Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi
Abstract
Here, 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 studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere 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 communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype 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.more »
- Authors:
-
- Kent State Univ., Kent, OH (United States)
- Publication Date:
- Research Org.:
- Kent State Univ., Kent, OH (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1247639
- Alternate Identifier(s):
- OSTI ID: 1359565
- Grant/Contract Number:
- SC0004335; SC000433
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Journal of Microbiological Methods
- Additional Journal Information:
- Journal Volume: 123; Journal Issue: C; Journal ID: ISSN 0167-7012
- Publisher:
- Elsevier
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; fungi; forest litter; PCR primers; environmental samples; functional gene; endopolygalacturonase
Citation Formats
Gacura, Matthew D., Sprockett, Daniel D., Heidenreich, Bess, and Blackwood, Christopher B. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi. United States: N. p., 2016.
Web. doi:10.1016/j.mimet.2016.02.013.
Gacura, Matthew D., Sprockett, Daniel D., Heidenreich, Bess, & Blackwood, Christopher B. Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi. United States. https://doi.org/10.1016/j.mimet.2016.02.013
Gacura, Matthew D., Sprockett, Daniel D., Heidenreich, Bess, and Blackwood, Christopher B. Wed .
"Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi". United States. https://doi.org/10.1016/j.mimet.2016.02.013. https://www.osti.gov/servlets/purl/1247639.
@article{osti_1247639,
title = {Comparison of pectin-degrading fungal communities in temperate forests using glycosyl hydrolase family 28 pectinase primers targeting Ascomycete fungi},
author = {Gacura, Matthew D. and Sprockett, Daniel D. and Heidenreich, Bess and Blackwood, Christopher B.},
abstractNote = {Here, 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 studywe developed primers for the amplification of GH28 coding genes from a database of 293 GH28 sequences from40 fungal genomes. The primerswere 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 communitieswere up to 39% Basidiomycetes. Analysis of leaf samples indicated that both forest stand and ecosystemtype 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.},
doi = {10.1016/j.mimet.2016.02.013},
journal = {Journal of Microbiological Methods},
number = C,
volume = 123,
place = {United States},
year = {Wed Feb 17 00:00:00 EST 2016},
month = {Wed Feb 17 00:00:00 EST 2016}
}
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