Using QIIME to Evaluate the Microbial Communities Within Hydrocarbon Environments View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2015

AUTHORS

Luke K. Ursell , Adam Robbins-Pianka , Nicole Scott , Antonio Gonzalez , Dan Knights , Jai Ram Rideout , Ajay Kshatriya , J. Gregory Caporaso , Rob Knight

ABSTRACT

Interest in the microbiology of hydrocarbon-rich environments has increased rapidly in recent years, with applications ranging from oil spill cleanup to reservoir management. Modern techniques for reading out microbial communities using high-throughput sequencing produce vast amounts of data that cannot be processed by traditional methods. Here, we describe the use of the QIIME (Quantitative Insights into Microbial Ecology) pipeline for analyzing hydrocarbon-rich samples. This pipeline starts with the raw data from high-throughput sequence analysis and produces graphical and statistical analyses suitable for publication or for decision support. We illustrate the use of the QIIME pipeline using several recent datasets including sediments and water from the Deepwater Horizon spill and crude oil from a hydraulically fractured oil field in the United States, allowing better understanding of the microbiology of these systems. QIIME is a free, open-source software and can be deployed on systems ranging from laptops to cloud computing environments. More... »

PAGES

89-113

References to SciGraph publications

  • 2010-01. Fast UniFrac: facilitating high-throughput phylogenetic analyses of microbial communities including analysis of pyrosequencing and PhyloChip data in THE ISME JOURNAL
  • 2010-05. QIIME allows analysis of high-throughput community sequencing data in NATURE METHODS
  • 2012-08. Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms in THE ISME JOURNAL
  • 2014-05. Comparison of bacterial community in aqueous and oil phases of water-flooded petroleum reservoirs using pyrosequencing and clone library approaches in APPLIED MICROBIOLOGY AND BIOTECHNOLOGY
  • 2012-03. An improved Greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea in THE ISME JOURNAL
  • 2013-01. Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing in NATURE METHODS
  • 2014-12. The Earth Microbiome project: successes and aspirations in BMC BIOLOGY
  • 2011-09. Bayesian community-wide culture-independent microbial source tracking in NATURE METHODS
  • 2009-09. The 'rare biosphere': a reality check in NATURE METHODS
  • 2012-07. Comparison of Illumina paired-end and single-direction sequencing for microbial 16S rRNA gene amplicon surveys in THE ISME JOURNAL
  • 2014-07. Metagenomics reveals sediment microbial community response to Deepwater Horizon oil spill in THE ISME JOURNAL
  • 2012-12. The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome in GIGASCIENCE
  • 2010-08. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences in GENOME BIOLOGY
  • 2013-12. EMPeror: a tool for visualizing high-throughput microbial community data in GIGASCIENCE
  • Book

    TITLE

    Hydrocarbon and Lipid Microbiology Protocols

    ISBN

    978-3-662-49309-0
    978-3-662-49310-6

    Identifiers

    URI

    http://scigraph.springernature.com/pub.10.1007/8623_2015_175

    DOI

    http://dx.doi.org/10.1007/8623_2015_175

    DIMENSIONS

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