Tropical fungal diversity: closing the gap between species estimates and species discovery

Aime, M. Catherine; Brearley, Francis Q.

doi:10.1007/s10531-012-0338-7

Cited by 29 publications

(21 citation statements)

References 21 publications

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“…If so, it may be possible to make predictions about fungal community shifts in disturbed tropical landscapes using trait-based approaches that have informed plant community ecology for decades [82,83]. The fact that almost 40 % of the shared fungi across sites were unidentified at the level of order is not surprising, as the majority of the undescribed fungal species likely reside in tropical forests [19,84], highlighting the need for more intensive taxonomic surveys in these regions.…”

Section: Discussionmentioning

confidence: 99%

“…One key group of soil organisms likely to be impacted by tropical land-use change is soil fungi, which are critical components of forest ecosystems in their roles as decomposers, mutualists, and pathogens [16][17][18][19]. Compositional changes in fungal communities have been linked to altered plant dynamics [20], changes in nutrient cycling [21,22], and shifts in soil carbon pools and fluxes [23].…”

Section: Introductionmentioning

confidence: 99%

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Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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Human land use alters soil microbial composition and function in a variety of systems, although few comparable studies have been done in tropical forests and tropical agricultural production areas. Logging and the expansion of oil palm agriculture are two of the most significant drivers of tropical deforestation, and the latter is most prevalent in Southeast Asia. The aim of this study was to compare soil fungal communities from three sites in Malaysia that represent three of the most dominant land-use types in the Southeast Asia tropics: a primary forest, a regenerating forest that had been selectively logged 50 years previously, and a 25-year-old oil palm plantation. Soil cores were collected from three replicate plots at each site, and fungal communities were sequenced using the Illumina platform. Extracellular enzyme assays were assessed as a proxy for soil microbial function. We found that fungal communities were distinct across all sites, although fungal composition in the regenerating forest was more similar to the primary forest than either forest community was to the oil palm site. Ectomycorrhizal fungi, which are important associates of the dominant Dipterocarpaceae tree family in this region, were compositionally distinct across forests, but were nearly absent from oil palm soils. Extracellular enzyme assays indicated that the soil ecosystem in oil palm plantations experienced altered nutrient cycling dynamics, but there were few differences between regenerating and primary forest soils. Together, these results show that logging and the replacement of primary forest with oil palm plantations alter fungal community and function, although forests regenerating from logging had more similarities with primary forests in terms of fungal composition and nutrient cycling potential. Since oil palm agriculture is currently the mostly rapidly expanding equatorial crop and logging is pervasive across tropical ecosystems, these findings may have broad applicability.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

et al. 2014

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“…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.…”

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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

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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 ...

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“…However, recent metagenomics studies suggested that actual numbers might be closer to 3.5 to 5.1 million species or much higher than this [3]. This uncertainty in the numbers is partially due to lack of advanced molecular based thorough studies in the tropics where incredibly rich diversity has been reported [4]. Hawksworth [5] also suggested that much of the undescribed fungal species could be present in the tropics and it is reviewed in Aime and Brearley [4].…”

Section: Introductionmentioning

confidence: 99%

Molecular phylogeny of wood decay fungi of hardwood and their ability to produce laccase that correlates with triphenylmethane dye decolorization

Dona¹,

Deraniyagala²,

Wijesinghe³

et al. 2019

Preprint

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21Though Sri Lanka belongs to one of the 34 biodiversity hotspots of the world, its microfolora 22 specially fungi are not well studied and underrepresented in the global literature. Here we report 23 the fungal species diversity of decaying hardwood of a Sri Lankan dry zone forest for the first 24 time. Decaying hardwoods were collected from historically important Dimbulagala forest reserve, 25 Sri Lanka and fungi associated with these woods were isolated. Out of 35 fungal species identified 26 using morphological and molecular methods, 11 species were first records in Sri Lanka. All the 27 tested isolates were able to utilize wood as the sole carbon source and produced varying degrees 28 of laccase. Isolates of Perenniporia tephropora, Coriolopsis caperata, Gymnopilus dilepis, 29 Fusarium solani and Vanderbylia fraxinea were among the top six laccase producers. Except 30 Fusarium solani, the rest of the isolates showed more than 70% decolorization of the of 31 triphenylmethane dye and there was a significant positive correlation between laccase production 32 and dye decolorization. To the best of our knowledge laccase production and dye decolorization 33 ability of Vanderbylia fraxinea and Gymnopilus dilepis have never been reported in the fungal 34 kingdom before. Perenniporia tephropora was isolated from one of the strongest decay resistant 35 hardwood species, Ebony (Diospyros ebenum) also known as dark wood and V. fraxinea was 36 isolated from another medicinally important hardwood Neem (Azadirachta indica). Findings of 37 this study confirms that decaying hardwood of Sri Lanka provide unexplode a unique niche for 38 discovering fungal species with biotechnological applications such as high laccase producers and 39 dye decolorizers. 40 41 48metagenomics studies suggested that actual numbers might be closer to 3.5 to 5.1 million species 49 or much higher than this [3]. This uncertainty in the numbers is partially due to lack of advanced 50 molecular based thorough studies in the tropics where incredibly rich diversity has been reported 51 [4]. Hawksworth [5] also suggested that much of the undescribed fungal species could be present 52 in the tropics and it is reviewed in Aime and Brearley [4]. 53Sri Lanka, a tropical island in the Indian ocean along with the Western Ghats, belongs to one of 54 the 34 biodiversity hotspots in the world. Though its plant and animal diversity is well studied 55 [6,7], microbial studies, especially fungal studies remain in its infancy. Furthermore, biodiversity 56 hotspot concept of Sri Lanka should not be an exception for microbial diversity including fungi. 57However, most of the fungal studies in Sri Lanka have mainly focused on macro-fungi using 58 morphological characters [8]. Moreover, these studies have mainly concentrated on the wet zone 59 forests. On the other hand, dry zone forest ecosystems in the country spread over 22 % of area in 60 Sri Lanka, whereas the total forest cover is about 26.6%. Dimbulagala (7°51'40.5"N 61 81°07'05.5"E) is an isolated hill co...

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Tropical fungal diversity: closing the gap between species estimates and species discovery

Cited by 29 publications

References 21 publications

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

Responses of Soil Fungi to Logging and Oil Palm Agriculture in Southeast Asian Tropical Forests

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

Molecular phylogeny of wood decay fungi of hardwood and their ability to produce laccase that correlates with triphenylmethane dye decolorization

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