First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and its host Pinus sylvestris

Peršoh, Derek; Melcher, Martina; Flessa, Fabienne; Rambold, Gerhard

doi:10.1016/j.funbio.2010.04.009

Cited by 76 publications

(71 citation statements)

References 58 publications

(61 reference statements)

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“…Actually only the polythetic approach has led to a situation where we can now see clearly that ITS is less well-suited than certain protein-coding genes for species segregation in many fungal groups. Another hypothesis from Peršoh et al (2010) and Peršoh (2013) is to give independent rules from the code for mgDNA, i.e. it would be not a real species name, but an ''indication'' that there might be something new (a new species) related to the taxon given in the name, or the name of the closest physical type appended by a number.…”

Section: Conclusion and An Alternative Dna-based Systemmentioning

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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Section: Conclusion and An Alternative Dna-based Systemmentioning

confidence: 99%

Can we use environmental DNA as holotypes?

et al. 2018

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“…These microorganisms display a remarkable diversity, in fact, more than 100 endophytic taxa have been detected in some plant species (Stone et al 2004). Endophytic fungi can also show host, organ and tissue specificity (Chapela et al 1991;Bettucci et al 1997;Mostert et al 2000;Ragazzi et al 2004;Schulz and Boyle 2006;Peršoh et al 2010;Yuan et al 2011).…”

Section: Introductionmentioning

confidence: 99%

Identification of Acremonium isolates from grapevines and evaluation of their antagonism towards Plasmopara viticola

et al. 2015

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Some endophytic fungal genera in Vitis vinifera, including Acremonium, have been reported as antagonists of Plasmopara viticola. Endophytic Acremonium isolates from an asymptomatic grapevine cultivar Inzolia from Italy were identified by morphological features and multigene phylogenies of ITS, 18S and 28S genes, and their intra-specific genomic diversity was analyzed by RAPD analysis. Culture filtrates (CFs) obtained from Acremonium isolates were tested in vitro for their inhibitory activity against the P. viticola sporangia germination. Among 94 isolates, 68 belonged to the Acremonium persicinum and 26 to the Acremonium sclerotigenum. RAPD analysis grouped the A. persicinum isolates into 15 clusters and defined 31 different strains. The A. sclerotigenum isolates, instead, were clustered into 22 groups and represented 25 strains. All A. persicinum CFs inhibited sporangia germination of P. viticola, while not all those of A. sclerotigenum had inhibitory effect. A different degree of inhibition was observed between strains of the same species, while some strains of different species showed identical inhibitory effect. No correlation was found between RAPD groups and inhibitory activity in both Acremonium species.

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“…Ascomycota was found to be the most common EF in plants by both culture‐dependent and culture‐independent methods. This is consistent with previous finding that Ascomycota was the dominant group in soils, marine environments, mangroves and endophytic community (Gazis and Chaverri, 2010; Peršoh et al ., 2010; Simões et al ., 2015; Khan et al ., 2017). Forty‐three taxa were recovered of culturable endophytes, while 1989 OTUs were obtained in Illumina Miseq sequencing, which supported the fact that only a very small portion of endophytes can be cultured (Fig.…”

Section: Discussionmentioning

confidence: 99%

Endophytic fungal community of Dysphania ambrosioides from two heavy metal‐contaminated sites: evaluated by culture‐dependent and culture‐independent approaches

Parmar

et al. 2018

Microbial Biotechnology

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SummaryEndophytic fungal communities of Dysphania ambrosioides, a hyperaccumulator growing at two Pb‐Zn‐contaminated sites, were investigated through culture‐dependent and culture‐independent approaches. A total of 237 culturable endophytic fungi (EF) were isolated from 368 tissue (shoot and roots) segments, and the colonization rate (CR) ranged from 9.64% to 65.98%. The isolates were identified to 43 taxa based on morphological characteristics and rDNA ITS sequence analysis. Among them, 13 taxa (30.23%) were common in plant tissues from both sites; however, dominant EF were dissimilar. In culture‐dependent study, 1989 OTUs were obtained through Illumina Miseq sequencing, and dominant EF were almost same in plant tissues from both sites. However, some culturable EF were not observed in total endophytic communities. We suggest that combination of both culture‐dependent and culture‐independent methods will provide more chances for the precise estimation of endophytic fungal community than using either of them. The tissue had more influence on the culturable fungal community structure, whereas the location had more influence on the total fungal community structure (including culturable and unculturable). Both culture‐dependent and culture‐independent studies illustrated that endophytic fungal communities of D. ambrosioides varied across the sites, which suggested that HM concentration of the soil may have some influence on endophytic fungal diversity.

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First fungal community analyses of endophytic ascomycetes associated with Viscum album ssp. austriacum and its host Pinus sylvestris

Cited by 76 publications

References 58 publications

Can we use environmental DNA as holotypes?

Can we use environmental DNA as holotypes?

Identification of Acremonium isolates from grapevines and evaluation of their antagonism towards Plasmopara viticola

Endophytic fungal community of Dysphania ambrosioides from two heavy metal‐contaminated sites: evaluated by culture‐dependent and culture‐independent approaches

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