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Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi.
- Source :
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Journal of microbiological methods [J Microbiol Methods] 2016 Apr; Vol. 123, pp. 108-13. Date of Electronic Publication: 2016 Feb 17. - Publication Year :
- 2016
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Abstract
- Fungi have developed a wide assortment of enzymes to break down pectin, a prevalent polymer in plant cell walls that is important in plant defense and structure. One enzyme family used to degrade pectin is the glycosyl hydrolase family 28 (GH28). In this study we developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from 40 fungal genomes. The primers were used to successfully amplify GH28 pectinases from all Ascomycota cultures tested, but only three out of seven Basidiomycota cultures. In addition, we further tested the primers in PCRs on metagenomic DNA extracted from senesced tree leaves from different forest ecosystems, followed by cloning and sequencing. Taxonomic specificity for Ascomycota GH28 genes was tested by comparing GH28 composition in leaves to internal transcribed spacer (ITS) amplicon composition using pyrosequencing. All sequences obtained from GH28 primers were classified as Ascomycota; in contrast, ITS sequences indicated that fungal communities were up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystem type were important in structuring fungal communities. However, site played the prominent role in explaining GH28 composition, whereas ecosystem type was more important for ITS composition, indicating possible genetic drift between populations of fungi. Overall, these primers will have utility in understanding relationships between fungal community composition and ecosystem processes, as well as detection of potentially pathogenic Ascomycetes.<br /> (Copyright © 2016 Elsevier B.V. All rights reserved.)
- Subjects :
- Ascomycota classification
Ascomycota genetics
Forests
Fungal Proteins metabolism
Multigene Family
Pectins metabolism
Phylogeny
Polygalacturonase metabolism
Trees growth & development
Ascomycota enzymology
DNA Primers genetics
Fungal Proteins genetics
Polygalacturonase genetics
Polymerase Chain Reaction methods
Trees microbiology
Subjects
Details
- Language :
- English
- ISSN :
- 1872-8359
- Volume :
- 123
- Database :
- MEDLINE
- Journal :
- Journal of microbiological methods
- Publication Type :
- Academic Journal
- Accession number :
- 26899925
- Full Text :
- https://doi.org/10.1016/j.mimet.2016.02.013