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Applied and Environmental Microbiology, July 2008, p. 4516-4529, Vol. 74, No. 14
0099-2240/08/$08.00+0 doi:10.1128/AEM.02751-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity in Marine Sediments from the Gulf of Mexico 
,
Liyou Wu,1,3,
Laurie Kellogg,1
Allan H. Devol,2
James M. Tiedje,4 and
Jizhong Zhou1,3,*
Institute for Environmental Genomics and Department of Botany and Microbiology, University of Oklahoma, Norman, Oklahoma 73019,1 School of Oceanography, University of Washington, Seattle, Washington 982954,2 Environmental Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831,3 Center for Microbial Ecology, Michigan State University, East Lansing, Michigan 488244
Received 6 December 2007/ Accepted 21 May 2008
Marine sediments of coastal margins are important sites of carbon sequestration and nitrogen cycling. To determine the metabolic potential and structure of marine sediment microbial communities, two cores were collected each from the two stations (GMT at a depth of 200 m and GMS at 800 m) in the Gulf of Mexico, and six subsamples representing different depths were analyzed from each of these two cores using functional gene arrays containing 
2,000 probes targeting genes involved in carbon fixation; organic carbon degradation; contaminant degradation; metal resistance; and nitrogen, sulfur, and phosphorous cycling. The geochemistry was highly variable for the sediments based on both site and depth. A total of 930 (47.1%) probes belonging to various functional gene categories showed significant hybridization with at least 1 of the 12 samples. The overall functional gene diversity of the samples from shallow depths was in general lower than those from deep depths at both stations. Also high microbial heterogeneity existed in these marine sediments. In general, the microbial community structure was more similar when the samples were spatially closer. The number of unique genes at GMT increased with depth, from 1.7% at 0.75 cm to 18.9% at 25 cm. The same trend occurred at GMS, from 1.2% at 0.25 cm to 15.2% at 16 cm. In addition, a broad diversity of geochemically important metabolic functional genes related to carbon degradation, nitrification, denitrification, nitrogen fixation, sulfur reduction, phosphorus utilization, contaminant degradation, and metal resistance were observed, implying that marine sediments could play important roles in biogeochemical cycling of carbon, nitrogen, phosphorus, sulfate, and various metals. Finally, the Mantel test revealed significant positive correlations between various specific functional genes and functional processes, and canonical correspondence analysis suggested that sediment depth, PO43–, NH4+, Mn(II), porosity, and Si(OH)4 might play major roles in shaping the microbial community structure in the marine sediments.
* Corresponding author. Mailing address: Institute for Environmental Genomics, University of Oklahoma, Norman, OK 73019. Phone: (405) 325-6073. Fax: (405) 325-7552. E-mail: jzhou{at}ou.edu
Published ahead of print on 30 May 2008.
Supplemental material for this article may be found at http://aem.asm.org/.
L.W. and J.Z. contributed equally to this study.
Applied and Environmental Microbiology, July 2008, p. 4516-4529, Vol. 74, No. 14
0099-2240/08/$08.00+0 doi:10.1128/AEM.02751-07
Copyright © 2008, American Society for Microbiology. All Rights Reserved.
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