Table of Contents

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

These data were published in Turk-Kubo et al. (2021). Table 1, Figure 3, Table S1, Table S2

Meaning different No Data values:

UD = undetected
na = not applicable
- - = parameter not measured
DNQ = detected, not quantified
Empty cells = means that the value reported in the average nifH L-1 column is quantified. 

Samples were collected using standard oceanographic techniques. A CTD Rosette with 24 10L Niskin bottles was lowered to the maximum sampling depth and then brought back to the surface. Methodology described in depth in Turk-Kubo et al. (2021)

Samples for the measurement of nitrate plus nitrite and phosphate (PO43−) concentrations were filtered through precombusted GF/F filters and analyzed using standard techniques on a Lachat QuikChem 8000 Flow Injection Analyzer. Chl a samples from each depth were filtered onto GF/F filters, extracted in the dark at 3 °C in 90% acetone for 24 h and measured fluorometrically using a Turner Fluorometer TD-700 as described in Welschmeyer et al.

For DNA collection and extraction, seawater was filtered through SterivexTM filters using gentle peristaltic pumping and flash-frozen in liquid N2. DNA was extracted using the DNeasy Plant Kit (Qiagen, Germantown, MD) using modifications to the manufacturer’s guidelines described in detail in Moisander et al. 2007. On-column steps were automated using a QIACube (Qiagen). DNA was quantified using the Picogreen® dsDNA Quantitation kit (Molecular Probes, Eugene, OR).

Gene-based abundance estimates of UCYN-A1, UCYN-A2, Crocosphaera (UCYN-B), Trichodesmium, Richelia associated with Hemiaulus (Het-2), and gamma A (γ-24774A11) were determined using Taqman® qPCR assays. Protocols used for all aspects of qPCR analysis, including reaction conditions, the use of linearized plasmids and inhibition reactions, and calculation of unknowns follow those described in detail by Goebel et al. 2010, apart from a 64 °C annealing temperature for the UCYN-A2 assay. The LOD and LOQ for all assays ranged between 25-31 and 200-250 nifH copies l−1, respectively. Targets with nifH copies >LOD and <LOQ are detected not quantified (DNQ).

Methodology described in depth in Turk-Kubo et al. (2021). 

NSF Award Abstract:
Nitrogen is a nutrient whose availability limits growth and productivity of ecosystems. Nitrogen is extremely abundant in the atmosphere in the inert form of gaseous N2, but most organisms cannot reduce N2 into a biologically available form. In all environments, including agricultural soils, there are microorganisms that can make available the N from gaseous N2 by reducing it to the biologically available form, ammonium. In the vast expanses of the open ocean, few organisms are known to have this ability, and recently a unique symbiosis between a single-celled cyanobacterium and a single-celled algae was discovered, which appears to be very widely distributed and likely of global biogeochemical significance. The cyanobacterium in this symbiotic partnership has very unusual metabolism and genomic streamlining. Little is known of the symbiosis because it is not detectable except by modern molecular biological techniques. Recent work has shown this symbiosis to be very widely spread through the oceans, and that there is previously unrecognized diversity in both the cyanobacterial and algal hosts. This research will examine the environmental distributions and the biogeochemical significance of this diversity in coastal US waters. The investigators will engage the public in ocean sciences through internship programs at local high schools and for undergraduate students at Stanford, and by documenting their field research in a 'virtual cruise' blog.

In the marine environment, the contribution of N2 fixation to the fixed nitrogen (N) pool is poorly quantified, in part due to an incomplete understanding on the abundance, activity, and physiology of diazotrophs. The symbiotic unicellular cyanobacteria (UCYN-A) is a poorly characterized, yet globally important, group of marine diazotrophs. UCYN-A is widely distributed in the marine environment, and lives symbiotically with a picoeukaryotic prymnesiophyte alga. We now know that there are multiple ecotypes of UCYN-A, which may be adapted to specific locations in the water-column and different oceanic provinces. Typically N2 fixation was considered unimportant in coastally influenced and non-tropical waters, however recent data shows that multiple subclades of UCYN-A are present. The distribution and rate of N2 fixation by UCYN-A subclades in coastal/nearshore environments is a major unknown in the oceanic N cycle. Its presence in nearshore waters may change the paradigm of the balance between basin N sources (N2 fixation) and sinks (denitrification). Likewise, significant N2 fixation by UCYN-A will need to be considered when determining estimates of new production in coastally influenced waters. This project aims to quantify the significance of different UCYN-A subclades to coastal/nearshore N budgets. It tackles the issue of determining N2 fixation rates by different UCYN-A subclades in coastal waters through rigorous fieldwork off the west coast of North America. The temporal and spatial distribution of UCYN-A subclades, as well as the rates of N2 fixation, will be determined by coupling N2 fixation measurements of bulk communities and individual cells (nanoSIMS) with molecular assays to study these widespread, but dilute, diazotrophic symbionts and their hosts. Additionally the investigators will conduct experiments aimed at constraining the effects of light and nutrient ratios (N/P) on UCYN-A N2 fixation rates, and the prymnesiophyte host's rate of carbon fixation. They will conduct this work through seasonal sampling of a coastal site in the Southern California Bight (Scripps Pier) and on two process cruises in the coastal waters between central California and the Baja Peninsula. The cruise work will provide an opportunity to understand the temporal dynamics of the UCYN-A/prymnesiophyte associations over larger spatial scales. Finally, evidence suggests that unidentified UCYN-A subclades and hosts exist and the investigators have developed a strategy to identify and quantify their temporal and spatial distributions as well as their N2 fixation activities. Data on the coastal distribution, ecology and activity of UCYN-A is critical for obtaining a better understanding of their contribution to fixed N to the marine environment. The group-specific and bulk rates of N2 fixation measured in this study of coastally influenced waters, will provide data for future modeling efforts, which will make an important contribution to constraining oceanic N2 fixation inputs.