Table of Contents

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

Samples collected from the Monterey Bay Time Series from May 2014 to February 2016. These data include CTD, nutrient, chlorophyll a and paeopigment concentration data. 

These data were published in Tolar et al., submitted (Table S1)

The water column in Monterey Bay (coastal California, USA) was sampled near-monthly from May 2014-February 2016 at stations M1 (36.747 ºN, 122.022 ºW) and M2 (36.697 ºN, 122.378 ºW), on board the RV Western Flyer or RV Rachel Carson using a CTD Rosette sampler (Sea-Bird Scientific, Bellevue, WA). For each hydrocast, the CTD collected data on conductivity, temperature, depth, dissolved oxygen (DO), total CO2, and transmissivity (turbidity). Additional samples were collected from 11-12 depths from the cast (0, 5, 10, 20, 30, 40, 60, 80, 100, 150, 200 m; 500 m included for 2015-2016) to measure nutrients (ammonia, nitrite, nitrate, silicate, phosphate), chlorophyll a and phaeopigment concentrations. These were processed using established methods as part of the Monterey Bay Time Series (http://www3.mbari.org/bog/Projects/CentralCal/summary/ts_methods_and_materials.htm; Pennington and Chavez 2000). Light penetration depth (LPD; 0.1-50 % of surface light) was estimated by secchi disk.

Approximately 1 L sample seawater was filtered using a peristaltic pump onto duplicate filters – 10 µm polycarbonate (PCTE, Sterlitech; pre-filter), 0.2 µm GVWP (Millipore; final filter) – for molecular analysis from 6-10 depths per site per month (0-500 m depth). Samples were immediately frozen on liquid N2 and stored at -80°C upon return to laboratory until processing.

DNA was co-extracted with RNA using previously described methods (Smith et al. 2014a), with slight modification – both 0.1 and 0.5 mm sterile glass beads (BioSpec) were used for bead beating on the FastPrep (Thermo) and fresh -mercaptoethanol was added to Lysis/Binding buffer (10 µL per mL) immediately before extraction. Concentration of DNA was measured using a Qubit fluorometer (Invitrogen). Gene abundance was determined using published methods for total archaeal amoA (Francis et al. 2005), water column group A (WCA) and water column group B (WCB) amoA (Beman et al. 2008); modified to TaqMan assay, (Mosier and Francis 2011), and two archaeal nirK groups (AnirKa and AnirKb; Lund et al. 2012). 

Water samples were collected from 6-10 depths for nitrification rate measurements using 15NH4Cl as a tracer. Sample seawater was spiked with 15NH4Cl, and placed in ship-board seawater flow-through incubators for 24 h. Incubations were carried out in the dark or at estimated in situ light using stainless steel tubes with pre-drilled evenly spaced and sized holes (Pennington and Chavez 2000; Smith et al. 2014). At the end of incubations, samples were filtered (0.2 µm) and frozen at -20 ºC. δ15N values were measured from NOx in each sample, converted to N2O via the bacterial denitrification assay (Sigman et al. 2001) using a ThermoFinnigan Gas Bench and PreCon trace gas concentration system interfaced with the Delta VPLUS isotope-ratio mass spectrometer (Bremen, Germany) at the UC Davis Stable Isotope Facility.

BCO-DMO processing notes:

• Units (%) removed from column Light_Penetration_Depth
• Adjusted column header names

Description from NSF award abstract:
Because the first and rate-limiting step of nitrification, ammonia oxidation, was long believed to be restricted to a few groups within the domain Bacteria, the discovery of ammonia-oxidizing archaea (AOA) - members of one of the most abundant microbial groups on the planet (now known as the Thaumarchaeota) - has seriously challenged our understanding of the microbial ecology and biogeochemistry of the nitrogen cycle. AOA are now believed to be responsible for the majority of nitrification in the sea, and occur in the marine water column as two taxonomically distinct groups, namely the Water Column Group A (WCA) and B (WCB) ecotypes. An open question in marine biogeochemistry is whether the taxonomic definition of WCA and WCB and their observed distributions correspond to distinct ecological and biogeochemical niches. To fill this critical knowledge gap, this project will examine linkages between patterns of ecotype-specific archaeal ammonia monooxygenase (amoA) gene abundance and expression and 15N-based nitrification rates across multiple depths (0-500m) and two stations within the Monterey Bay Time Series (MBTS). Acquiring quantitative expressional and biogeochemical activity data from a wide array of water column samples from the MBTS, bimonthly over the course of two years, will yield valuable new insights into how archaeal ammonia oxidation and AOA ecotype dynamics are influenced by changes in ocean conditions.

The discovery of AOA has served to refocus attention on nitrification in the ocean; however, there are still an alarmingly low number of direct measurements of oceanic ammonia oxidation rates. This paucity of data has made it difficult to accurately quantify the degree to which nitrification supports primary production in the global ocean. One major goal of this project is to ascertain whether a quantitative relationship between the abundance of AOA genes and transcripts and instantaneous rates of nitrification exists for the coastal ocean. Prior collaboration indicated a strong correlation between 15N-based nitrification rates and archaeal amoA gene copies in surface waters of northern Monterey Bay. This study will acquire a more holistic understanding of this relationship by performing these measurements as part of the MBTS, not only at depths in the euphotic zone - where the biogeochemical importance of nitrification is hotly debated - but also within disphotic and aphotic waters of the mesopelagic. By conducting this research as part of the 23 year MBTS, the resultant dataset will be incorporated into a larger oceanographic framework. These efforts will also directly connect to a goal of the MBTS to determine spatiotemporal patterns in new and regenerated primary production by providing new quantitative insights into processes responsible for regenerated nitrogen production in the photic zone. Additionally, the extensive collections of microbial sequence and biogeochemical data generated through this study will provide a valuable resource to the scientific community and, ultimately, help reveal new information about the ecology and factors regulating nitrification in the ocean, greatly advancing our ability to model its role in N and C cycles under present and future conditions.