↓ Skip to main content

Microbial Environmental Genomics (MEG)

Overview of attention for book
Cover of 'Microbial Environmental Genomics (MEG)'

Table of Contents

  1. Altmetric Badge
    Book Overview
  2. Altmetric Badge
    Chapter 1 "Deciphering Archaeal Communities" Omics Tools in the Study of Archaeal Communities.
  3. Altmetric Badge
    Chapter 2 Investigating the Endobacteria Which Thrive in Arbuscular Mycorrhizal Fungi
  4. Altmetric Badge
    Chapter 3 GenoSol Platform: A Logistic and Technical Platform for Conserving and Exploring Soil Microbial Diversity.
  5. Altmetric Badge
    Chapter 4 Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons
  6. Altmetric Badge
    Chapter 5 Fungal Communities in Soils: Soil Organic Matter Degradation.
  7. Altmetric Badge
    Chapter 6 DNA-Based Characterization and Identification of Arbuscular Mycorrhizal Fungi Species.
  8. Altmetric Badge
    Chapter 7 Molecular Identification of Soil Eukaryotes and Focused Approaches Targeting Protist and Faunal Groups Using High-Throughput Metabarcoding.
  9. Altmetric Badge
    Chapter 8 Identification and In Situ Distribution of a Fungal Gene Marker: The Mating Type Genes of the Black Truffle
  10. Altmetric Badge
    Chapter 9 Stable-Isotope Probing RNA to Study Plant/Fungus Interactions
  11. Altmetric Badge
    Chapter 10 Targeted Gene Capture by Hybridization to Illuminate Ecosystem Functioning.
  12. Altmetric Badge
    Chapter 11 Hybridization of Environmental Microbial Community Nucleic Acids by GeoChip.
  13. Altmetric Badge
    Chapter 12 Reconstruction of Transformation Processes Catalyzed by the Soil Microbiome Using Metagenomic Approaches.
  14. Altmetric Badge
    Chapter 13 MG-RAST, a Metagenomics Service for Analysis of Microbial Community Structure and Function.
  15. Altmetric Badge
    Chapter 14 Analysis of Active Methylotrophic Communities: When DNA-SIP Meets High-Throughput Technologies.
  16. Altmetric Badge
    Chapter 15 Functional Metagenomics: Construction and High-Throughput Screening of Fosmid Libraries for Discovery of Novel Carbohydrate-Active Enzymes.
  17. Altmetric Badge
    Chapter 16 Metatranscriptomics of Soil Eukaryotic Communities
  18. Altmetric Badge
    Chapter 17 Analysis of Ancient DNA in Microbial Ecology.
Attention for Chapter 4: Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons
Altmetric Badge

Citations

dimensions_citation
24 Dimensions

Readers on

mendeley
37 Mendeley
You are seeing a free-to-access but limited selection of the activity Altmetric has collected about this research output. Click here to find out more.
Chapter title
Sample Preparation for Fungal Community Analysis by High-Throughput Sequencing of Barcode Amplicons
Chapter number 4
Book title
Microbial Environmental Genomics (MEG)
Published in
Methods in molecular biology, January 2016
DOI 10.1007/978-1-4939-3369-3_4
Pubmed ID
Book ISBNs
978-1-4939-3367-9, 978-1-4939-3369-3
Authors

Karina Engelbrecht Clemmensen, Katarina Ihrmark, Mikael Brandström Durling, Björn D. Lindahl

Editors

Francis Martin, Stephane Uroz

Abstract

Fungal species participate in vast numbers of processes in the landscape around us. However, their often cryptic growth, inside various substrates and in highly diverse species assemblages, has been a major obstacle to thorough analysis of fungal communities, hampering exhaustive description of the fungal kingdom. Recent technological developments allowing rapid, high-throughput sequencing of mixed communities from many samples at once are currently having a tremendous impact in fungal community ecology. Universal DNA extraction followed by amplification and sequencing of fungal species-level barcodes such as the nuclear internal transcribed spacer (ITS) region now enable identification and relative quantification of fungal community members across well-replicated experimental settings.Here, we present the sample preparation procedure presently used in our laboratory for fungal community analysis by high-throughput sequencing of amplified ITS2 markers. We focus on the procedure optimized for studies of total fungal communities in humus-rich soils, wood, and litter. However, this procedure can be applied to other sample types and markers. We focus on the laboratory-based part of sample preparation, that is, the procedure from the point where samples enter the laboratory until amplicons are submitted for sequencing. Our procedure comprises four main parts: (1) universal DNA extraction, (2) optimization of PCR conditions, (3) production of tagged ITS amplicons, and (4) preparation of the multiplexed amplicon mix to be sequenced. The presented procedure is independent of the specific high-throughput sequencing technology used, which makes it highly versatile.

Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 37 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 37 100%

Demographic breakdown

Readers by professional status Count As %
Student > Master 9 24%
Researcher 9 24%
Student > Ph. D. Student 4 11%
Student > Bachelor 3 8%
Student > Doctoral Student 2 5%
Other 4 11%
Unknown 6 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 17 46%
Environmental Science 6 16%
Biochemistry, Genetics and Molecular Biology 5 14%
Veterinary Science and Veterinary Medicine 1 3%
Earth and Planetary Sciences 1 3%
Other 1 3%
Unknown 6 16%