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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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An X, Han S, Ren X, Sichone J, Fan Z, Wu X, Zhang Y, Wang H, Cai W, Sun F. Succession of Fungal Community during Outdoor Deterioration of Round Bamboo. J Fungi (Basel) 2023; 9:691. [PMID: 37367627 DOI: 10.3390/jof9060691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/09/2023] [Accepted: 06/14/2023] [Indexed: 06/28/2023] Open
Abstract
Bamboo's mechanical and aesthetic properties are significantly influenced by fungi. However, few studies have been conducted to investigate the structure and dynamics of fungal communities in bamboo during its natural deterioration. In this study, fungal community succession and characteristic variations of round bamboo in roofed and unroofed environments over a period of 13 weeks of deterioration were deciphered using high-throughput sequencing and multiple characterization methods. A total of 459 fungal Operational Taxonomic Units (OTUs) from eight phyla were identified. The fungal community's richness of roofed bamboo samples showed an increasing trend, whereas that of unroofed bamboo samples presented a declining trend during deterioration. Ascomycota and Basidiomycota were the dominant phyla throughout the deterioration process in two different environments: Basidiomycota was found to be an early colonizer of unroofed bamboo samples. Principal Coordinates Analysis (PCoA) analysis suggested that the deterioration time had a greater impact on fungal community variation compared to the exposure conditions. Redundancy analysis (RDA) further revealed that temperature was a major environmental factor that contributed to the variation in fungal communities. Additionally, the bamboo epidermis presented a descending total amount of cell wall components in both roofed and unroofed conditions. The correlation analysis between the fungal community and relative abundance of three major cell wall components elucidated that Cladosporium was negatively correlated with hemicellulose in roofed samples, whereas they presented a positive correlation with hemicellulose and a negative correlation with lignin in unroofed samples. Furthermore, the contact angle decreased during the deterioration process in the roofed as well as unroofed samples, which could arise from the degradation of lignin. Our findings provide novel insights into the fungal community succession on round bamboo during its natural deterioration and give useful information for round bamboo protection.
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Affiliation(s)
- Xiaojiao An
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Shuaibo Han
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Xin Ren
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - John Sichone
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Zhiwei Fan
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
| | - Xinxing Wu
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Yan Zhang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Hui Wang
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
| | - Wei Cai
- Anji Zhujing Bamboo Technology Co., Ltd., Huzhou 313300, China
| | - Fangli Sun
- School of Chemical and Materials Engineering, National Engineering & Technology Research Center for the Comprehensive Utilization of Wood-Based Resources, Zhejiang A&F University, Hangzhou 311300, China
- Microbes and Insects Control Institute of Bio-Based Materials, Zhejiang A&F University, Hangzhou 311300, China
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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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Schiro G, Chen Y, Blankinship JC, Barberán A. Ride the dust: Linking dust dispersal and spatial distribution of microorganisms across an arid landscape. Environ Microbiol 2022; 24:4094-4107. [PMID: 35384241 DOI: 10.1111/1462-2920.15998] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 04/01/2022] [Accepted: 04/03/2022] [Indexed: 11/30/2022]
Abstract
In arid ecosystems, where the soil is directly exposed to the action of the wind due to sparse vegetation, dust aerosolization is a consequence of soil degradation and concomitantly, a major vector of microbial dispersal. Disturbances such as livestock grazing or fire can exacerbate wind erosion and dust production. Here, we sampled surface soils in 29 locations across an arid landscape in southwestern USA and characterized their prokaryotic and fungal communities. At four of these locations, we also sampled potential fugitive dust. By comparing the composition of soil and dust samples, we determined the role of dust dispersal in structuring the biogeography of soil microorganisms across the landscape. For Bacteria/Archaea, we found dust associated taxa to have on average, higher regional occupancies compared to soil associated taxa. Complementarily, we found dust samples to harbor a higher amount of widely distributed taxa compared to soil samples. Overall, our study shows how dust dispersal plays a role in the spatial distribution of soil Bacteria/Archaea, but not soil Fungi, and might inform indicators of soil health and stability in arid ecosystems. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Gabriele Schiro
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Yongjian Chen
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Joseph C Blankinship
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
| | - Albert Barberán
- Department of Environmental Science, University of Arizona, Tucson, Arizona, 85721, USA
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Jang J, Kim M, Baek S, Shin J, Shin J, Shin SG, Kim YM, Cho KH. Hydrometeorological Influence on Antibiotic-Resistance Genes (ARGs) and Bacterial Community at a Recreational Beach in Korea. JOURNAL OF HAZARDOUS MATERIALS 2021; 403:123599. [PMID: 32791479 DOI: 10.1016/j.jhazmat.2020.123599] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 06/29/2020] [Accepted: 07/27/2020] [Indexed: 06/11/2023]
Abstract
We investigated the occurrence and distribution of antibiotic-resistance genes (ARGs) and the composition of a bacterial community under conditions of rainfall on a recreational beach in Korea. Seawater samples, collected every 1‒5 hours in June 2018 and May 2019, were analyzed using quantitative real-time polymerase chain reaction and next-generation sequencing. We found a substantial influence of rainfall and tidal levels on the relative abundance of total ARGs and bacterial operational taxonomic units (OTUs), which showed 1.9 × 103 and 1.1 × 101 fold increases, respectively. In particular, the elevated levels of ARGs were maintained for up to 32 hours after rainfall. An increased abundance of sewage-related ARGs and bacterial OTUs suggested that combined sewer overflow (CSO) may be the major factor contributing to the increase in the number and diversity of ARGs and related bacterial communities. Network analysis of ARGs and OTUs indicated that, at the genus level, Acinetobacter, Pseudomonas, and Prevotella were the main potential pathogens carrying the observed ARGs in the recreational seawater. Overall, these findings highlight the potential threat to public health on beaches, and indicate the requirement for more adequate monitoring, with greater efforts to mitigate the propagation of ARGs arising from CSOs.
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Affiliation(s)
- Jiyi Jang
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Minjeong Kim
- Korea Atomic Energy Research Institute, 111, Daedeok-daero 989beon-gil, Yuseong-gu, Daejeon, 34057, Republic of Korea
| | - Sangsoo Baek
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea
| | - Jingyeong Shin
- Department of Civil and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Juhee Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongnam National University of Science and Technology, 6, Naedong-ro 139beon-gil, Naedong-myeon, Jinju, 52725, Republic of Korea
| | - Seung Gu Shin
- Department of Energy Engineering, Future Convergence Technology Research Institute, Gyeongnam National University of Science and Technology, 6, Naedong-ro 139beon-gil, Naedong-myeon, Jinju, 52725, Republic of Korea
| | - Young Mo Kim
- Department of Civil and Environmental Engineering, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Kyung Hwa Cho
- School of Urban and Environmental Engineering, Ulsan National Institute of Science and Technology, 50, UNIST-gil, Eonyang-eup, Ulju-gun, Ulsan, 44919, Republic of Korea.
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6
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Diversity, community composition, and bioactivity of cultivable fungal endophytes in saline and dry soils in deserts. FUNGAL ECOL 2021. [DOI: 10.1016/j.funeco.2020.101019] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Moelling K, Broecker F. Air Microbiome and Pollution: Composition and Potential Effects on Human Health, Including SARS Coronavirus Infection. JOURNAL OF ENVIRONMENTAL AND PUBLIC HEALTH 2020; 2020:1646943. [PMID: 32565838 PMCID: PMC7256708 DOI: 10.1155/2020/1646943] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 01/06/2020] [Accepted: 05/11/2020] [Indexed: 12/14/2022]
Abstract
Polluted air poses a significant threat to human health. Exposure to particulate matter (PM) and harmful gases contributes to cardiovascular and respiratory diseases, including allergies and obstructive lung disease. Air pollution may also be linked to cancer and reduced life expectancy. Uptake of PM has been shown to cause pathological changes in the intestinal microbiota in mice and humans. Less is known about the effects of pollution-associated microbiota on human health. Several recent studies described the microbiomes of urban and rural air samples, of the stratosphere and sand particles, which can be transported over long distances, as well as the air of indoor environments. Here, we summarize the current knowledge on airborne bacterial, viral, and fungal communities and discuss their potential consequences on human health. The current data suggest that bacterial pathogens are typically too sparse and short-lived in air to pose a significant risk for infecting healthy people. However, airborne fungal spores may exacerbate allergies and asthma. Little information is available on viruses including phages, and future studies are likely to detect known and novel viruses with a yet unknown impact on human health. Furthermore, varying experimental protocols have been employed in the recent microbiome and virome studies. Therefore, standardized methodologies will be required to allow for better comparisons between studies. Air pollution has been linked to more severe outcomes of SARS (severe acute respiratory syndrome) coronavirus (SARS-CoV) infections. This may have contributed to severe SARS-CoV-2 outbreaks, especially those in China, Northern Italy, Iran, and New York City.
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Affiliation(s)
- Karin Moelling
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
- Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Felix Broecker
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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Waters SM, Purdue SK, Armstrong R, Detrés Y. Metagenomic investigation of African dust events in the Caribbean. FEMS Microbiol Lett 2020; 367:5809963. [PMID: 32189002 DOI: 10.1093/femsle/fnaa051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 03/17/2020] [Indexed: 11/14/2022] Open
Abstract
African dust from the Sahara and Sahel regions of Northern Africa is blown intercontinental distances and is the highest portion of atmospheric dust generated each year. During the Northern Hemisphere summer months (boreal summer), these dust events travel into the Caribbean and southern United States. While viability assays, microscopy and bacterial amplicon analyses have shown that dust-associated microbes may be diverse, the specific microbial taxa that are transported intercontinental distances with these dust events remain poorly characterized. To provide new insights into these issues, five metagenomes of Saharan dust events occurring in the Caribbean, collected in the summer months of 2002 and 2008, were analyzed. The data revealed that similar microbial composition existed between three out of the five of the distinct dust events and that fungi were a prominent feature of the metagenomes compared to other environmental samples. These results have implications for better understanding of microbial transport through the atmosphere and may implicate that the dust-associated microbial load transiting the Atlantic with Saharan dust is similar from year to year.
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Affiliation(s)
- Samantha Marie Waters
- Universities Space Research Association, Space Biosciences Division, Ames Research Center, Moffett Field, CA 94035, USA
| | - S K Purdue
- Atmospheric Science, Rosenstiel School of Marine and Atmospheric Science, University of Miami, Miami, FL 33149, USA
| | - R Armstrong
- NOAA Center for Atmospheric Sciences (NCAS), Department of Marine Sciences, University of Puerto Rico-Mayaguez, Puerto Rico 00682, USA
| | - Y Detrés
- NOAA Center for Atmospheric Sciences (NCAS), Department of Marine Sciences, University of Puerto Rico-Mayaguez, Puerto Rico 00682, USA
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9
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Zhang X, Xia S, Zhao R, Wang H. Effect of temperature on opportunistic pathogen gene markers and microbial communities in long-term stored roof-harvested rainwater. ENVIRONMENTAL RESEARCH 2020; 181:108917. [PMID: 31759642 DOI: 10.1016/j.envres.2019.108917] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 11/07/2019] [Accepted: 11/10/2019] [Indexed: 06/10/2023]
Abstract
Roof-harvested rainwater (RHRW) has received increasing attention in recent years as an alternative water source for domestic use, yet its biological stability during storage is not fully understood. This study investigated the effects of temperature (4 °C, 20 °C and 30 °C) on the microbiological characteristics of RHRW over a storage period of 60 days by targeting different microbial groups including total bacteria and fecal indictor Escherichia coli, bacterial opportunistic pathogen genera and species (Legionella spp, Legionella pneumophila, Mycobacterium spp, Mycobacterium avium, Pseudomonas aeruginosa), and two amoebas (Acanthamoeba and Vermamoeba vermiformis). The rainwater chemistry demonstrated no obvious change during storage. The highest biomass was observed in RHRW stored at 30 °C, as measured by heterotrophic bacterial counts, adenosine triphosphate, and 16S rRNA gene numbers. Gene markers of E. coli, Legionella spp., P. aeruginosa, and V. vermiformis were detected in fresh RHRW and can persist during RHRW storage; whereas P. aeruginosa was the only species demonstrated significant regrowth at higher storage temperatures (P < 0.05). Acanthamoeba spp. was only detected in RHRW after 50 days of storage at three investigated temperatures, highlighting increased health risks in long-term stored RHRW. Bacterial community compositions were significantly different in RHRW stored at different temperatures, with increased variations among triplicate storage bottles noted at higher temperatures along with storage time. The results provide insights into RHRW storage practices in terms of mitigating microbial contamination risks.
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Affiliation(s)
- Xiaodong Zhang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China
| | - Siqing Xia
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China
| | - Renzun Zhao
- Civil, Architectural and Environmental Engineering Department, North Carolina Agricultural and Technical State University, Greensboro, NC 27411, USA
| | - Hong Wang
- State Key Laboratory of Pollution Control and Resource Reuse, College of Environmental Science and Engineering, Tongji University, Shanghai, 200092, China; Shanghai Institute of Pollution Control and Ecological Security, Shanghai, 200092, China.
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Systematic Analysis of Impact of Sampling Regions and Storage Methods on Fecal Gut Microbiome and Metabolome Profiles. mSphere 2020; 5:5/1/e00763-19. [PMID: 31915218 PMCID: PMC6952195 DOI: 10.1128/msphere.00763-19] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The gastrointestinal microbiome and metabolome can provide a new angle to understand the development of health and disease. Stool samples are most frequently used for large-scale cohort studies. Standardized procedures for stool sample handling and storage can be a determining factor for performing microbiome or metabolome studies. In this study, we focused on the effects of stool sampling regions and stool sample storage conditions on variations in the gut microbiome composition and metabolome profile. The contribution of human gastrointestinal (GI) microbiota and metabolites to host health has recently become much clearer. However, many confounding factors can influence the accuracy of gut microbiome and metabolome studies, resulting in inconsistencies in published results. In this study, we systematically investigated the effects of fecal sampling regions and storage and retrieval conditions on gut microbiome and metabolite profiles from three healthy children. Our analysis indicated that compared to homogenized and snap-frozen samples (standard control [SC]), different sampling regions did not affect microbial community alpha diversity, while a total of 22 of 176 identified metabolites varied significantly across different sampling regions. In contrast, storage conditions significantly influenced the microbiome and metabolome. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles. Sample storage in RNALater showed a significant level of variation in both microbiome and metabolome profiles, independent of the storage or retrieval conditions. The effect of RNALater on the metabolome was stronger than the effect on the microbiome, and individual variability between study participants outweighed the effect of RNALater on the microbiome. We conclude that homogenizing stool samples was critical for metabolomic analysis but not necessary for microbiome analysis. Short-term room temperature storage had a minimal effect on the microbiome and metabolome profiles and is recommended for short-term fecal sample storage. In addition, our study indicates that the use of RNALater as a storage medium of stool samples for microbial and metabolomic analyses is not recommended. IMPORTANCE The gastrointestinal microbiome and metabolome can provide a new angle to understand the development of health and disease. Stool samples are most frequently used for large-scale cohort studies. Standardized procedures for stool sample handling and storage can be a determining factor for performing microbiome or metabolome studies. In this study, we focused on the effects of stool sampling regions and stool sample storage conditions on variations in the gut microbiome composition and metabolome profile.
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Zhong S, Zhang L, Jiang X, Gao P. Comparison of chemical composition and airborne bacterial community structure in PM 2.5 during haze and non-haze days in the winter in Guilin, China. THE SCIENCE OF THE TOTAL ENVIRONMENT 2019; 655:202-210. [PMID: 30471588 DOI: 10.1016/j.scitotenv.2018.11.268] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/15/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
Haze is a typical type of air pollution and frequently has occurred in the winter in Guilin city recently, but information relating to chemical compositions and airborne bacterial community structure of atmospheric particulate matter (PM2.5) during haze days remains very limited. In this study, the PM2.5 concentration, chemical components including water-soluble ions and metal elements, and bacterial community compositions of PM2.5 on both haze and non-haze days were characterized, and the relationships between them were studied. The results showed that levels of the secondary aerosol particles of SO42-, NO3-, and NH4+ in haze PM2.5 associated with local fuel combustion and vehicle emissions were significantly higher than non-haze samples. Similar trends were observed for the detected trace metal elements. High-throughput sequencing results indicated that higher PM2.5 concentration caused lower bacterial richness and diversity. However, the airborne bacterial community structure remained stable, and no significant difference was found between haze and non-haze PM2.5. Firmicutes, Proteobacteria, and Bacteroidetes were the most abundant phyla accounting for a total of 97.2% on average. In contrast to non-haze PM2.5, the bacterial community structure of haze PM2.5 was mostly positively correlated with SO42-, NO3-, NH4+, K+, and Cl-, suggesting these secondary aerosol particles were probably of great importance on haze pollution and variability of the bacterial compositions of PM2.5.
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Affiliation(s)
- Shan Zhong
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi 541004, China
| | - Lishan Zhang
- School of Life and Environmental Sciences, Guilin University of Electronic Technology, Guilin, Guangxi 541004, China
| | - Xiaoying Jiang
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China
| | - Pin Gao
- College of Environmental Science and Engineering, Donghua University, Shanghai 201620, China.
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Madronich S, Björn LO, McKenzie RL. Solar UV radiation and microbial life in the atmosphere. Photochem Photobiol Sci 2018; 17:1918-1931. [PMID: 29978175 DOI: 10.1039/c7pp00407a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Many microorganisms are alive while suspended in the atmosphere, and some seem to be metabolically active during their time there. One of the most important factors threatening their life and activity is solar ultraviolet (UV) radiation. Quantitative understanding of the spatial and temporal survival patterns in the atmosphere, and of the ultimate deposition of microbes to the surface, is limited by a number factors some of which are discussed here. These include consideration of appropriate spectral sensitivity functions for biological damage (e.g. inactivation), and the estimation of UV radiation impingent on a microorganism suspended in the atmosphere. We show that for several bacteria (E. coli, S. typhimurium, and P. acnes) the inactivation rates correlate well with irradiances weighted by the DNA damage spectrum in the UV-B spectral range, but when these organisms show significant UV-A (or visible) sensitivities, the correlations become clearly non-linear. The existence of these correlations enables the use of a single spectrum (here DNA damage) as a proxy for sensitivity spectra of other biological effects, but with some caution when the correlations are strongly non-linear. The radiative quantity relevant to the UV exposure of a suspended particle is the fluence rate at an altitude above ground, while down-welling irradiance at ground-level is the quantity most commonly measured or estimated in satellite-derived climatologies. Using a radiative transfer model that computes both quantities, we developed a simple parameterization to exploit the much larger irradiance data bases to estimate fluence rates, and present the first fluence-rate based climatology of DNA-damaging UV radiation in the atmosphere. The estimation of fluence rates in the presence of clouds remains a particularly challenging problem. Here we note that both reductions and enhancements in the UV radiation field are possible, depending mainly on cloud optical geometry and prevailing solar zenith angles. These complex effects need to be included in model simulations of the atmospheric life cycle of the organisms.
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Woo C, An C, Xu S, Yi SM, Yamamoto N. Taxonomic diversity of fungi deposited from the atmosphere. ISME JOURNAL 2018; 12:2051-2060. [PMID: 29849168 PMCID: PMC6051994 DOI: 10.1038/s41396-018-0160-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 11/17/2022]
Abstract
Fungi release spores into the global atmosphere. The emitted spores are deposited to the surface of the Earth by sedimentation (dry deposition) and precipitation (wet deposition), and therefore contribute to the global cycling of substances. However, knowledge is scarce regarding the diversities of fungi deposited from the atmosphere. Here, an automatic dry and wet deposition sampler and high-throughput sequencing plus quantitative PCR were used to observe taxonomic diversities and flux densities of atmospheric fungal deposition. Taxon-specific fungal deposition velocities and aerodynamic diameters (da) were determined using a collocated cascade impactor for volumetric, particle-size-resolved air sampling. Large multicellular spore-producing dothideomycetes (da ≥ 10.0 μm) were predominant in dry deposition, with a mean velocity of 0.80 cm s–1 for all fungal taxa combined. Higher taxonomic richness was observed in fungal assemblages in wet deposition than in dry deposition, suggesting the presence of fungal taxa that are deposited only in wet form. In wet deposition, agaricomycetes, including mushroom-forming fungi, and sordariomycetes, including plant pathogenic species, were enriched, indicating that such fungal spores serve as nuclei in clouds, and/or are discharged preferentially during precipitation. Moreover, this study confirmed that fungal assemblage memberships and structures were significantly different between dry and wet deposition (P-test, p < 0.001). Overall, these findings suggest taxon-specific involvement of fungi in precipitation, and provide important insights into potential links between environmental changes that can disturb regional microbial communities (e.g., deforestation) and changes in precipitation patterns that might be mediated by changes in microbial communities in the atmosphere.
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Affiliation(s)
- Cheolwoon Woo
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Choa An
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Siyu Xu
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seung-Muk Yi
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea.,Institute of Health and Environment, Seoul National University, Seoul, 08826, Republic of Korea
| | - Naomichi Yamamoto
- Department of Environmental Health Sciences, Graduate School of Public Health, Seoul National University, Seoul, 08826, Republic of Korea. .,Institute of Health and Environment, Seoul National University, Seoul, 08826, Republic of Korea.
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14
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Vüllers F, Fritz B, Roslizar A, Striegel A, Guttmann M, Richards BS, Hölscher H, Gomard G, Klampaftis E, Kavalenka MN. Self-Cleaning Microcavity Array for Photovoltaic Modules. ACS APPLIED MATERIALS & INTERFACES 2018; 10:2929-2936. [PMID: 29284257 DOI: 10.1021/acsami.7b15579] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Development of self-cleaning coatings is of great interest for the photovoltaic (PV) industry, as soiling of the modules can significantly reduce their electrical output and increase operational costs. We fabricated flexible polymeric films with novel disordered microcavity array (MCA) topography from fluorinated ethylene propylene (FEP) by hot embossing. Because of their superhydrophobicity with water contact angles above 150° and roll-off angles below 5°, the films possess self-cleaning properties over a wide range of tilt angles, starting at 10°, and contaminant sizes (30-900 μm). Droplets that impact the FEP MCA surface with velocities of the same order of magnitude as that of rain bounce off the surface without impairing its wetting properties. Additionally, the disordered MCA topography of the films enhances the performance of PV devices by improving light incoupling. Optical coupling of the FEP MCA films to a glass-encapsulated multicrystalline silicon solar cell results in 4.6% enhancement of the electrical output compared to that of an uncoated device.
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Affiliation(s)
- Felix Vüllers
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Benjamin Fritz
- Light Technology Institute (LTI), Karlsruhe Institute of Technology (KIT) , Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Aiman Roslizar
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Andreas Striegel
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Markus Guttmann
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Bryce S Richards
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Light Technology Institute (LTI), Karlsruhe Institute of Technology (KIT) , Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Hendrik Hölscher
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Guillaume Gomard
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
- Light Technology Institute (LTI), Karlsruhe Institute of Technology (KIT) , Engesserstrasse 13, 76131 Karlsruhe, Germany
| | - Efthymios Klampaftis
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Maryna N Kavalenka
- Institute of Microstructure Technology (IMT), Karlsruhe Institute of Technology (KIT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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15
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Hagh-Doust N, Akbarinia M, Safaie N, Yousefzadeh H, Bálint M. Community analysis of Persian oak fungal microbiome under dust storm conditions. FUNGAL ECOL 2017. [DOI: 10.1016/j.funeco.2017.05.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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16
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Schmidt SK, Vimercati L, Darcy JL, Arán P, Gendron EM, Solon AJ, Porazinska D, Dorador C. A Naganishia in high places: functioning populations or dormant cells from the atmosphere? Mycology 2017; 8:153-163. [PMID: 30123637 PMCID: PMC6059072 DOI: 10.1080/21501203.2017.1344154] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/15/2017] [Indexed: 12/16/2022] Open
Abstract
Here, we review the current state of knowledge concerning high-elevation members of the extremophilic Cryptococcus albidus clade (now classified as the genus Naganishia). These fungi dominate eukaryotic microbial communities across the highest elevation, soil-like material (tephra) on volcanoes such as Llullaillaco, Socompa, and Saírecabur in the Atacama region of Chile, Argentina, and Bolivia. Recent studies indicate that Naganishia species are among the most resistant organisms to UV radiation, and a strain of N. friedmannii from Volcán Llullaillaco is the first organism that is known to grow during the extreme, diurnal freeze-thaw cycles that occur on a continuous basis at elevations above 6000 m.a.s.l. in the Atacama region. These and other extremophilic traits discussed in this review may serve a dual purpose of allowing Naganishia species to survive long-distance transport through the atmosphere and to survive the extreme conditions found at high elevations. Current evidence indicates that there are frequent dispersal events between high-elevation volcanoes of Atacama region and the Dry Valleys of Antarctica via "Rossby Wave" merging of the polar and sub-tropical jet streams. This dispersal hypothesis needs further verification, as does the hypothesis that Naganishia species are flexible "opportunitrophs" that can grow during rare periods of water (from melting snow) and nutrient availability (from Aeolian inputs) in one of the most extreme terrestrial habitats on Earth.
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Affiliation(s)
- Steven K Schmidt
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Lara Vimercati
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - John L Darcy
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Pablo Arán
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
| | - Eli M.S Gendron
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
- Molecular, Cellular, and Developmental Biology Department, University of Colorado, Boulder, CO, USA
| | - Adam J Solon
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Dorota Porazinska
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO, USA
| | - Cristina Dorador
- Laboratorio de Complejidad Microbiana y Ecología Funcional, Instituto Antofagasta & Centre for Biotechnology and Bioengineering (CeBiB), Universidad de Antofagasta, Antofagasta, Chile
- Departamento de Biotecnología, Facultad de Ciencias del Mar y Recursos Biológicos, Universidad de Antofagasta, Antofagasta, Chile
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17
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Farenhorst A, Li R, Jahan M, Tun HM, Mi R, Amarakoon I, Kumar A, Khafipour E. Bacteria in drinking water sources of a First Nation reserve in Canada. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 575:813-819. [PMID: 27693149 DOI: 10.1016/j.scitotenv.2016.09.138] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 09/15/2016] [Accepted: 09/16/2016] [Indexed: 06/06/2023]
Abstract
Approximately 20% of the 600 First Nations reserves across Canada are under a drinking water advisory, often due to unacceptable levels of bacteria. In this study, we detected fecal bacteria at an alarmingly high frequency in drinking water sources in a fly-in First Nations community, most notably in buckets/drums of homes without running water where Escherichia coli levels ranged from 20 to 62,000CFU/100mL. The water leaving the water treatment plant was free of E. coli and its free residual chlorine concentration (0.67mg/L) was within the range typically observed for treated water in Canada. Water samples from taps in homes served by cisterns, and those sampled from the water truck and community standpipe, always showed unacceptable levels of E. coli (1 to 2100CFU/100mL) and free residual chlorine concentrations below the 0.2mg/L required to prevent bacterial regrowth. Samples from taps in homes served by piped water had lower levels of E. coli (0 to 2CFU/100mL). DNA- and RNA-based 16S rRNA Illumina sequencing demonstrated that piped and cisterns water distribution systems showed an abundance of viable cells of Alphaproteobacteria indicative of biofilm formation in pipes and cisterns. The alpha diversity, based on observed OTUs and three other indices, was lowest in water truck samples that supplied water to the cistern and the low free residual chlorine concentration (0.07mg/L) and predominance of Betaproteobacteria (63% of viable cells) that were immediately detected after the truck had filled up at the water treatment plant was indicative of contamination by particulate matter. Given these findings, First Nation residents living without running water and relying on inadequate water distribution systems are at higher risk of contracting water-born illnesses. We urge all governments in Canada to expand their investments in supporting and sustaining water as a human right in Canada's First Nations communities.
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Affiliation(s)
- Annemieke Farenhorst
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
| | - Ru Li
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Musarrat Jahan
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Hein Min Tun
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ruidong Mi
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Inoka Amarakoon
- Department of Soil Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ayush Kumar
- Department of Microbiology, University of Manitoba, MB R3T 2N2, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada
| | - Ehsan Khafipour
- Department of Animal Science, University of Manitoba, Winnipeg, MB R3T 2N2, Canada; Department of Medical Microbiology, University of Manitoba, Winnipeg, MB R3T 2N2, Canada.
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