Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons

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Published inApplied and Environmental Microbiology Vol. 69; no. 1; pp. 327 - 333
Main Authors Landeweert, Renske, Leeflang, Paula, Kuyper, Thom W., Hoffland, Ellis, Rosling, Anna, Wernars, Karel, Smit, Eric
Format Journal Article
LanguageEnglish
Published Washington, DC American Society for Microbiology 01.01.2003
Subjects
amplification
Basidiomycota - classification
Basidiomycota - genetics
Biological and medical sciences
Deoxyribonucleic acid
diversity
DNA
dna extraction
DNA, Fungal - analysis
DNA, Fungal - isolation & purification
environmental-samples
forest soil
Fundamental and applied biological sciences. Psychology
fungal communities
Fungi
gradient gel-electrophoresis
growth
Microbiology
Molecular Sequence Data
Mycorrhizae
Phylogeny
Picea - microbiology
Pinus - microbiology
Plant Microbiology
Plant Roots - microbiology
primers
ribosomal-rna
Sequence Analysis, DNA
Soil - analysis
Soil horizons
Soil Microbiology
Soil types
Soils
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Abstract Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue Spotlights in the Current Issue AEM About AEM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AEM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0099-2240 Online ISSN: 1098-5336 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to AEM .asm.org, visit: AEM       
AbstractList Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (greater than or equal to99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had greater than or equal to98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Classifications Services AEM Citing Articles Google Scholar PubMed Related Content Social Bookmarking CiteULike Delicious Digg Facebook Google+ Mendeley Reddit StumbleUpon Twitter current issue Spotlights in the Current Issue AEM About AEM Subscribers Authors Reviewers Advertisers Inquiries from the Press Permissions & Commercial Reprints ASM Journals Public Access Policy AEM RSS Feeds 1752 N Street N.W. • Washington DC 20036 202.737.3600 • 202.942.9355 fax • journals@asmusa.org Print ISSN: 0099-2240 Online ISSN: 1098-5336 Copyright © 2014 by the American Society for Microbiology.   For an alternate route to AEM .asm.org, visit: AEM       
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology ([>=]99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had [>=]98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (> or = 99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had > or = 98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (> or = 99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had > or = 98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (greater than or equal to 99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had greater than or equal to 98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (> or = 99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had > or = 98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification techniques, the ectomycorrhizal (EM) fungal community under coniferous vegetation was analyzed. Soil samples were taken at different depths from four horizons of a podzol profile. A basidiomycete-specific primer pair (ITS1F-ITS4B) was used to amplify fungal internal transcribed spacer (ITS) sequences from total DNA extracts of the soil horizons. Amplified basidiomycete DNA was cloned and sequenced, and a selection of the obtained clones was analyzed phylogenetically. Based on sequence similarity, the fungal clone sequences were sorted into 25 different fungal groups, or operational taxonomic units (OTUs). Out of 25 basidiomycete OTUs, 7 OTUs showed high nucleotide homology (≥99%) with known EM fungal sequences and 16 were found exclusively in the mineral soil. The taxonomic positions of six OTUs remained unclear. OTU sequences were compared to sequences from morphotyped EM root tips collected from the same sites. Of the 25 OTUs, 10 OTUs had ≥98% sequence similarity with these EM root tip sequences. The present study demonstrates the use of molecular techniques to identify EM hyphae in various soil types. This approach differs from the conventional method of EM root tip identification and provides a novel approach to examine EM fungal communities in soil.
Author Thom W. Kuyper
Karel Wernars
Paula Leeflang
Renske Landeweert
Ellis Hoffland
Eric Smit
Anna Rosling
AuthorAffiliation Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen, 1 Department MGB, National Institute of Public Health and the Environment, NL-3720 BA Bilthoven, 2 Laboratory of Soil Science and Geology, Wageningen University, NL-6700 AA, Wageningen, The Netherlands, 3 Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden 4
AuthorAffiliation_xml – name: Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen, 1 Department MGB, National Institute of Public Health and the Environment, NL-3720 BA Bilthoven, 2 Laboratory of Soil Science and Geology, Wageningen University, NL-6700 AA, Wageningen, The Netherlands, 3 Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden 4
Author_xml – sequence: 1
  givenname: Renske
  surname: Landeweert
  fullname: Landeweert, Renske
  organization: Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen
– sequence: 2
  givenname: Paula
  surname: Leeflang
  fullname: Leeflang, Paula
  organization: Department MGB, National Institute of Public Health and the Environment, NL-3720 BA Bilthoven
– sequence: 3
  givenname: Thom W.
  surname: Kuyper
  fullname: Kuyper, Thom W.
  organization: Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen
– sequence: 4
  givenname: Ellis
  surname: Hoffland
  fullname: Hoffland, Ellis
  organization: Subdepartment of Soil Quality, Wageningen University, NL-6700 EC Wageningen, Laboratory of Soil Science and Geology, Wageningen University, NL-6700 AA, Wageningen, The Netherlands
– sequence: 5
  givenname: Anna
  surname: Rosling
  fullname: Rosling, Anna
  organization: Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden
– sequence: 6
  givenname: Karel
  surname: Wernars
  fullname: Wernars, Karel
  organization: Department MGB, National Institute of Public Health and the Environment, NL-3720 BA Bilthoven
– sequence: 7
  givenname: Eric
  surname: Smit
  fullname: Smit, Eric
  organization: Department MGB, National Institute of Public Health and the Environment, NL-3720 BA Bilthoven
BackLink http://pascal-francis.inist.fr/vibad/index.php?action=getRecordDetail&idt=14587854$$DView record in Pascal Francis
https://www.ncbi.nlm.nih.gov/pubmed/12514012$$D View this record in MEDLINE/PubMed
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ContentType Journal Article
Copyright 2003 INIST-CNRS
Copyright American Society for Microbiology Jan 2003
Copyright © 2003, American Society for Microbiology 2003
Wageningen University & Research
Copyright_xml – notice: 2003 INIST-CNRS
– notice: Copyright American Society for Microbiology Jan 2003
– notice: Copyright © 2003, American Society for Microbiology 2003
– notice: Wageningen University & Research
DBID AAYXX
CITATION
IQODW
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Corresponding author. Mailing address: Sub-Dept of Soil Quality, Wageningen University, Box 8005, NL-6700 EC, Wageningen, The Netherlands. Phone: 31 317 48 23 39. Fax: 31 317 48 37 66. E-mail: renske.landeweert@wur.nl.
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Molecular identification techniques based on total DNA extraction provide a unique tool for identification of mycelium in soil. Using molecular identification...
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SubjectTerms amplification
Basidiomycota - classification
Basidiomycota - genetics
Biological and medical sciences
Deoxyribonucleic acid
diversity
DNA
dna extraction
DNA, Fungal - analysis
DNA, Fungal - isolation & purification
environmental-samples
forest soil
Fundamental and applied biological sciences. Psychology
fungal communities
Fungi
gradient gel-electrophoresis
growth
Microbiology
Molecular Sequence Data
Mycorrhizae
Phylogeny
Picea - microbiology
Pinus - microbiology
Plant Microbiology
Plant Roots - microbiology
primers
ribosomal-rna
Sequence Analysis, DNA
Soil - analysis
Soil horizons
Soil Microbiology
Soil types
Soils
Title Molecular Identification of Ectomycorrhizal Mycelium in Soil Horizons
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