Dataset: Potential nitrification rates and ammonia oxidizer gene abundances collected on R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007

Final no updates expectedDOI: 10.1575/1912/bco-dmo.654371.1Version 1 (2016-08-18)Dataset Type:Cruise Results

Lead Principal Investigator: Christopher Francis (Stanford University)

BCO-DMO Data Manager: Hannah Ake (Woods Hole Oceanographic Institution)


Project: Spatial and Temporal Dynamics of Nitrogen-Cycling Microbial Communities Across Physicochemical Gradients in the San Francisco Bay Estuary (N-Cycling Microbial Communities)


Abstract

Potential nitrification rates and ammonia oxidizer gene abundances collected on R/V Endeavor (SQO-Delta) in the San Francisco Bay Delta during September and October 2007

Surface sediment samples were collected for potential nitrification rates, using sediment slurries with filtered site water. Ammonia oxidizer gene abundances (AOA and AOB amoA) were quantified using qPCR, and clone libraries for each gene were sequenced using Sanger sequencing.

Related Manuscript: Damasheck et al., 2015

 


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Related Publications

General

Damashek, J., Smith, J. M., Mosier, A. C., & Francis, C. A. (2015). Benthic ammonia oxidizers differ in community structure and biogeochemical potential across a riverine delta. Frontiers in Microbiology, 5. doi:10.3389/fmicb.2014.00743
Methods

Francis, C. A., Roberts, K. J., Beman, J. M., Santoro, A. E., & Oakley, B. B. (2005). Ubiquity and diversity of ammonia-oxidizing archaea in water columns and sediments of the ocean. Proceedings of the National Academy of Sciences, 102(41), 14683–14688. doi:10.1073/pnas.0506625102
Methods

Legendre, P., and Legendre, L. (2012). Numerical Ecology, 3rd Edn. San Francisco, CA: Elsevier.
Methods

Lozupone, C., Hamady, M., & Knight, R. (2006). UniFrac - An online tool for comparing microbial community diversity in a phylogenetic context. BMC Bioinformatics, 7(1), 371. doi:10.1186/1471-2105-7-371
Methods

Mosier, A. C., & Francis, C. A. (2008). Relative abundance and diversity of ammonia-oxidizing archaea and bacteria in the San Francisco Bay estuary. Environmental Microbiology, 10(11), 3002–3016. doi:10.1111/j.1462-2920.2008.01764.x