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Applied and Environmental Microbiology, July 2008, p. 4440-4453, Vol. 74, No. 14
0099-2240/08/$08.00+0     doi:10.1128/AEM.02692-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.

Characterization of Nitrifying, Denitrifying, and Overall Bacterial Communities in Permeable Marine Sediments of the Northeastern Gulf of Mexico ^,

Heath J. Mills,^1,2 Evan Hunter,¹ Mike Humphrys,¹ Lee Kerkhof,³ Lora McGuinness,³ Markus Huettel,¹ and Joel E. Kostka^1*

Department of Oceanography, Florida State University, Tallahassee, Florida 32306,¹ Department of Oceanography, Texas A&M University, College Station, Texas 77843,² Institute of Marine and Coastal Sciences, Rutgers University, New Brunswick, New Jersey 08901³

Received 29 November 2007/ Accepted 12 May 2008

Sandy or permeable sediment deposits cover the majority of the shallow ocean seafloor, and yet the associated bacterial communities remain poorly described. The objective of this study was to expand the characterization of bacterial community diversity in permeable sediment impacted by advective pore water exchange and to assess effects of spatial, temporal, hydrodynamic, and geochemical gradients. Terminal restriction fragment length polymorphism (TRFLP) was used to analyze nearly 100 sediment samples collected from two northeastern Gulf of Mexico subtidal sites that primarily differed in their hydrodynamic conditions. Communities were described across multiple taxonomic levels using universal bacterial small subunit (SSU) rRNA targets (RNA- and DNA-based) and functional markers for nitrification (amoA) and denitrification (nosZ). Clonal analysis of SSU rRNA targets identified several taxa not previously detected in sandy sediments (i.e., Acidobacteria, Actinobacteria, Chloroflexi, Cyanobacteria, and Firmicutes). Sequence diversity was high among the overall bacterial and denitrifying communities, with members of the Alphaproteobacteria predominant in both. Diversity of bacterial nitrifiers (amoA) remained comparatively low and did not covary with the other gene targets. TRFLP fingerprinting revealed changes in sequence diversity from the family to species level across sediment depth and study site. The high diversity of facultative denitrifiers was consistent with the high permeability, deeper oxygen penetration, and high rates of aerobic respiration determined in these sediments. The high relative abundance of Gammaproteobacteria in RNA clone libraries suggests that this group may be poised to respond to short-term periodic pulses of growth substrates, and this observation warrants further investigation.

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* Corresponding author. Mailing address: Department of Oceanography, Florida State University, FSU Collins Research Lab, 255 Atomic Way, Bldg. 42, Tallahassee, FL 32306-4470. Phone: (850) 644-5719. Fax: (850) 644-2581. E-mail: jkostka{at}ocean.fsu.edu

Published ahead of print on 16 May 2008.

Supplemental material for this article may be found at http://aem.asm.org/.

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Applied and Environmental Microbiology, July 2008, p. 4440-4453, Vol. 74, No. 14
0099-2240/08/$08.00+0     doi:10.1128/AEM.02692-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.