A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

Kittelmann, Sandra; Naylor, Graham E.; Koolaard, J.; Janssen, Peter H.

doi:10.1371/journal.pone.0036866

Cited by 105 publications

(119 citation statements)

References 58 publications

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“…Notably, this method was developed more than 20 years ago (Muyzer et al, 1993) and has been an efficient method for microbial diversity studies in several environments, such as in soil (Bresolin et al, 2010), in plants Miguel et al, 2016) and in animals (Kittelmann et al, 2012). The different intensities of the bands in the electrophoretic profile of DGGE were interpreted as different community structures.…”

Section: Discussionmentioning

confidence: 99%

Diversity and distribution of the endophytic fungal community in eucalyptus leaves

Miguel¹,

Delvaux²,

Oliveira³

et al. 2017

Afr. J. Microbiol. Res.

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Eucalyptus species are among the most widely grown and most economically valuable trees worldwide. In Brazil, eucalyptus is of major environmental and economic importance because it generates thousands of jobs and offers an alternative to using wood from native forests. In forest ecosystems, plant shoots are considered a common habitat for various microorganisms, and plants of the family Myrtaceae are an important source of fungal biodiversity. However, very little is known about the diversity and microbial distribution in eucalyptus leaves. This study aimed at showing the diversity and distribution of endophytic fungi in the leaves of eucalyptus plants aged 18 and 72 months. The leaves were collected at the onset of the rainy period, during the rainy period, and during the dry period. Diversity was measured using DNA extraction, 18S rRNA subunit amplifi cation, denaturing gradient gel electrophoresis (DGGE), and sequencing of eluted bands. The endophytic fungal community was affected by plant location. Differences observed in the distribution of the phylogenetic groups found in the upper, middle and lower thirds of the tree canopy indicate that the endophytic community distribution in eucalyptus is dependent on leaf position. The age of the plants affected the diversity of endophytic fungi in Eucalyptus "urograndis". Phylogenetic analysis showed that the phyla Basidiomycota and Ascomycota dominate in the environments studied. The description of endophytic fungal diversity in this important forest species is an important step for assessing this genetic resource in the search for metabolites and processes tha t can contribute to improving plant development.

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Section: Discussionmentioning

confidence: 99%

Diversity and distribution of the endophytic fungal community in eucalyptus leaves

Miguel¹,

Delvaux²,

Oliveira³

et al. 2017

Afr. J. Microbiol. Res.

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“…Recently it was proposed that the phylogeny and taxonomy of ITS sequences after revision was suitable for the analysis of high-throughput sequencing datasets (Kittelmann et al 2012). It was reported that ITS sequences are more taxonomically informative than 18S rRNA sequences and are the common target in DNA based studies (Anderson and Parkin 2007).…”

Section: Introductionmentioning

confidence: 99%

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Liu

Cai

et al. 2015

World J Microbiol Biotechnol

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Both the internal transcribed spacer (ITS) region and 18S rRNA genes are broadly applied in molecular fingerprinting studies of fungi. However, the differences in those two ribosomal RNA regions are still largely unknown. In the current study, three sets of most suitable subunit ribosomes in ITS and 18S rRNA were compared using denaturing gradient gel electrophoresis (DGGE) under the optimum experimental conditions. Ten samples from both aquatic and soil environments were tested. The results revealed that the ITS region produced range-weighted richness in the range 36-361, which was significantly higher than that produced by 18S rDNA. There was a similar tendency in terms of the Shannon-Weaver diversity index and community dynamics in both water and soil samples. Samples from water and soil were better separated using ITS than 18S rDNA in principal component analysis of DGGE bands. Our study suggests that the ITS region is more precise and has more potential than 18S rRNA genes in fungal community analysis.

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“…The sequences of the five clones were submitted to GenBank (EU414755-EU414759) under the generic name Anaeromyces, since these sequences clustered close to the Anaeromyces clade at that time. However, more detailed analysis has since suggested that this isolate is quite distinct from Anaeromyces (Kittelmann et al 2012).…”

Section: Phylogenetic Analysismentioning

confidence: 99%

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces

Callaghan¹,

Podmirseg²,

Hohlweck³

et al. 2015

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The novel anaerobic fungus Buwchfawromyces eastonii gen. nov., sp. nov., belonging to order Neocallimastigales (phylum Neocallimastigomycota) is described. Morphologically similar to Piromyces but genetically quite distinct, this fungus (isolate GE09) was first isolated from buffalo faeces in west Wales and then subsequently isolated from sheep, cattle and horse in the same area. Phylogenetic analysis of LSU and ITS sequence confirmed that B. eastonii isolates formed a distinct clade close to the polycentric Anaeromyces spp. The morphology of GE09 is monocentric with monoflagellate zoospores. However, the sporangial stalk (sporangiophore) is often distinctly swollen and the proximal regions of the rhizoidal system twisted in appearance.publishersversionPeer reviewe

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A Proposed Taxonomy of Anaerobic Fungi (Class Neocallimastigomycetes) Suitable for Large-Scale Sequence-Based Community Structure Analysis

Cited by 105 publications

References 58 publications

Diversity and distribution of the endophytic fungal community in eucalyptus leaves

Diversity and distribution of the endophytic fungal community in eucalyptus leaves

Comparison of ITS and 18S rDNA for estimating fungal diversity using PCR–DGGE

Buwchfawromyces eastonii gen. nov., sp. nov.: a new anaerobic fungus (Neocallimastigomycota) isolated from buffalo faeces

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