Fungal ecology catches fire

Hibbett, David S.; Öhman, Anders; Kirk, Paul M.

doi:10.1111/j.1469-8137.2009.03042.x

Cited by 98 publications

(96 citation statements)

References 13 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Molecular community analyses provide the resolution required to identify species and functional groups. Methodological development in molecular fungal ecology is currently undergoing a boom (Hibbett et al, 2009), and in combination with careful field manipulations and measurements of environmental and functional parameters, such as elemental concentrations and enzyme activities. DNA-based methods may enable us to elucidate environmental drivers of fungal community assembly, as well as the functional roles of fungal communities in ecosystems.…”

Section: Discussionmentioning

confidence: 99%

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

2010

View full text Add to dashboard Cite

Ectomycorrhizal fungi dominate the humus layers of boreal forests. They depend on carbohydrates that are translocated through roots, via fungal mycelium to microsites in the soil, wherein they forage for nutrients. Mycorrhizal fungi are therefore sensitive to disruptive disturbances that may restrict their carbon supply. By disrupting root connections, we induced a sudden decline in mycorrhizal mycelial abundance and studied the consequent effects on growth and activity of free living, saprotrophic fungi and bacteria in pine forest humus, using molecular community analyses in combination with enzyme activity measurements. Ectomycorrhizal fungi had decreased in abundance 14 days after root severing, but the abundance of certain free-living ascomycetes was three times higher within 5 days of the disturbance compared with undisturbed controls. Root disruption also increased laccase production by an order of magnitude and cellulase production by a factor of 5. In contrast, bacterial populations seemed little affected. The results indicate that access to an external carbon source enables mycorrhizal fungi to monopolise the humus, but disturbances may induce rapid growth of opportunistic saprotrophic fungi that presumably use the dying mycorrhizal mycelium. Studies of such functional shifts in fungal communities, induced by disturbance, may shed light on mechanisms behind nutrient retention and release in boreal forests. The results also highlight the fundamental problems associated with methods that study microbial processes in soil samples that have been isolated from living roots.

show abstract

Section: Discussionmentioning

confidence: 99%

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

2010

View full text Add to dashboard Cite

show abstract

“…Large molecular data sets are being generated at an extraordinary rate (3)(4)(5)(6), but diversity estimations and taxonomic identification at all taxonomic levels are constrained by the lack of accurate, comprehensive taxonomic databases and information on the accuracy of classification tools for comparison of environmental survey data. The detection of emergent fungal diseases, the determination of biogeographical patterns, and definition of strategies for conservation of fungi are just a few examples of research areas that are challenged by the lack of reliable databases and tools (7,8). The large number of sequences generated from platforms of high-throughput sequencing also demand fast and accurate algorithms for sequence analysis and taxonomic classification of fungi.…”

mentioning

confidence: 99%

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

Porras-Alfaro

Liu

Kuske

et al. 2014

Appl Environ Microbiol

102

View full text Add to dashboard Cite

We compared the classification accuracy of two sections of the fungal internal transcribed spacer (ITS) region, individually and combined, and the 5= section (about 600 bp) of the large-subunit rRNA (LSU), using a naive Bayesian classifier and BLASTN. A hand-curated ITS-LSU training set of 1,091 sequences and a larger training set of 8,967 ITS region sequences were used. Of the factors evaluated, database composition and quality had the largest effect on classification accuracy, followed by fragment size and use of a bootstrap cutoff to improve classification confidence. The naive Bayesian classifier and BLASTN gave similar results at higher taxonomic levels, but the classifier was faster and more accurate at the genus level when a bootstrap cutoff was used. All of the ITS and LSU sections performed well (>97.7% accuracy) at higher taxonomic ranks from kingdom to family, and differences between them were small at the genus level (within 0.66 to 1.23%). When full-length sequence sections were used, the LSU outperformed the ITS1 and ITS2 fragments at the genus level, but the ITS1 and ITS2 showed higher accuracy when smaller fragment sizes of the same length and a 50% bootstrap cutoff were used. In a comparison using the larger ITS training set, ITS1 and ITS2 had very similar accuracy classification for fragments between 100 and 200 bp. Collectively, the results show that any of the ITS or LSU sections we tested provided comparable classification accuracy to the genus level and underscore the need for larger and more diverse classification training sets. Fungi are one of the most diverse groups of eukaryotic organisms on Earth, with estimates that range from 1.5 to 5.1 million species (1, 2). The use of next-generation sequencing (NGS) is playing a major role in the discovery of new species and ecological studies of fungi. Large molecular data sets are being generated at an extraordinary rate (3-6), but diversity estimations and taxonomic identification at all taxonomic levels are constrained by the lack of accurate, comprehensive taxonomic databases and information on the accuracy of classification tools for comparison of environmental survey data. The detection of emergent fungal diseases, the determination of biogeographical patterns, and definition of strategies for conservation of fungi are just a few examples of research areas that are challenged by the lack of reliable databases and tools (7,8). The large number of sequences generated from platforms of high-throughput sequencing also demand fast and accurate algorithms for sequence analysis and taxonomic classification of fungi.The entire internal transcribed spacer (ITS) rRNA region (approximately 600 bp in length) is composed of two hypervariable regions (ITS1 and ITS2) with the highly conserved 5.8S rRNA gene between them (Fig. 1). The ITS region has been used for many years for diversity estimations and taxonomic identification of fungal isolates and uncultured taxa (9-11) and was adapted as the barcode region for Fungi by the Consortium for the Barcode ...

show abstract

“…Next generation sequencing (NGS) permits deep interrogation of hyperdiverse fungal communities (Hibbett et al 2009). Data generation has become expedient and sequence analysis/annotation more streamlined via available pipelines (e.g.…”

mentioning

confidence: 99%

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

et al. 2015

View full text Add to dashboard Cite

Fungal ecology catches fire

Cited by 98 publications

References 13 publications

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

Disruption of root carbon transport into forest humus stimulates fungal opportunists at the expense of mycorrhizal fungi

From Genus to Phylum: Large-Subunit and Internal Transcribed Spacer rRNA Operon Regions Show Similar Classification Accuracies Influenced by Database Composition

Scraping the bottom of the barrel: are rare high throughput sequences artifacts?

Contact Info

Product

Resources

About