Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate?

Hawksworth, David L.

doi:10.1007/s10531-012-0335-x

Cited by 193 publications

(117 citation statements)

References 28 publications

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“…In the present study, the use of Ion Torrent sequencing revealed a high diversity of fungi associated with the phyllosphere of P. abies while sample barcoding allowed their assignment to particular type of samples (damaged and undamaged) as well as to individual study sites ( Table 1). The detected richness of fungal taxa were one or two orders of magnitude as compared to similar studies which were based on fungal culturing [18,25,26], showing that such detection methods allow in depth analysis of fungal communities, and challenges our understanding of the global fungal diversity [10,11]. Shannon diversity index of fungal communities was high in all study sites (Table 1) repeatedly demonstrating a high efficacy of the detection method.…”

Section: Discussionmentioning

confidence: 73%

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae)

et al. 2015

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The aim of this study was to assess diversity and composition of fungal communities in damaged and undamaged shoots of Norway spruce (Picea abies) following recent invasion of the spruce bud scale (Physokermes piceae) in Lithuania. Sampling was done in July 2013 and included 50 random lateral shoots from 10 random trees in each of five visually undamaged and five damaged 40-50 years-old pure stands of P. abies. DNA was isolated from 500 individual shoots, subjected to amplification of the internal transcribed spacer of fungal ribosomal DNA (ITS rDNA), barcoded and sequenced. Clustering of 149426 high-quality sequences resulted in 1193 non-singleton contigs of which 1039 (87.1%) were fungal. In total, there were 893 fungal taxa in damaged shoots and 608 taxa in undamaged shoots (p<0.0001). Furthermore, 431 (41.5%) fungal taxa were exclusively in damaged shoots, 146 (14.0%) were exclusively in undamaged shoots and 462 (44.5%) were common to both types of samples. Correspondence analysis showed that study sites representing damaged and undamaged shoots were separated from each other, indicating that in these fungal communities were largely different, and therefore heavily affected by P. piceae. In conclusion, the results demonstrated that invasive alien tree pests may have a profound effect on fungal mycobiota associated with the phyllosphere of P. abies, and therefore, in addition to their direct negative effect owing physical damage of the tissue, they may also indirectly determine health, sustainability and ultimately distribution of the forest tree species.Keywords: forest health, pathogens, pest insects, climate change, fungal community Introduction Norway spruce (Picea abies) is one of the dominant tree species distributed in a larger part of the north temperate and boreal forests of Europe, and therefore is of tremendous socioeconomic importance [33]. It appears that the climate has been the major determinant of the distributional limits of the tree species and these limits track climate change so closely that even short-term climatic variation can lead to significant range adjustments with consequences for practical forestry and society [39]. The recent observations suggest that the range limit of P. abies has begun to change more rapidly than in the past, and a further projection predicts its range expansion in the north and much greater contraction in the south of the present limit [3]. Climate change can affect forests directly (storms, droughts, high

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Section: Discussionmentioning

confidence: 73%

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae)

et al. 2015

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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%

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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“…Roughly 100 000 species of Fungi have been described (Kirk et al 2008), but only about a quarter of these (26 540 species) are represented by a sequence of any locus, and only 267 species are represented by a genome sequence in GenBank (although this is increasing rapidly). These numbers pale in comparison to estimates of actual fungal diversity, which range from hundreds of thousands to many millions of species (Blackwell 2011, Hawksworth 2012. For the foreseeable future, fungal metagenomic and metatranscriptomic studies will have to contend with huge numbers of unidentified genes and organisms.…”

Section: Achieving Genome-enabled Mycologymentioning

confidence: 99%

Toward genome-enabled mycology

2013

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Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genomeenabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of Mycologia presents the first complete fungal genomes in the history of the journal, reflecting the ongoing transformation of mycology into a genomeenabled science. Here, we consider the prospects for genome-enabled mycology and the technical and social challenges that will need to be overcome to grow the database of complete fungal genomes and enable all fungal biologists to make use of the new data.

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Global species numbers of fungi: are tropical studies and molecular approaches contributing to a more robust estimate?

Cited by 193 publications

References 28 publications

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae)

High-Throughput Sequencing Reveals Drastic Changes in Fungal Communities in the Phyllosphere of Norway Spruce (Picea abies) Following Invasion of the Spruce Bud Scale (Physokermes piceae)

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

Toward genome-enabled mycology

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