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Direct analysis of sulfate reducing bacterial communities in gas hydrate-impacted marine sediments by PCR-DGGE

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Formolo,  M.
Department of Biogeochemistry, Max Planck Institute for Marine Microbiology, Max Planck Society;

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Citation

Bagwell, C., Formolo, M., Ye, Q., Yeager, C., Lyons, T., & Zhang, C. (2009). Direct analysis of sulfate reducing bacterial communities in gas hydrate-impacted marine sediments by PCR-DGGE. Journal of Basic Microbiology, 49, S87-S92.


Cite as: http://hdl.handle.net/21.11116/0000-0001-CCB1-1
Abstract
Molecular investigations of the sulfate reducing bacteria that target the dissimilatory sulfite- reductase subunit A gene (dsrA) are plagued by the nonspecific performance of conventional PCR primers. Here we describe the incorporation of the FailSafe™ PCR System to optimize en- vironmental analysis of dsrA by PCR amplification and denaturing gradient gel electrophoresis. PCR–DGGE analysis of dsrA composition revealed that SRB diversity was greater and more variable throughout the vertical profile of a marine sediment core obtained from a gas hydrate site (GC234) in the Gulf of Mexico than in a sediment core collected from a nearby site devoid of gas hydrates (NBP). Depth profiled dsrB abundance corresponded with sulfate reduction rates at both sites, though measurements were higher at GC234. This study exemplifies the numeri- cal and functional importance of sulfate reducing bacteria in deep-sea sedimentary environ- ments, and incremental methodological advancements, as described herein, will continue to streamline the analysis of sulfate reducer communities in situ.