USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

Vaz, Aline B. M.; Fonseca, Paula Luize Camargos; Leite, Laura Hora Rios; Badotti, Fernanda; Salim, Anna C. M.; Araújo, Flávio Marcos Gomes; Cuadros-Orellana, Sara; Duarte, Ângelo; Rosa, Carlos A.; Oliveira, Guilherme; Goés-Neto, Aristóteles

doi:10.11646/phytotaxa.295.1.1

Cited by 23 publications

(23 citation statements)

References 63 publications

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“…Ascomycota were dominant, particularly in wood of the 1 st decay class where their frequency increased to over 89% of all fungi detected. Dominance of Ascomycota in deadwood was also observed by Vaz et al (2017). Many Ascomycota taxa detected were soft rot fungi, meaning that they can break down cellulose and hemi-cellulose, but not harder structural substances such as lignin (Mäkelä et al, 2015).…”

Section: Discussionmentioning

confidence: 72%

“…In the six 3-30-year-old Q. petraea logs there were 264 307 different OTUs, which is 127-fold more than the 2 080 OTUs found in nine samples of 3-year-old Q. rubra logs using high-throughput sequencing (by van der Wal et al, 2017), but less than the 687 662 and 1 861 279 OTUs found in 20 samples of broadleaved trees from two locations in neotropical Atlantic forests using massively parallel sequencing (Vaz et al, 2017). There were also 277 fungal taxa, which is more than the 141 taxa detected in deadwood of Quercus robur L. using the classical method based on isolation and microscopic analysis (Kwaśna et al, 2016b), the 100 taxa detected in neotropical Atlantic forests (Vaz et al, 2017), and the 15 species detected in Q. rubra logs (by van der Wal et al, 2017). In two other tree species, beech and Scots pine, respectively 96 and 138 fungal taxa were detected by isolation and microscopic analysis (Fukasawa et al, 2009;Kwaśna et al, 2016b).…”

Section: Discussionmentioning

confidence: 90%

“…Both approaches are selective; inconspicuous or non-fruiting species can be missed during surveys, and only a small portion of the microfungal community can be cultured in vitro. Recently, nucleic acid techniques have been applied to extract and identify fungal species colonizing deadwood in boreal forests (Allmér et al, 2006;Kulhánková et al, 2006;Ovaskainen et al, 2010;Rajala et al, 2010Rajala et al, , 2011Rajala et al, , 2012Rajala et al, , 2015Kebli et al, 2011;Lindner et al, 2011, van der Wal et al, 2017Vaz et al, 2017). This approach is not restricted to any functional or taxonomic groups.…”

Section: Introductionmentioning

confidence: 99%

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Abundance and diversity of fungi in oak wood

Behnke‐Borowczyk¹,

Kwaśna²,

Kokot³

et al. 2019

Dendrobiology

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Deadwood is an important functional and structural component of forest ecosystems since it regulates nutrient cycling, serves as a carbon (C) pool, increases the C content in the soil, and is a source of resources, including water, for a wide range of saproxylic and non-saproxylic organisms. The abundance and diversity of wood-inhabiting fungi in six fallen, horizontally lying logs of Quercus petraea, in the 1 st , 2 nd and 3 rd decay classes, in the Drawa National Park in Poland in 2015, were studied using the Illumina sequencing technique. The total number of OTUs obtained (264 307) included sequences of culturable fungi (242 369 = 91.70%) and non-culturable fungi (7 056 = 2.66%). The dead oak wood was colonized by 277 taxa. Culturable fungi of Zygomycota, Ascomycota and Basidiomycota comprised 75% of taxa detected and were represented by 14, 139 and 53 taxa respectively. Non-culturable organisms were represented by 70 taxa. Fungi were classified into 18 groups: (i) typical soft rot fungi, (ii) phytopathogens potentially hazardous to trees, (iii) epiphytes and endophytes or weak, opportunistic pathogens, (iv) ectomycorrhizal species, (v) ericoid mycorrhizal species, (vi) crust fungi, (vii) resupinate basidiomycetes, (viii) saprotrophs and soil fungi, (ix) opportunistic human pathogens causing superficial or systemic mycoses, (x) pathogens of warm-or cold-blooded animals, (xi) ascomycetous yeasts, (xii) basidiomycetous yeasts, (xiii) antagonists of fungi, (xiv) producers of metabolites effective against pathogens, (xv) hyperparasites, (xvi) lichen-forming species, (xvii) partners of other fungi, (xviii) species rare or uncommon in nature. It was shown that: (i) coarse, woody debris of oak is host to abundant and diverse mycobiota, (ii) abundance and diversity of fungi increase with the decay continuum, (iii) oak logs can be a habitat of phytopathogens potentially hazardous to forest health, (iv) different phytopathogens favour wood in different decay classes, (v) abundance of pathogens decreases, and of ericoid mycorrhizal (or soil) species increases with the decay continuum. Maintaining different types of deadwood increases fungal diversity, but also the risk of diseases.

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Section: Discussionmentioning

confidence: 72%

Section: Discussionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

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Abundance and diversity of fungi in oak wood

Behnke‐Borowczyk¹,

Kwaśna²,

Kokot³

et al. 2019

Dendrobiology

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“…Yet, despite these factors being well documented, after more than a decade of use there is no clear consensus as to what extent metabarcoding is quantitative. Many studies report their findings in a quantitative manner where the relative read abundance (RRA) (Deagle et al, 2018) is interpreted as the relative abundance of biomass (Kowalczyk et al, 2011;Soininen et al, 2015;Sousa et al, 2016;Vaz et al, 2017).…”

Section: Introductionmentioning

confidence: 99%

How quantitative is metabarcoding: A meta‐analytical approach

et al. 2018

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Metabarcoding has been used in a range of ecological applications such as taxonomic assignment, dietary analysis and the analysis of environmental DNA. However, after a decade of use in these applications there is little consensus on the extent to which proportions of reads generated corresponds to the original proportions of species in a community. To quantify our current understanding, we conducted a structured review and meta‐analysis. The analysis suggests that a weak quantitative relationship may exist between the biomass and sequences produced (slope = 0.52 ± 0.34, p < 0.01), albeit with a large degree of uncertainty. None of the tested moderators, sequencing platform type, the number of species used in a trial or the source of DNA, were able to explain the variance. Our current understanding of the factors affecting the quantitative performance of metabarcoding is still limited: additional research is required before metabarcoding can be confidently utilized for quantitative applications. Until then, we advocate the inclusion of mock communities when metabarcoding as this facilitates direct assessment of the quantitative ability of any given study.

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“…However, methodological biases, limitations of the markers and bioinformatic analysis, may lead to misleading conclusions (Lindahl et al 2013, Vaz et al 2017. Operational taxonomic units are based on sequences with ≥ 97% similarity.…”

Section: Comparison Between Culture-dependent and Culture-independentmentioning

confidence: 99%

Can ITS sequence data identify fungal endophytes from cultures? A case study from Rhizophora apiculata

Doilom¹

2017

Mycosphere

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Culture-based studies have recovered fungal endophytes from numerous plant hosts, while direct examination of sporulating cultures has enabled identification. However, many endophytes cannot be identified due to the fact that they only form mycelia sterilia in culture. Although next generation sequencing (NGS), as well as ITS sequence analyses have been used to identify endophytes, identification is still rudimentary. In this study, we isolated fungal endophytes from Rhizophora apiculata in Thailand and established how many can be identified to species level based on ITS sequence data. Endophytic fungi were isolated from leaves, petioles and aerial roots of R. apiculata in four provinces of Thailand. One hundred and fifty four isolates were obtained and initially grouped into 20 morphotypes based on cultural characteristics. Nine were sporulating morphotypes, which were assigned to seven genera (Colletotrichum, Diaporthe, Hypoxylon, Neopestalotiopsis, Neodevriesia, Pestalotiopsis and Phyllosticta), and eleven morphotypes were non-sporulating mycelia sterilia. Sequence similarity comparison and phylogenetic analysis of the ITS regions were further used to identify taxa. While ITS sequence data is reliable to assign isolates at the generic rank, and can be useful to identify taxa to species level in a small number of fungal genera, it cannot generally be used to determine specific species in most genera. ITS analysis classified 30 representative isolates into 20 taxonomic units residing in 15 known genera: Allophoma sp., Colletotrichum spp., Diaporthe spp., Hortaea werneckii, Hypoxylon griseobrunneum, Hypoxylon sp., Pestalotiopsis sp., Phanerochaete sp., Phyllosticta spp., Pseudopithomyces maydicus, Preussia sp., Nemania sp., Neodevriesia sp., Neopestalotiopsis sp., Rigidoporus vinctus, Schizophyllum sp. and one unidentified genus. Of the morphotypes, four were identified to species. The results from Blast searches and ITS phylogeny of the 15 genera and the one unidentified genus are discussed. Twenty-five of the 30 isolates could not be identified and thus an estimated 20 isolates are likely to be new species and one a new genus. This is remarkable, as endophytes of a single host in Thailand, may yield 75% or more of new species. This is not akin to the OTUs generated in NGS platforms, which are generally short sequences with high possibility to not match with sequences in GenBank, not because they are new, but because of the quality of the sequence data.

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USING Next-Generation Sequencing (NGS) TO UNCOVER DIVERSITY OF WOOD-DECAYING FUNGI IN NEOTROPICAL ATLANTIC FORESTS

Cited by 23 publications

References 63 publications

Abundance and diversity of fungi in oak wood

Abundance and diversity of fungi in oak wood

How quantitative is metabarcoding: A meta‐analytical approach

Can ITS sequence data identify fungal endophytes from cultures? A case study from Rhizophora apiculata

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