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Abstract

To better describe the community structure of sulfate-reducing bacteria in environmental systems, we compared several dissimilatory sulfite reductase (dsr) primer sets for terminal restriction fragment length polymorphism application. A new reverse primer that increased allelic diversity estimates up to 5-fold was applied to hydrocarbon seep samples to examine the relationship between guild activity and diversity.

A major scientific challenge in ecology is to link community function with community structure. For the sulfate-reducing microorganisms (SRM) that make up a large polyphyletic guild, with species belonging to at least five bacterial phyla and two archaeal phyla (14), community diversity of SRM is often assessed by using the dissimilatory (bi)sulfite reductase (dSir [EC 1.8.99.3]) subunits encoded by dsrA and dsrB gene sequences as functional markers (1, 5, 11). While these genes exhibit high conservation, considerable polymorphisms exist at the traditionally targeted primer sites (18, 20). While a number of molecular methods have recently been employed to address the functional gene content of communities, such as functional gene arrays (19) or metatranscriptome sequencing (for example, reference 16), there is still a need for relatively inexpensive and high-throughput methods, like community fingerprinting.