Introducing DNA-based methods to compare fungal microbiota and concentrations in indoor, outdoor, and personal air

An, Choa; Woo, Cheolwoon; Yamamoto, Naomichi

doi:10.1007/s10453-017-9490-6

Cited by 18 publications

(24 citation statements)

References 81 publications

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“…DNA libraries were constructed according to a protocol reported elsewhere [ 32 ]. Briefly, the fungal internal transcribed spacer 1 (ITS1) region was amplified with universal fungal primers ITS1F and ITS2 [ 33 , 34 ] along with adapter sequences for Illumina MiSeq.…”

Section: Methodsmentioning

confidence: 99%

“…The full sequence processing protocol is available elsewhere [ 32 ]. Briefly, the paired-end reads were joined with a minimum allowed overlap of 10 bp in QIIME version 1.8.0 [ 35 ].…”

Section: Methodsmentioning

confidence: 99%

“…Quantitative PCR (qPCR) was performed to quantify gene copy numbers (GCN) of fungal ITS1 using a method reported elsewhere [ 32 ]. The same primers were used for sequencing (ITS1F and ITS2).…”

Section: Methodsmentioning

confidence: 99%

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Taxonomic diversity of fungi deposited from the atmosphere

Woo

et al. 2018

The ISME Journal

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Fungi release spores into the global atmosphere. The emitted spores are deposited to the surface of the Earth by sedimentation (dry deposition) and precipitation (wet deposition), and therefore contribute to the global cycling of substances. However, knowledge is scarce regarding the diversities of fungi deposited from the atmosphere. Here, an automatic dry and wet deposition sampler and high-throughput sequencing plus quantitative PCR were used to observe taxonomic diversities and flux densities of atmospheric fungal deposition. Taxon-specific fungal deposition velocities and aerodynamic diameters (da) were determined using a collocated cascade impactor for volumetric, particle-size-resolved air sampling. Large multicellular spore-producing dothideomycetes (da ≥ 10.0 μm) were predominant in dry deposition, with a mean velocity of 0.80 cm s–1 for all fungal taxa combined. Higher taxonomic richness was observed in fungal assemblages in wet deposition than in dry deposition, suggesting the presence of fungal taxa that are deposited only in wet form. In wet deposition, agaricomycetes, including mushroom-forming fungi, and sordariomycetes, including plant pathogenic species, were enriched, indicating that such fungal spores serve as nuclei in clouds, and/or are discharged preferentially during precipitation. Moreover, this study confirmed that fungal assemblage memberships and structures were significantly different between dry and wet deposition (P-test, p < 0.001). Overall, these findings suggest taxon-specific involvement of fungi in precipitation, and provide important insights into potential links between environmental changes that can disturb regional microbial communities (e.g., deforestation) and changes in precipitation patterns that might be mediated by changes in microbial communities in the atmosphere.

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Section: Methodsmentioning

confidence: 99%

“…The full sequence processing protocol is available elsewhere [ 32 ]. Briefly, the paired-end reads were joined with a minimum allowed overlap of 10 bp in QIIME version 1.8.0 [ 35 ].…”

Section: Methodsmentioning

confidence: 99%

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Taxonomic diversity of fungi deposited from the atmosphere

Woo

et al. 2018

The ISME Journal

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“…Taxon-specific plant quantity was estimated by multiplying the DNA sequencing-derived relative abundance of each taxon by the total plant quantity by the universal plant-specific qPCR, as previously described (Yamamoto et al, 2014;Dannemiller et al, 2014;An et al, 2018). The calculated genus-level deposition flux densities were confirmed to be biologically reproducible with a cumulative coefficient of variation of 91% on an arithmetic scale ( Fig.…”

Section: Calculationsmentioning

confidence: 99%

Plant assemblages in atmospheric deposition

Dong¹,

Woo²,

Yamamoto³

2019

Preprint

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<p><strong>Abstract.</strong> Plants disperse spores, pollen, and fragments into the atmosphere. The emitted plant particles return to the pedosphere by sedimentation (dry deposition) and/or by precipitation (wet deposition) and constitute part of the global cycle of substances. However, little is known regarding the taxonomic diversities and flux densities of plant particles deposited from the atmosphere. Here, plant assemblages were examined in atmospheric deposits collected in Seoul in South Korea. A custom-made automatic sampler was used to collect dry and wet deposition samples for which plant assemblages and quantities were determined using high-throughput sequencing and quantitative PCR with universal plant-specific primers targeting the internal transcribed spacer 2 (ITS2) region. Dry deposition was dominant for atmospheric deposition of plant particles (87&#8201;%). The remaining 13&#8201;% was deposited by precipitation, i.e., wet deposition, via rainout (in-cloud scavenging) and/or washout (below-cloud scavenging). Plant assemblage structures did not differ significantly between dry and wet deposition, indicating that washout, which is likely taxon-independent, predominated rainout, which is likely taxon-dependent, for wet deposition of atmospheric plant particles. A small number of plant genera were detected only in wet deposition, indicating that they might be specifically involved in precipitation through acting as nucleation sites in the atmosphere. Future interannual monitoring will control for the seasonality of atmospheric plant assemblages observed at our sampling site. Future global monitoring is also proposed to investigate geographical differences and investigate whether endemic species are involved in plant-mediated bioprecipitation in regional ecological systems.</p>

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“…In total, 1 261 572 reads from 43 libraries were mapped onto 97 % OTUs (Table S1). Taxonomic assignment was performed using the SINTAX algorithm with a cutoff value of 0.5 (Edgar, 2018) against the ITS2 database (Sickel et al, 2015;Ankenbrand et al, 2015). P tests were performed using mothur v.1.39.5 (Schloss et al, 2009) to compare taxonomic structures.…”

Section: Dna Sequence Processing and Analysesmentioning

confidence: 99%

Plant assemblages in atmospheric deposition

Woo

Yamamoto

2019

Atmos. Chem. Phys.

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Abstract. Plants disperse spores, pollen, and fragments into the atmosphere. The emitted plant particles return to the pedosphere by sedimentation (dry deposition) and/or by precipitation (wet deposition) and constitute part of the global cycle of substances. However, little is known regarding the taxonomic diversities and flux densities of plant particles deposited from the atmosphere. Here, plant assemblages were examined in atmospheric deposits collected in Seoul in South Korea. A custom-made automatic sampler was used to collect dry and wet deposition samples for which plant assemblages and quantities were determined using high-throughput sequencing and quantitative polymerase chain reaction (PCR) with universal plant-specific primers targeting the internal transcribed spacer 2 (ITS2) region. Dry deposition was dominant for atmospheric deposition of plant particles (87 %). The remaining 13 % was deposited by precipitation, i.e., wet deposition, via rainout (in-cloud scavenging) and/or washout (below-cloud scavenging). Plant assemblage structures did not differ significantly between dry and wet deposition, indicating a possibility that washout, which is possibly taxon-independent, predominated rainout, which is possibly taxon-dependent, for wet deposition of atmospheric plant particles. A small number of plant genera were detected only in wet deposition, indicating that they might be specifically involved in precipitation through acting as nucleation sites in the atmosphere. Future interannual monitoring will control for the seasonality of atmospheric plant assemblages observed at our sampling site. Future global monitoring is also proposed to investigate geographical differences and investigate whether endemic species are involved in plant-mediated bioprecipitation in regional ecological systems.

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Introducing DNA-based methods to compare fungal microbiota and concentrations in indoor, outdoor, and personal air

Cited by 18 publications

References 81 publications

Taxonomic diversity of fungi deposited from the atmosphere

Taxonomic diversity of fungi deposited from the atmosphere

Plant assemblages in atmospheric deposition

Plant assemblages in atmospheric deposition

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