Table of Contents

• Coverage
• Dataset Description
  • Methods & Sampling
• Data Files
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

This dataset contains data related to spatiotemporal characterization of nirK and nirS Abundance in San Francisco Bay. Data include sampling information (e.g. latitude, longitude, date, water temperature), bottom chemistry (e.g. salinity, nitrate, ammonium), sediment chemistry (e.g. porosity, total carbon, Mg, C/N), and sediment nirK and nirS gene abundance per ng DNA and per gram dry sediment.

nirK = copper-containing nitrite reductase
nirS = cytochrome-cd1 nitrite reductase

These data were published in Lee and Franics, 2017:
Lee, J. A., and C. A. Francis. 2017. Spatiotemporal characterization of San Francisco Bay denitrifying communities: a comparison of nirK and nirS diversity and abundance. Microbial Ecology 73(2): 271-284. doi: 10.1007/s00248-016-0865-y

For related datasets, click on the project link at the top of the page.

Field sampling:

Sampling was conducted between July 2011 and June 2012 aboard monthly full-bay cruises on the R/V Polaris carried out by the US Geological Survey (USGS; Menlo Park, CA, external link). Sediment samples were collected by overboard Van Veen grab. Surface cores were collected using sterile 1-cc and 6-cc cut-off syringes, placed immediately on dry ice, and stored at -80C until processing. Bottom water was caught in the grab simultaneously with the sediment. Due to logistical difficulties, no samples were collected at site 21 in December 2011, or at any sites in April 2012.

Sediment and water chemical measurements. Salinity and temperature were measured

on-site using a YSI 556 MPS handheld multiparameter instrument (YSI Inc, OH). Subsamples of water for nutrient analyses were filtered through a 0.2 um PES syringe filter, placed on dry ice, and then stored at -80C until processing. Bottom water NO2- and NO3- concentrations were measured using a WestCo SmartChem 200 Discrete Analyzer (Unity Scientific, Brookfield, CT), and NH4+ was measured using the salicylate-hypochlorite method. In preparation for sediment chemical measurements, frozen sediment samples were thawed and air-dried, then ground, sieved, and homogenized. Total C and N were measured on a Carlo Erba NA1500 Elemental Analyzer (Val de Reuil, France) using an atropine standard curve, and total content of specific elements (Al, Cl, Mg, Na, P, S, Cu, Fe, Mn, Pb) was measured on a Spectro Xepos HE XRF Spectrometer (Kleve, Germany). Sediment samples were weighed before and after drying for calculation of gravimetric water content.

Nucleic acid extraction and gene abundance measurements:

Total DNA was extracted in triplicate, from the surface 1-cm of sediment of each of 3 cores from each site, using the FastDNA Spin Kit for Soil (MP Biomedicals, Solon, OH) following the manufacturer’s instructions. Abundances of nirK, nirS, and bacterial 16S rRNA genes were measured using quantitative real-time PCR on the StepOnePlus Real-Time PCR system (Applied Biosystems, Foster City, CA), as described in Lee and Francis (2017). Each of the three DNA extractions from each sample was quantified in a separate reaction, with each reaction run in triplicate. A fresh 8-point standard curve was run on each reaction plate using 10-fold dilutions of a linearized plasmid containing an amplicon of the appropriate gene that had previously been PCR-amplified from San Francisco Bay sediment and sequenced.

            From DNA samples collected at each site in July 2011, October 2011, January 2012, and May 2012, nirK and nirS gene fragments were PCR amplified, cloned, and sequenced, as described in Lee and Francis (2017). The nucleotide sequences reported in this study have been deposited in GenBank under accession numbers KR060094 - KR060621 (for nirK) and KR060622 - KR061281 (for nirS).

Description from the NSF award abstract:

This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).

Although nitrogen (N) acts as a limiting nutrient in many marine ecosystems, from estuaries to the open ocean, N in excess can be extremely detrimental. Eutrophication is of particular concern in estuaries, with over half of the estuaries in the United States experiencing its effects. Harmful levels of N in estuaries can be diminished through tightly coupled processes in the microbial nitrogen cycle, including nitrification (chemoautotrophic oxidation of ammonia to nitrite and nitrate) and denitrification (the dissimilatory reduction of nitrate to N2 gas). In fact, coupled nitrification-denitrification can remove up to 50% of external dissolved inorganic nitrogen inputs to estuaries, thereby reducing the risk of eutrophication. Despite the biogeochemical importance of both nitrification and denitrification in estuarine systems, surprisingly little is known regarding the underlying microbial communities responsible for these processes, or how they are influenced by key physical/chemical factors.

The investigators will work in San Francisco Bay - the largest estuary on the west coast of the United States - using molecular, biogeochemical and cultivation approaches to explore how the distribution, diversity, abundance, and activities of key N-cycling communities are influenced by environmental gradients over temporal and spatial scales. Denitrifying communities will be studied using functional genes (nirK and nirS) encoding the key denitrification enzyme nitrite reductase, while genes encoding ammonia monooxygenase subunit A (amoA) will be used to study both ammonia-oxidizing bacteria (AOB) and the recently-discovered ammonia-oxidizing archaea (AOA)- members of one of the most ubiquitous and abundant prokaryotic groups on the planet, the mesophilic Crenarchaeota. Analyzing sediments from sites spanning a range of physical and chemical conditions in the Bay, seasonally over the course of several years, will represent an unprecedented opportunity to examine spatial, physical/chemical, and temporal effects on both denitrifier and ammonia-oxidizer communities in this large, urban estuary. Concurrently, an intensive cultivation effort will also be undertaken, in order to compile a novel culture collection of estuarine denitrifiers and ammonia-oxidizers, for which virtually nothing is currently known. Taken together, these complimentary approaches will help reveal how complex physical/chemical gradients influence the diversity and functioning of key estuarine N-cycling communities over time and space.