Sequences, the environment and fungi

Mitchell, Julian; Zuccaro, Alga

doi:10.1016/j.mycol.2005.11.004

Cited by 72 publications

(50 citation statements)

References 83 publications

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“…For example, the conditions that we select to do the PCR can give us biased results. Sometimes it is difficult to understand whether the fungi identified by this technique actually exist in the natural system (Mitchell and Zuccaro 2006). Therefore, in order to obtain a better resolution in species identification, richness and distribution patterns of microbes, a combination of both approaches (i.e.…”

Section: Introductionmentioning

confidence: 99%

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

et al. 2018

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This study is unique as it compares traditional and high-resolution culture-independent approaches using the same set of samples to study the saprotrophic fungi on Vitis vinifera. We identified the saprotrophic communities of table grape (Red Globe) and wine grape (Carbanate Gernischet) in China using both traditional and culture-independent techniques. The traditional approach used direct observations based on morphology, single spore isolation and phylogenetic analysis yielding 45 taxa which 19 were commonly detected in both cultivars. The same set of samples were then used for Illumina sequencing which analyzed ITS1 sequence data and detected 226 fungal OTUs, of which 176 and 189 belong to the cultivars Carbanate Gernischet and Red Globe, respectively. There were 139 OTUs shared between the two V. vinifera cultivars and 37 and 50 OTUs were specific to Carbanate Gernischet and Red Globe cultivars respectively. In the Carbanate Gernischet cultivar, Ascomycota accounted for 77% of the OTUs and in Red Globe, almost all sequenced were Ascomycota. The fungal taxa overlap at the genus and species level between the traditional and culture-independent approach was relatively low. In the traditional approach we were able to identify the taxa to species level, while in the culture-independent method we were frequently able to identify the taxa to family or genus level. This is remarkable as we used the same set of samples collected in China for both approaches. We recommend the use of traditional techniques to accurately identify taxa. Culture-independent method can be used to get a better understanding about the organisms that are present in a host in its natural environment. We identified primary and secondary plant pathogens and endophytes in the saprotrophic fungal communities, which support previous observations, that dead plant material in grape vineyards can be the primary sources of disease. Finally, based on present and previous findings, we provide a worldwide checklist of 905 fungal taxa on Vitis species, which includes their mode of life and distribution.

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Section: Introductionmentioning

confidence: 99%

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

et al. 2018

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“…Species in the environment may not be cultivatable or even visible (Mitchell and Zuccaro 2006;Stewart 2012). DNA metabarcoding has therefore become an important tool and is now commonly used to understand species diversity and community structure in complex communities of microorganisms (Heeger et al 2018;Jayawardena et al 2018b).…”

Section: Introductionmentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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The advantages and disadvantages of giving a valid name to a sequence of DNA detected from environmental specimens is presently a hot debate amongst the mycological community. The idea of using intracellular DNA (''mgDNA'') from environmental samples as holotypes seems at face value, to be a good idea, considering the expansion of knowledge among these 'dark taxa' or 'dark matter fungi' that it could provide (i.e. sequence based taxa without physical specimens and formal nomenclature). However, the limitations of using mgDNA as holotypes needs careful thought, i.e. can we use a short mgDNA fragment, which may contain a small amount of genetic information, to allow discrimination between species? What is the point and are the potential problems of giving valid scientific names to mgDNA? Numerous mycologists and taxonomists, who have many years of experience working on the taxonomy and phylogeny of different groups of fungi, are concerned about the consequences of providing valid names to mgDNA. There has been much debate, through several publications on the considerable problems of using mgDNA as holotypes. The proponents have tried to debate the virtues of using mgDNA as holotypes. Those against have shown that identification to species using mgDNA does not work in many fungal groups, while those for have shown cases where species can be identified with mgDNA. Different disciplines have different reasons and opinions for using mgDNA as holotypes, however even groups of the same disciplines have dissimilar ideas. In this paper we explore the use of mgDNA as holotypes. We provide evidences and opinions as to the use of mgDNA as holotypes from our own experiences. In no way do we attempt to degrade the study of DNA from environmental samples and the expansion of knowledge in to the dark taxa, but relate the issues to fungal taxonomy. In fact we show the value of using sequence data from these approaches, in dealing with the discovery of already named taxa, taxa numbers and ecological roles. We discuss the advantages and the pitfalls of using mgDNA from environmental samples as holotypes. The impacts of expanding the nomenclatural concept to allow using mgDNA from environmental samples as holotypes are also discussed. We provide evidence from case studies on Botryosphaeria, Colletotrichum, Penicillium and Xylaria. The case studies show that we cannot use mgDNA due to their short fragments and the fact that most ITS sequence data presently result from environmental sequencing. We conclude from the evidence that it is highly undesirable to use mgDNA as holotypes in naming fungal species. If this approach adopted, it would result in numerous problems where species identification cannot be confirmed due to limited sequence data available for the holotypes. We also propose an alternative DNA-based system for naming DNA based species which would provide considerably less problems and should be adopted.

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“…This lack of knowledge arises, in part, from the enormous complexity of soil microbial communities, which are estimated to contain more than 4,000 different genomic equivalents in a single gram of soil [1]. Because of their broad ecological range, ready adaptation abilities, and wide spectrum of nutrient sources, filamentous and yeast-like fungi are able to colonize many different niches or substrates [2]. As integral components in the soil ecosystem, fungi play an important role as major decomposers of plant residues, releasing nutrients that sustain and stimulate plant growth [3].…”

Section: Introductionmentioning

confidence: 99%

“…Cultivation-independent approaches using rRNA gene sequence analysis have been used to explore the taxonomic diversity of soil microbial communities. Recent technological advances in DNA-based methodologies have allowed rapid and accurate identification of fungal and yeast species from a wide variety of samples [2]. Concerning rDNA genes, the small subunit 16S has been successfully used to assess bacterial diversity in natural ecosystems, offering the possibility to discover new species [6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani

Val-Moraes

Pedrinho

Lemos

et al. 2013

Applied and Environmental Soil Science

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Fungi constitute an important part of the soil ecosystem, playing key roles in decomposition, cycling processes, and biotic interactions. Molecular methods have been used to assess fungal communities giving a more realistic view of their diversity. For this purpose, total DNA was extracted from bulk soils cultivated with tomato (STC), vegetables (SHC), and native forest (SMS) from three sites of the Taquara Branca river basin in Sumaré County, São Paulo State, Brazil. This metagenomic DNA was used as a template to amplify fungal 18S rDNA sequences, and libraries were constructed in Escherichia coli by cloning PCR products. The plasmid inserts were sequenced and compared to known rDNA sequences in the GenBank database. Of the sequenced clones, 22 were obtained from the SMS sample, 18 from the SHC sample, and 6 from the STC sample. Although most of the clone sequences did not match the sequences present in the database, individual amplified sequences matched with Glomeromycota (SMS), Fungi incertae sedis (SMS), and Neocallimastigomycota (SHC). Most of the sequences from the amplified taxa represent uncultured fungi. The molecular analysis of variance (AMOVA) indicated that fluctuations observed of haplotypes in the composition may be related to herbicide application.

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Sequences, the environment and fungi

Cited by 72 publications

References 83 publications

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

Biodiversity of fungi on Vitis vinifera L. revealed by traditional and high-resolution culture-independent approaches

Can we use environmental DNA as holotypes?

Molecular Identification of Fungal Communities in a Soil Cultivated with Vegetables and Soil Suppressiveness toRhizoctonia solani

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