | - Lisa A. Brenner
- University of Colorado, Anschutz Medical Campus, Aurora, Colorado, USA
| | - Megan A. Carney
- School of the Environment, Florida Agricultural and Mechanical University, Tallahassee, Florida, USA
| | - Ashvini Chauhan
- University of Arizona, School of Anthropology and Center for Regional Food Studies, Tucson, Arizona, USA
| | - Mauna Dasari
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Leslie G. Dietz
- University of Oregon, Biology and the Built Environment Center, Eugene, Oregon, USA
| | - Michael Friedman
- American International College of Arts and Sciences of Antigua, Antigua and Barbuda, West Indies
| | - Laura Grieneisen
- Department of Genetics, Cell, and Development, University of Minnesota, Minneapolis, Minnesota, USA
| | | | - Patrick F. Horve
- University of Oregon, Institute of Molecular Biology, Eugene, Oregon, USA
| | - Ally Hunter
- Department of Student Development, University of Massachusetts, Amherst, Massachusetts, USA
| | - Sierra Jech
- University of Colorado Boulder, Department of Ecology and Evolutionary Biology, Boulder, Colorado, USA
| | - Anna Jorgensen
- Department of Landscape Architecture, University of Sheffield, Sheffield, United Kingdom
| | - Christopher A. Lowry
- Department of Integrative Physiology, Center for Neuroscience, and Center for Microbial Exploration, University of Colorado Boulder, Boulder, Colorado, USA
| | - Ioana Man
- Architectural Association School of Architecture, London, United Kingdom
| | - Gwynne Mhuireach
- Department of Architecture, University of Oregon, Eugene, Oregon, USA
| | - Edauri Navarro-Pérez
- Program of Environmental Life Sciences, School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Euan G. Ritchie
- School of Life and Environmental Sciences and Centre for Integrative Ecology, Deakin University, Burwood, VIC, Australia
| | - Justin D. Stewart
- Department of Ecological Science, Faculty of Earth and Life Sciences, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Harry Watkins
- St. Andrews Botanic Garden, Canongate, St. Andrews, Fife, United Kingdom
- Bio-integrated Design Lab, Bartlett School of Architecture, London, United Kingdom
| | - Philip Weinstein
- School of Public Health, The University of Adelaide, Adelaide, SA, Australia
| | - Suzanne L. Ishaq
- University of Maine, School of Food and Agriculture, Orono, Maine, USA
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10
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Concentrations, Size Distribution, and Community Structure Characteristics of Culturable Airborne Antibiotic-Resistant Bacteria in Xinxiang, Central China. ATMOSPHERE 2021. [DOI: 10.3390/atmos12081077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Antimicrobial resistance is considered an important threat to global health and has recently attracted significant attention from the public. In this study, the concentrations and size distribution characteristics of culturable airborne total bacteria (TB) and four antibiotic-resistant bacteria (tetracycline-resistant bacteria (TRB), ciprofloxacin-resistant bacteria (CRB), erythromycin-resistant bacteria (ERB), and ampicillin-resistant bacteria (ARB)) were investigated for approximately one year to explore their variations under different seasons, diurnal periods, and air quality levels. The concentrations of TB and four antibiotic-resistant bacteria in winter and night were higher than during other seasons and diurnal periods. Their maximum concentrations were detected from air under moderate pollution or heavy pollution. PM2.5, PM10, SO2, and NO2 were positively related to TB and four antibiotic-resistant bacteria (p < 0.01), whereas O3 and wind speed were negatively related to them (p < 0.05). The particle size of TB and four antibiotic-resistant bacteria were mainly distributed in stage V (1.1–2.2 µm). Bacillus was the dominant genus of ARB (75.97%) and CRB (25.67%). Staphylococcus and Macrococcus were the dominant genera of TRB (46.05%) and ERB (47.67%), respectively. The opportunistic pathogens of Micrococcus, Sphingomonas, Enterococcus, Rhodococcus, and Stenotrophomonas were also identified. This study provides important references for understanding the threat of bioaerosols to human health.
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Robinson JM, Cando-Dumancela C, Antwis RE, Cameron R, Liddicoat C, Poudel R, Weinstein P, Breed MF. Exposure to airborne bacteria depends upon vertical stratification and vegetation complexity. Sci Rep 2021; 11:9516. [PMID: 33947905 PMCID: PMC8096821 DOI: 10.1038/s41598-021-89065-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/20/2021] [Indexed: 02/02/2023] Open
Abstract
Exposure to biodiverse aerobiomes supports human health, but it is unclear which ecological factors influence exposure. Few studies have investigated near-surface green space aerobiome dynamics, and no studies have reported aerobiome vertical stratification in different urban green spaces. We used columnar sampling and next generation sequencing of the bacterial 16S rRNA gene, combined with geospatial and network analyses to investigate urban green space aerobiome spatio-compositional dynamics. We show a strong effect of habitat on bacterial diversity and network complexity. We observed aerobiome vertical stratification and network complexity that was contingent on habitat type. Tree density, closer proximity, and canopy coverage associated with greater aerobiome alpha diversity. Grassland aerobiomes exhibited greater proportions of putative pathogens compared to scrub, and also stratified vertically. We provide novel insights into the urban ecosystem with potential importance for public health, whereby the possibility of differential aerobiome exposures appears to depend on habitat type and height in the airspace. This has important implications for managing urban landscapes for the regulation of aerobiome exposure.
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Affiliation(s)
- Jake M Robinson
- Department of Landscape Architecture, The University of Sheffield, Sheffield, S10 2TN, UK.
- inVIVO Planetary Health of the Worldwide Universities Network, NJ, 10704, USA.
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia.
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia.
| | - Christian Cando-Dumancela
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
| | - Rachael E Antwis
- School of Science, Engineering and Environment, University of Salford, Salford, M5 4WX, UK
| | - Ross Cameron
- Department of Landscape Architecture, The University of Sheffield, Sheffield, S10 2TN, UK
| | - Craig Liddicoat
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Ravin Poudel
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL, 32603, USA
| | - Philip Weinstein
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
- School of Public Health and the Environment Institute, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Martin F Breed
- College of Science and Engineering, Flinders University, Bedford Park, SA, 5042, Australia
- The Healthy Urban Microbiome Initiative (HUMI), Adelaide, Australia
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Núñez A, García AM, Moreno DA, Guantes R. Seasonal changes dominate long-term variability of the urban air microbiome across space and time. ENVIRONMENT INTERNATIONAL 2021; 150:106423. [PMID: 33578068 DOI: 10.1016/j.envint.2021.106423] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/25/2021] [Accepted: 01/25/2021] [Indexed: 05/24/2023]
Abstract
Compared to soil or aquatic ecosystems, the atmosphere is still an underexplored environment for microbial diversity. In this study, we surveyed the composition, variability and sources of microbes (bacteria and fungi) in the near surface atmosphere of a highly populated area, spanning ~ 4,000 Km2 around the city center of Madrid (Spain), in different seasonal periods along two years. We found a core of abundant bacterial genera robust across space and time, most of soil origin, while fungi were more sensitive to environmental conditions. Microbial communities showed clear seasonal patterns driven by variability of environmental factors, mainly temperature and accumulated rain, while local sources played a minor role. We also identified taxa in both groups characteristic of seasonal periods, but not of specific sampling sites or plant coverage. The present study suggests that the near surface atmosphere of urban environments contains an ecosystem stable across relatively large spatial and temporal scales, with a rather homogenous composition, modulated by climatic variations. As such, it contributes to our understanding of the long-term changes associated to the human exposome in the air of highly populated areas.
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Affiliation(s)
- Andrés Núñez
- Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid, Spain; Department of Genetics and Microbiology, Facultad de Biología, Universidad de Murcia, Murcia, Spain
| | - Ana M García
- Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid, Spain
| | - Diego A Moreno
- Escuela Técnica Superior de Ingenieros Industriales, Universidad Politécnica de Madrid (ETSII-UPM), Madrid, Spain; Facultad de Farmacia, Universidad de Castilla-La Mancha (FF-UCLM), Albacete, Spain.
| | - Raúl Guantes
- Department of Condensed Matter Physics and Material Science Institute 'Nicolás Cabrera', Science Faculty, Universidad Autónoma de Madrid, Madrid, Spain; Institute for Condensed Matter Physics (IFIMAC), Science Faculty, Universidad Autónoma de Madrid, Madrid, Spain.
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13
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Stewart JD, Kremer P, Shakya KM, Conway M, Saad A. Outdoor Atmospheric Microbial Diversity Is Associated With Urban Landscape Structure and Differs From Indoor-Transit Systems as Revealed by Mobile Monitoring and Three-Dimensional Spatial Analysis. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.620461] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Microbes are abundant inhabitants of the near-surface atmosphere in urban areas. The distribution of microbial communities may benefit or hinder human wellbeing and ecosystem function. Surveys of airborne microbial diversity are uncommon in both natural and built environments and those that investigate diversity are stationary in the city, thus missing continuous exposure to microbes that covary with three-dimensional urban structure. Individuals in cities are generally mobile and would be exposed to diverse urban structures outdoors and within indoor-transit systems in a day. We used mobile monitoring of microbial diversity and geographic information system spatial analysis, across Philadelphia, Pennsylvania, USA in outdoor and indoor-transit (subways and train cars) environments. This study identifies to the role of the three-dimensional urban landscape in structuring atmospheric microbiomes and employs mobile monitoring over ~1,920 kilometers to measure continuous biodiversity. We found more diverse communities outdoors that significantly differ from indoor-transit air in microbial community structure, function, likely source environment, and potentially pathogenic fraction of the community. Variation in the structure of the urban landscape was associated with diversity and function of the near-surface atmospheric microbiome in outdoor samples.
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Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020. [PMID: 32877224 PMCID: PMC7642895 DOI: 10.1152/ajplung.00360.2020 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
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Affiliation(s)
- Kent A. Willis
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D. Stewart
- 2Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- 1Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,3Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama,4Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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15
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Willis KA, Stewart JD, Ambalavanan N. Recent advances in understanding the ecology of the lung microbiota and deciphering the gut-lung axis. Am J Physiol Lung Cell Mol Physiol 2020; 319:L710-L716. [PMID: 32877224 DOI: 10.1152/ajplung.00360.2020] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
A rapidly expanding new field of lung research has been produced by the emergence of culture-independent next-generation sequencing technologies. While pulmonary microbiome research lags behind the exploration of the microbiome in other organ systems, the field is maturing and has recently produced multiple exciting discoveries. In this mini-review, we will explore recent advances in our understanding of the lung microbiome and the gut-lung axis from an ecological perspective.
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Affiliation(s)
- Kent A Willis
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
| | - Justin D Stewart
- Department of Ecological Science, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Namasivayam Ambalavanan
- Division of Neonatology, Department of Pediatrics, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Pathology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama.,Department of Cell, Developmental and Integrative Biology, College of Medicine, The University of Alabama at Birmingham, Birmingham, Alabama
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