Microarray-Based Analysis of Functional Genes in Sediments from the Gulf of Mexico

Author(s): Wu, L.Y.; Kellogg, L.E.; Schadt, C.W.; Devol, A.H.; Tiedje, J.M.; Zhou, J.Z. | Abstract: Marine sediments play important roles in global biogeochemical processes such as carbon degradation and nutrient cycles. To determine the metabolic potential and structure of marine sediment microbial communities, marine sediments were collected from two collection stations (GMT and GMS) in the Gulf of Mexico and analyzed with a functional gene array containing g2000 probes from the genes involved in carbon fixation, organic carbon degradation, contaminant degradation, metal resistance, and nitrogen, sulfur, and phosphorous cycling. Several environmental variables were also measured, including ammonium, nitrate, sulfate, phosphorus, and sulfate reduction. A total of 1343 genes or 67% of the probes showed significant hybridization with at least one of the 12 samples. A total of 722 genes were detected at GMT and 844 were detected at GMS. Two times more genes on the array hybridized in the deep sediments (GMT-11 and GMS-11) than those in the top sediments (GMT-1, GMS-1). Simpson s reciprocal diversity index (1/D) indicated much higher levels of genetic diversity in the deep sediment samples (204.9 for GMT-11 and 201.6 for GMS-11) than the top sediment samples (e.g., 118.4 for GMT-1, and 121.9 for GMS-1). We found no overall correlation among the measured environmental variables and the functional gene community. However, specific gene groups showed significant relationships with specific environmental variables. Our results indicate that while geochemistry may not explain changes in community structure, overall; geochemistry may be related to specific functional guilds. Additionally, distance plays a large role in community structure for these sediment cores where near-neighbor shows the greatest similarity.