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Book Chapter

Chapter 8: Identification and Evaluation of Molecular Bioindicators of Natural Hydrocarbon Seepage in Gulf of Mexico Sediments

By
Matthew Ashby
Matthew Ashby
Taxon Biosciences, Inc., Tiburon, California, U.S.A. E-mail: ashbym@taxon.com.
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Sa Vanna Baker Leyva
Sa Vanna Baker Leyva
Taxon Biosciences, Inc., Tiburon, California, U.S.A. E-mail: ashbym@taxon.com.
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Kimberley Cook
Kimberley Cook
Taxon Biosciences, Inc., Tiburon, California, U.S.A. E-mail: ashbym@taxon.com.
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Patrick Mulroy
Patrick Mulroy
Taxon Biosciences, Inc., Tiburon, California, U.S.A. E-mail: ashbym@taxon.com.
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Karen Nelson
Karen Nelson
The J. Craig Venter Institute, Rockville, Maryland, U.S.A.
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Michael A. Abrams
Michael A. Abrams
Apache Corp., Houston, Texas, U.S.A.
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Dago Dimster-Denk
Dago Dimster-Denk
Taxon Biosciences, Inc., Tiburon, California, U.S.A. E-mail: ashbym@taxon.com.
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Published:
January 01, 2013

Abstract

Microbial communities inhabiting prolific hydrocarbon seeps in the Gulf of Mexico have been characterized by culture-independent DNA profiling of 16S ribosomal RNA (rRNA) genes. High-throughput 454 pyrosequencing was combined with serial analysis of ribosomal DNA (SARD) to vastly increase the number and, hence, sensitivity and accuracy of microbial 16S rRNA gene detection. This approach enabled the detection of more than 5 million ribosomal sequence tags and revealed that approximately one-third of the sequence tags showed a similar distribution among the sediment piston-core samples compared to the major hydrocarbon constituents present in the seeps. Numerous correlated distributions or associations were found between particular microbial DNA sequences and specific hydrocarbons, suggesting a biochemical role in the transformation of these compounds. Quantitative polymerase chain reaction (qPCR) primers were designed to target these 16S rRNA gene sequences and were found to accurately detect and serve as sensitive bioindicators for these hydrocarbons in blind tests. The results underscore the need for a thorough characterization of geochemistry and microbiology to fully understand the dynamics of these biogeochemical associations.

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Contents

Geophysical Developments Series

Hydrocarbon Seepage: From Source to Surface

Fred Aminzadeh
Fred Aminzadeh
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Timothy B. Berge
Timothy B. Berge
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David L. Connolly
David L. Connolly
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Society of Exploration Geophysicists
Volume
16
ISBN electronic:
9781560803119
Publication date:
January 01, 2013

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