Table of Contents

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

Sediment cores were collected in the northwest Pacific Ocean off the coast of San Francisco, CA on the R/V Oceanus during cruise OC1703A in March 2017 and in the northeast Atlantic off the coast of Woods Hole, MA on the R/V Atlantis during cruise AT36 in July 2016. Sediment cores in the northwest Pacific were 15–30 cm long and collected at five sites (100–4475 water depths) using an MC-800 multicore (Ocean Instruments). Sediment cores in the northeast Atlantic were 15 cm long and collected at two sites (1252–1496 water depth) using an MC-400 multicore (Ocean Instruments). Both multicores were modified with Go-Pro cameras in custom pressure housing to provide real-time video feeds and guide sampling (MISO Facility, Woods Hole Oceanographic Institute). Cores were stored at 4ºC for ≤24 hours until they were sectioned on board in 2.5, 3 or 5 cm depth increments. At each site, sediment porewater was extracted from triplicate cores in the Pacific and single cores in the Atlantic using either a porewater pressing bench (two cores/site in the Pacific; KC Denmark Research Equipment, Silkeborg, Denmark) under a stream of argon gas or Rhizon samplers (one core/site in the Pacific, all cores in the Atlantic; Rhizosphere Research Products, Wageningen, The Netherlands). Extracted water was either preserved with zinc acetate or filtered via 0.2 μm filters and frozen at −20°C.

Concentrations of nitrate, nitrite, ammonium, sulfate, sulfide, phosphate, bromide, and acetate were measured in pore water extracted from two cores at each site. Ammonium concentrations were obtained using a colorimetric assay (Bower et al.,1980). Phosphate concentrations were obtained using a Malachite Green Phosphate Assay Kit (BioAssay Systems; Hayward, CA; Cat# POMG-25H), following the manufacturer’s instructions. The analysis of nitrite and nitrate was performed using a microphotometry assay (Schnetger and Lehners, 2014). Concentrations of sulfide were measured in pore water preserved with zinc acetate via the colorimetric Cline Assay (Cline 1969). Optical densities of ammonium, phosphate, nitrite, nitrate and sulfide were obtained with a Lab BioTek Synergy HT microplate reader (Winooski, VT). Check standards for each nutrient were run in duplicate or triplicate along with samples. Sulfate, bromide, acetate and formate concentrations were determined with a Dionex DX-500 Ion Chromatograph, AS11 column, 5-50% sodium hydroxide gradient (Dionex Corporation, Sunnyvale CA) in the Stanford Environmental Measurements Facility. Samples and standards were diluted with ultrapure water before analysis. Check standards were analyzed every 10–15 samples. Oxygen concentrations were measured directly in the sediment through pre-drilled holes in the core tubes using an optical oxygen meter, FirestingO2 (FSO2-4, PyroScience, Aachen, Germany), and the robust oxygen probe (OCROB10, PyroScience). A two-point calibration was performed (0 and 100% air saturation), and the measurement was compensated for temperature and ambient pressure using internal or external sensors, as well as seawater salinity (35 g/L).

BCO-DMO Processing:
- renamed fields to conform with BCO-DMO naming conventions;
- converted longitude negative values to indicate West direction.

Missing Data Notation:
blq = below limit of quantification; 
nm = no measurement;
nd = no data/not applicable (used in Notes column only);
ppt = precipate formed & no data collected (used inPO4_uM column only).

NSF Award Abstract:
Life requires nitrogen for growth. Atmospheric nitrogen (N2) is the most abundant form of nitrogen on the surface of the planet, but most organisms cannot assimilate N2 directly. Habitats can therefore be nitrogen limited, meaning the demand for "bioavailable" nitrogen exceeds the supply, and its availability controls the overall growth and productivity of the community. A small subset of microorganisms, termed diazotrophs, convert N2 to bioavailable forms of nitrogen, including ammonium and nitrogenous organic matter, in a process known as N2 fixation. Diazotrophs are the largest natural source of bioavailable nitrogen on the planet, and the rate at which they fix N2 can control the rates at which other important microbial processes occur, such as the production and consumption of greenhouse gases. Understanding diazotrophs in the environment - their identity, distribution, activity levels, and biogeochemical controls - is therefore essential to understanding overall microbial community activity and biogeochemical cycling. The goal of this project is to characterize N2 fixation in deep-sea sediments, a generally understudied but expansive habitat, covering nearly two thirds of our planet. The project will have broader impacts via educational outreach, support and training of early career scientists, and scientific impact: since rates of marine methane, carbon dioxide, and nitrous oxide cycling are affected by nitrogen availability, the results will inform our understanding of greenhouse gas cycling in the marine environment, and therefore climate stability, a topic central to global security.

N2 fixation is a critical and intensely studied metabolism in the marine photic zone. Much less is known about N2 fixation in deep-sea sediments, but it could be an important factor in both benthic productivity and ocean-scale elemental cycling. Several observations have suggested or directly detected N2 fixation at localized areas of enhanced productivity on the seafloor (e.g., methane seeps and hydrothermal vents), raising the possibility that deep-sea N2 fixation is widespread. However, few measurements of N2 fixation have been made outside of these anomalous areas, and thus little is known about N2 fixation in the vast majority of the deep ocean floor. Preliminary data suggest N2 fixation does occur in typical deep marine sediment, and is mediated by a diverse set of yet unidentified microorganisms. This project will combine techniques from molecular biology and geochemistry to systematically investigate N2 fixation in representative deep-sea sediments collected along a depth profile (500 to 4500 m water depth) offshore California. The project will determine the (1) rates and distribution of N2 fixation (2) abundance, diversity, and distribution of genes and transcripts associated with N2 fixation (nif) (3) phylogenetic identity of the biological mediators (diazotrophs) and (4) physiochemical controls on diazotrophic community structure and activity. For context, the activity of the non-diazotrophic bacterial community will also be characterized. The results may lead to upward revisions of the estimates of new nitrogen production in the seafloor, and therefore change our understanding of the current balance of the marine nitrogen cycle. Together, this hypothesis-driven characterization of N2 fixation in deep-sea sediments will shed light on an expansive, climatically important, and traditionally understudied habitat, and facilitate more accurate extrapolation of the rates and distribution of N2 fixation on the whole seafloor as well as the metabolic response of the seafloor community to environmental change.