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Navarro A, Del Moral A, Weber B, Weber J, Molinero A, Delgado R, Párraga J, Martínez-Checa F. Microbial composition of Saharan dust plumes deposited as red rain in Granada (Southern Spain). THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 913:169745. [PMID: 38163611 DOI: 10.1016/j.scitotenv.2023.169745] [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: 10/16/2023] [Revised: 12/26/2023] [Accepted: 12/26/2023] [Indexed: 01/03/2024]
Abstract
During durst storms, also biological material is transported from arid areas such as the Sahara Desert. In the present work, rain samples containing significant amounts of mineral dust have been collected in Granada during different red rain episodes. Biological features (bacteria, biofilm, pollen grain and fungal spore) as well as size-particle distribution and mineralogical composition were studied by SEM. Nanobacteria were observed for the first time in red rain samples. A preliminary metabarcoding analysis was performed on three red rain samples. Here, Bacillota made up 18 % and Pseudomonadota 23 % of the whole prokaryotic community. The fungal community was characterized by a high abundance of Ascomycota and, dependent on the origin, the presence of Chytridiomycota. By means of 16S rRNA sequencing, 18 cultivable microorganisms were identified. In general, members of the phyla Pseudomonadota and Bacillota made up the majority of taxa. Some species, such as Peribacillus frigoritolerans and Bacillus halotolerans were isolated during three different red rain episodes. Generally, red rain carries a wide variety of microorganisms, being their ecosystem and health effects largely unknown.
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Affiliation(s)
- Azahara Navarro
- Department of Edaphology and Agricultural Chemistry, University of Granada, Granada, Spain
| | - Ana Del Moral
- Department of Microbiology, University of Granada, Granada, Spain.
| | - Bettina Weber
- Institute of Plant Sciences, University of Graz, Graz, Austria; Multiphase Chemistry Department, Max Planck Institute for Chemistry, Mainz, Germany
| | - Jens Weber
- Institute of Plant Sciences, University of Graz, Graz, Austria
| | - Alberto Molinero
- Department of Edaphology and Agricultural Chemistry, University of Granada, Granada, Spain
| | - Rafael Delgado
- Department of Edaphology and Agricultural Chemistry, University of Granada, Granada, Spain
| | - Jesús Párraga
- Department of Edaphology and Agricultural Chemistry, University of Granada, Granada, Spain
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Genomic microbiome analyses of surface sand samples from the Kyzyl-Kum Desert (Uzbekistan): characterization and comparative study. Arch Microbiol 2023; 205:90. [PMID: 36780035 DOI: 10.1007/s00203-023-03432-z] [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: 06/06/2022] [Accepted: 02/02/2023] [Indexed: 02/14/2023]
Abstract
The Kyzyl-Kum Desert extends over an area of 300,000 Km2, in the region bordering Kazakhstan, Uzbekistan and Turkmenistan and is mainly covered by sand dunes. The Kyzyl-Kum desert is also known for its large deposits of minerals of economic interests, the exploitation of which is affecting the local ecosystem and increasing the desertification. We examined the bacterial biodiversity of surface sand samples from several sites from the Kyzyl-Kum desert using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. We also examined several physicochemical parameters of the sand samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Actinobacteria, Proteobacteria and Bacteroidetes. The most abundant genera in our samples were found to belong to the Arthrobacter, Adhaeribacter and Roseomonas genera. We found that the relative abundance of members belonging to the Actinobacteria phylum, commonly found in desertic areas, increase in abundance in sites with higher content of organic matter and sulfur, whereas members of the Proteobacteria and Bacteroidetes phyla seems to diminish in abundance in coarse silt and fine-grained soils and those rich in magnesium, suggesting that those parameters might influence the bacterial community composition in this desertic area. This study is the first to provide new insights into the prokaryotic community composition from this unusual desert site.
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Spatio-Temporal Evolution of a Typical Sandstorm Event in an Arid Area of Northwest China in April 2018 Based on Remote Sensing Data. REMOTE SENSING 2022. [DOI: 10.3390/rs14133065] [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
Northwest China is significantly affected by sandstorm disasters. To mitigate the negative impacts of sandstorm events, it is critical to understand the spatio-temporal variations in typical sand and dust storms and their influencing factors. In this work, using ground-based measurements of particulate matter and remote sensing data such as MODIS, OMI, and CALIPSO data, the sources of aerosol pollution and aerosol optical properties of a typical sandstorm event that occurred in Northwest China in 2018 was studied. In addition, the HYSPLIT model was used to explore the air mass trajectories in order to analyze the sand and dust migration process during the sandstorm event. Furthermore, the wind erosion sensitivity of Northwest China was analyzed via single factor analysis and multi-factor superposition of wind field intensity, soil drought index, vegetation coverage, and relief amplitude. Finally, the region of the study area having a high comprehensive wind erosion sensitivity was identified. The results showed that the PM10 concentrations exceeded 400 µg/m3 and the PM2.5/PM10 ratio did not exceeded 0.6 during the sandstorm event, indicating that natural particulate matter was dominant in the ambient air. At the epicenter of pollution, the aerosol optical depth (AOD) at 550 nm was 0.75–1. By combining AOD data with wind speed and direction data from field observation stations, it was found that the sandstorm event in 2018 mainly occurred between 1 April and 3 April, and affected all of Northwest China on 2 April and 3 April. The absorbed aerosol index (AAI) ranged between 2.5 and 4, indicating that the Taklimakan Desert was the main source of sandstorm events in Northwest China. The CALIPSO total attenuated backscatter coefficient at 532 nm indicated that the main component of tropospheric aerosol in this region was distributed in the range of 0–12.5 km. The simulated airflow track showed that it had the same dust source regions as AAI index studies. Moreover, investigation of wind erosion sensitivity in the study areas indicated that the Taklimakan Desert and other desert regions were the main ecologically sensitive areas. These conclusions can provide references and suggestions for the mitigation of damage caused by sandstorm events, in addition to the enhancement of ecological governance.
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Vergadi E, Rouva G, Angeli M, Galanakis E. Infectious Diseases Associated with Desert Dust Outbreaks: A Systematic Review. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19116907. [PMID: 35682493 PMCID: PMC9180817 DOI: 10.3390/ijerph19116907] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 02/04/2023]
Abstract
Background: Desert dust outbreaks and dust storms are the major source of particulate matter globally and pose a major threat to human health. We investigated the microorganisms transported with desert dust particles and evaluated their potential impact on human health. Methods: A systematic review of all reports on the association between non-anthropogenic desert dust pollution, dust microorganisms and human health is conducted. Results: In total, 51 articles were included in this review. The affected regions studied were Asia (32/51, 62.7%) followed by Europe (9/51, 17.6%), America (6/51, 11.8%), Africa (4/51, 7.8%) and Australia (1/51, 2.0%). The Sahara Desert was the most frequent source of dust, followed by Asian and American deserts. In 39/51 studies the dust-related microbiome was analyzed, while, in 12/51 reports, the association of desert dust with infectious disease outbreaks was examined. Pathogenic and opportunistic agents were isolated from dust in 24/39 (61.5%) and 29/39 (74.4%) of the studies, respectively. A significant association of dust events with infectious disease outbreaks was found in 10/12 (83.3%) reports. The infectious diseases that were mostly investigated with dust outbreaks were pneumonia, respiratory tract infections, COVID-19, pulmonary tuberculosis and coccidioidomycosis. Conclusions: Desert dust outbreaks are vehicles of a significant number of pathogenic or opportunistic microorganisms and limited data indicate an association between dust events and infectious disease outbreaks. Further research is required to strengthen the correlation between dust events and infectious diseases and subsequently guide preventive public health measures.
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Iakovides M, Tsiamis G, Tziaras T, Stathopoulou P, Nikolaki S, Iakovides G, Stephanou EG. Two-year systematic investigation reveals alterations induced on chemical and bacteriome profile of PM 2.5 by African dust incursions to the Mediterranean atmosphere. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 815:151976. [PMID: 34843760 DOI: 10.1016/j.scitotenv.2021.151976] [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: 09/07/2021] [Revised: 11/22/2021] [Accepted: 11/22/2021] [Indexed: 06/13/2023]
Abstract
PM2.5 atmospheric samples were regularly collected between January 2013 and March 2015 at a central location of Eastern Mediterranean (Island of Crete) during African dust events (DES) and periods of absence of such episodes as controls (CS). The elemental composition and microbiome DES and CS were thoroughly investigated. Fifty-six major and trace elements were determined by inductively coupled plasma-mass spectrometry. Relative mass abundances (RMA) of major crustal elements and lanthanoids were higher in DES than in CS. Conversely in CS, RMAs were higher for most anthropogenic transition metals. Lanthanum-to-other lanthanoids concentration ratios for DES approached the corresponding reference values for continental crust and several African dust source regions, while in CS they exceeded these values. USEPA's UNMIX receptor model, applied in all PM2.5 samples, established that African dust is the dominant contributing source (by 80%) followed by road dust/fuel oil emissions (17%) in the receptor area. Potential source contribution function (PSCF) identified dust hotspots in Tunisia, Libya and Egypt. The application of 16S rRNA gene amplicon sequencing revealed high variation of bacterial composition and diversity between DES and CS samples. Proteobacteria, Actinobacteria and Bacteroides were the most dominant in both DES and CS samples, representing ~88% of the total bacterial diversity. Cutibacterium, Tumebacillus and Sphingomonas dominated the CS samples, while Rhizobium and Brevundimonas were the most prevalent genera in DES. Mutual exclusion/co-occurrence network analysis indicated that Sphingomonas and Chryseobacterium exhibited the highest degrees of mutual exclusion in CS, while in DES the corresponding species were Brevundimonas, Delftia, Rubellimicrobium, Flavobacterium, Blastococcus, and Pseudarthrobacter. Some of these microorganisms are emerging global opportunistic pathogens and an increase in human exposure to them as a result of environmental changes, is inevitable.
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Affiliation(s)
- Minas Iakovides
- Department of Chemistry, University of Crete, 71003 Heraklion, Greece
| | - George Tsiamis
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St, 30100 Agrinio, Greece
| | | | - Panagiota Stathopoulou
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St, 30100 Agrinio, Greece
| | - Sofia Nikolaki
- Laboratory of Systems Microbiology and Applied Genomics, Department of Environmental Engineering, University of Patras, 2 Seferi St, 30100 Agrinio, Greece
| | - Giannis Iakovides
- Department of Mathematics and Applied Mathematics, University of Crete, 71003 Heraklion, Greece
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High Proportions of Radiation-Resistant Strains in Culturable Bacteria from the Taklimakan Desert. BIOLOGY 2022; 11:biology11040501. [PMID: 35453702 PMCID: PMC9030528 DOI: 10.3390/biology11040501] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/19/2022] [Accepted: 03/23/2022] [Indexed: 12/18/2022]
Abstract
Simple Summary Radiation-resistant extremophiles have frequently been found in the Taklimakan Desert, which is known for its harsh conditions. However, there is no systemic study investigating the diversity and proportion of radiation-resistant strains among culturable bacteria. The results of this study revealed the distribution of culturable bacteria in the Taklimakan Desert and indicated high proportions of radiation-resistant strains in the culturable bacteria. The study helps to better understand the ecological origin of radio-resistance and to quantitatively describe the desert as a common habitat for radiation-resistant extremophiles. Abstract The Taklimakan Desert located in China is the second-largest shifting sand desert in the world and is known for its harsh conditions. Types of γ-rays or UV radiation-resistant bacterial strains have been isolated from this desert. However, there is no information regarding the proportions of the radiation-resistant strains in the total culturable microbes. We isolated 352 bacterial strains from nine sites across the Taklimakan Desert from north to south. They belong to Actinobacteria, Firmicutes, Proteobacteria, and Bacteroidetes. The phylum Actinobacteria was the most predominant in abundance and Firmicutes had the highest species richness. Bacteroidetes had the lowest abundance and was found in four sites only, while the other three phyla were found in every site but with different distribution profiles. After irradiating with 1000 J/m2 and 6000 J/m2 UV-C, the strains with survival rates higher than 10% occupied 72.3% and 36.9% of all culturable bacteria, respectively. The members from Proteobacteria had the highest proportions, with survival rates higher than 10%. After radiation with 10 kGy γ-rays, Kocuria sp. TKL1057 and Planococcus sp. TKL1152 showed higher radiation-resistant capabilities than Deinococcus radiodurans R1. Besides obtaining several radiation-resistant extremophiles, this study measured the proportions of the radiation-resistant strains in the total culturable microbes for the first time. This study may help to better understand the origin of radioresistance, especially by quantitatively comparing proportions of radiation-resistant extremophiles from different environments in the future.
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Mališová L, Španělová P, Sedláček I, Pajer P, Musílek M, Puchálková B, Jakubů V, Žemličková H, Šafránková R. The first case of Planococcus glaciei found in blood, a report from the Czech Republic. Folia Microbiol (Praha) 2021; 67:121-127. [PMID: 34590203 DOI: 10.1007/s12223-021-00919-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 09/07/2021] [Indexed: 11/27/2022]
Abstract
The isolation of Planococcus glaciei (designed strain CNCTC 7660) from blood of a patient with appendicitis is reported. Species P. glaciei (type strain CGMCC 1.6846 T) was for the first time identified as an environmental bacterium acquired from a glacier in China in 2009. To reveal the identity of the isolate CNCTC 7660, the 16S rDNA sequencing and the whole genome sequencing (Illumina MiSeq, Oxford Nanopore) were performed. The level of 16S rDNA gene sequencing similarity between CNCTC 7660 and CGMCC 1.6846 T was 99.55%. Phylogenetic analysis and average nucleotide analysis (ANI) based on the whole genome sequencing confirmed that the isolate CNCTC 7660 and CGMCC1.6846 T had ANI value above the taxonomic threshold for belonging to the same species (95%). The G + C content of CNCTC 7660 DNA was 46.8% (mol/mol). Except for the growth temperature, strains CGMCC1.6846 T and CNCTC 7660 were distinguished also biochemically. Due to the lack of information about the pathogenicity of P. glaciei, the possibility that it exerts pathogenicity in persons is suggested. But for understanding the nature of this species, further cases are needed.
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Affiliation(s)
- Lucia Mališová
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
| | - Petra Španělová
- Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic.
| | - Ivo Sedláček
- Department of Experimental Biology, Faculty of Science, Czech Collection of Microorganisms, Masaryk University, Brno, Czech Republic
| | - Petr Pajer
- Military Health Institute, Military Medical Agency, Prague, Czech Republic
| | - Martin Musílek
- National Reference Laboratory for Meningococcal Infections, National Institute of Public Health, Prague, Czech Republic
| | - Blanka Puchálková
- Department of Clinical Microbiology, Karlovy Vary Regional Hospital, Hradec Kralove, Czech Republic
| | - Vladislav Jakubů
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Helena Žemličková
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czech Republic
- Department of Microbiology, 3Rd Faculty of Medicine, Charles University, University Hospital Kralovske Vinohrady and National Institute of Public Health, Prague, Czech Republic
- Department of Clinical Microbiology, Faculty of Medicine and University Hospital, Charles University, Hradec Kralove, Czech Republic
| | - Renáta Šafránková
- Czech National Collection of Type Cultures, National Institute of Public Health, Prague, Czech Republic
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Xie Z, Du S, Ma T, Hou J, Zeng X, Li Y. High time-resolved characterization of airborne microbial community during a typical haze pollution process. JOURNAL OF HAZARDOUS MATERIALS 2021; 415:125722. [PMID: 34088212 DOI: 10.1016/j.jhazmat.2021.125722] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/04/2021] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Variations of bioaerosol characteristics during the process of haze pollution have rarely been explored. In this study, high time-resolved variations of the community structures of bacteria, fungi, and ammonia-oxidizing microorganisms (AOMs) were assessed during a typical haze pollution process. The impacts of meteorological factors, water-soluble inorganic ions (WSII), and organic dicarboxylic acids (DCA) on the airborne microbial community were systematically evaluated. The results showed that the bacterial community varied greatly during the formation stages of haze pollution, and tended to stabilize with the further development of haze pollution. Nevertheless, variations of the fungal community lasted throughout the whole haze pollution process. Furthermore, Nitrososphaera absolutely dominated the ammonia-oxidizing archaea (AOA) and declined as PM2.5 burst. Network analysis identified relatively weak interactions and co-occurrence patterns between dominant fungal genera. Importantly, dust source ions and PM2.5 acidity exerted the most significant impacts on bacterial and fungal communities. These results identify the high time-resolved variations of airborne microbial communities during the formation and development of haze pollution process, and provide valuable data to better understand the interaction between bioaerosols and haze pollution.
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Affiliation(s)
- Zhengsheng Xie
- School of Water and Environment, Chang'an University, Xi'an 710054, China.
| | - Shengli Du
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Tianfeng Ma
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Junli Hou
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Xuelin Zeng
- School of Water and Environment, Chang'an University, Xi'an 710054, China
| | - Yanpeng Li
- School of Water and Environment, Chang'an University, Xi'an 710054, China; Key Laboratory of Subsurface Hydrology and Ecological Effects in Arid Region (Chang'an University), Ministry of Education, Xi'an 710054, China.
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Osman JR, Wang Y, Jaubert C, Nguyen TN, Fernandes GR, DuBow MS. The bacterial communities of surface soils from desert sites in the eastern Utah (USA) portion of the Colorado Plateau. Microbiol Res 2020; 244:126664. [PMID: 33359841 DOI: 10.1016/j.micres.2020.126664] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 09/11/2020] [Accepted: 11/27/2020] [Indexed: 01/05/2023]
Abstract
Desert-like areas located in the eastern portion of the state of Utah (USA) have geographic features that can resemble the surface of the planet Mars, characterized by red-colored hills, soils and sandstones. We examined the bacterial biodiversity of surface soil samples from several sites from the Colorado Plateau Desert in eastern Utah using pyrosequencing of PCR amplified bacterial 16S rRNA genes from total extracted soil DNA. The sample sites cover the Great Basin, Goblin Valley State Park and nearby regions on the Colorado Plateau. We also examined several physicochemical parameters of the soil samples to investigate any possible correlations between bacterial community structure and environmental drivers. The predominant bacterial phyla present in the samples were found to belong to members of the Proteobacteria, Actinobacteria, Bacteroidetes, and Gemmatimonadetes. The most abundant genera in our samples were found to belong to the Cesiribacter, Lysobacter, Adhaeribacter, Microvirga and Pontibacter genera. We found that the relative abundance of Proteobacteria and Gemmatimonadetes were significantly correlated with soil pH and a low concentration of organic matter, suggesting that, in these relatively high-altitude desert soils, these two parameters may be of primary importance to influence bacterial community composition.
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Affiliation(s)
- Jorge R Osman
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Yang Wang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Chloé Jaubert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Tuyet-Nga Nguyen
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Gustavo R Fernandes
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France.
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Pompilio A, Di Bonaventura G. Ambient air pollution and respiratory bacterial infections, a troubling association: epidemiology, underlying mechanisms, and future challenges. Crit Rev Microbiol 2020; 46:600-630. [PMID: 33059504 DOI: 10.1080/1040841x.2020.1816894] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
The World Health Organization attributed more than four million premature deaths to ambient air pollution in 2016. Numerous epidemiologic studies demonstrate that acute respiratory tract infections and exacerbations of pre-existing chronic airway diseases can result from exposure to ambient (outdoor) air pollution. In this context, the atmosphere contains both chemical and microbial pollutants (bioaerosols), whose impact on human health remains unclear. Therefore, this review: summarises the findings from recent studies on the association between exposure to air pollutants-especially particulate matter and ozone-and onset or exacerbation of respiratory infections (e.g. pneumonia, cystic fibrosis lung infection, and tuberculosis); discusses the mechanisms underlying the relationship between air pollution and respiratory bacterial infections, which is necessary to define prevention and treatment strategies; demonstrates the relevance of air pollution modelling in investigating and preventing the impact of exposure to air pollutants on human health; and outlines future actions required to improve air quality and reduce morbidity and mortality related to air pollution.
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Affiliation(s)
- Arianna Pompilio
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
| | - Giovanni Di Bonaventura
- Department of Medical, Oral and Biotechnological Sciences, and Center for Advanced Studies and Technology (CAST), "G. d'Annunzio" University of Chieti-Pescara, Chieti, Italy
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González-Toril E, Osuna S, Viúdez-Moreiras D, Navarro-Cid I, Toro SDD, Sor S, Bardera R, Puente-Sánchez F, de Diego-Castilla G, Aguilera Á. Impacts of Saharan Dust Intrusions on Bacterial Communities of the Low Troposphere. Sci Rep 2020; 10:6837. [PMID: 32321958 PMCID: PMC7176723 DOI: 10.1038/s41598-020-63797-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 03/31/2020] [Indexed: 11/30/2022] Open
Abstract
We have analyzed the bacterial community of a large Saharan dust event in the Iberian Peninsula and, for the first time, we offer new insights regarding the bacterial distribution at different altitudes of the lower troposphere and the replacement of the microbial airborne structure as the dust event receeds. Samples from different open-air altitudes (surface, 100 m and 3 km), were obtained onboard the National Institute for Aerospace Technology (INTA) C-212 aircrafts. Samples were collected during dust and dust-free air masses as well two weeks after the dust event. Samples related in height or time scale seems to show more similar community composition patterns compared with unrelated samples. The most abundant bacterial species during the dust event, grouped in three different phyla: (a) Proteobacteria: Rhizobiales, Sphingomonadales, Rhodobacterales, (b) Actinobacteria: Geodermatophilaceae; (c) Firmicutes: Bacillaceae. Most of these taxa are well known for being extremely stress-resistant. After the dust intrusion, Rhizobium was the most abundant genus, (40-90% total sequences). Samples taken during the flights carried out 15 days after the dust event were much more similar to the dust event samples compared with the remaining samples. In this case, Brevundimonas, and Methylobacterium as well as Cupriavidus and Mesorizobium were the most abundant genera.
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Affiliation(s)
- Elena González-Toril
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Susana Osuna
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Daniel Viúdez-Moreiras
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Ivan Navarro-Cid
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Silvia Díaz Del Toro
- Department of Genetics, Physiology and Microbiology. Biology Faculty. C/José Antonio Novais, 12, Universidad Complutense de Madrid (UCM), 28040, Madrid, Spain
| | - Suthyvann Sor
- Aerodinamic Department (INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Rafael Bardera
- Aerodinamic Department (INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain
| | - Fernando Puente-Sánchez
- Systems Biology Program. Centro Nacional de Biotecnología. C/ Darwin n° 3, Campus de Cantoblanco, 28049, Madrid, Spain
| | | | - Ángeles Aguilera
- Centro de Astrobiología (CSIC-INTA). Carretera de Ajalvir Km 4, Torrejón de Ardoz, 28850, Madrid, Spain.
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Fu P, Bai L, Cai Z, Li R, Yung KKL. Fine particulate matter aggravates intestinal and brain injury and affects bacterial community structure of intestine and feces in Alzheimer's disease transgenic mice. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2020; 192:110325. [PMID: 32078839 DOI: 10.1016/j.ecoenv.2020.110325] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 02/09/2020] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Fine particulate matter (PM2.5) was a risk factor for neurological disorders when emerging studies revealed that PM2.5 affected the bacterial community structure of gut in Alzheimer's disease (AD) patients. The purpose of this study was to explore the effects of PM2.5 on intestinal and brain injury and on bacterial community structure in the intestine and feces of APP/PS1 transgenic mice exposed to PM2.5 for eight weeks with a real-world whole-body inhalation exposure system in Taiyuan, China. The brain and intestinal tissues were collected to evaluate histopathological changes by HE staining. TNF-α and IL-6 levels in intestines, brains, and serums, and Aβ-42 levels in brains were detected. Intestinal and fecal samples were subjected to 16S rRNA gene sequencing. Results showed that PM2.5 significantly aggravated the pathological injury in intestines and brains in AD mice with elevated pro-inflammatory cytokine levels. The estimators of Shannon, Simpson, Chao1, and ACE indexes reflected the diversity and richness of the bacterial community. Compared with the FA-WT group, the FA-AD group had lower diversity and richness when the PM2.5-AD group had the highest ones. PCA and NMDS revealed the specific influence of PM2.5 on the bacterial community of intestine and feces because that the PM2.5-FA and PM2.5-AD group clumped visibly closer than the other groups in both bacterial communities of intestine and feces. The KEGG pathway analysis predicted the vital functional genes and metabolic pathways in the bacterial community of PM2.5-AD mice. This study indicated the histopathological changes and inflammation in the intestine and brain were seriously caused in PM2.5-AD mice when the α-diversity of the bacterial community in intestine and feces was visibly changed.
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Affiliation(s)
- Pengfei Fu
- Department of Biology, Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Hong Kong Special Administrative Region
| | - Lirong Bai
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China
| | - Zongwei Cai
- State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong Special Administrative Region
| | - Ruijin Li
- Institute of Environmental Science, Shanxi University, Taiyuan, PR China.
| | - Ken Kin Lam Yung
- Department of Biology, Golden Meditech Center for NeuroRegeneration Sciences, Hong Kong Baptist University, Hong Kong Special Administrative Region; Institute of Environmental Science, Shanxi University, Taiyuan, PR China; State Key Laboratory of Environmental and Biological Analysis, Hong Kong Baptist University, Hong Kong Special Administrative Region.
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13
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Wang Y, Osman JR, DuBow MS. Bacterial Communities on the Surface of the Mineral Sandy Soil from the Desert of Maine (USA). Curr Microbiol 2020; 77:1429-1437. [PMID: 32193606 DOI: 10.1007/s00284-020-01946-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 03/07/2020] [Indexed: 12/19/2022]
Abstract
The Desert of Maine, not a real desert, is a 160,000 m2 tourist attraction of glacial silt which resembles a desert, surrounded by a pine forest in the state of Maine located in the northeastern USA. Though not a true desert, the soil of the Desert of Maine has a sandy texture with poor water-holding abilities, nutrient retention capabilities, and a relatively low pH value (pH 5.09). Samples from this site may be of interest to examine the bacterial diversity present on mineral sandy loam soils with an acidic pH, low concentrations of organic materials though surrounded by a pine forest, and compare it with true desert soil microbial populations. Two surface sand samples from the Desert of Maine were obtained, and pyrosequencing of PCR amplified 16S rRNA genes from total extracted DNA was used to assess bacterial diversity, community structure, and the relative abundance of major bacterial taxa. We found that the soil samples from the Desert of Maine displayed high levels of bacterial diversity, with a predominance of members belonging to the Proteobacteria and Actinobacteria phyla. Bacteria from the most abundant genus, Acidiphilium, represent 12.5% of the total 16S rDNA sequences. In total, 1394 OTUs were observed in the two samples, with 668 OTUs being observed in both samples. By comparing Desert of Maine bacterial populations with studies on similar soil environments, we found that the samples contained less Acidobacteria than soils from acid soil forests, and less Firmicutes plus more Proteobacteria than oligotrophic desert soils. Interestingly, our samples were found to be highly similar in their composition to an oak forest soil in France.
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Affiliation(s)
- Yang Wang
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
| | - Jorge R Osman
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France
- Laboratoire de Géologie de Lyon, Université Claude Bernard Lyon-1, UMR5276, Lyon, France
| | - Michael S DuBow
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Univ Paris-Sud, Bâtiment 409, 91405, Orsay, France.
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14
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Goulart MC, Cueva‐Yesquén LG, Hidalgo Martinez KJ, Attili‐Angelis D, Fantinatti‐Garboggini F. Comparison of specific endophytic bacterial communities in different developmental stages of Passiflora incarnata using culture-dependent and culture-independent analysis. Microbiologyopen 2019; 8:e896. [PMID: 31454177 PMCID: PMC6813437 DOI: 10.1002/mbo3.896] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 12/12/2022] Open
Abstract
Plants and endophytic microorganisms have coevolved unique relationships over many generations. Plants show a specific physiological status in each developmental stage, which may determine the occurrence and dominance of specific endophytic populations with a predetermined ecological role. This study aimed to compare and determine the structure and composition of cultivable and uncultivable bacterial endophytic communities in vegetative and reproductive stages (RS) of Passiflora incarnata. To that end, the endophytic communities were assessed by plating and Illumina-based 16S rRNA gene amplicon sequencing. Two hundred and four cultivable bacterial strains were successfully isolated. From the plant's RS, the isolated strains were identified mainly as belonging to the genera Sphingomonas, Curtobacterium, and Methylobacterium, whereas Bacillus was the dominant genus isolated from the vegetative stage (VS). From a total of 133,399 sequences obtained from Illumina-based sequencing, a subset of 25,092 was classified in operational taxonomy units (OTUs). Four hundred and sixteen OTUs were obtained from the VS and 66 from the RS. In the VS, the most abundant families were Pseudoalteromonadaceae and Alicyclobacillaceae, while in the RS, Enterobacteriaceae and Bacillaceae were the most abundant families. The exclusive abundance of specific bacterial populations for each developmental stage suggests that plants may modulate bacterial endophytic community structure in response to different physiological statuses occurring at the different plant developmental stages.
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Affiliation(s)
- Marcela C. Goulart
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Luis G. Cueva‐Yesquén
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Kelly J. Hidalgo Martinez
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Derlene Attili‐Angelis
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
| | - Fabiana Fantinatti‐Garboggini
- Graduate Program in Genetics and Molecular Biology, Institute of BiologyUniversity of Campinas (UNICAMP)CampinasBrazil
- Division of Microbial Resources (DRM), Research Center for Agricultural, Biological and Chemical (CPQBA)University of Campinas (UNICAMP)PaulíniaBrazil
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15
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Variation of bacterial biodiversity from saline soils and estuary sediments present near the Mediterranean Sea coast of Camargue (France). Antonie van Leeuwenhoek 2018; 112:351-365. [PMID: 30232678 DOI: 10.1007/s10482-018-1164-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2017] [Accepted: 09/07/2018] [Indexed: 10/28/2022]
Abstract
Salinity is an important environmental factor influencing microbial community composition. To better understand this influence, we determined the bacterial communities present in 17 different sites of brackish sediment (underwater) and soil (surface) samples from the Camargue region (Rhône river delta) in southern France during the fall of 2013 and 2014 using pyrosequencing of the V3-V4 regions of the 16S rRNA genes amplified by PCR. This region is known for abundant flora and fauna and, though saline, 30% of rice consumed in France is grown here. We found that bacterial abundance in 1 g of soil or sediment, calculated by qPCR, was higher in sediments than in surface soil samples. Members belonging to the Proteobacteria, Bacteroidetes, Chloroflexi and Firmicutes phyla dominated the bacterial communities of sediment samples, while members belonging to the Proteobacteria, Bacteroidetes, Gemmatimonadetes, Actinobacteria, Firmicutes and Acidobacteria phyla dominated the bacterial communities of the soil samples. The most abundant bacterial genera present in the saline sediments and soils from the Camargue belonged mostly to halophilic and sulphate reducing bacteria, suggesting that the Camargue may be a valuable system to investigate saline, yet agriculturally productive, sediment and soil microbial ecosystem.
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16
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Behzad H, Mineta K, Gojobori T. Global Ramifications of Dust and Sandstorm Microbiota. Genome Biol Evol 2018; 10:1970-1987. [PMID: 29961874 PMCID: PMC6097598 DOI: 10.1093/gbe/evy134] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/28/2018] [Indexed: 12/17/2022] Open
Abstract
Dust and sandstorm events inject substantial quantities of foreign microorganisms into global ecosystems, with the ability to impact distant environments. The majority of these microorganisms originate from deserts and drylands where the soil is laden with highly stress-resistant microbes capable of thriving under extreme environmental conditions, and a substantial portion of them survive long journeys through the atmosphere. This large-scale transmission of highly resilient alien microbial contaminants raises concerns with regards to the invasion of sensitive and/or pristine sink environments, and to human health-concerns exacerbated by increases in the rate of desertification. Further increases in the transport of dust-associated microbiota could extend the spread of foreign microbes to new ecosystems, increase their load in present sink environments, disrupt ecosystem balance, and potentially introduce new pathogens. Our present understanding of these microorganisms, their phylogenic affiliations and functional significance, is insufficient to determine their impact. The purpose of this review is to provide an overview of available data regarding dust and sandstorm microbiota and their potential ramifications on human and ecosystem health. We conclude by discussing current gaps in dust and sandstorm microbiota research, and the need for collaborative studies involving high-resolution meta-omic approaches in conjunction with extensive ecological time-series studies to advance the field towards an improved and sufficient understanding of these invisible atmospheric travelers and their global ramifications.
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Affiliation(s)
- Hayedeh Behzad
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
| | - Katsuhiko Mineta
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Computer, Electrical and Mathematical Sciences and Engineering Division (CEMSE), Thuwal, Saudi Arabia
| | - Takashi Gojobori
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, Saudi Arabia
- King Abdullah University of Science and Technology (KAUST), Biological and Environmental Sciences and Engineering Division (BESE), Thuwal, Saudi Arabia
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17
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Airborne Bacterial Communities in Three East Asian Cities of China, South Korea, and Japan. Sci Rep 2017; 7:5545. [PMID: 28717138 PMCID: PMC5514139 DOI: 10.1038/s41598-017-05862-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 06/05/2017] [Indexed: 02/01/2023] Open
Abstract
The global diversity of airborne bacteria has not yet been studied, despite its importance in human health and climate change. Here, we focused on the diversity of airborne bacteria and their correlations with meteorological/environmental conditions in China, South Korea, and Japan. Beijing (China) had more diverse airborne bacteria, followed by Seoul (South Korea) and Nagasaki (Japan), and seasonal variations were observed. Beijing and Seoul had more diverse airborne bacteria during the winter, whereas Nagasaki showed greater diversity during the summer. According to principal component analysis and Bray-Curtis similarity, higher similarity was observed between Beijing and Seoul than between Seoul and Nagasaki during all seasons except summer. Among meteorological/environmental variables, temperature and humidity were highly correlated with the diversity of airborne bacteria on the measurement day, whereas wind speeds and the frequency of northwest winds were highly correlated for 2–3-day moving averages. Thus, proximity and resuspension could enhance bacterial diversity in East Asian cities.
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18
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Alterations in the airborne bacterial community during Asian dust events occurring between February and March 2015 in South Korea. Sci Rep 2016; 6:37271. [PMID: 27849049 PMCID: PMC5110963 DOI: 10.1038/srep37271] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2016] [Accepted: 10/27/2016] [Indexed: 11/14/2022] Open
Abstract
During Asian dust events, a relatively high concentration of particulate matter is transported by wind from arid and semi-arid regions, such as the Gobi and Taklamakan deserts, to nearby countries, including China, Korea, and Japan. The dust particles contain various microorganisms, which can affect human health as well as the environmental microbe population. In the current study, we investigated the characteristics of the airborne bacterial community during Asian dust events between February and March 2015 in South Korea. Bacterial diversity indexes such as operational taxonomic units, Chao1 and Inverse Simpson index were increased, along with total 16S rRNA gene copy number during Asian dust events. The bacterial community structure during Asian dust events was clearly distinguishable from that during non-Asian dust days. The genera Bacillus and Modestobacter were increased 3.9- and 2.7-fold, respectively, while Escherichia-Shigella was decreased by 89.8%. A non-metric multidimensional scaling plot with metadata analysis revealed association of particulate matter concentration, but not temperature, humidity or wind speed, with bacterial community structure, suggesting that the newly transported dust particles contain various microorganisms that influence the airborne bacterial environment.
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19
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Mazar Y, Cytryn E, Erel Y, Rudich Y. Effect of Dust Storms on the Atmospheric Microbiome in the Eastern Mediterranean. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2016; 50:4194-202. [PMID: 27001166 DOI: 10.1021/acs.est.5b06348] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
We evaluated the impact of Saharan dust storms on the local airborne microbiome in a city in the Eastern Mediterranean area. Samples of particles with diameter less than 10 μm were collected during two spring seasons on both dusty and nondusty days. DNA was extracted, and partial 16S rRNA gene amplicons were sequenced using the Illumina platform. Bioinformatic analysis showed the effect of dust events on the diversity of the atmospheric microbiome. The relative abundance of desert soil-associated bacteria increased during dust events, while the relative abundance of anthropogenic-influenced taxa decreased. Quantitative polymerase chain reaction measurements of selected clinically significant antibiotic resistance genes (ARGs) showed that their relative abundance decreased during dust events. The ARG profiles on dust-free days were similar to those in aerosol collected in a poultry house, suggesting a strong agricultural influence on the local ambient profiles. We conclude that dust storms enrich the ambient airborne microbiome with new soil-derived bacteria that disappear as the dust settles, suggesting that the bacteria are transported attached to the dust particles. Dust storms do not seem to be an important vector for transport of probed ARGs.
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Affiliation(s)
- Yinon Mazar
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
| | - Eddie Cytryn
- Institute of Soil, Water and Environmental Sciences, The Volcani Center, Agriculture Research Organization, Bet Dagan 50250, Israel
| | - Yigal Erel
- The Fredy and Nadine Herrmann Institute of Earth Sciences, The Hebrew University of Jerusalem , Jerusalem 91904, Israel
| | - Yinon Rudich
- Department of Earth and Planetary Sciences, Weizmann Institute of Science , Rehovot 76100, Israel
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20
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Joly D, Faure D. Next-generation sequencing propels environmental genomics to the front line of research. Heredity (Edinb) 2015; 114:429-30. [PMID: 25873237 DOI: 10.1038/hdy.2015.23] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Affiliation(s)
- D Joly
- 1] GDR3692 Génomique Environnementale, CNRS, Gif-sur-Yvette Cedex, France [2] Laboratoire Evolution, Génomes, Comportement, Ecologie UMR9191 CNRS-IRD-Paris-Sud, Gif-sur-Yvette Cedex, France
| | - D Faure
- 1] GDR3692 Génomique Environnementale, CNRS, Gif-sur-Yvette Cedex, France [2] Institut for Integrative Biology of the Cell, I2BC, UMR9198 CNRS CEA Université Paris-Sud, Saclay Plant Sciences, Gif-sur-Yvette Cedex, France
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21
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Behzad H, Gojobori T, Mineta K. Challenges and opportunities of airborne metagenomics. Genome Biol Evol 2015; 7:1216-26. [PMID: 25953766 PMCID: PMC4453059 DOI: 10.1093/gbe/evv064] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/06/2015] [Indexed: 01/09/2023] Open
Abstract
Recent metagenomic studies of environments, such as marine and soil, have significantly enhanced our understanding of the diverse microbial communities living in these habitats and their essential roles in sustaining vast ecosystems. The increase in the number of publications related to soil and marine metagenomics is in sharp contrast to those of air, yet airborne microbes are thought to have significant impacts on many aspects of our lives from their potential roles in atmospheric events such as cloud formation, precipitation, and atmospheric chemistry to their major impact on human health. In this review, we will discuss the current progress in airborne metagenomics, with a special focus on exploring the challenges and opportunities of undertaking such studies. The main challenges of conducting metagenomic studies of airborne microbes are as follows: 1) Low density of microorganisms in the air, 2) efficient retrieval of microorganisms from the air, 3) variability in airborne microbial community composition, 4) the lack of standardized protocols and methodologies, and 5) DNA sequencing and bioinformatics-related challenges. Overcoming these challenges could provide the groundwork for comprehensive analysis of airborne microbes and their potential impact on the atmosphere, global climate, and our health. Metagenomic studies offer a unique opportunity to examine viral and bacterial diversity in the air and monitor their spread locally or across the globe, including threats from pathogenic microorganisms. Airborne metagenomic studies could also lead to discoveries of novel genes and metabolic pathways relevant to meteorological and industrial applications, environmental bioremediation, and biogeochemical cycles.
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Affiliation(s)
- Hayedeh Behzad
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Takashi Gojobori
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
| | - Katsuhiko Mineta
- Computational Bioscience Research Center, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia Computer, Electrical, and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Kingdom of Saudi Arabia
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