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Lu C, Xiao Z, Li H, Han R, Sun A, Xiang Q, Zhu Z, Li G, Yang X, Zhu YG, Chen QL. Aboveground plants determine the exchange of pathogens within air-phyllosphere-soil continuum in urban greenspaces. JOURNAL OF HAZARDOUS MATERIALS 2024; 465:133149. [PMID: 38056267 DOI: 10.1016/j.jhazmat.2023.133149] [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: 10/28/2023] [Revised: 11/20/2023] [Accepted: 11/29/2023] [Indexed: 12/08/2023]
Abstract
The microbiome in the air-phyllosphere-soil continuum of urban greenspaces plays a crucial role in re-connecting urban populations with biodiverse environmental microbiomes. However, little is known about whether plant type affects the airborne microbiomes, as well as the extent to which soil and phyllosphere microbiomes contribute to airborne microbiomes. Here we collected soil, phyllosphere and airborne microbes with different plant types (broadleaf tree, conifer tree, and grass) in urban parks. Despite the significant impacts of plant type on soil and phyllosphere microbiomes, plant type had no obvious effects on the diversity of airborne microbes but shaped airborne bacterial composition in urban greenspaces. Soil and phyllosphere microbiomes had a higher contribution to airborne bacteria in broadleaf trees (37.56%) compared to conifer trees (9.51%) and grasses (14.29%). Grass areas in urban greenspaces exhibited a greater proportion of potential pathogens compared to the tree areas. The abundance of bacterial pathogens in phyllosphere was significantly higher in grasses compared to broadleaf and conifer trees. Together, our study provides novel insights into the microbiome patterns in air-phyllosphere-soil continuum, highlighting the potential significance of reducing the proportion of extensively human-intervened grass areas in future urban environment designs to enhance the provision of ecosystem services in urban greenspaces.
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Affiliation(s)
- Changyi Lu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zufei Xiao
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hu Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ruixia Han
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Anqi Sun
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Qian Xiang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China
| | - Zhe Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham, Ningbo 315100, China
| | - Gang Li
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaoru Yang
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yong-Guan Zhu
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Urban and Regional Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, China
| | - Qing-Lin Chen
- Key Laboratory of Urban Environment and Health, Ningbo Urban Environment Observation and Research Station, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361021, China; Zhejiang Key Laboratory of Urban Environmental Processes and Pollution Control, CAS Haixi Industrial Technology Innovation Center in Beilun, Ningbo 315830, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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Huang Z, Yu X, Liu Q, Maki T, Alam K, Wang Y, Xue F, Tang S, Du P, Dong Q, Wang D, Huang J. Bioaerosols in the atmosphere: A comprehensive review on detection methods, concentration and influencing factors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:168818. [PMID: 38036132 DOI: 10.1016/j.scitotenv.2023.168818] [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: 08/24/2023] [Revised: 11/17/2023] [Accepted: 11/21/2023] [Indexed: 12/02/2023]
Abstract
In the past few decades, especially since the outbreak of the coronavirus disease (COVID-19), the effects of atmospheric bioaerosols on human health, the environment, and climate have received great attention. To evaluate the impacts of bioaerosols quantitatively, it is crucial to determine the types of bioaerosols in the atmosphere and their spatial-temporal distribution. We provide a concise summary of the online and offline observation strategies employed by the global research community to sample and analyze atmospheric bioaerosols. In addition, the quantitative distribution of bioaerosols is described by considering the atmospheric bioaerosols concentrations at various time scales (daily and seasonal changes, for example), under various weather, and different underlying surfaces. Finally, a comprehensive summary of the reasons for the spatiotemporal distribution of bioaerosols is discussed, including differences in emission sources, the impact process of meteorological factors and environmental factors. This review of information on the latest research progress contributes to the emergence of further observation strategies that determine the quantitative dynamics of public health and ecological effects of bioaerosols.
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Affiliation(s)
- Zhongwei Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Xinrong Yu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qiantao Liu
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Teruya Maki
- Department of Life Science, Faculty of Science and Engineering, Kindai University, Higashiosaka, Osaka, Japan
| | - Khan Alam
- Department of Physics, University of Peshawar, Peshawar 25120, Pakistan
| | - Yongkai Wang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Fanli Xue
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shihan Tang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Pengyue Du
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qing Dong
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China
| | - Danfeng Wang
- Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China
| | - Jianping Huang
- Key Laboratory for Semi-Arid Climate Change of the Ministry of Education, College of Atmospheric Sciences, Lanzhou University, Lanzhou 730000, China; Collaborative Innovation Center for Western Ecological Safety, Lanzhou University, Lanzhou 730000, China.
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3
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Lappan R, Thakar J, Molares Moncayo L, Besser A, Bradley JA, Goordial J, Trembath-Reichert E, Greening C. The atmosphere: a transport medium or an active microbial ecosystem? THE ISME JOURNAL 2024; 18:wrae092. [PMID: 38804464 PMCID: PMC11214262 DOI: 10.1093/ismejo/wrae092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Revised: 05/05/2024] [Accepted: 05/27/2024] [Indexed: 05/29/2024]
Abstract
The atmosphere may be Earth's largest microbial ecosystem. It is connected to all of Earth's surface ecosystems and plays an important role in microbial dispersal on local to global scales. Despite this grand scale, surprisingly little is understood about the atmosphere itself as a habitat. A key question remains unresolved: does the atmosphere simply transport microorganisms from one location to another, or does it harbour adapted, resident, and active microbial communities that overcome the physiological stressors and selection pressures the atmosphere poses to life? Advances in extreme microbiology and astrobiology continue to push our understanding of the limits of life towards ever greater extremes of temperature, pressure, salinity, irradiance, pH, and water availability. Earth's atmosphere stands as a challenging, but potentially surmountable, extreme environment to harbour living, active, resident microorganisms. Here, we confront the current understanding of the atmosphere as a microbial habitat, highlighting key advances and limitations. We pose major ecological and mechanistic questions about microbial life in the atmosphere that remain unresolved and frame the problems and technical pitfalls that have largely hindered recent developments in this space, providing evidence-based insights to drive future research in this field. New innovations supported by rigorous technical standards are needed to enable progress in understanding atmospheric microorganisms and their influence on global processes of weather, climate, nutrient cycling, biodiversity, and microbial connectivity, especially in the context of rapid global change.
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Affiliation(s)
- Rachael Lappan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- School of Earth, Atmosphere & Environment, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
| | - Jordan Thakar
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | - Laura Molares Moncayo
- School of Geography, Queen Mary University of London, London E1 4NS, United Kingdom
- Natural History Museum, London SW7 5BD, United Kingdom
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
| | - Alexi Besser
- School of Earth and Space Exploration, Arizona State University, Tempe, AZ 85287, United States
| | - James A Bradley
- Aix Marseille University, University of Toulon, CNRS, IRD, MIO, Marseille 13009, France
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, United Kingdom
| | - Jacqueline Goordial
- School of Environmental Sciences, University of Guelph, Guelph, Ontario N1G2W1, Canada
| | | | - Chris Greening
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, Victoria 3800, Australia
- Securing Antarctica’s Environmental Future, Monash University, Clayton, Victoria 3800, Australia
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4
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Hoetzinger M, Hahn MW, Andersson LY, Buckley N, Ramsin C, Buck M, Nuy JK, Garcia SL, Puente-Sánchez F, Bertilsson S. Geographic population structure and distinct intra-population dynamics of globally abundant freshwater bacteria. THE ISME JOURNAL 2024; 18:wrae113. [PMID: 38959851 PMCID: PMC11283720 DOI: 10.1093/ismejo/wrae113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 06/09/2024] [Indexed: 07/05/2024]
Abstract
Implications of geographic separation and temporal dynamics on the evolution of free-living bacterial species are widely unclear. However, the vast amount of metagenome sequencing data generated during the last decades from various habitats around the world provides an unprecedented opportunity for such investigations. Here, we exploited publicly available and new freshwater metagenomes in combination with the genomes of abundant freshwater bacteria to reveal geographic and temporal population structure. We focused on species that were detected across broad geographic ranges at high enough sequence coverage for meaningful population genomic analyses, associated with the predominant freshwater taxa acI, LD12, Polynucleobacter, and Candidatus Methylopumilus. Despite the broad geographic ranges, each species appeared as a sequence-discrete cluster, in contrast to abundant marine taxa, for which continuous diversity structures were reported on a global scale. Population differentiation increased significantly with spatial distance in all species, but notable dispersal barriers (e.g. oceanic) were not apparent. Yet, the different species showed contrasting rates of geographic divergence and strikingly different intra-population dynamics in time series within individual habitats. The change in an LD12 population over 7 years was minor (FST = 0.04) compared to differentiation between lakes, whereas a Polynucleobacter population displayed strong changes within merely 2 months (FST up to 0.54), similar in scale to differentiation between populations separated by thousands of kilometers. The slowly and steadily evolving LD12 population showed high strain diversity, whereas the dynamic Polynucleobacter population exhibited alternating clonal expansions of mostly two strains only. Based on the contrasting population structures, we propose distinct models of speciation.
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Affiliation(s)
- Matthias Hoetzinger
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
- Faculty of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1433 Ås, Norway
| | - Martin W Hahn
- Research Department for Limnology, University of Innsbruck, 5310 Mondsee, Austria
| | - Linnéa Y Andersson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Nathaniel Buckley
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Chelsea Ramsin
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Moritz Buck
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Julia K Nuy
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 104 05 Stockholm, Sweden
- Centre for Water and Environmental Research, University of Duisburg-Essen, 45141 Essen, Germany
| | - Sarahi L Garcia
- Department of Ecology, Environment, and Plant Sciences, Science for Life Laboratory, Stockholm University, 104 05 Stockholm, Sweden
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg, Germany
| | - Fernando Puente-Sánchez
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
| | - Stefan Bertilsson
- Department of Aquatic Sciences and Assessment, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden
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5
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Bao Y, Chen Y, Wang F, Xu Z, Zhou S, Sun R, Wu X, Yan K. East Asian monsoon manipulates the richness and taxonomic composition of airborne bacteria over China coastal area. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 875:162581. [PMID: 36889406 DOI: 10.1016/j.scitotenv.2023.162581] [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: 11/19/2022] [Revised: 01/23/2023] [Accepted: 02/27/2023] [Indexed: 06/18/2023]
Abstract
Airborne bacteria may have significant impacts on aerosol properties, public health and ecosystem depending on their taxonomic composition and transport. This study investigated the seasonal and spatial variations of bacterial composition and richness over the east coast of China and the roles of East Asian monsoon played through synchronous sampling and 16S rRNA sequencing analysis of airborne bacteria at Huaniao island of the East China Sea (ECS) and the urban and rural sites of Shanghai. Airborne bacteria showed higher richness over the land sites than Huaniao island with the highest values found in the urban and rural springs associated with the growing plants. For the island, the maximal richness occurred in winter as the result of prevailing terrestrial winds controlled by East Asian winter monsoon. Proteobacteria, Actinobacteria and Cyanobacteria were found to be top three phyla, together accounting for 75 % of total airborne bacteria. Radiation-resistant Deinococcus, Methylobacterium belonging to Rhizobiales (related to vegetation) and Mastigocladopsis_PCC_10914 originating from marine ecosystem were indicator genera for urban, rural and island sites, respectively. The Bray-Curits dissimilarity of taxonomic composition between the island and two land sites was the lowest in winter with the representative genera over island also typically from the soil. Our results reveal that seasonal change of monsoon wind directions evidently affects the richness and taxonomic composition of airborne bacteria in China coastal area. Particularly, prevailing terrestrial winds lead to the dominance of land-derived bacteria over the coastal ECS which may have a potential impact on marine ecosystem.
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Affiliation(s)
- Yang Bao
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ying Chen
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China; Institute of Eco-Chongming (IEC), National Observations and Research Station for Wetland Ecosystems of the Yangtze Estuary, Shanghai 202162, China.
| | - Fanghui Wang
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Zongjun Xu
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Shengqian Zhou
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
| | - Ruihua Sun
- Pudong New District Environmental Monitoring Station, Shanghai 200135, China
| | - Xiaowei Wu
- School of Environmental and Geographical Sciences, Shanghai Normal University, Shanghai 200233, China
| | - Ke Yan
- Shanghai Key Laboratory of Atmospheric Particle Pollution Prevention, Department of Environmental Science & Engineering, Institute of Atmospheric Sciences, Fudan University, Shanghai 200438, China
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6
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Apangu GP, Frisk CA, Adams-Groom B, Petch GM, Hanson M, Skjøth CA. Using qPCR and microscopy to assess the impact of harvesting and weather conditions on the relationship between Alternaria alternata and Alternaria spp. spores in rural and urban atmospheres. INTERNATIONAL JOURNAL OF BIOMETEOROLOGY 2023:10.1007/s00484-023-02480-w. [PMID: 37191729 DOI: 10.1007/s00484-023-02480-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Accepted: 04/16/2023] [Indexed: 05/17/2023]
Abstract
Alternaria is a plant pathogen and human allergen. Alternaria alternata is one of the most abundant fungal spores in the air. The purpose of this study was to examine whether Alternaria spp. spore concentrations can be used to predict the abundance and spatio-temporal pattern of A. alternata spores in the air. This was investigated by testing the hypothesis that A. alternata dominates airborne Alternaria spp. spores and varies spatio-temporally. Secondarily, we aimed at investigating the relationship between airborne Alternaria spp. spores and the DNA profile of A. alternata spores between two proximate (~ 7 km apart) sites. These were examined by sampling Alternaria spp. spores using Burkard 7-day and cyclone samplers for the period 2016-2018 at Worcester and Lakeside campuses of the University of Worcester, UK. Daily Alternaria spp. spores from the Burkard traps were identified using optical microscopy whilst A. alternata from the cyclone samples was detected and quantified using quantitative polymerase chain reaction (qPCR). The results showed that either A. alternata or other Alternaria species spores dominate the airborne Alternaria spore concentrations, generally depending on weather conditions. Furthermore, although Alternaria spp. spore concentrations were similar for the two proximate sites, A. alternata spore concentrations significantly varied for those sites and it is highly likely that the airborne samples contained large amounts of small fragments of A. alternata. Overall, the study shows that there is a higher abundance of airborne Alternaria allergen than reported by aerobiological networks and the majority is likely to be from spore and hyphal fragments.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK.
- Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, Hertfordshire, AL5 2JQ, UK.
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Beverley Adams-Groom
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
| | - Geoffrey M Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Edith Cowan University, 270 Joondalup Drive, Joondalup, WA, 6027, Australia
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000, Roskilde, Denmark
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Tuck AF. Natural Selection and Scale Invariance. Life (Basel) 2023; 13:life13040917. [PMID: 37109446 PMCID: PMC10144207 DOI: 10.3390/life13040917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/03/2023] [Accepted: 03/15/2023] [Indexed: 04/03/2023] Open
Abstract
This review points out that three of the essential features of natural selection—competition for a finite resource, variation, and transmission of memory—occur in an extremely simple, thermalized molecular population, one of colliding “billiard balls” subject to an anisotropy, a directional flux of energetic molecules. The emergence of scaling behavior, scale invariance, in such systems is considered in the context of the emergence of complexity driven by Gibbs free energy, the origins of life, and known chemistries in planetary and astrophysical conditions. It is suggested that the thermodynamic formalism of statistical multifractality offers a parallel between the microscopic and macroscopic views of non-equilibrium systems and their evolution, different from, empirically determinable, and therefore complementing traditional definitions of entropy and its production in living systems. Further, the approach supports the existence of a bridge between microscopic and macroscopic scales, the missing mesoscopic scale. It is argued that natural selection consequently operates on all scales—whether or not life results will depend on both the initial and the evolving boundary conditions. That life alters the boundary conditions ensures nonlinearity and scale invariance. Evolution by natural selection will have taken place in Earth’s fluid envelope; both air and water display scale invariance and are far from chemical equilibrium, a complex condition driven by the Gibbs free energy arising from the entropy difference between the incoming solar beam and the outgoing infrared radiation to the cold sink of space acting on the initial conditions within evolving boundary conditions. Symmetry breaking’s role in the atmospheric state is discussed, particularly in regard to aerosol fission in the context of airborne bacteria and viruses in both current and prebiotic times. Over 4.4 billion years, the factors operating to support natural selection will have evolved along with the entire system from relative simplicity to the current complexity.
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Fan C, Xie W, Hu W, Matsusaki H, Kojima T, Zhang D. Number size distribution of bacterial aerosols in terrestrial and marine airflows at a coastal site of Japan. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161238. [PMID: 36586682 DOI: 10.1016/j.scitotenv.2022.161238] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 06/17/2023]
Abstract
Size-differentiated concentration of bacterial aerosols is essential for investigating their dissemination via the atmosphere. In this study, the number size distribution of bacterial aerosols was measured at a coastal site in southwestern Japan (32.324°N, 129.993°E) using a size-segregated eight-stage (>11, 7.0-11, 4.7-7.0, 3.3-4.7, 2.1-3.3, 1.1-2.1, 0.65-1.1, and 0.43-0.65μm) sampler. The results showed that the distribution differed according to the source areas: terrestrial air, oceanic air, or a combination of the two. The distribution in the long-distance transported terrestrial air from the Asian continent was monomodal, with a peak of 3.3-4.7 μm. The distribution in local land breeze air was bimodal, with the peaks at 0.43-1.1 and 3.3-4.7 μm. A similar bimodal distribution was encountered when the local island air and long-distance transported terrestrial air mixed. In contrast, the size distribution did not show clear peaks in the air from either nearby or remote marine areas. According to the air mass backward trajectories, the further the distance the air moved in the 72 h before arriving at the site, the lower the concentration of total bacterial aerosols. The estimation of dry deposition fluxes of bacterial cells showed that the deposition was dominated by cells larger than 1.1 μm with a relative contribution from 70.5 % to 93.7 %, except for the local land breeze cases, where the contributions in the size ranges larger and smaller than 1.1 μm were similar. These results show the distinctive number size distributions and removal processes of bacterial aerosols in different types of air. In addition, they indicate that size-dependent characteristics of airborne bacteria should be considered when studying their activities and roles in the atmospheric environment.
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Affiliation(s)
- Chunlan Fan
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Wenwen Xie
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Wei Hu
- Institute of Surface-Earth System Science, School of Earth System Science, Tianjin University, Tianjin 300072, China
| | - Hiromi Matsusaki
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan
| | - Tomoko Kojima
- Department Earth and Environmental Science, Faculty of Advanced Science and Technology, Kumamoto University, Kumamoto 860-8555, Japan
| | - Daizhou Zhang
- Faculty of Environmental and Symbiotic Sciences, Prefectural University of Kumamoto, Kumamoto 862-8502, Japan.
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9
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Keuschnig C, Vogel TM, Barbaro E, Spolaor A, Koziol K, Björkman MP, Zdanowicz C, Gallet JC, Luks B, Layton R, Larose C. Selection processes of Arctic seasonal glacier snowpack bacterial communities. MICROBIOME 2023; 11:35. [PMID: 36864462 PMCID: PMC9979512 DOI: 10.1186/s40168-023-01473-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Arctic snowpack microbial communities are continually subject to dynamic chemical and microbial input from the atmosphere. As such, the factors that contribute to structuring their microbial communities are complex and have yet to be completely resolved. These snowpack communities can be used to evaluate whether they fit niche-based or neutral assembly theories. METHODS We sampled snow from 22 glacier sites on 7 glaciers across Svalbard in April during the maximum snow accumulation period and prior to the melt period to evaluate the factors that drive snowpack metataxonomy. These snowpacks were seasonal, accumulating in early winter on bare ice and firn and completely melting out in autumn. Using a Bayesian fitting strategy to evaluate Hubbell's Unified Neutral Theory of Biodiversity at multiple sites, we tested for neutrality and defined immigration rates at different taxonomic levels. Bacterial abundance and diversity were measured and the amount of potential ice-nucleating bacteria was calculated. The chemical composition (anions, cations, organic acids) and particulate impurity load (elemental and organic carbon) of the winter and spring snowpack were also characterized. We used these data in addition to geographical information to assess possible niche-based effects on snow microbial communities using multivariate and variable partitioning analysis. RESULTS While certain taxonomic signals were found to fit the neutral assembly model, clear evidence of niche-based selection was observed at most sites. Inorganic chemistry was not linked directly to diversity, but helped to identify predominant colonization sources and predict microbial abundance, which was tightly linked to sea spray. Organic acids were the most significant predictors of microbial diversity. At low organic acid concentrations, the snow microbial structure represented the seeding community closely, and evolved away from it at higher organic acid concentrations, with concomitant increases in bacterial numbers. CONCLUSIONS These results indicate that environmental selection plays a significant role in structuring snow microbial communities and that future studies should focus on activity and growth. Video Abstract.
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Affiliation(s)
- Christoph Keuschnig
- Formerly at Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully Cedex, France
- Currently at Interface Geochemistry, German Research Center for Geosciences, GFZ, Potsdam, Germany
| | - Timothy M Vogel
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully Cedex, France
| | - Elena Barbaro
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30170, Venice Mestre, Italy
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Andrea Spolaor
- Institute of Polar Sciences, ISP-CNR, Via Torino 155, 30170, Venice Mestre, Italy
- Department of Environmental Sciences, Informatics and Statistics, Ca' Foscari University of Venice, Via Torino 155, 30172, Venice, Italy
| | - Krystyna Koziol
- Department of Environmental Change and Geochemistry, Faculty of Geographical Sciences, the Kazimierz Wielki University in Bydgoszcz, Bydgoszcz, Poland
| | - Mats P Björkman
- Department of Earth Sciences, University of Gothenburg, Box 460, SE-40530, Gothenburg, Sweden
| | - Christian Zdanowicz
- Department of Earth Sciences, Uppsala University, Villavägen 16, SE-75236, Uppsala, Sweden
| | | | - Bartłomiej Luks
- Institute of Geophysics, Polish Academy of Sciences, Księcia Janusza 64, 01-452, Warsaw, Poland
| | - Rose Layton
- Formerly at Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully Cedex, France
| | - Catherine Larose
- Univ Lyon, CNRS, INSA Lyon, Université Claude Bernard Lyon 1, Ecole Centrale de Lyon, Ampère, UMR5005, 69134, Ecully Cedex, France.
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10
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Taushiba A, Dwivedi S, Zehra F, Shukla PN, Lawrence AJ. Assessment of indoor air quality and their inter-association in hospitals of northern India-a cross-sectional study. AIR QUALITY, ATMOSPHERE, & HEALTH 2023; 16:1023-1036. [PMID: 37213469 PMCID: PMC9985081 DOI: 10.1007/s11869-023-01321-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 02/01/2023] [Indexed: 05/23/2023]
Abstract
This study was commenced to evaluate the indoor and outdoor air quality concentrations of PM2.5, sub-micron particles (PM>2.5, PM1.0-2.5, PM0.50 -1.0, PM0.25-0.50, and PM<0.25), heavy metals, and microbial contaminants along with their identification in three different hospitals of Lucknow City. The study was conducted from February 2022 to April 2022 in hospitals situated in the commercial, residential, and industrial belts of the city. The indoor concentration trend of particulate matter as observed during the study suggested that most of the highest concentrations belonged to the hospital situated in an industrial area. The highest obtained indoor and outdoor concentrations for PM1.0-2.5, PM0.50-1.0, PM0.25-0.50, and PM<0.25 are 40.44 µg/m3, 56.08 µg/m3, 67.20 µg/m3, 74.50 µg/m3, 61.9 µg/m3, 79.3 µg/m3, 82.0 µg/m3, and 93.9 µg/m3, respectively, which belonged to hospital C situated in the industrial belt. However, for PM>2.5, the highest indoor concentration obtained belonged to hospital B, i.e., 30.7 µg/m3, which is situated in the residential belt of the city. Regarding PM2.5, the highest indoor and outdoor concentrations obtained are 149.41 µg/m3 and 227.45 µg/m3, which were recorded at hospital A and hospital C, respectively. The present study also observed that a high bacterial load of 1389.21 CFU/m3 is recorded in hospital B, and the fungi load was highest in hospital C with 786.34 CFU/m3. Henceforth, the present study offers thorough information on the various air pollutants in a crucial indoor setting, which will further aid the researchers in the field to identify and mitigate the same more precisely.
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Affiliation(s)
- Anam Taushiba
- Department of Chemistry, Isabella Thoburn College, Lucknow, India
- Department of Environmental Science, Integral University, Lucknow, India
| | - Samridhi Dwivedi
- Department of Chemistry, Isabella Thoburn College, Lucknow, India
| | - Farheen Zehra
- Department of Chemistry, Isabella Thoburn College, Lucknow, India
| | - Pashupati Nath Shukla
- Department of Pharmacology & Microbial Technology, National Botanical Research Institute, Lucknow, India
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11
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Sorkheh M, Asgari HM, Zamani I, Ghanbari F. The Relationship Between Dust Sources and Airborne Bacteria in the Southwest of Iran. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:82045-82063. [PMID: 35748994 PMCID: PMC9244375 DOI: 10.1007/s11356-022-21563-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 06/14/2022] [Indexed: 05/30/2023]
Abstract
The biological agents are carried from deserts and dried lands to long distances by high dust volumes. Their adverse effects can be reduced by specifying and controlling dust sources and their related biological agents. Thus, the current work examined the relationship between the bacteria in air and soil samples by taking samples from the soil surface of two dust sources, as well as from air samples during spring from Khorramshahr and Abadan cities. The dust event is the most influential factor on airborne bacteria. There is an insignificant negative (-0.06), insignificant positive (0.14), and weak positive (0.24) correlation between airborne bacteria and UV radiation, relative humidity, and temperature, respectively. After preparing a 16S ribosomal DNA (rDNA) clone library from the soil and air samples, operational taxonomic unit picking and taxonomic assignment were conducted using QIIME Virtual Box. In the present work, Bacillus was the dominant species. The relationship between dust sources and air samples was determined by principal component analysis. Bacteria in the Hoor-Al-Azim dust source and airborne bacteria on dusty and non-dusty days showed a more significant correlation compared to bacteria in the Shadegan dust source. Source Tracker software was used to estimate the contribution of dust sources. The primary source of dust was associated with the dried areas of Hoor-Al-Azim on the non-dusty and dusty days. Finally, the long transport of airborne bacteria was assessed by moderate resolution imaging spectroradiometer (MODIS) and the back trajectory model of Hybrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) data. The research findings can help decision-makers prioritize dust sources to control the adverse effects of dust.
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Affiliation(s)
- Maryam Sorkheh
- Faculty of Marine Natural Resources, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - Hossein Mohammad Asgari
- Department of Marine Environment, Faculty of Marine Natural Resources, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran.
| | - Isaac Zamani
- Department of Marine Biology, Faculty of Marine Science and Oceanography, Khorramshahr University of Marine Science and Technology, Khorramshahr, Iran
| | - Farshid Ghanbari
- Research Center for Environmental Contaminants (RCEC), Abadan University of Medical Sciences, Abadan, Iran
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12
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Maki T, Noda J, Morimoto K, Aoki K, Kurosaki Y, Huang Z, Chen B, Matsuki A, Miyata H, Mitarai S. Long-range transport of airborne bacteria over East Asia: Asian dust events carry potentially nontuberculous Mycobacterium populations. ENVIRONMENT INTERNATIONAL 2022; 168:107471. [PMID: 36081221 DOI: 10.1016/j.envint.2022.107471] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 07/30/2022] [Accepted: 08/11/2022] [Indexed: 06/15/2023]
Abstract
The nontuberculous mycobacterial pulmonary disease (NTM-PD) caused by Mycobacterium species has increased in prevalence all over the world. The distributions of NTM-PD are possibly determined by the westerly wind traveling at high altitudes over East Asia. However, the long-range transport of Mycobacterium species has not been demonstrated by analyzing the bacterial communities in aerosols such as desert mineral particles and anthropogenic pollutants transported by the westerly wind. Here, airborne bacterial compositions were investigated including Mycobacterium species in high-elevation aerosols, which were captured in the snow cover at 2,450 m altitude on Mt. Tateyama. This was further compared to the ground-level or high-altitude aerosols collected at six sampling sites distributed from Asian-dust source region (Tsogt-Ovoo) to downwind areas in East Asia (Asian continental cities; Erenhot, Beijing, Yongin, Japanese cities; Yonago, Suzu, Noto Peninsula). The cell concentrations and taxonomic diversities of airborne bacteria decreased from the Asian continent to the Japan area. Terrestrial bacterial populations belonging to Firmicutes and Actinobacteria showed higher relative abundance at high-elevation and Japanese cities. Additionally, Mycobacterium species captured in the snow cover on Mt. Tateyama increased in relative abundance in correspondence to the increase of black carbon concentrations. The relative abundance of Mycobacterium sequences was higher in the aerosol samples of Asian continental cities and Japanese cities than in the desert area. Presumably, anthropogenic pollution over East Asia carries potential Mycobacterium species, which induce NTM-PD, thereby impacting upon the public health.
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Affiliation(s)
- Teruya Maki
- Department of Life Science, Faculty of Science and Technology, Kindai University 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan.
| | - Jun Noda
- Environment Health Sciences, Graduate School of Veterinary Science, Rakuno Gakuen University, Hokkaido 069-8501, Japan
| | - Kozo Morimoto
- Division of Clinical Research, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo 204-8522, Japan; Respiratory Disease Center, Fukujuji Hospital, Japan Anti-Tuberculosis Association, Tokyo 204-8522, Japan
| | - Kazuma Aoki
- Department of Natural and Environmental Sciences, Faculty of Science, University of Toyama 3190 Gofuku, Toyama 930-8555, Japan
| | - Yasunori Kurosaki
- Arid Land Research Center, Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Zhongwei Huang
- Collaborative Innovation Center for West Ecological Safety (CIWES), Lanzhou University, Lanzhou 730000, China
| | - Bin Chen
- Institute of Atmospheric Physics, Chinese Academy of Sciences, Beijing 100029, China
| | - Atsushi Matsuki
- Institute of Nature and Environmental Technology, Kanazawa University, Kakumamachi, Kanazawa 920-1192, Japan
| | - Hiroki Miyata
- Department of Life Science, Faculty of Science and Technology, Kindai University 3-4-1 Kowakae, Higashiosaka, Osaka 577-8502, Japan
| | - Satoshi Mitarai
- Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan; Department of Mycobacterium Reference and Research, The Research Institute of Tuberculosis, Japan Anti-Tuberculosis Association, Tokyo 204-8533, Japan
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13
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Weagle CL, Saint-Louis R, Dumas-Lefebvre É, Chavanne C, Dumont D, Chang RYW. Sea-air transfer of a tracer dye observed during the Tracer Release Experiment with implications for airborne contaminant exposure. MARINE POLLUTION BULLETIN 2022; 182:113945. [PMID: 35905703 DOI: 10.1016/j.marpolbul.2022.113945] [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: 04/07/2022] [Revised: 07/06/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Rhodamine water tracer (RWT) released during the 2021 Tracer Release Experiment in the St. Lawrence Estuary provides a proxy for the water-soluble fractions of contaminant spills. Measurements of total and size-resolved aerosols were taken onboard a research vessel throughout the experiment. Size-resolved aerosol measurements show airborne transmission of water-soluble RWT in a bimodal distribution peaking at 5.2 μm and 0.9 μm. Highest aerosol RWT (30.5 pg m-3) was observed in the 12-hour daytime period following the first dye release (Sept. 5), while the lowest (8.8 pg m-3) was observed in the subsequent nighttime sample. Available wind and RWT patch information were used to identify factors contributing to the factor-of-three variation in aerosol RWT concentrations. Negligible correlations were found between aerosol RWT and wind speed and sample time-of-day. Wind direction is isolated as the key variable for consideration in identifying the impact of contaminant spills on coastal and inland communities.
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Affiliation(s)
- Crystal L Weagle
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Richard Saint-Louis
- Département De Biologie, Chimie et Géographie, Université du Québec à Rimouski, Rimouski, QC G5L 2Z9, Canada
| | - Élie Dumas-Lefebvre
- Institut des Sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Cédric Chavanne
- Institut des Sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Dany Dumont
- Institut des Sciences de la mer de Rimouski, Université du Québec à Rimouski, Rimouski, QC G5L 3A1, Canada
| | - Rachel Y-W Chang
- Department of Physics and Atmospheric Science, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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de Lorenzo V. Environmental Galenics: large-scale fortification of extant microbiomes with engineered bioremediation agents. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210395. [PMID: 35757882 PMCID: PMC9234819 DOI: 10.1098/rstb.2021.0395] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Contemporary synthetic biology-based biotechnologies are generating tools and strategies for reprogramming genomes for specific purposes, including improvement and/or creation of microbial processes for tackling climate change. While such activities typically work well at a laboratory or bioreactor scale, the challenge of their extensive delivery to multiple spatio-temporal dimensions has hardly been tackled thus far. This state of affairs creates a research niche for what could be called Environmental Galenics (EG), i.e. the science and technology of releasing designed biological agents into deteriorated ecosystems for the sake of their safe and effective recovery. Such endeavour asks not just for an optimal performance of the biological activity at stake, but also the material form and formulation of the agents, their propagation and their interplay with the physico-chemical scenario where they are expected to perform. EG also encompasses adopting available physical carriers of microorganisms and channels of horizontal gene transfer as potential paths for spreading beneficial activities through environmental microbiomes. While some of these propositions may sound unsettling to anti-genetically modified organisms sensitivities, they may also fall under the tag of TINA (there is no alternative) technologies in the cases where a mere reduction of emissions will not help the revitalization of irreversibly lost ecosystems. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología-CSIC, Campus de Cantoblanco, Madrid 28049, Spain
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15
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Long-Term Studies of Biological Components of Atmospheric Aerosol: Trends and Variability. ATMOSPHERE 2022. [DOI: 10.3390/atmos13050651] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Background: Biological components of atmospheric aerosol affect the quality of atmospheric air. Long-term trends in changes of the concentrations of total protein (a universal marker of the biogenic component of atmospheric aerosol) and culturable microorganisms in the air are studied. Methods: Atmospheric air samples are taken at two locations in the south of Western Siberia and during airborne sounding of the atmosphere. Sample analysis is carried out in the laboratory using standard culture methods (culturable microorganisms) and the fluorescence method (total protein). Results: Negative trends in the average annual concentration of total protein and culturable microorganisms in the air are revealed over more than 20 years of observations. For the concentration of total protein and culturable microorganisms in the air, intra-annual dynamics is revealed. The ratio of the maximum and minimum values of these concentrations reaches an order of magnitude. The variability of concentrations does not exceed, as a rule, two times for total protein and three times for culturable microorganisms. At the same time, for the data obtained in the course of airborne sounding of the atmosphere, a high temporal stability of the vertical profiles of the studied concentrations was found. The detected biodiversity of culturable microorganisms in atmospheric air samples demonstrates a very high variability at all observation sites. Conclusions: The revealed long-term changes in the biological components of atmospheric aerosol result in a decrease in their contribution to the atmospheric air quality index.
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16
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Tajiki F, Asgari HM, Zamani I, Ghanbari F. Assessing the relationship between airborne fungi and potential dust sources using a combined approach. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2022; 29:17799-17810. [PMID: 34676476 DOI: 10.1007/s11356-021-17028-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/10/2021] [Indexed: 06/13/2023]
Abstract
Dust events impose negative socio-economic, health, and environmental impacts on vulnerable areas and reflect their sources' physiochemical and biological characteristics. This study aimed to assess the impact of two dust sources on the concentration and diversity of airborne fungi in one of the dustiest areas in the world. This study is the first attempt to investigate the relationship between dust sources fungal community and those in airborne dust. Also, the contribution of dust sources to airborne fungi was estimated. Air masses arriving at the study area were assessed using local wind rose and the HYSPLIT model. Sampling was carried out from airborne dust at the Arvand Free Zone as target areas and soil in the dried parts of the Hor al-Azim and Shadegan wetlands as source areas to explore the relationship between fungi in the dust sources and the downwind area. The samples were analyzed in the lab to extract DNA. The internal transcribed spacer (ITS) regions of the rDNA gene were amplified using the primers ITS1F and ITS4, and then PCR products were sent to the lab for sequencing. The raw DNA data were processed using the QIIME virtual box to pick operational taxonomic units and taxonomy assignments. The most common fungi at the genus level were in the order of Penicillium > Aspergillus > Alternaria > Fusarium > Paradendryphiella > Talaromyces. The similarity between air and soil fungal genera was investigated using richness and diversity indices, the phylogenetic tree, and principal component analysis. The results showed that the community structures of ambient fungi in the Hor al-Azim and Shadegan dust sources were more similar to those on dusty days than non-dusty days. The source tracker model was used to quantify the contributions of known dust sources to airborne fungi. The results showed that the main source of airborne fungi was Hor al-Azim on dusty and non-dusty days. This study's results can help managers identify and prioritize dust sources regarding fungal species.
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Affiliation(s)
- Forough Tajiki
- Department of Environment, Faculty of Natural Resources, Khorramshahr University of Marine Sciences and Technology, P.B. 699, Khorramshahr, Iran
| | - Hossein Mohammad Asgari
- Department of Environment, Faculty of Natural Resources, Khorramshahr University of Marine Sciences and Technology, P.B. 699, Khorramshahr, Iran.
| | - Isaac Zamani
- Department of Marine Biology, Faculty of Marine and Oceanic Sciences, Khorramshahr University of Marine Sciences and Technology, P.B. 699, Khorramshahr, Iran
| | - Farshid Ghanbari
- Research Center for Environmental Contaminants (RCEC), Abadan Faculty of Medical Sciences, Abadan, Iran
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Drautz-Moses DI, Luhung I, Gusareva ES, Kee C, Gaultier NE, Premkrishnan BNV, Lee CF, Leong ST, Park C, Yap ZH, Heinle CE, Lau KJX, Purbojati RW, Lim SBY, Lim YH, Kutmutia SK, Aung NW, Oliveira EL, Ng SG, Dacanay J, Ang PN, Spence S, Phung WJ, Wong A, Kennedy RJ, Kalsi N, Sasi SP, Chandrasekaran L, Uchida A, Junqueira ACM, Kim HL, Hankers R, Feuerle T, Corsmeier U, Schuster SC. Vertical stratification of the air microbiome in the lower troposphere. Proc Natl Acad Sci U S A 2022; 119:e2117293119. [PMID: 35131944 PMCID: PMC8851546 DOI: 10.1073/pnas.2117293119] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/11/2021] [Indexed: 12/11/2022] Open
Abstract
The troposphere constitutes the final frontier of global ecosystem research due to technical challenges arising from its size, low biomass, and gaseous state. Using a vertical testing array comprising a meteorological tower and a research aircraft, we conducted synchronized measurements of meteorological parameters and airborne biomass (n = 480) in the vertical air column up to 3,500 m. The taxonomic analysis of metagenomic data revealed differing patterns of airborne microbial community composition with respect to time of day and height above ground. The temporal and spatial resolution of our study demonstrated that the diel cycle of airborne microorganisms is a ground-based phenomenon that is entirely absent at heights >1,000 m. In an integrated analysis combining meteorological and biological data, we demonstrate that atmospheric turbulence, identified by potential temperature and high-frequency three-component wind measurements, is the key driver of bioaerosol dynamics in the lower troposphere. Multivariate regression analysis shows that at least 50% of identified airborne microbial taxa (n = ∼10,000) are associated with either ground or height, allowing for an understanding of dispersal patterns of microbial taxa in the vertical air column. Due to the interconnectedness of atmospheric turbulence and temperature, the dynamics of microbial dispersal are likely to be impacted by rising global temperatures, thereby also affecting ecosystems on the planetary surface.
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Affiliation(s)
- Daniela I Drautz-Moses
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Irvan Luhung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elena S Gusareva
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Carmon Kee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Nicolas E Gaultier
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | | | - Choou Fook Lee
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - See Ting Leong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Changsook Park
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Zhei Hwee Yap
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Cassie E Heinle
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Kenny J X Lau
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Rikky W Purbojati
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Serene B Y Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Yee Hui Lim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Shruti Ketan Kutmutia
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ngu War Aung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Elaine L Oliveira
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Soo Guek Ng
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Justine Dacanay
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Poh Nee Ang
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Sam Spence
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Wen Jia Phung
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Anthony Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ryan J Kennedy
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Namrata Kalsi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Santhi Puramadathil Sasi
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Lakshmi Chandrasekaran
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Akira Uchida
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
| | - Ana Carolina M Junqueira
- Departamento de Genética, Instituto de Biologia, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, Brazil
| | - Hie Lim Kim
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551
- The Asian School of the Environment, Nanyang Technological University, Singapore 637459
| | - Rudolf Hankers
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Thomas Feuerle
- Institute of Flight Guidance, Technische Universität, 38108 Braunschweig, Germany
| | - Ulrich Corsmeier
- Institute of Meteorology and Climate Research, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Stephan C Schuster
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore 637551;
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18
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Louca S. The rates of global bacterial and archaeal dispersal. THE ISME JOURNAL 2022; 16:159-167. [PMID: 34282284 PMCID: PMC8692594 DOI: 10.1038/s41396-021-01069-8] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 06/28/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
The phylogenetic resolution at which microorganisms display geographic endemism, the rates at which they disperse at global scales, and the role of humans on global microbial dispersal are largely unknown. Answering these questions is necessary for interpreting microbial biogeography, ecology, and macroevolution and for predicting the spread of emerging pathogenic strains. To resolve these questions, I analyzed the geographic and evolutionary relationships between 36,795 bacterial and archaeal ("prokaryotic") genomes from ∼7000 locations around the world. I find clear signs of continental-scale endemism, including strong correlations between phylogenetic divergence and geographic distance. However, the phylogenetic scale at which endemism generally occurs is extremely small, and most "species" (defined by an average nucleotide identity ≥ 95%) and even closely related strains (average nucleotide identity ≥ 99.9%) are globally distributed. Human-associated lineages display faster dispersal rates than other terrestrial lineages; the average net distance between any two human-associated cell lineages diverging 50 years ago is roughly 580 km. These results suggest that many previously reported global-scale microbial biogeographical patterns are likely the result of recent or current environmental filtering rather than geographic endemism. For human-associated lineages, estimated transition rates between Europe and North America are particularly high, and much higher than for non-human associated terrestrial lineages, highlighting the role that human movement plays in global microbial dispersal. Dispersal was slowest for hot spring- and terrestrial subsurface-associated lineages, indicating that these environments may act as "isolated islands" of microbial evolution.
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Affiliation(s)
- Stilianos Louca
- Department of Biology, University of Oregon, Eugene, OR, USA.
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, USA.
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19
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Apangu GP, Frisk CA, Petch GM, Muggia L, Pallavicini A, Hanson M, Skjøth CA. Environmental DNA reveals diversity and abundance of Alternaria species in neighbouring heterogeneous landscapes in Worcester, UK. AEROBIOLOGIA 2022; 38:457-481. [PMID: 36471880 PMCID: PMC9715499 DOI: 10.1007/s10453-022-09760-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 09/28/2022] [Indexed: 05/05/2023]
Abstract
UNLABELLED Alternaria is a pathogenic and allergenic fungus affecting 400 plant species and 334 million people globally. This study aimed at assessing the diversity of Alternaria species in airborne samples collected from closely located (7 km apart) and heterogeneous sites (rural, urban and unmanaged grassland) in Worcester and Lakeside, the UK. A secondary objective was to examine how the ITS1 subregion varies from ITS2 in Alternaria species diversity and composition. Airborne spores were collected using Burkard 7-day and multi-vial Cyclone samplers for the period 5 July 2016-9 October 2019. Air samples from the Cyclone were amplified using the ITS1and ITS2 subregions and sequenced using Illumina MiSeq platform whereas those from the Burkard sampler were identified and quantified using optical microscopy. Optical microscopy and eDNA revealed a high abundance of Alternaria in the rural, urban and unmanaged sites. ITS1 and ITS2 detected five and seven different Alternaria species at the three sampling sites, respectively. A. dactylidicola, A. metachromatica and A. infectoria were the most abundant. The rural, urban and unmanaged grassland sites had similar diversity (PERMANOVA) of the species due to similarity in land use and proximity of the sites. Overall, the study showed that heterogeneous and neighbouring sites with similar land uses can have similar Alternaria species. It also demonstrated that an eDNA approach can complement the classical optical microscopy method in providing more precise information on fungal species diversity in an environment for targeted management. Similar studies can be replicated for other allergenic and pathogenic fungi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10453-022-09760-9.
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Affiliation(s)
- Godfrey Philliam Apangu
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Protecting Crops and the Environment, Rothamsted Research, West Common, Harpenden, AL5 2JQ Hertfordshire UK
| | - Carl Alexander Frisk
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Present Address: Department of Urban Greening and Vegetation Ecology, Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Geoffrey M. Petch
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Lucia Muggia
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via Giorgieri 10, 34127 Trieste, Italy
| | - Mary Hanson
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ Worcester UK
- Department of Environmental Science, Aarhus University, Frederiksborgvej 399, 4000 Roskilde, Denmark
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20
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Alsante AN, Thornton DCO, Brooks SD. Ocean Aerobiology. Front Microbiol 2021; 12:764178. [PMID: 34777320 PMCID: PMC8586456 DOI: 10.3389/fmicb.2021.764178] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/27/2021] [Indexed: 12/12/2022] Open
Abstract
Ocean aerobiology is defined here as the study of biological particles of marine origin, including living organisms, present in the atmosphere and their role in ecological, biogeochemical, and climate processes. Hundreds of trillions of microorganisms are exchanged between ocean and atmosphere daily. Within a few days, tropospheric transport potentially disperses microorganisms over continents and between oceans. There is a need to better identify and quantify marine aerobiota, characterize the time spans and distances of marine microorganisms’ atmospheric transport, and determine whether microorganisms acclimate to atmospheric conditions and remain viable, or even grow. Exploring the atmosphere as a microbial habitat is fundamental for understanding the consequences of dispersal and will expand our knowledge of biodiversity, biogeography, and ecosystem connectivity across different marine environments. Marine organic matter is chemically transformed in the atmosphere, including remineralization back to CO2. The magnitude of these transformations is insignificant in the context of the annual marine carbon cycle, but may be a significant sink for marine recalcitrant organic matter over long (∼104 years) timescales. In addition, organic matter in sea spray aerosol plays a significant role in the Earth’s radiative budget by scattering solar radiation, and indirectly by affecting cloud properties. Marine organic matter is generally a poor source of cloud condensation nuclei (CCN), but a significant source of ice nucleating particles (INPs), affecting the formation of mixed-phase and ice clouds. This review will show that marine biogenic aerosol plays an impactful, but poorly constrained, role in marine ecosystems, biogeochemical processes, and the Earth’s climate system. Further work is needed to characterize the connectivity and feedbacks between the atmosphere and ocean ecosystems in order to integrate this complexity into Earth System models, facilitating future climate and biogeochemical predictions.
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Affiliation(s)
- Alyssa N Alsante
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Daniel C O Thornton
- Department of Oceanography, Texas A&M University, College Station, TX, United States
| | - Sarah D Brooks
- Department of Atmospheric Sciences, Texas A&M University, College Station, TX, United States
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21
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Wang M, Kriticos DJ, Ota N, Brooks A, Paini D. A general trait-based modelling framework for revealing patterns of airborne fungal dispersal threats to agriculture and native flora. THE NEW PHYTOLOGIST 2021; 232:1506-1518. [PMID: 34338336 DOI: 10.1111/nph.17659] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Accepted: 07/23/2021] [Indexed: 06/13/2023]
Abstract
Fungal plant pathogens are of economic and ecological importance to global agriculture and natural ecosystems. Long-distance atmospheric dispersal of fungal spores (LAD) can pose threats to agricultural and native vegetation lands. An understanding of such patterns of fungal spore dispersal and invasion pathways can provide valuable insights into plant protection. Spore traits affect their dispersal abilities. We propose a general trait-based framework for modelling LAD to reveal dispersal patterns and pathways, and assess subsequent threats of arrival (TOA) quantitatively in the context of biosecurity. To illustrate the framework, we present a study of Australia and its surrounding land masses. The overall dispersal pattern covered almost the entire continent of Australia. Fungal spores in the size class of 10 and 20 µm (aerodynamic diameter) posed the greatest TOA. Our study shows the effects of morphological traits on these potential TOA, and how they varied between source regions, size classes, and seasons. Our framework revealed spore dispersal patterns and pathways. It also facilitates comparisons of spatio-temporal dispersal dynamics among fungal classes, gaining insights into atmospheric long-distance dispersal of fungi as a whole, and provides a basis for assessing fungal pest threats in potential source regions based on easily measured spore characteristics.
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Affiliation(s)
- Ming Wang
- Health & Biosecurity, CSIRO, Canberra, ACT, 2601, Australia
| | - Darren J Kriticos
- Health & Biosecurity, CSIRO, Canberra, ACT, 2601, Australia
- School of Biological Sciences, The University of Queensland, Brisbane, QLD, 4072, Australia
| | - Noboru Ota
- Health & Biosecurity, CSIRO, Canberra, ACT, 2601, Australia
| | - Aaron Brooks
- Health & Biosecurity, CSIRO, Canberra, ACT, 2601, Australia
| | - Dean Paini
- Health & Biosecurity, CSIRO, Canberra, ACT, 2601, Australia
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22
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Regional Relative Risk, a Physics-Based Metric for Characterizing Airborne Infectious Disease Transmission. Appl Environ Microbiol 2021; 87:e0126221. [PMID: 34432495 DOI: 10.1128/aem.01262-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Airborne infectious disease transmission events occur over a wide range of spatial scales and can be an important means of disease transmission. Physics- and biology-based models can assist in predicting airborne transmission events, overall disease incidence, and disease control strategy efficacy. We describe a new theory that extends current approaches for the case in which an individual is infected by a single airborne particle, including the scenario in which numerous infectious particles are present in the air but only one causes infection. A single infectious particle can contain more than one pathogenic microorganism and be physically larger than the pathogen itself. This approach allows robust relative risk estimates even when there is wide variation in (i) individual exposures and (ii) the individual response to that exposure (the pathogen dose-response function can take any mathematical form and vary by individual). Based on this theory, we propose the regional relative risk-a new metric, distinct from the traditional relative risk metric, that compares the risk between two regions. In theory, these regions can range from individual rooms to large geographic areas. In this paper, we apply the regional relative risk metric to outdoor disease transmission events over spatial scales ranging from 50 m to 20 km, demonstrating that in many common cases minimal input information is required to use the metric. Also, we demonstrate that the model predictions are consistent with data from prior outbreaks. Future efforts could apply and validate this theory for other spatial scales, such as transmission within indoor environments. This work provides context for (i) the initial stages of an airborne disease outbreak and (ii) larger-scale disease spread, including unexpected low-probability disease "sparks" that potentially affect remote populations, a key practical issue in controlling airborne disease outbreaks. IMPORTANCE Airborne infectious disease transmission events occur over a wide range of spatial scales and can be important to disease outbreaks. We describe a new physics- and biology-based theory for the important case in which individuals are infected by a single airborne particle (even though numerous infectious particles can be emitted into the air and inhaled). Based on this theory, we propose a new epidemiological metric, regional relative risk, that compares the risk between two geographic regions (in theory, regions can range from individual rooms to large areas). Our modeling of transmission events predicts that for many scenarios of interest, minimal information is required to use this metric for locations 50 m to 20 km downwind. This prediction is consistent with data from prior disease outbreaks. Future efforts could apply and validate this theory for other spatial scales, such as indoor environments. Our results may be applicable to many airborne diseases a priori, as these results depend on the physics of airborne particulate dispersion.
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23
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Jeong SY, Kim TG. Effects of dispersal on species distribution, abundance, diversity and interaction in a bacterial biofilm metacommunity. J Appl Microbiol 2021; 132:459-469. [PMID: 34176204 DOI: 10.1111/jam.15194] [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: 02/02/2021] [Revised: 06/01/2021] [Accepted: 06/18/2021] [Indexed: 11/30/2022]
Abstract
AIMS Dispersal effects on biofilms have not been adequately studied despite their strong potential impacts on biofilm development. We investigated the effects of dispersal on biofilm metacommunity. METHODS AND RESULTS A bacterial consortium was allowed to form biofilms on 12 glass beads attached to disposable plates (compartmentalized or not), and biofilms were scrutinized on days 5, 10 and 15 using quantitative PCR and MiSeq sequencing. Biofilm population density was lesser by 2 orders of magnitude on day 5 when dispersal was allowed (p < 0.05). Then, the population rapidly increased by 4.4 orders with dispersal (p < 0.05) but did not change without dispersal. Community analyses revealed that dispersal increased the species diversity at all sampling times (p < 0.05). Dispersal affected the community structure and increased the homogeneity of local communities (p < 0.05). Distance-decay analysis showed that dispersal reduced the dissimilarity among local communities at all distance levels. Furthermore, dispersal reduced the variability of diversity, population and community structure. Network analysis revealed that dispersal increased the clustering coefficient, network density and connectivity. CONCLUSIONS Dispersal increased the species diversity, population and interaction and reduced the variability of the diversity, population and structure among local communities. SIGNIFICANCE AND IMPACT OF STUDY Our results suggest that dispersal can induce the niche complementarity and mass effects.
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Affiliation(s)
- So-Yeon Jeong
- Department of Microbiology, Pusan National University, Pusan, Korea
| | - Tae Gwan Kim
- Department of Microbiology, Pusan National University, Pusan, Korea
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24
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Pendergraft MA, Grimes DJ, Giddings SN, Feddersen F, Beall CM, Lee C, Santander MV, Prather KA. Airborne transmission pathway for coastal water pollution. PeerJ 2021; 9:e11358. [PMID: 34164231 PMCID: PMC8191489 DOI: 10.7717/peerj.11358] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 04/06/2021] [Indexed: 12/18/2022] Open
Abstract
Each year, over one hundred million people become ill and tens of thousands die from exposure to viruses and bacteria from sewage transported to the ocean by rivers, estuaries, stormwater, and other coastal discharges. Water activities and seafood consumption have been emphasized as the major exposure pathways to coastal water pollution. In contrast, relatively little is known about the potential for airborne exposure to pollutants and pathogens from contaminated seawater. The Cross Surfzone/Inner-shelf Dye Exchange (CSIDE) study was a large-scale experiment designed to investigate the transport pathways of water pollution along the coast by releasing dye into the surfzone in Imperial Beach, CA. Additionally, we leveraged this ocean-focused study to investigate potential airborne transmission of coastal water pollution by collecting complementary air samples along the coast and inland. Aerial measurements tracked sea surface dye concentrations along 5+ km of coast at 2 m × 2 m resolution. Dye was detected in the air over land for the first 2 days during two of the three dye releases, as far as 668 m inland and 720 m downwind of the ocean. These coordinated water/air measurements, comparing dye concentrations in the air and upwind source waters, provide insights into the factors that lead to the water-to-air transfer of pollutants. These findings show that coastal water pollution can reach people through an airborne pathway and this needs to be taken into account when assessing the full impact of coastal ocean pollution on public health. This study sets the stage for further studies to determine the details and importance of airborne exposure to sewage-based pathogens and toxins in order to fully assess the impact of coastal pollution on public health.
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Affiliation(s)
- Matthew A Pendergraft
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Derek J Grimes
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Sarah N Giddings
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Falk Feddersen
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Charlotte M Beall
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America
| | - Christopher Lee
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States
| | - Mitchell V Santander
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States
| | - Kimberly A Prather
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, California, United States of America.,Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California, United States
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25
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Jeong SY, Kim TG. Comparison of five membrane filters to collect bioaerosols for airborne microbiome analysis. J Appl Microbiol 2020; 131:780-790. [PMID: 33331057 DOI: 10.1111/jam.14972] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Revised: 11/29/2020] [Accepted: 12/11/2020] [Indexed: 11/27/2022]
Abstract
AIMS Recovering DNA of airborne micro-organisms (AM) from air is a challenging task. We compared five membrane filters for bioaerosol sampling-mixed cellulose ester (MCE), polyethersulfone (PES), polyamide (PA), polytetrafluorethylene (PTFE) and polyvinylidene fluoride (PVDF)-based on their bacterial, fungal and eukaryotic DNA recoveries. METHODS AND RESULTS Bacterial, fungal and eukaryotic populations were quantified using quantitative PCR. With a bacterial consortium, PTFE exhibited the best recovery efficiency (113%), followed by PA (92%), PES (86%), MCE (48%) and PVDF (1%). When filters were compared with air, PA was used as a control to normalize results from the others. The bacterial, fungal and eukaryotic DNA recovery ratios were markedly greater in PES (9·3, 11·5 and 10·3 respectively) than in the remaining. Eukaryotic MiSeq sequencing revealed that PES recovered a more diverse and considerably richer assemblage (richness ratios, 4·97 vs ≤ 1·16 for PES vs the others). Rank abundance distribution analysis showed that distribution tails were longer (>4 times) in PES, but these did not differ between the remaining and PA. Community comparison showed that PES exhibited a lower variation across trials than the PA, while the remaining did not. CONCLUSIONS PES filter markedly outperformed the other filters in quantitative and qualitative recovery of AM. SIGNIFICANCE AND IMPACT OF THE STUDY Our findings demonstrated the importance of filter selection for sampling AM.
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Affiliation(s)
- S-Y Jeong
- Department of Microbiology, Pusan National University, Pusan, Korea
| | - T G Kim
- Department of Microbiology, Pusan National University, Pusan, Korea
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26
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Franco Ortega S, Ferrocino I, Adams I, Silvestri S, Spadaro D, Gullino ML, Boonham N. Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR. J Fungi (Basel) 2020; 6:jof6040372. [PMID: 33348656 PMCID: PMC7766667 DOI: 10.3390/jof6040372] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/10/2020] [Accepted: 12/14/2020] [Indexed: 01/16/2023] Open
Abstract
The airborne mycobiota has been understudied in comparison with the mycobiota present in other agricultural environments. Traditional, culture-based methods allow the study of a small fraction of the organisms present in the atmosphere, thus missing important information. In this study, the aerial mycobiota in a rice paddy has been examined during the cropping season (from June to September 2016) using qPCRs for two important rice pathogens (Pyricularia oryzae and Bipolaris oryzae) and by using DNA metabarcoding of the fungal ITS region. The metabarcoding results demonstrated a higher alpha diversity (Shannon–Wiener diversity index H′ and total number of observed species) at the beginning of the trial (June), suggesting a higher level of community complexity, compared with the end of the season. The main taxa identified by HTS analysis showed a shift in their relative abundance that drove the cluster separation as a function of time and temperature. The most abundant OTUs corresponded to genera such as Cladosporium, Alternaria, Myrothecium, or Pyricularia. Changes in the mycobiota composition were clearly dependent on the average air temperature with a potential impact on disease development in rice. In parallel, oligotyping analysis was performed to obtain a sub-OTU identification which revealed the presence of several oligotypes of Pyricularia and Bipolaris with relative abundance changing during monitoring.
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Affiliation(s)
- Sara Franco Ortega
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
| | - Ilario Ferrocino
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
| | - Ian Adams
- FERA, National Agri-Food Innovation Campus, Sand Hutton, York YO41 1LZ, UK;
| | - Simone Silvestri
- Ente Nazionale per la Risicultura (ENTERISI), Strada per Ceretto 4, 27030 Castello d’Agogna (PV), Italy;
| | - Davide Spadaro
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
- Correspondence:
| | - Maria Lodovica Gullino
- Centre of Competence for the Innovation in the Agro-Environmental Sector—AGROINNOVA, University of Turin, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy; (S.F.O.); (M.L.G.)
- Department of Agricultural, Forestry and Food Sciences (DiSAFA), University of Torino, Via Paolo Braccini 2, I-10095 Grugliasco (TO), Italy;
| | - Neil Boonham
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, UK;
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27
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Woo C, Yamamoto N. Falling bacterial communities from the atmosphere. ENVIRONMENTAL MICROBIOME 2020; 15:22. [PMID: 33902752 PMCID: PMC8066439 DOI: 10.1186/s40793-020-00369-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 11/28/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND Bacteria emitted into the atmosphere eventually settle to the pedosphere via sedimentation (dry deposition) or precipitation (wet deposition), constituting a part of the global cycling of substances on Earth, including the water cycle. In this study, we aim to investigate the taxonomic compositions and flux densities of bacterial deposition, for which little is known regarding the relative contributions of each mode of atmospheric deposition, the taxonomic structures and memberships, and the aerodynamic properties in the atmosphere. RESULTS Precipitation was found to dominate atmospheric bacterial deposition, contributing to 95% of the total flux density at our sampling site in Korea, while bacterial communities in precipitation were significantly different from those in sedimentation, in terms of both their structures and memberships. Large aerodynamic diameters of atmospheric bacteria were observed, with an annual mean of 8.84 μm, which appears to be related to their large sedimentation velocities, with an annual mean of 1.72 cm s- 1 for all bacterial taxa combined. The observed mean sedimentation velocity for atmospheric bacteria was larger than the previously reported mean sedimentation velocities for fungi and plants. CONCLUSIONS Large aerodynamic diameters of atmospheric bacteria, which are likely due to the aggregation and/or attachment to other larger particles, are thought to contribute to large sedimentation velocities, high efficiencies as cloud nuclei, and large amounts of precipitation of atmospheric bacteria. Moreover, the different microbiotas between precipitation and sedimentation might indicate specific bacterial involvement and/or selective bacterial growth in clouds. Overall, our findings add novel insight into how bacteria participate in atmospheric processes and material circulations, including hydrological circulation, on Earth.
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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
| | - 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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28
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Piriyakarnsakul S, Takarada K, Heab KE, Nasu M, Hata M, Furuuchi M. Optimal fluorescent-dye staining time for the real-time detection of microbes: a study of Saccharomyces cerevisiae. J Appl Microbiol 2020; 128:1694-1702. [PMID: 31925843 DOI: 10.1111/jam.14577] [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: 09/09/2019] [Revised: 12/27/2019] [Accepted: 01/06/2020] [Indexed: 11/28/2022]
Abstract
AIMS To provide information on the time-dependent behaviour of microbe staining by fluorescent dyes in the order of seconds, which is important in terms of the recent rapid and online techniques for microbe measurements and/or environmental microbe analysis. METHODS AND RESULTS For combinations of yeast (Saccharomyces cerevisiae) and typical dyes, including DAPI (4',6-diamidino-2-phenylindole) and Auramine-O, a suspension of yeast cells in ultrapure water was injected into a dye solution in a micro cuvette placed inside a spectrofluorometer and the fluorescence intensity of the resulting solution was measured at 1 s intervals, starting immediately after the mixing and continued until the time for the maximum intensity using various concentrations of yeast and dyes. The relaxation time τ, which corresponds to ~63·2% of the maximum fluorescence intensity, was shown to decrease to below 1 s with increasing DAPI concentration, whereas it remained constant for 2-3 s with increasing Auramine-O concentration, for example at a yeast concentration of 100 µg ml-1 . CONCLUSIONS For the conditions of yeast >10 µg ml-1 , DAPI >1 µg ml-1 and Auramine-O >0·1 µg ml-1 , τ could be adjusted to below 5 s to achieve a rapid and stable staining. SIGNIFICANCE AND IMPACT OF THE STUDY Design and operating conditions for rapid and online measurements of microbes can be optimized.
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Affiliation(s)
- S Piriyakarnsakul
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - K Takarada
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - K E Heab
- Graduate School of Natural Science and Technology, Kanazawa University, Kanazawa, Japan
| | - M Nasu
- Faculty of Pharmacy, Osaka Ohtani University, Osaka, Japan
| | - M Hata
- Faculty of Geoscience and Civil Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan
| | - M Furuuchi
- Faculty of Geoscience and Civil Engineering, Institute of Science and Engineering, Kanazawa University, Kanazawa, Japan.,Faculty of Environmental Management, Prince of Songkla University, Hat Yai, Thailand
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Accessing the Life in Smoke: A New Application of Unmanned Aircraft Systems (UAS) to Sample Wildland Fire Bioaerosol Emissions and Their Environment. FIRE-SWITZERLAND 2019. [DOI: 10.3390/fire2040056] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Wildland fire is a major producer of aerosols from combustion of vegetation and soils, but little is known about the abundance and composition of smoke’s biological content. Bioaerosols, or aerosols derived from biological sources, may be a significant component of the aerosol load vectored in wildland fire smoke. If bioaerosols are injected into the upper troposphere via high-intensity wildland fires and transported across continents, there may be consequences for the ecosystems they reach. Such transport would also alter the concept of a wildfire’s perimeter and the disturbance domain of its impact. Recent research has revealed that viable microorganisms are directly aerosolized during biomass combustion, but sampling systems and methodology for quantifying this phenomenon are poorly developed. Using a series of prescribed fires in frequently burned forest ecosystems, we report the results of employing a small rotary-wing unmanned aircraft system (UAS) to concurrently sample aerosolized bacteria and fungi, particulate matter, and micrometeorology in smoke plumes versus background conditions. Airborne impaction-based bioaerosol sampling indicated that microbial composition differed between background air and smoke, with seven unique organisms in smoke vs. three in background air. The air temperature was negatively correlated with the number of fungal colony-forming units detected. Our results demonstrate the utility of a UAS-based sampling platform for active sampling of viable aerosolized microbes in smoke arising from wildland fires. This methodology can be extended to sample viable microbes in a wide variety of emissions sampling pursuits, especially those in hazardous and inaccessible environments.
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Grewling Ł, Bogawski P, Kryza M, Magyar D, Šikoparija B, Skjøth CA, Udvardy O, Werner M, Smith M. Concomitant occurrence of anthropogenic air pollutants, mineral dust and fungal spores during long-distance transport of ragweed pollen. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2019; 254:112948. [PMID: 31377333 DOI: 10.1016/j.envpol.2019.07.116] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Revised: 07/17/2019] [Accepted: 07/22/2019] [Indexed: 06/10/2023]
Abstract
Large-scale synoptic conditions are able to transport considerable amounts of airborne particles over entire continents by creating substantial air mass movement. This phenomenon is observed in Europe in relation to highly allergenic ragweed (Ambrosia L.) pollen grains that are transported from populations in Central Europe (mainly the Pannonian Plain and Balkans) to the North. The path taken by atmospheric ragweed pollen often passes through the highly industrialised mining region of Silesia in Southern Poland, considered to be one of the most polluted areas in the EU. It is hypothesized that chemical air pollutants released over Silesia could become mixed with biological material and be transported to less polluted regions further North. We analysed levels of air pollution during episodes of long-distance transport (LDT) of ragweed pollen to Poland. Results show that, concomitantly with pollen, the concentration of air pollutants with potential health-risk, i.e. SO2, and PM10, have also significantly increased (by 104% and 37%, respectively) in the receptor area (Western Poland). Chemical transport modelling (EMEP) and air mass back-trajectory analysis (HYSPLIT) showed that potential sources of PM10 include Silesia, as well as mineral dust from the Ukrainian steppe and the Sahara Desert. In addition, atmospheric concentrations of other allergenic biological particles, i.e. Alternaria Nees ex Fr. spores, also increased markedly (by 115%) during LDT episodes. We suggest that the LDT episodes of ragweed pollen over Europe are not a "one-component" phenomenon, but are often related to elevated levels of chemical air pollutants and other biotic and abiotic components (fungal spores and desert dust).
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Affiliation(s)
- Łukasz Grewling
- Laboratory of Aeropalynology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-489 Poznań, Poland.
| | - Paweł Bogawski
- Laboratory of Biological Spatial Information, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-489 Poznań, Poland
| | - Maciej Kryza
- Department of Climatology and Atmosphere Protection, University of Wroclaw, Wroclaw, Poland
| | - Donat Magyar
- Department of Air Hygiene and Aerobiology, National Public Health Institute, Hungary
| | - Branko Šikoparija
- BioSense Institute - Research Institute for Information Technologies in Biosystems, University of Novi Sad, Novi Sad, Serbia
| | - Carsten Ambelas Skjøth
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
| | - Orsolya Udvardy
- Department of Air Hygiene and Aerobiology, National Public Health Institute, Hungary
| | - Małgorzata Werner
- Department of Climatology and Atmosphere Protection, University of Wroclaw, Wroclaw, Poland
| | - Matt Smith
- School of Science and the Environment, University of Worcester, Henwick Grove, WR2 6AJ, Worcester, United Kingdom
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Microbial communities in the tropical air ecosystem follow a precise diel cycle. Proc Natl Acad Sci U S A 2019; 116:23299-23308. [PMID: 31659049 PMCID: PMC6859341 DOI: 10.1073/pnas.1908493116] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This manuscript describes a precise diel cycle carried out by airborne microbiota in the tropics. 795 metagenomes from air samples taken from a single site show that fungi, bacteria, and plants all adhere to a specific timing for their presence in the near-surface atmosphere. The airborne community composition thereby shows an unexpected robustness, with the majority of the dynamics in taxa composition occurring within 24 h, but not across days, weeks, or months. Environmental parameters are the main drivers for the observed phenomenon, with temperature being the most important one. The atmosphere is vastly underexplored as a habitable ecosystem for microbial organisms. In this study, we investigated 795 time-resolved metagenomes from tropical air, generating 2.27 terabases of data. Despite only 9 to 17% of the generated sequence data currently being assignable to taxa, the air harbored a microbial diversity that rivals the complexity of other planetary ecosystems. The airborne microbial organisms followed a clear diel cycle, possibly driven by environmental factors. Interday taxonomic diversity exceeded day-to-day and month-to-month variation. Environmental time series revealed the existence of a large core of microbial taxa that remained invariable over 13 mo, thereby underlining the long-term robustness of the airborne community structure. Unlike terrestrial or aquatic environments, where prokaryotes are prevalent, the tropical airborne biomass was dominated by DNA from eukaryotic phyla. Specific fungal and bacterial species were strongly correlated with temperature, humidity, and CO2 concentration, making them suitable biomarkers for studying the bioaerosol dynamics of the atmosphere.
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Abstract
Culturable eubacterial isolates were collected at various altitudes in Earth’s atmosphere, including ~1.5 m above ground in Tallahassee, FL, USA; ~10.0 m above sea level over the mid-Atlantic ridge (~15° N); ~ 20 km above ground over the continental United States; ~20 km above sea level over the Pacific Ocean near southern California; and from the atmosphere of Carlsbad Cavern, Carlsbad Cavern National Park, NM, USA. Isolates were screened for the presence of inducible virus-like particles (VLP) through the use of mitomycin C and epifluorescent direct counts. We determined that 92.7% of the isolates carried inducible VLP counts in exposed versus non-exposed culture controls and that the relationship was statistically significant. Further statistical analyses revealed that the number of isolates that demonstrated VLP production did not vary among collection sites. These data demonstrate a high prevalence of VLP generation in isolates collected in the lower atmosphere and at extreme altitudes. They also show that species of eubacteria that are resistant to the rigors of atmospheric transport play a significant role in long-range atmospheric inter- and intra-continental dispersion of VLP and that long-range atmospheric transport of VLP may enhance rates of evolution at the microbial scale in receiving environments.
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Abundance and survival of microbial aerosols in the troposphere and stratosphere. ISME JOURNAL 2019; 13:2789-2799. [PMID: 31316133 DOI: 10.1038/s41396-019-0474-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 06/17/2019] [Accepted: 06/28/2019] [Indexed: 01/03/2023]
Abstract
Bioaerosol transport in the atmosphere disperses microbial species between continents, affects human and plant health, and may influence hydrologic cycling. However, there have been few quantitative observations of bioaerosols at altitudes more than a few kilometers above the surface. Lack of data on bioaerosol distributions in the atmosphere has impeded efforts to assess the aerial dissemination of microbes and their vertical extent in the biosphere. In this study, a helium balloon payload system was used to sample microbial cells and dust particles in air masses as high as 38 km above sea level over three locations in the southwestern United States. The cell concentrations at altitudes between 3 and 29 km were highly similar (2-5 × 105 cells m-3) and approximately threefold lower than those observed in the convective boundary layer (CBL; 1 × 106 cells m-3), decreasing to 8 × 104 cells m-3 at 35-38 km. The detection of adenosine triphosphate (ATP) and recovery of bacteria possessing extreme tolerance to desiccation and shortwave ultraviolet radiation confirmed that certain microorganisms have the capacity to persist at lower altitudes of the stratosphere. Our data and related calculations provide constraints on the upper altitudinal boundary for microbial habitability in the biosphere.
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Mhuireach GÁ, Betancourt-Román CM, Green JL, Johnson BR. Spatiotemporal Controls on the Urban Aerobiome. Front Ecol Evol 2019. [DOI: 10.3389/fevo.2019.00043] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Dommergue A, Amato P, Tignat-Perrier R, Magand O, Thollot A, Joly M, Bouvier L, Sellegri K, Vogel T, Sonke JE, Jaffrezo JL, Andrade M, Moreno I, Labuschagne C, Martin L, Zhang Q, Larose C. Methods to Investigate the Global Atmospheric Microbiome. Front Microbiol 2019; 10:243. [PMID: 30967843 PMCID: PMC6394204 DOI: 10.3389/fmicb.2019.00243] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Accepted: 01/29/2019] [Indexed: 11/13/2022] Open
Abstract
The interplay between microbes and atmospheric physical and chemical conditions is an open field of research that can only be fully addressed using multidisciplinary approaches. The lack of coordinated efforts to gather data at representative temporal and spatial scales limits aerobiology to help understand large scale patterns of global microbial biodiversity and its causal relationships with the environmental context. This paper presents the sampling strategy and analytical protocols developed in order to integrate different fields of research such as microbiology, -omics biology, atmospheric chemistry, physics and meteorology to characterize atmospheric microbial life. These include control of chemical and microbial contaminations from sampling to analysis and identification of experimental procedures for characterizing airborne microbial biodiversity and its functioning from the atmospheric samples collected at remote sites from low cell density environments. We used high-volume sampling strategy to address both chemical and microbial composition of the atmosphere, because it can help overcome low aerosol and microbial cell concentrations. To account for contaminations, exposed and unexposed control filters were processed along with the samples. We present a method that allows for the extraction of chemical and biological data from the same quartz filters. We tested different sampling times, extraction kits and methods to optimize DNA yield from filters. Based on our results, we recommend supplementary sterilization steps to reduce filter contamination induced by handling and transport. These include manipulation under laminar flow hoods and UV sterilization. In terms of DNA extraction, we recommend a vortex step and a heating step to reduce binding to the quartz fibers of the filters. These steps have led to a 10-fold increase in DNA yield, allowing for downstream omics analysis of air samples. Based on our results, our method can be integrated into pre-existing long-term monitoring field protocols for the atmosphere both in terms of atmospheric chemistry and biology. We recommend using standardized air volumes and to develop standard operating protocols for field users to better control the operational quality.
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Affiliation(s)
- Aurelien Dommergue
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Pierre Amato
- Institut de Chimie de Clermont-Ferrand, UMR6096 CNRS–Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Romie Tignat-Perrier
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Olivier Magand
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Alban Thollot
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Muriel Joly
- Institut de Chimie de Clermont-Ferrand, UMR6096 CNRS–Université Clermont Auvergne-Sigma, Clermont-Ferrand, France
| | - Laetitia Bouvier
- Laboratory for Meteorological Physics (LaMP), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Karine Sellegri
- Laboratory for Meteorological Physics (LaMP), Université Clermont Auvergne, Clermont-Ferrand, France
| | - Timothy Vogel
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
| | - Jeroen E. Sonke
- Géosciences Environnement Toulouse, Centre National de la Recherche Scientifique, Institut de Recherche pour le Développement, Université de Toulouse, Toulouse, France
| | - Jean-Luc Jaffrezo
- Institut des Géosciences de l’Environnement, Univ. Grenoble Alpes, CNRS, IRD, Grenoble INP, Grenoble, France
| | - Marcos Andrade
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andrés, La Paz, Bolivia
- Department of Atmospheric and Oceanic Sciences, University of Maryland, College Park, MD, United States
| | - Isabel Moreno
- Laboratory for Atmospheric Physics, Institute for Physics Research, Universidad Mayor de San Andrés, La Paz, Bolivia
| | | | - Lynwill Martin
- South African Weather Service, Stellenbosch, South Africa
| | - Qianggong Zhang
- Key Laboratory of Tibetan Environment Changes and Land Surface Processes, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Catherine Larose
- CNRS UMR 5005, Environmental Microbial Genomics, Laboratoire Ampère, École Centrale de Lyon, Université de Lyon, Ecully, France
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Pulschen AA, de Araujo GG, de Carvalho ACSR, Cerini MF, Fonseca LDM, Galante D, Rodrigues F. Survival of Extremophilic Yeasts in the Stratospheric Environment during Balloon Flights and in Laboratory Simulations. Appl Environ Microbiol 2018; 84:e01942-18. [PMID: 30266724 PMCID: PMC6238051 DOI: 10.1128/aem.01942-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022] Open
Abstract
The high-altitude atmosphere is a harsh environment with extremely low temperatures, low pressure, and high UV irradiation. For this reason, it has been proposed as an analogue for Mars, presenting deleterious factors similar to those on the surface of that planet. We evaluated the survival of extremophilic UV-resistant yeasts isolated from a high-elevation area in the Atacama Desert under stratospheric conditions. As biological controls, intrinsically resistant Bacillus subtilis spores were used. Experiments were performed in two independent stratospheric balloon flights and with an environmental simulation chamber. The three following different conditions were evaluated: (i) desiccation, (ii) desiccation plus exposure to stratospheric low pressure and temperature, and (3) desiccation plus exposure to the full stratospheric environment (UV, low pressure, and temperature). Two strains, Naganishia (Cryptococcus) friedmannii 16LV2 and Exophiala sp. strain 15LV1, survived full exposures to the stratosphere in larger numbers than did B. subtilis spores. Holtermanniella watticus (also known as Holtermanniella wattica) 16LV1, however, suffered a substantial loss in viability upon desiccation and did not survive the stratospheric UV exposure. The remarkable resilience of N. friedmannii and Exophiala sp. 15LV1 under the extreme Mars-like conditions of the stratosphere confirms its potential as a eukaryotic model for astrobiology. Additionally, our results with N. friedmannii strengthen the recent hypothesis that yeasts belonging to the Naganishia genus are fit for aerial dispersion, which might account for the observed abundance of this species in high-elevation soils.IMPORTANCE Studies of eukaryotic microorganisms under conditions of astrobiological relevance, as well as the aerial dispersion potential of extremophilic yeasts, are still lacking in the literature compared to works with bacteria. Using stratospheric balloon flights and a simulation chamber, we demonstrate that yeasts isolated from an extreme environment are capable of surviving all stressors found in the stratosphere, including intense UV irradiation, scoring an even higher survival than B. subtilis spores. Notably, the yeast N. friedmannii, which displayed one of the highest tolerances to the stratospheric environment in the experiments, was recently proposed to be adapted to airborne transportation, although such a hypothesis had not yet been tested. Our results strengthen such an assumption and can help explain the observed distribution and ecology of this particular yeast species.
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Affiliation(s)
| | | | | | - Maria Fernanda Cerini
- Graduate Program in Biomolecular Physics, São Carlos Institute of Physics, University of São Paulo, São Paulo, Brazil
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | | | - Douglas Galante
- Graduate Program in Biomolecular Physics, São Carlos Institute of Physics, University of São Paulo, São Paulo, Brazil
- Brazilian Synchrotron Light Laboratory, Brazilian Center for Research in Energy and Materials, Campinas, São Paulo, Brazil
| | - Fabio Rodrigues
- Department of Fundamental Chemistry, Institute of Chemistry, University of São Paulo, São Paulo, Brazil
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Kobziar LN, Pingree MRA, Larson H, Dreaden TJ, Green S, Smith JA. Pyroaerobiology: the aerosolization and transport of viable microbial life by wildland fire. Ecosphere 2018. [DOI: 10.1002/ecs2.2507] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Affiliation(s)
- Leda N. Kobziar
- Department of Natural Resources and Society University of Idaho, College of Natural Resources 875 Perimeter Drive Moscow Idaho 83844 USA
| | - Melissa R. A. Pingree
- Department of Natural Resources and Society University of Idaho, College of Natural Resources 875 Perimeter Drive Moscow Idaho 83844 USA
| | - Heather Larson
- University of Florida 53 Weaver View Circle #101 Weaverville North Carolina 28787 USA
| | - Tyler J. Dreaden
- Forest Health Research and Education Center USDA‐Forest Service, Southern Research Station 1405 Veterans Drive Lexington Kentucky 40546 USA
| | - Shelby Green
- Department of Environmental Science University of Idaho, College of Natural Resources 875 Perimeter Drive Moscow Idaho 83844 USA
| | - Jason A. Smith
- School of Forest Resources and Conservation University of Florida 136 Newins‐Ziegler Hall Gainesville Florida 32611 USA
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Leyronas C, Morris CE, Choufany M, Soubeyrand S. Assessing the Aerial Interconnectivity of Distant Reservoirs of Sclerotinia sclerotiorum. Front Microbiol 2018; 9:2257. [PMID: 30337908 PMCID: PMC6178138 DOI: 10.3389/fmicb.2018.02257] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 09/05/2018] [Indexed: 12/26/2022] Open
Abstract
Many phytopathogenic fungi are disseminated as spores via the atmosphere from short to long distances. The distance of dissemination determines the extent to which plant diseases can spread and novel genotypes of pathogens can invade new territories. Predictive tools including models that forecast the arrival of spores in areas where susceptible crops are grown can help to more efficiently manage crop health. However, such models are difficult to establish for fungi with broad host ranges because sources of inoculum cannot be readily identified. Sclerotinia sclerotiorum, the pandemic agent of white mold disease, can attack >400 plant species including economically important crops. Monitoring airborne inoculum of S. sclerotiorum in several French cropping areas has shown that viable ascospores are present in the air almost all the time, even when no susceptible crops are nearby. This raises the hypothesis of a distant origin of airborne inoculum. The objective of the present study was to determine the interconnectivity of reservoirs of S. sclerotiorum from distant regions based on networks of air mass movement. Viable airborne inoculum of S. sclerotiorum was collected in four distinct regions of France and 498 strains were genotyped with 16 specific microsatellite markers and compared among the regions. Air mass movements were inferred using the HYSPLIT model and archived meteorological data from the global data assimilation system (GDAS). The results show that up to 700 km could separate collection sites that shared the same haplotypes. There was low or no genetic differentiation between strains collected from the four sites. The rate of aerial connectivity between two sites varied according to the direction considered. The results also show that the aerial connectivity between sites is a better indicator of the probability of the incoming component (PIC) of inoculum at a given site from another one than is geographic distance. We identified the links between specific sites in the trajectories of air masses and we quantified the frequencies at which the directional links occurred as a proof-of-concept for an operational method to assess the arrival of airborne inoculum in a given area from distant origins.
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Smith DJ, Ravichandar JD, Jain S, Griffin DW, Yu H, Tan Q, Thissen J, Lusby T, Nicoll P, Shedler S, Martinez P, Osorio A, Lechniak J, Choi S, Sabino K, Iverson K, Chan L, Jaing C, McGrath J. Airborne Bacteria in Earth's Lower Stratosphere Resemble Taxa Detected in the Troposphere: Results From a New NASA Aircraft Bioaerosol Collector (ABC). Front Microbiol 2018; 9:1752. [PMID: 30154759 PMCID: PMC6102410 DOI: 10.3389/fmicb.2018.01752] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 07/13/2018] [Indexed: 01/26/2023] Open
Abstract
Airborne microorganisms in the upper troposphere and lower stratosphere remain elusive due to a lack of reliable sample collection systems. To address this problem, we designed, installed, and flight-validated a novel Aircraft Bioaerosol Collector (ABC) for NASA's C-20A that can make collections for microbiological research investigations up to altitudes of 13.7 km. Herein we report results from the first set of science flights-four consecutive missions flown over the United States (US) from 30 October to 2 November, 2017. To ascertain how the concentration of airborne bacteria changed across the tropopause, we collected air during aircraft Ascent/Descent (0.3 to 11 km), as well as sustained Cruise altitudes in the lower stratosphere (~12 km). Bioaerosols were captured on DNA-treated gelatinous filters inside a cascade air sampler, then analyzed with molecular and culture-based characterization. Several viable bacterial isolates were recovered from flight altitudes, including Bacillus sp., Micrococcus sp., Arthrobacter sp., and Staphylococcus sp. from Cruise samples and Brachybacterium sp. from Ascent/Descent samples. Using 16S V4 sequencing methods for a culture-independent analysis of bacteria, the average number of total OTUs was 305 for Cruise samples and 276 for Ascent/Descent samples. Some taxa were more abundant in the flight samples than the ground samples, including OTUs from families Lachnospiraceae, Ruminococcaceae and Erysipelotrichaceae as well as the following genera: Clostridium, Mogibacterium, Corynebacterium, Bacteroides, Prevotella, Pseudomonas, and Parabacteroides. Surprisingly, our results revealed a homogeneous distribution of bacteria in the atmosphere up to 12 km. The observation could be due to atmospheric conditions producing similar background aerosols across the western US, as suggested by modeled back trajectories and satellite measurements. However, the influence of aircraft-associated bacterial contaminants could not be fully eliminated and that background signal was reported throughout our dataset. Considering the tremendous engineering challenge of collecting biomass at extreme altitudes where contamination from flight hardware remains an ever-present issue, we note the utility of using the stratosphere as a proving ground for planned life detection missions across the solar system.
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Affiliation(s)
- David J. Smith
- NASA Ames Research Center, Space Biosciences DivisionMoffett Field, CA, United States
| | | | - Sunit Jain
- Second Genome Inc.South San Francisco, CA, United States
| | - Dale W. Griffin
- United States Geological Survey, Environmental HealthSt. Petersburg, FL, United States
| | - Hongbin Yu
- Climate and Radiation Laboratory, NASA Goddard Space Flight CenterGreenbelt, MD, United States
| | - Qian Tan
- Earth Science Division, Bay Area Environmental Research InstituteMoffett Field, CA, United States
| | - James Thissen
- Lawrence Livermore National LaboratoryLivermore, CA, United States
| | - Terry Lusby
- NASA Ames Research Center, Space Biosciences DivisionMoffett Field, CA, United States
| | - Patrick Nicoll
- Space Biosciences Division, Blue Marble Space Institute of ScienceMoffett Field, CA, United States
| | - Sarah Shedler
- Biological Oceanography Department, University of South Florida, College of Marine SciencesSt. Petersburg, FL, United States
| | - Paul Martinez
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Alejandro Osorio
- Jacobs Technology Inc., NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Jason Lechniak
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Samuel Choi
- Jacobs Technology Inc., NASA Armstrong Flight Research CenterPalmdale, CA, United States
| | - Kayleen Sabino
- Second Genome Inc.South San Francisco, CA, United States
| | | | - Luisa Chan
- Second Genome Inc.South San Francisco, CA, United States
| | - Crystal Jaing
- Lawrence Livermore National LaboratoryLivermore, CA, United States
| | - John McGrath
- NASA Armstrong Flight Research CenterPalmdale, CA, United States
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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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Araújo CA, Dias LP, Ferreira PC, Mittmann J, Pupin B, Brancini G, Braga GÚ, Rangel DE. Responses of entomopathogenic fungi to the mutagen 4-nitroquinoline 1-oxide. Fungal Biol 2018; 122:621-628. [DOI: 10.1016/j.funbio.2018.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2018] [Revised: 03/09/2018] [Accepted: 03/15/2018] [Indexed: 01/11/2023]
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42
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Ballard ZS, Brown C, Ozcan A. Mobile Technologies for the Discovery, Analysis, and Engineering of the Global Microbiome. ACS NANO 2018; 12:3065-3082. [PMID: 29553706 DOI: 10.1021/acsnano.7b08660] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The microbiome has been heralded as a gauge of and contributor to both human health and environmental conditions. Current challenges in probing, engineering, and harnessing the microbiome stem from its microscopic and nanoscopic nature, diversity and complexity of interactions among its members and hosts, as well as the spatiotemporal sampling and in situ measurement limitations induced by the restricted capabilities and norm of existing technologies, leaving some of the constituents of the microbiome unknown. To facilitate significant progress in the microbiome field, deeper understanding of the constituents' individual behavior, interactions with others, and biodiversity are needed. Also crucial is the generation of multimodal data from a variety of subjects and environments over time. Mobile imaging and sensing technologies, particularly through smartphone-based platforms, can potentially meet some of these needs in field-portable, cost-effective, and massively scalable manners by circumventing the need for bulky, expensive instrumentation. In this Perspective, we outline how mobile sensing and imaging technologies could lead the way to unprecedented insight into the microbiome, potentially shedding light on various microbiome-related mysteries of today, including the composition and function of human, animal, plant, and environmental microbiomes. Finally, we conclude with a look at the future, propose a computational microbiome engineering and optimization framework, and discuss its potential impact and applications.
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DasSarma P, DasSarma S. Survival of microbes in Earth's stratosphere. Curr Opin Microbiol 2017; 43:24-30. [PMID: 29156444 DOI: 10.1016/j.mib.2017.11.002] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 11/01/2017] [Accepted: 11/03/2017] [Indexed: 12/18/2022]
Abstract
The remarkable survival of microorganisms high above the surface of the Earth is of increasing interest. At stratospheric levels, multiple stressors including ultraviolet and ionizing radiation, low temperatures, hypobaric conditions, extreme desiccation, and nutrient scarcity are all significant challenges. Our understanding of which microorganisms are capable of tolerating such stressful conditions has been addressed by stratospheric sample collection and survival assays, through launching and recovery, and exposure to simulated conditions in the laboratory. Here, we review stratospheric microbiology studies providing our current perspective on microbial life at extremely high altitudes and discuss implications for health and agriculture, climate change, planetary protection, and astrobiology.
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Affiliation(s)
- Priya DasSarma
- University of Maryland School of Medicine and Institute of Marine and Environmental Technology, 701 East Pratt Street, Baltimore, MD 21202, USA
| | - Shiladitya DasSarma
- University of Maryland School of Medicine and Institute of Marine and Environmental Technology, 701 East Pratt Street, Baltimore, MD 21202, USA.
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Innocente E, Squizzato S, Visin F, Facca C, Rampazzo G, Bertolini V, Gandolfi I, Franzetti A, Ambrosini R, Bestetti G. Influence of seasonality, air mass origin and particulate matter chemical composition on airborne bacterial community structure in the Po Valley, Italy. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:677-687. [PMID: 28363180 DOI: 10.1016/j.scitotenv.2017.03.199] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Revised: 03/02/2017] [Accepted: 03/21/2017] [Indexed: 05/26/2023]
Abstract
The integration of chemical and biological data in aerosol studies represents a new challenge in atmospheric science. In this perspective it will be possible to gain a clearer and deeper comprehension of biogeochemical cycles in the atmosphere. In this view, this study aimed to investigate the relationships occurring between bacterial populations and PM chemical composition in one of the most polluted and urbanized areas in Europe: the Po Valley (Italy). Moreover, seasonality, long- and short-range transports were also evaluated to investigate the influence on airborne bacterial communities. PM samples were collected in two cities of the Po Valley (Milan and Venice) characterized by different meteorological conditions and atmospheric pollutant sources. Samples were analysed for water-soluble inorganic ions (WSIIs) and bacterial community structure. Chemical and biological data were jointly processed by using redundancy discriminate analysis (RDA), while the influence of atmospheric circulation was evaluated by using wind ground data and back-trajectories analysis. Results showed strong seasonal shifts of bacterial community structure in both cities, while a different behaviour was observed for air mass circulation at Milan ad Venice sites: long-range transport significantly affected bacterial populations in Milan whereas local ground wind had more influence in the Venice area. Moreover, difference in taxonomic composition can be mostly addressed to the characteristics of sampling sites. This evidence could suggest that, while PM composition is influenced by long-range transport, bacterial populations are affected, besides transport, by other factors (i.e., season and sampling site location). This perspective allow to better understand and explain airborne bacterial community behaviour.
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Affiliation(s)
- Elena Innocente
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Università Ca' Foscari Venezia, Campus Scientifico, Via Torino 155, 30172 Mestre, VE, Italy.
| | - Stefania Squizzato
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Università Ca' Foscari Venezia, Campus Scientifico, Via Torino 155, 30172 Mestre, VE, Italy; Center for Air Resources Engineering and Science, Clarkson University, Box 5708, Potsdam, NY 13699-5708, USA
| | - Flavia Visin
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Università Ca' Foscari Venezia, Campus Scientifico, Via Torino 155, 30172 Mestre, VE, Italy
| | - Chiara Facca
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Università Ca' Foscari Venezia, Campus Scientifico, Via Torino 155, 30172 Mestre, VE, Italy
| | - Giancarlo Rampazzo
- Department of Environmental Sciences, Informatics and Statistics (DAIS), Università Ca' Foscari Venezia, Campus Scientifico, Via Torino 155, 30172 Mestre, VE, Italy
| | - Valentina Bertolini
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Isabella Gandolfi
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Andrea Franzetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Roberto Ambrosini
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
| | - Giuseppina Bestetti
- Department of Earth and Environmental Sciences (DISAT), University of Milano-Bicocca, Piazza della Scienza 1, 20126 Milano, Italy
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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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Costello MJ, Chaudhary C. Marine Biodiversity, Biogeography, Deep-Sea Gradients, and Conservation. Curr Biol 2017; 27:R511-R527. [DOI: 10.1016/j.cub.2017.04.060] [Citation(s) in RCA: 166] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Weerasundara L, Amarasekara RWK, Magana-Arachchi DN, Ziyath AM, Karunaratne DGGP, Goonetilleke A, Vithanage M. Microorganisms and heavy metals associated with atmospheric deposition in a congested urban environment of a developing country: Sri Lanka. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 584-585:803-812. [PMID: 28185730 DOI: 10.1016/j.scitotenv.2017.01.121] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 06/06/2023]
Abstract
The presence of bacteria and heavy metals in atmospheric deposition were investigated in Kandy, Sri Lanka, which is a typical city in the developing world with significant traffic congestion. Atmospheric deposition samples were analyzed for Al, Cr, Mn, Fe, Ni, Cu, Zn, Cd and Pb which are heavy metals common to urban environments. Al and Fe were found in high concentrations due to the presence of natural sources, but may also be re-suspended by vehicular traffic. Relatively high concentrations of toxic metals such as Cr and Pb in dissolved form were also found. High Zn loads can be attributed to vehicular emissions and the wide use of Zn coated roofing materials. The metal loads in wet deposition showed higher concentrations compared to dry deposition. The metal concentrations among the different sampling sites significantly differ from each other depending on the traffic conditions. Industrial activities are not significant in Kandy City. Consequently, the traffic exerts high influence on heavy metal loadings. As part of the bacterial investigations, nine species of culturable bacteria, namely; Sphingomonas sp., Pseudomonas aeruginosa, Pseudomonas monteilii, Klebsiella pneumonia, Ochrobactrum intermedium, Leclercia adecarboxylata, Exiguobacterium sp., Bacillus pumilus and Kocuria kristinae, which are opportunistic pathogens, were identified. This is the first time Pseudomonas monteilii and Ochrobactrum intermedium has been reported from a country in Asia. The culturable fraction constituted ~0.01 to 10%. Pigmented bacteria and endospore forming bacteria were copious in the atmospheric depositions due to their capability to withstand harsh environmental conditions. The presence of pathogenic bacteria and heavy metals creates potential human and ecosystem health risk.
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Affiliation(s)
- Lakshika Weerasundara
- Environmental Chemodynamics Project, National Institute of Fundamental Studies, Kandy, Sri Lanka
| | - R W K Amarasekara
- Cell Biology, National Institute of Fundamental Studies, Kandy, Sri Lanka
| | | | - Abdul M Ziyath
- Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia
| | - D G G P Karunaratne
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Peradeniya, Sri Lanka
| | - Ashantha Goonetilleke
- Science and Engineering Faculty, Queensland University of Technology (QUT), Brisbane, Australia
| | - Meththika Vithanage
- Environmental Chemodynamics Project, National Institute of Fundamental Studies, Kandy, Sri Lanka.
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Sherwood AR, Dittbern MN, Johnston ET, Conklin KY. A metabarcoding comparison of windward and leeward airborne algal diversity across the Ko'olau mountain range on the island of O'ahu, Hawai'i 1. JOURNAL OF PHYCOLOGY 2017; 53:437-445. [PMID: 27988936 DOI: 10.1111/jpy.12502] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 11/07/2016] [Indexed: 06/06/2023]
Abstract
Airborne algae from sites on the windward (n = 3) and leeward (n = 3) sides of the Ko'olau Mountain range of O'ahu, Hawai'i, were sampled for a 16 d period during January and February 2015 using passive collection devices and were characterized using Illumina MiSeq sequencing of the universal plastid amplicon marker. Amplicons were assigned to 3,023 operational taxonomic units (OTUs), which included 1,189 cyanobacteria, 1,009 heterotrophic bacteria, and 304 Eukaryota (of which 284 were algae and land plants). Analyses demonstrated substantially more OTUs at windward than leeward O'ahu sites during the sampling period. Removal of nonalgal OTUs revealed a greater number of algal reads recovered from windward (839,853) than leeward sites (355,387), with the majority of these being cyanobacteria. The 1,234 total algal OTUs included cyanobacteria, diatoms, cryptophytes, brown algae, chlorophyte green algae, and charophyte green algae. A total of 208 algal OTUs were identified from leeward side samplers (including OTUs in common among samplers) and 1,995 algal OTUs were identified from windward samplers. Barcoding analyses of the most abundant algal OTUs indicated that very few were shared between the windward and leeward sides of the Ko'olau Mountains, highlighting the localized scale at which these airborne algae communities differ. Back trajectories of air masses arriving on O'ahu during the sampling period were calculated using the NOAA HY-SPLIT model and suggested that the sampling period was composed of three large-scale meteorological events, indicating a diversity of potential sources of airborne algae outside of the Hawaiian Islands.
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Affiliation(s)
- Alison R Sherwood
- Department of Botany, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i, 96822, USA
| | - Monica N Dittbern
- Department of Botany, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i, 96822, USA
| | - Emily T Johnston
- Department of Botany, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i, 96822, USA
| | - Kimberly Y Conklin
- Department of Botany, University of Hawai'i, 3190 Maile Way, Honolulu, Hawai'i, 96822, USA
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González-Delgado A, Shukla MK, DuBois DW, Flores-Márgez JP, Hernández Escamilla JA, Olivas E. Microbial and size characterization of airborne particulate matter collected on sticky tapes along US-Mexico border. J Environ Sci (China) 2017; 53:207-216. [PMID: 28372745 DOI: 10.1016/j.jes.2015.10.037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Revised: 10/10/2015] [Accepted: 10/26/2015] [Indexed: 06/07/2023]
Abstract
Particulate matter (PM) emissions from various sources can affect significantly human health and environmental quality especially in the Chihuahuan Desert region along US-Mexico border. The objective of this study was to use the low-cost sticky tape method to collect airborne PM for size characterization and identification of fungal spores. Sticky tape samplers were placed at 1.0 and 2.0m above the ground surface at experimental sites in Ciudad Juárez, Mexico and at 0.6, 1.2 and 1.8m at New Mexico sites, USA. Soil samples were collected in both countries to determine fungal diversity, texture and moisture content. Dust particles collected from all of the experimental sites had a dominant texture of clay (<0.002mm). The dominant textures identified from soil samples collected from the US and Mexican sites were loam and sandy clay loam, respectively. Alternaria, Penicillium and Fusarium were frequently found funguses in the US sites while Alternaria and Aspergillus were commonly observed in the Mexican sites. The sticky tapes also showed a similar diversity of fungal microorganisms present in the airborne PM at both Mexico and US sites. Alternaria, Penicillium and Aspergillus were the three groups of airborne fungal microorganisms consistently present in the US and Mexican sites. The low-cost sticky tape method has the potential to be used for characterizing different airborne microorganisms and dust particles.
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Affiliation(s)
- Amir González-Delgado
- Plant and Environmental Sciences Department, New Mexico State University, MSC 3Q Skeen Hall Room N 127, P.O. Box 30003, Las Cruces, NM 88003-8003, USA.
| | - Manoj K Shukla
- Plant and Environmental Sciences Department, New Mexico State University, MSC 3Q Skeen Hall Room N 127, P.O. Box 30003, Las Cruces, NM 88003-8003, USA
| | - David W DuBois
- Plant and Environmental Sciences Department, New Mexico State University, MSC 3Q Skeen Hall Room N 127, P.O. Box 30003, Las Cruces, NM 88003-8003, USA
| | - Juan P Flores-Márgez
- Universidad Autónoma de Ciudad Juárez, UACJ, Av. Plutarco Elías Calles 1020, Fovisste Chamizal, Ciudad Juárez, Chihuahua C.P. 32310, Mexico
| | - Joel A Hernández Escamilla
- Universidad Autónoma de Ciudad Juárez, UACJ, Av. Plutarco Elías Calles 1020, Fovisste Chamizal, Ciudad Juárez, Chihuahua C.P. 32310, Mexico
| | - Evangelina Olivas
- Universidad Autónoma de Ciudad Juárez, UACJ, Av. Plutarco Elías Calles 1020, Fovisste Chamizal, Ciudad Juárez, Chihuahua C.P. 32310, Mexico
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50
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Grinn-Gofroń A, Sadyś M, Kaczmarek J, Bednarz A, Pawłowska S, Jedryczka M. Back-trajectory modelling and DNA-based species-specific detection methods allow tracking of fungal spore transport in air masses. THE SCIENCE OF THE TOTAL ENVIRONMENT 2016; 571:658-669. [PMID: 27405520 DOI: 10.1016/j.scitotenv.2016.07.034] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/01/2016] [Accepted: 07/05/2016] [Indexed: 06/06/2023]
Abstract
Recent advances in molecular detection of living organisms facilitate the introduction of novel methods to studies of the transport of fungal spores over large distances. Monitoring the migration of airborne fungi using microscope based spore identification is limited when different species produce very similar spores. In our study, DNA-based monitoring with the use of species-specific probes allowed us to track the aerial movements of two important fungal pathogens of oilseed rape (Brassica napus L.), i.e., Leptosphaeria maculans and Leptosphaeria biglobosa, which have identical spore shape and size. The fungi were identified using dual-labelled fluorescent probes that were targeted to a β-tubulin gene fragment of either Leptosphaeria species. Spore identification by Real-Time PCR techniques capable of detecting minute amounts of DNA of selected fungal species was combined with back-trajectory analysis, allowing the tracking of past movements of air masses using the Hybrid Single Particle Lagrangian Integrated Trajectory model. Over a study period spanning the previous decade (2006-2015) we investigated two specific events relating to the long distance transport of Leptosphaeria spp. spores to Szczecin in North-West Poland. Based on the above mentioned methods and the results obtained with the additional spore sampler located in nearby Szczecin, and operating at the ground level in an oilseed rape field, we have demonstrated that on both occasions the L. biglobosa spores originated from the Jutland Peninsula. This is the first successful attempt to combine analysis of back-trajectories of air masses with DNA-based identification of economically important pathogens of oilseed rape in Europe. In our studies, the timing of L. biglobosa ascospore dispersal in the air was unlikely to result in the infection of winter oilseed rape grown as a crop plant. However, the fungus could infect other host plants, such as vegetable brassicas, cruciferous weeds, spring rapeseed and winter rapeseed growing as a volunteer plant.
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Affiliation(s)
- Agnieszka Grinn-Gofroń
- Department of Plant Taxonomy and Phytogeography, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
| | - Magdalena Sadyś
- Rothamsted Research, West Common, Harpenden, Hertfordshire AL5 2JQ, UK
| | - Joanna Kaczmarek
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland
| | - Aleksandra Bednarz
- Department of Plant Taxonomy and Phytogeography, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
| | - Sylwia Pawłowska
- Department of Plant Taxonomy and Phytogeography, University of Szczecin, Wąska 13, 71-415 Szczecin, Poland
| | - Malgorzata Jedryczka
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, 60-479 Poznan, Poland.
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