Dataset: Nitrite reductase genes sequence accessions
Deployment: RMP_2004_Sediment

Sediment samples (upper 5-cm) were collected in conjunction with the Regional Monitoring Program (RMP) managed by the San Francisco Estuary Institute (http://www.sfei.org/). Surface sediment was retrieved using a modified Van Veen grab, and cores were taken from each grab sample using sterile, cut-off 5 mL syringes and immediately placed on dry ice prior to storage at –80C. DNA was extracted from approximately 250–300 mg of sediment from the upper 5 mm of the cores using the FastDNA SPIN kit for soil (MP Biomedicals) with a 30 s bead beating time at speed 5.5. Duplicate DNA extractions were performed for each sediment core. Sediment DNA extracts were PCR amplified with primers targeting nirK and nirS: nirK583FdegCF(5′-TCATGGTGCTGCCGCGYGANGG; Santoro et al., 2006) and nirK5R (Braker et al., 1998); nirS1F and nirS6R (Braker et al., 1998). Clone libraries of nirK and nirS gene fragments were constructed using the TOPO TA cloning(R) kit (Invitrogen) and 28–45 clones from each library were sequenced (ABI 3100 Capillary Sequencer). Sequences reported in this study have been deposited in GenBank under Accession No. GQ454031 to GQ454413 for nirK and GQ453671 to GQ454030 for nirS.