Towards a unified paradigm for sequence‐based identification of fungi

Kõljalg, Urmas; Nilsson, R. Henrik; Abarenkov, Kessy; Tedersoo, Leho; Taylor, Andy F. S.; Bahram, Mohammad; Bates, Scott T.; Bruns, Thomas D.; Bengtsson‐Palme, Johan; Callaghan, Tony M.; Douglas, Brian; Drenkhan, Tiia; Eberhardt, Ursula; Dueñas, Margarita; Grebenc, Tine; Griffith, Gareth; Hartmann, Martin; Kirk, Paul M.; Kohout, Petr; Larsson, Ellen; Lindahl, Björn D.; Lücking, Robert; Martín, María P.; Matheny, P. Brandon; Nguyen, Nhu; Niskanen, Tuula; Oja, Jane; Peay, Kabir G.; Peintner, Ursula; Peterson, Marko; Põldmaa, Kadri; Saag, Lauri; Saar, Irja; Schüßler, Arthur; Scott, James A.; Senés, Carolina; Smith, Matthew E.; Suija, Ave; Taylor, D. Lee; Tellería, M. Teresa; Weiß, Michael; Larsson, Karl‐Henrik

doi:10.1111/mec.12481

Cited by 3,007 publications

(1,932 citation statements)

References 29 publications

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“…Lineages are designated by a slash (/) followed by the dominant genus, genera, or higher level taxon. Blast searching was performed against UNITE database (Koljalg et al., 2013). Relative abundances of guilds, lineages, and exploration types were calculated for each plot.…”

Section: Methodsmentioning

confidence: 99%

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Vowles

Lindwall

Ekblad

et al. 2017

Ecology and Evolution

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Mycorrhizal associations are widespread in high‐latitude ecosystems and are potentially of great importance for global carbon dynamics. Although large herbivores play a key part in shaping subarctic plant communities, their impact on mycorrhizal dynamics is largely unknown. We measured extramatrical mycelial (EMM) biomass during one growing season in 16‐year‐old herbivore exclosures and unenclosed control plots (ambient), at three mountain birch forests and two shrub heath sites, in the Scandes forest‐tundra ecotone. We also used high‐throughput amplicon sequencing for taxonomic identification to investigate differences in fungal species composition. At the birch forest sites, EMM biomass was significantly higher in exclosures (1.36 ± 0.43 g C/m2) than in ambient conditions (0.66 ± 0.17 g C/m2) and was positively influenced by soil thawing degree‐days. At the shrub heath sites, there was no significant effect on EMM biomass (exclosures: 0.72 ± 0.09 g C/m2; ambient plots: 1.43 ± 0.94). However, EMM biomass was negatively related to Betula nana abundance, which was greater in exclosures, suggesting that grazing affected EMM biomass positively. We found no significant treatment effects on fungal diversity but the most abundant ectomycorrhizal lineage/cortinarius, showed a near‐significant positive effect of herbivore exclusion (p = .08), indicating that herbivory also affects fungal community composition. These results suggest that herbivory can influence fungal biomass in highly context‐dependent ways in subarctic ecosystems. Considering the importance of root‐associated fungi for ecosystem carbon balance, these findings could have far‐reaching implications.

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Section: Methodsmentioning

confidence: 99%

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Vowles

Lindwall

Ekblad

et al. 2017

Ecology and Evolution

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“…Taxonomy was assigned to each OTU consensus sequence using the UNITE database (Kõljalg et al. 2013) in Mothur, which provides a naïve Bayes classifier with a minimum bootstrap value of 60%. Raw sequence data were deposited in the NCBI Sequence Read Archive and are available under the project number PRJNA286207.…”

Section: Methodsmentioning

confidence: 99%

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Roy‐Bolduc

Laliberté

Hijri

2015

Ecology and Evolution

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Ectomycorrhizal (EM) fungi are ubiquitous in temperate and boreal forests, comprising over 20,000 species forming root symbiotic associations with Pinaceae and woody angiosperms. As much as 100 different EM fungal species can coexist and interact with the same tree species, forming complex multispecies networks in soils. The degree of host specificity and structural properties of these interaction networks (e.g., nestedness and modularity) may influence plant and fungal community assembly and species coexistence, yet their structure has been little studied in northern coniferous forests, where trees depend on EM fungi for nutrient acquisition. We used high‐throughput sequencing to characterize the composition and diversity of bulk soil and root‐associated fungal communities in four co‐occurring Pinaceae in a relic foredune plain located at Îles de la Madeleine, Québec, Canada. We found high EM fungal richness across the four hosts, with a total of 200 EM operational taxonomic units (OTUs), mainly belonging to the Agaricomycetes. Network analysis revealed an antinested pattern in both bulk soil and roots EM fungal communities. However, there was no detectable modularity (i.e., subgroups of interacting species) in the interaction networks, indicating a low level of specificity in these EM associations. In addition, there were no differences in EM fungal OTU richness or community structure among the four tree species. Limited shared resources and competitive exclusion typically restrict the number of taxa coexisting within the same niche. As such, our finding of high EM fungal richness and low host specificity highlights the need for further studies to determine the mechanisms enabling such a large number of EM fungal species to coexist locally on the same hosts.

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“…Alpha diversity estimators, including Chao1, Simpson's index, and Shannon's index, were performed by the Quantitative Insights into Microbial Ecology software (Version 1.8.0, http://qiime.org/scripts/assign_taxonomy.html; Kuczynski et al, 2011). The taxonomy of ITS sequences was analyzed by RDP Classifier against the UNITE database (release 7.0, http://unite.ut.ee/index.php; Koljalg et al, 2013) using a confidence threshold of 70 %. RDP Classifier was used to determine the taxonomic composition at the phylum, class, order, family, genus, and species levels (Koiv et al, 2015;Miettinen et al, 2015).…”

Section: Sequence Analysesmentioning

confidence: 99%

Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

Wei

Chen

et al. 2017

Atmos. Chem. Phys.

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Abstract. Fungi are ubiquitous throughout the near-surface atmosphere, where they represent an important component of primary biological aerosol particles. This study combined internal transcribed spacer region sequencing and quantitative real-time polymerase chain reaction (qPCR) to investigate the ambient fungi in fine (PM 2.5 , 50 % cutoff aerodynamic diameter D a50 = 2.5 µm, geometric standard deviation of collection efficiency σ g = 1.2) and submicron (PM 1 , D a50 = 1 µm, σ g = 1.2) particles at the summit of Mt. Tai located in the North China Plain, China. Fungal abundance values were 9.4 × 10 4 and 1.3 × 10 5 copies m −3 in PM 2.5 and PM 1 , respectively. Most of the fungal sequences were from Ascomycota and Basidiomycota, which are known to actively discharge spores into the atmosphere. The fungal community showed a significant seasonal shift across different size fractions according to Metastats analysis and the Kruskal-Wallis rank sum test. The abundance of Glomerella and Zasmidium increased in larger particles in autumn, whereas Penicillium, Bullera, and Phaeosphaeria increased in smaller particles in winter. Environmental factors, namely Ca 2+ , humidity, and temperature, were found to be crucial for the seasonal variation in the fungal community. This study might serve as an important reference for fungal contribution to primary biological aerosol particles.

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Towards a unified paradigm for sequence‐based identification of fungi

Cited by 3,007 publications

References 29 publications

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

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Towards a unified paradigm for sequence‐based identification of fungi

Cited by 3,007 publications

References 29 publications

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest‐tundra ecotone

High richness of ectomycorrhizal fungi and low host specificity in a coastal sand dune ecosystem revealed by network analysis

Fungi diversity in PM&lt;sub&gt;2. 5&lt;/sub&gt; and PM&lt;sub&gt;1&lt;/sub&gt; at the summit of Mt. Tai: abundance, size distribution, and seasonal variation

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Fungi diversity in PM<sub>2. 5</sub> and PM<sub>1</sub> at the summit of Mt. Tai: abundance, size distribution, and seasonal variation