MICROBIOLOGY OF AQUATIC SYSTEMS Changes in Sediment Bacterial Community in Response to Long-Term Nutrient Enrichment in a Subtropical Seagrass-Dominated Estuary Rafael Guevara & Makoto Ikenaga & Amanda L. Dean & Cristina Pisani & Joseph N. Boyer Received: 25 May 2012 /Accepted: 4 April 2014 # Springer Science+Business Media New York 2014 Abstract Florida Bay exhibits a natural gradient of strong P limitation in the east which shifts to weak P or even N limitation at the western boundary. This nutrient gradient greatly affects seagrass abundance and productivity across the bay. We assessed the effects of N and P additions on sediment bacterial community structure in relation to the existing nutrient gradient in Florida Bay. Sediment samples from 24 permanent 0.25 m 2 plots in each of six sites across Florida Bay were fertilized with granular N and P in a factorial design for 26 months. Sediment bacterial community structure was analyzed using PCR-denaturing gradient gel electropho- resis (DGGE) analysis of 16S ribosomal RNA (rRNA) genes and a cloning strategy from DGGE bands. The phylogenetic positions of 16S rRNA sequences mostly fell into common members found in marine sediments such as sulfate-reducing Deltaproteobacteria, Gammaproteobacteria, Spirochaetes, and Bacteriodetes. Twenty-eight common DGGE bands were found in all sediment samples; however, some DGGE bands were only found or were better represented in eastern sites. Bacterial community diversity (Shannon-Weiner index) showed similar values throughout all sediment samples. The N treatment had no effect on the bacterial community struc- tures across the bay. Conversely, the addition of P significantly influenced the bacterial community structure at all but the most western site, where P is least limiting due to inputs from the Gulf of Mexico. P additions enhanced DGGE band se- quences related to Cytophagales, Ectothiorhodospiraceae, and Desulfobulbaceae, suggesting a shift toward bacterial com- munities with increased capability to degrade polymeric or- ganic matter. In addition, a band related to Deferribacteres was enhanced in eastern sites. Thus, indigenous environmental conditions were the primary determining factors controlling the bacterial communities, while the addition of P was a secondary determining factor. This P-induced change in com- munity composition tended to be proportional to the amount of P limitation obviated by the nutrient additions. Introduction Both natural and anthropogenic additions of nutrients to coast- al ecosystems are important drivers of community structure and function of aquatic ecosystems [1]. Much information has been generated concerning nutrient effects on species diversi- ty of phytoplankton [ 2 –4 ], bacterioplankton [ 5 –10 ], seagrasses [ 11–15], macroalgae [ 11, 16, 17], benthic microalgae [18–22], and sediment bacterial community struc- ture in habitats dominated by Spartina alterniflora [5, 23, 24]. However, despite the ecological and economic importance of seagrass meadows, the bacterial diversity response to nutrient additions has been poorly studied in these habitats. Sediment bacterial communities play an important role in nutrient cy- cling and are influenced by environmental conditions. Bacterial activities in sediments have been shown to be affect- ed by nutrient additions. Nilsson et al. [25] showed that nutrient additions had a significant effect on bacterial biomass and activity. Lopez et al. [26] found that the addition of N to Posidonia oceanica plots significantly increased ammonifica- tion rates and bacterial exoenzymatic activities and enhanced bacterial decomposition of seagrass-derived carbon. R. Guevara : A. L. Dean : C. Pisani : J. N. Boyer (*) Southeast Environmental Research Center, OE-148, Florida International University, Miami, FL 33199, USA e-mail: jnboyer@mail.plymouth.edu M. Ikenaga Laboratory of Soil Science, Faculty of Agriculture, Kagoshima University, 1-21-24 Korimoto, Kagoshima 890-0081, Japan J. N. Boyer Center for the Environment, Plymouth State University, 17 High Street, MSC-63, Plymouth NH 03264, USA Microb Ecol DOI 10.1007/s00248-014-0418-1 Author's personal copy