The coastal Everglades landscape may be viewed as an oligotrophic gradient of P limitation in the freshwater marsh to N limitation at the marine boundary of the estuaries (Boyer 2003). Sediment bacteria are known to play an important role in nutrient cycling and recognized to be influenced by the environmental conditions. However, the general questions linking between sediment bacterial communities and ecosystem functioning remain unanswered. For example: 1) Do bacterial communities change along aquatic P and N gradients, and if so, how? 2) Are the bacterial communities influenced more by changes in salinity or plant community types? 3) Do sediment nutrient concentrations have a significant effect on the distribution of bacterial communities? One approach to answer these questions is to fully characterize the bacterial communities in such a gradient and relate their distribution to the existing conditions. In previous study, we investigated the sediment bacterial communities in Everglades marsh, mangrove forest, and Florida Bay seagrass meadow using PCR-DGGE and sequence analyses, and estimated that the salinity was the primary factor to change the bacterial communities for the large succession between Everglades marsh, mangrove forest and Florida Bay (Ikenaga and Boyer in prep.). In this study, we focused on evaluating the effects of P and N gradients on sediment bacterial communities. Eastern Florida Bay is considered a P limited system whereas the western bay is more N limited. Sediment samples were collected in six sites distributed throughout Florida Bay where P, N, and both P and N application plots, and control plots were previously established (Armitage et al. 2005). These sites have undergone bimonthly fertilizer application since October 2002. We then investigated the bacterial communities using PCR-DGGE analysis. Based on the DGGE patterns, many different types of bacteria were found to inhabit the sediments irrespective of sampling sites and fertilizer applications (47-56 bands). Shannon-Weaver index showed that bacterial diversity in east, as influenced by the runoff from Everglades, was higher than in western bay. Cluster analysis showed that the bacterial communities changed largely according to the natural aquatic nutrient gradient existing in Florida bay. The application of fertilizers was not as strong as an influence on bacterial communities. However some effect of P applications on the bacterial communities was found in a few DGGE bands, especially P and NP application plots in eastern and central sites, where P is more limiting. Therefore, the addition of N had no effect on sediment bacterial communities. Second, the addition of P had small effect, but only in P limited areas. Finally, the sediment fertilization experiments were overshadowed by the effects of the natural ecosystem nutrient and salinity gradient on the distribution of bacterial community types.