High Diversity of Fungi in Air Particulate Matter

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High Diversity of Fungi in Air Particulate Matter

High Diversity of Fungi in Air Particulate Matter

Janine Fröhlich-Nowoisky, Viviane R. Després, Ulrich Pöschl

01 Apr 2009-pp 10066

TL;DR: By DNA analysis, pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter are found, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction.

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Abstract: Fungal spores can account for large proportions of air particulate matter, and they may potentially influence the hydrological cycle and climate as nuclei for water droplets and ice crystals in clouds, fog, and precipitation. Moreover, some fungi are major pathogens and allergens. The diversity of airborne fungi is, however, not well-known. By DNA analysis we found pronounced differences in the relative abundance and seasonal cycles of various groups of fungi in coarse and fine particulate matter, with more plant pathogens in the coarse fraction and more human pathogens and allergens in the respirable fine particle fraction (<3 μm). Moreover, the ratio of Basidiomycota to Ascomycota was found to be much higher than previously assumed, which might also apply to the biosphere.

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Journal Article•DOI•

Emerging fungal threats to animal, plant and ecosystem health.

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Matthew C. Fisher¹, Daniel A. Henk¹, Cheryl J. Briggs², John S. Brownstein³, Lawrence C. Madoff⁴, Sarah L. McCraw⁵, Sarah J. Gurr⁵ - Show less +3 more•Institutions (5)

Imperial College London¹, University of California, Santa Barbara², Boston Children's Hospital³, University of Massachusetts Medical School⁴, University of Oxford⁵

12 Apr 2012-Nature

TL;DR: It is argued that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.

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Abstract: The past two decades have seen an increasing number of virulent infectious diseases in natural populations and managed landscapes. In both animals and plants, an unprecedented number of fungal and fungal-like diseases have recently caused some of the most severe die-offs and extinctions ever witnessed in wild species, and are jeopardizing food security. Human activity is intensifying fungal disease dispersal by modifying natural environments and thus creating new opportunities for evolution. We argue that nascent fungal infections will cause increasing attrition of biodiversity, with wider implications for human and ecosystem health, unless steps are taken to tighten biosecurity worldwide.

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2,408 citations

Journal Article•DOI•

Primary biological aerosol particles in the atmosphere: a review

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Viviane R. Després¹, J. Alex Huffman², Susannah M. Burrows³, Corinna Hoose⁴, Aleksandr S. Safatov, G. A. Buryak, Janine Fröhlich-Nowoisky³, W. Elbert³, Meinrat O. Andreae³, Ulrich Pöschl³, Ruprecht Jaenicke¹ - Show less +7 more•Institutions (4)

University of Mainz¹, University of Denver², Max Planck Society³, Karlsruhe Institute of Technology⁴

22 Feb 2012-Tellus B

TL;DR: A review of the current knowledge on major categories of primary biological aerosol particles (PBAP): bacteria and archaea, fungal spores and fragments, pollen, viruses, algae and cyanobacteria, biological crusts and lichens and others like plant or animal fragments and detritus is presented in this article.

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Abstract: Atmospheric aerosol particles of biological origin are a very diverse group of biological materials and structures, including microorganisms, dispersal units, fragments and excretions of biological organisms. In recent years, the impact of biological aerosol particles on atmospheric processes has been studied with increasing intensity, and a wealth of new information and insights has been gained. This review outlines the current knowledge on major categories of primary biological aerosol particles (PBAP): bacteria and archaea, fungal spores and fragments, pollen, viruses, algae and cyanobacteria, biological crusts and lichens and others like plant or animal fragments and detritus. We give an overview of sampling methods and physical, chemical and biological techniques for PBAP analysis (cultivation, microscopy, DNA/RNA analysis, chemical tracers, optical and mass spectrometry, etc.). Moreover, we address and summarise the current understanding and open questions concerning the influence of PBAP on the atmosphere and climate, i.e. their optical properties and their ability to act as ice nuclei (IN) or cloud condensation nuclei (CCN). We suggest that the following research activities should be pursued in future studies of atmospheric biological aerosol particles: (1) develop efficient and reliable analytical techniques for the identification and quantification of PBAP; (2) apply advanced and standardised techniques to determine the abundance and diversity of PBAP and their seasonal variation at regional and global scales (atmospheric biogeography); (3) determine the emission rates, optical properties, IN and CCN activity of PBAP in field measurements and laboratory experiments; (4) use field and laboratory data to constrain numerical models of atmospheric transport, transformation and climate effects of PBAP. Keywords: primary biological atmospheric aerosol; climate; cloud condensation nuclei; biology; atmospheric ice nuclei (Published: 22 February 2012) Citation: Tellus B 2012, 64 , 15598, DOI: 10.3402/tellusb.v64i0.15598

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1,034 citations

Cites background or methods from "High Diversity of Fungi in Air Part..."

...Depending on biological species, age and ambient conditions, the diameter of fungal spores can vary ( 1 50 mm); most frequently it is in the range of 2 10 mm (Elbert et al., 2007; Wang et al., 2008; Fröhlich-Nowoisky et al., 2009; Huffman et al., 2010)....
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...soil DNA extraction kit (Després et al., 2007; Fröhlich-Nowoisky et al., 2009)); Fast Prep 120 agitator together with Spin column of MolBio Laboratories (DeSantis et al....
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...Amplification of the internal transcribed spacer (ITS) regions between the 18S and 28S ribosomal ribonucleic acid (rRNA) genes provides good target regions to identify fungi to genus and often to species level (O’Brien et al., 2005; Fröhlich-Nowoisky et al., 2009)....
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...To our knowledge, from the few studies that have reported DNA analyses of fungi in atmospheric aerosol samples, some had neither found the expected high abundance of, e.g. Cladosporium sp. nor a high species richness (in particular Basidiomycota), which may well be due to limitations of the applied PCR primers (e.g. Després et al., 2007; Fierer et al., 2008; Bowers et al., 2009), although over 1500 fungal DNA sequences from 5 urban air samples were measured by Fierer et al. (2008) and several dozens of filter samples of urban, rural and highalpine air were analysed by Després et al. (2007)....
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...…the generally accepted levels of discrimination are 97 99% similarity for species and 95 97% for genera; for fungi, clustering sequences with 97% or greater sequence similarity are accepted (O’Brien et al., 2005; Bowers et al., 2009; Fröhlich-Nowoisky et al., 2009; Georgakopoulos et al., 2009)....
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Journal Article•DOI•

Ice nucleation by particles immersed in supercooled cloud droplets

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Benjamin J. Murray¹, Daniel O'Sullivan¹, J. D. Atkinson¹, Michael E. Webb¹•Institutions (1)

University of Leeds¹

10 Sep 2012-Chemical Society Reviews

TL;DR: Aerosol species which have been identified in the past as potentially important ice nuclei are introduced and their ice-nucleating ability when immersed in a supercooled droplet is addressed and the importance of ice nucleation by different aerosol types is estimated.

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Abstract: The formation of ice particles in the Earth's atmosphere strongly affects the properties of clouds and their impact on climate. Despite the importance of ice formation in determining the properties of clouds, the Intergovernmental Panel on Climate Change (IPCC, 2007) was unable to assess the impact of atmospheric ice formation in their most recent report because our basic knowledge is insufficient. Part of the problem is the paucity of quantitative information on the ability of various atmospheric aerosol species to initiate ice formation. Here we review and assess the existing quantitative knowledge of ice nucleation by particles immersed within supercooled water droplets. We introduce aerosol species which have been identified in the past as potentially important ice nuclei and address their ice-nucleating ability when immersed in a supercooled droplet. We focus on mineral dusts, biological species (pollen, bacteria, fungal spores and plankton), carbonaceous combustion products and volcanic ash. In order to make a quantitative comparison we first introduce several ways of describing ice nucleation and then summarise the existing information according to the time-independent (singular) approximation. Using this approximation in combination with typical atmospheric loadings, we estimate the importance of ice nucleation by different aerosol types. According to these estimates we find that ice nucleation below about −15 °C is dominated by soot and mineral dusts. Above this temperature the only materials known to nucleate ice are biological, with quantitative data for other materials absent from the literature. We conclude with a summary of the challenges our community faces.

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943 citations

Journal Article•DOI•

ITS as an environmental DNA barcode for fungi: an in silico approach reveals potential PCR biases

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Eva Bellemain¹, Tor Carlsen², Christian Brochmann¹, Eric Coissac³, Pierre Taberlet³, Håvard Kauserud² - Show less +2 more•Institutions (3)

American Museum of Natural History¹, University of Oslo², Centre national de la recherche scientifique³

09 Jul 2010-BMC Microbiology

TL;DR: It is found that ascomycetes will more easily amplify than basidiomycete ITS sequences using these regions as targets, and this bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi.

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Abstract: Background: During the last 15 years the internal transcribed spacer (ITS) of nuclear DNA has been used as a target for analyzing fungal diversity in environmental samples, and has recently been selected as the standard marker for fungal DNA barcoding. In this study we explored the potential amplification biases that various commonly utilized ITS primers might introduce during amplification of different parts of the ITS region in samples containing mixed templates ('environmental barcoding'). We performed in silico PCR analyses with commonly used primer combinations using various ITS datasets obtained from public databases as templates. Results: Some of the ITS primers, such as ITS1-F, were hampered with a high proportion of mismatches relative to the target sequences, and most of them appeared to introduce taxonomic biases during PCR. Some primers, e.g. ITS1-F, ITS1 and ITS5, were biased towards amplification of basidiomycetes, whereas others, e.g. ITS2, ITS3 and ITS4, were biased towards ascomycetes. The assumed basidiomycete-specific primer ITS4-B only amplified a minor proportion of basidiomycete ITS sequences, even under relaxed PCR conditions. Due to systematic length differences in the ITS2 region as well as the entire ITS, we found that ascomycetes will more easily amplify than basidiomycetes using these regions as targets. This bias can be avoided by using primers amplifying ITS1 only, but this would imply preferential amplification of 'non-dikarya' fungi. Conclusions: We conclude that ITS primers have to be selected carefully, especially when used for high-throughput sequencing of environmental samples. We suggest that different primer combinations or different parts of the ITS region should be analyzed in parallel, or that alternative ITS primers should be searched for.

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832 citations

Journal Article•DOI•

Bioaerosols in the Earth system: Climate, health, and ecosystem interactions

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Janine Fröhlich-Nowoisky¹, Christopher J. Kampf², Christopher J. Kampf¹, Bettina Weber¹, J. Alex Huffman³, Christopher Pöhlker¹, Meinrat O. Andreae¹, Naama Lang-Yona¹, Susannah M. Burrows⁴, Sachin S. Gunthe⁵, W. Elbert¹, Hang Su¹, Peter Hoor², Eckhard Thines², Thorsten Hoffmann², Viviane R. Després², Ulrich Pöschl¹ - Show less +13 more•Institutions (5)

Max Planck Society¹, University of Mainz², University of Denver³, Pacific Northwest National Laboratory⁴, Indian Institute of Technology Madras⁵

15 Dec 2016-Atmospheric Research

TL;DR: A review of the state of bioaerosol research, highlights recent advances, and outlines future perspectives in terms of identification, characterization, transport and transformation processes, as well as their interactions with climate, health, and ecosystems, focusing on the role bio-aerosols play in the Earth system.

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588 citations

Cites background from "High Diversity of Fungi in Air Part..."

...…atmospheric abundance andfluxes of emission and transport of different types of bioaerosol particles are poorly constrained (Bowers et al., 2012, 2010, 2009; Burrows et al., 2009a, 2009b; Fröhlich-Nowoisky et al., 2012, 2009; Heald and Spracklen, 2009; Jaenicke, 2005; Sesartic and Dallafior, 2011)....
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...…sequences available in online databases like the National Center for Biotechnology Information (NCBI; Boreson et al., 2004; Després et al., 2007; Fahlgren et al., 2011; Fierer et al., 2008; Fröhlich-Nowoisky et al., 2009, 2012, 2014; Huffman et al., 2013; Maron et al., 2005; Urbano et al., 2011)....
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...…Bowers et al., 2013; Brown et al., 1964; DeLeon-Rodriguez et al., 2013; Delort et al., 2010; Després et al., 2012; Favero-Longo et al., 2014; Fröhlich-Nowoisky et al., 2009; Marshall and Chalmers, 1997; Sesartic and Dallafior, 2011; Smets et al., 2016), but their interactions with different…...
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...…public health (e.g., Adhikari et al., 2006; Brodie et al., 2007; Brown and Hovmøller, 2002; Després et al., 2012; Douwes, 2003; Fisher et al., 2012; Fröhlich-Nowoisky et al., 2009; Gorny et al., 2002; Kellogg andGriffin, 2006), and the potential impacts of airborne transmission of genetically…...
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Instability and decay of the primary structure of DNA

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Tomas Lindahl¹•Institutions (1)

University of Cambridge¹

22 Apr 1993-Nature

TL;DR: The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.

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Abstract: Although DNA is the carrier of genetic information, it has limited chemical stability. Hydrolysis, oxidation and nonenzymatic methylation of DNA occur at significant rates in vivo, and are counteracted by specific DNA repair processes. The spontaneous decay of DNA is likely to be a major factor in mutagenesis, carcinogenesis and ageing, and also sets limits for the recovery of DNA fragments from fossils.

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Abstract: On applique la methode d'Efron (1981, 1982) a la construction d'intervalles de confiance bases sur des distributions du bootstrap

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3,858 citations

"High Diversity of Fungi in Air Part..." refers methods in this paper

...As shown in Table 1, estimates of the actual species richness (S*) based on the Chao-1 estimator approach (21, 24) are an approximate factor of 3 higher than the measured species richness values (S), suggesting that the total number of fungal species in the investigated air samples was 1,000....
[...]

Journal Article•DOI•

Emerging fungal threats to animal, plant and ecosystem health.

[...]

Matthew C. Fisher¹, Daniel A. Henk¹, Cheryl J. Briggs², John S. Brownstein³, Lawrence C. Madoff⁴, Sarah L. McCraw⁵, Sarah J. Gurr⁵ - Show less +3 more•Institutions (5)

Imperial College London¹, University of California, Santa Barbara², Boston Children's Hospital³, University of Massachusetts Medical School⁴, University of Oxford⁵

12 Apr 2012-Nature

...read moreread less

2,408 citations

Journal Article•DOI•

Determination of microbial diversity in environmental samples: pitfalls of PCR‐based rRNA analysis

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Friedrich von Wintzingerode¹, Ulf B. Göbel¹, Erko Stackebrandt²•Institutions (2)

Charité¹, Deutsche Sammlung von Mikroorganismen und Zellkulturen²

01 Nov 1997-Fems Microbiology Reviews

TL;DR: Specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis are covered.

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Abstract: After nearly 10 years of PCR-based analysis of prokaryotic small-subunit ribosomal RNAs for ecological studies it seems necessary to summarize reported pitfalls of this approach which will most likely lead to an erroneous description on the microbial diversity of a given habitat. The following article will cover specific aspects of sample collection, cell lysis, nucleic acid extraction, PCR amplification, separation of amplified DNA, application of nucleic probes and data analysis.

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2,171 citations

"High Diversity of Fungi in Air Part..." refers background in this paper

...PCR errors can also introduce some sequence variability (56)....
[...]

Journal Article•DOI•

A higher-level phylogenetic classification of the Fungi

[...]

David S. Hibbett¹, Manfred Binder¹, Joseph F. Bischoff², Meredith Blackwell³, Paul F. Cannon⁴, Ove E. Eriksson⁵, Sabine M. Huhndorf⁶, Timothy Y. James⁷, Paul M. Kirk⁴, Robert Lücking⁶, H. Thorsten Lumbsch⁶, François Lutzoni⁷, P. Brandon Matheny¹, David J. McLaughlin⁸, Martha J. Powell⁹, Scott A. Redhead, Conrad L. Schoch¹⁰, Joseph W. Spatafora¹⁰, Joost A. Stalpers¹¹, Rytas Vilgalys⁷, M. Catherine Aime¹², André Aptroot, Robert Bauer¹³, Dominik Begerow¹⁴, Gerald L. Benny¹⁵, Lisa A. Castlebury¹², Pedro W. Crous¹¹, Yu-Cheng Dai, Walter Gams¹¹, David M. Geiser¹⁶, Gareth W. Griffith¹⁷, Cécile Gueidan⁷, David L. Hawksworth¹⁸, Geir Hestmark¹⁹, Kentaro Hosaka⁶, Richard A. Humber¹², Kevin D. Hyde²⁰, Joseph E. Ironside¹⁷, Urmas Kõljalg²¹, Cletus P. Kurtzman¹², Karl-Henrik Larsson²², Robert W. Lichtwardt²³, Joyce E. Longcore²⁴, Jolanta Miadlikowska⁷, Andrew N. Miller²⁵, Jean-Marc Moncalvo²⁶, Sharon E. Mozley-Standridge²⁷, Franz Oberwinkler¹³, Erast Parmasto²⁸, Valérie Reeb⁷, Jack D. Rogers²⁹, Claude Roux, Leif Ryvarden¹⁹, José Paulo Sampaio³⁰, Arthur Schüssler³¹, Junta Sugiyama, R. Greg Thorn³², Leif Tibell³³, Wendy A. Untereiner³⁴, Christopher Walker³⁵, Zheng Wang¹, Alex Weir³⁶, Michael Weiss¹³, Merlin M. White³⁷, Katarina Winka⁵, Yi-Jian Yao, Ning Zhang³⁸ - Show less +63 more•Institutions (38)

Clark University¹, National Institutes of Health², Louisiana State University³, CABI⁴, Umeå University⁵, Field Museum of Natural History⁶, Duke University⁷, University of Minnesota⁸, University of Alabama⁹, Oregon State University¹⁰, Centraalbureau voor Schimmelcultures¹¹, United States Department of Agriculture¹², University of Tübingen¹³, Max Planck Society¹⁴, University of Florida¹⁵, Pennsylvania State University¹⁶, Aberystwyth University¹⁷, Complutense University of Madrid¹⁸, University of Oslo¹⁹, University of Hong Kong²⁰, University of Tartu²¹, University of Gothenburg²², University of Kansas²³, University of Maine²⁴, University of Illinois at Urbana–Champaign²⁵, Royal Ontario Museum²⁶, Georgia State University²⁷, Estonian University of Life Sciences²⁸, Washington State University²⁹, Nova Southeastern University³⁰, Ludwig Maximilian University of Munich³¹, University of Western Ontario³², Uppsala University³³, Brandon University³⁴, Royal Botanic Garden Edinburgh³⁵, State University of New York at Purchase³⁶, Boise State University³⁷, Cornell University³⁸

01 May 2007-Fungal Biology

TL;DR: A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community.

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2,096 citations

"High Diversity of Fungi in Air Part..." refers background in this paper

...On the other hand, 70% of the detected species were found only in 1 sample (SI Text, and Table S3)....
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...More information about the taxonomic classes and families of the detected fungi is available online (SI Text) (26)....
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...The results are summarized in Table S5, Table S6, and Table S7 and additional information is given in SI Text....
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...More information about the differences between coarse and fine particle samples and about fungal spore size is available online (SI Text and Table S3, Table S4, Table S5, Table S6, Table S7, and Table S8)....
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