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The Southern Ocean Carbon and Climate Observations and Modeling (SOCCOM) project has deployed 194 profiling floats equipped with biogeochemical (BGC) sensors, making it one of the largest contributors to global BGC-Argo. Post-deployment quality control (QC) of float-based oxygen, nitrate, and pH data is a crucial step in the processing and dissemination of such data, as in situ chemical sensors remain in early stages of development. In situ calibration of chemical sensors on profiling floats using atmospheric reanalysis and empirical algorithms can bring accuracy to within 3 μmol O2 kg–1, 0.5 μmol NO3– kg–1, and 0.007 pH units. Routine QC efforts utilizing these methods can be conducted manually through visual inspection of data to assess sensor drifts and offsets, but more automated processes are preferred to support the growing number of BGC floats and reduce subjectivity among delayed-mode operators. Here we present a methodology and accompanying software designed to easily visualize float data against select reference datasets and assess QC adjustments within a quantitative framework. The software is intended for global use and has been used successfully in the post-deployment calibration and QC of over 250 BGC floats, including all floats within the SOCCOM array. Results from validation of the proposed methodology are also presented which help to verify the quality of the data adjustments through time.

Continuous monitoring of dissolved oxygen, pH and carbon dioxide are of great importance in oceanography. Sensors are the optimal tools for in situ measurements from mobile platforms, like A utonomous U nderwater V ehicles (AUVs) or Argo profiling floats, and for shipboard deployments. A validation study of small, versatile, easy-to-use, stand-alone optodes is presented. Each analyte can be read out with the identical optoelectronics which greatly minimizes the costs of the hardware needed. Several deployments were performed to evaluate the applicability of the sensors. The deployments varied in terms of duration (profiling, long-term monitoring 5 days to 8 weeks) and environmental conditions (salinity: 6–33 PSS; temperature: 9–25 °C). A set of sensors was successfully deployed at a mooring buoy, in an aquaculture facility and in the Monterey Bay Aquarium Open Sea Exhibition. They were also integrated in an AUV and a profiling float. The performance of the optodes was evaluated in comparison with commercially available sensors for dissolved oxygen (Aanderaa Data Instruments AS, Sea-Bird Scientific, OxyGuard®), pH (Hach, Satlantic) and carbon dioxide (Turner design). The data collected by our optodes and the commercially available sensors is generally in good agreement showing that the new, compact sensor device in combination with sensor foils (pO 2 , pH, pCO 2 ) can be a valuable tool for many applications in oceanography. The data also revealed the importance of the calibration strategy since inappropriate calibration resulted in an offset in the measured parameter. The efficiency of simple biofouling protection strategy (copper guard) for prolong measurements in highly dynamic environments was also demonstrated.

Six profiling floats equipped with nitrate and oxygen sensors were deployed at Ocean Station P in the Gulf of Alaska. The resulting six calendar years and 10 float years of nitrate and oxygen data were used to determine an average annual cycle for net community production (NCP) in the top 35 m of the water column. NCP became positive in February as soon as the mixing activity in the surface layer began to weaken, but nearly 3 months before the traditionally defined mixed layer began to shoal from its winter time maximum. NCP displayed two maxima, one toward the end of May and another in August with a summertime minimum in June corresponding to the historical peak in mesozooplankton biomass. The average annual NCP was determined to be 1.5 ± 0.6 mol C m−2 yr−1 using nitrate and 1.5 ± 0.7 mol C m−2 yr−1 using oxygen. The results from oxygen data proved to be quite sensitive to the gas exchange model used as well as the accuracy of the oxygen measurement. Gas exchange models optimized for carbon dioxide flux generally ignore transport due to gas exchange through the injection of bubbles, and these models yield NCP values that are two to three time higher than the nitrate-based estimates. If nitrate and oxygen NCP rates are assumed to be related by the Redfield model, we show that the oxygen gas exchange model can be optimized by tuning the exchange terms to reproduce the nitrate NCP annual cycle.

Aanderaa optode sensors for dissolved oxygen show remarkable stability when deployed on profiling floats, but these sensors suffer from poor calibration because of an apparent drift during storage (storage drift). It has been suggested that measurement of oxygen in air, during the period when a profiling float is on the surface, can be used to improve sensor calibration and to determine the magnitude of sensor drift while deployed in the ocean. The effect of air calibration on oxygen measurement quality with 47 profiling floats that were equipped with Aanderaa oxygen optode sensors is assessed. Recalibrated oxygen concentration measurements were compared to Winkler oxygen titrations that were made at the float deployment stations and to the World Ocean Atlas 2009 oxygen climatology. Recalibration of the sensor using air oxygen reduces the sensor error, defined as the difference from Winkler oxygen titrations in the mixed layer near the time of deployment, by about tenfold when compared to errors obtained with the factory calibration. The relative error of recalibrated sensors is −1 with a mean of 0.2% ± 0.5% yr−1. Given that storage drift for optode sensors is only negative, it is concluded that there is no evidence for sensor drift after they are deployed and that other processes are responsible for the linear changes.

International audience; Recently, measurements of oxygen concentration in the ocean -one of the most classical parameters in chemical oceanography-are experiencing a revival. This is not surprising, given the key role of oxygen for assessing the status of the marine carbon cycle and feeling the pulse of the biological pump. The revival, however, has to a large extent been driven by the availability of robust optical oxygen sensors and their painstakingly thorough characterization. For autonomous observations, oxygen optodes are the sensors of choice: They are used abundantly on Biogeochemical-Argo floats, gliders and other autonomous oceanographic observation platforms. Still, data quality and accuracy are often suboptimal, in some part because sensor and data treatment are not always straightforward and/or sensor characteristics are not adequately taken into account. Here, we want to summarize the current knowledge about oxygen optodes, their working principle as well as their behavior with respect to oxygen, temperature, hydrostatic pressure, and response time. The focus will lie on the most widely used and accepted optodes made by Aanderaa and Sea-Bird. We revisit the essentials and caveats of in-situ in air calibration as well as of time response correction for profiling applications, and provide requirements for a successful field deployment. In addition, all required steps to post-correct oxygen optode data will be discussed. We hope this summary will serve as a comprehensive, yet concise reference to help people get started with oxygen observations, ensure successful sensor deployments and acquisition of highest quality data, and facilitate post-treatment of oxygen data. In the end, we hope that this will lead to more and higher-quality oxygen observations and help to advance our understanding of ocean biogeochemistry in a changing ocean.

The prasinophyte order Mamiellales contains several widespread marine picophytoplankton (≤2 μm diameter) taxa, including Micromonas and Ostreococcus. Complete genome sequences are available for two Micromonas isolates, CCMP1545 and RCC299. We performed in silico analyses of nitrogen transporters and related assimilation genes in CCMP1545 and RCC299 and compared these with other green lineage organisms as well as Chromalveolata, fungi, bacteria, and archaea. Phylogenetic reconstructions of ammonium transporter (AMT) genes revealed divergent types contained within each Mamiellales genome. Some were affiliated with plant and green algal AMT1 genes and others with bacterial AMT2 genes. Land plant AMT2 genes were phylogenetically closer to archaeal transporters than to Mamiellales AMT2 genes. The Mamiellales represent the first green algal genomes to harbor AMT2 genes, which are not found in Chlorella and Chlamydomonas or the chromalveolate algae analyzed but are present in oomycetes. Fewer nitrate transporter (NRT) than AMT genes were identified in the Mamiellales. NRT1 was found in all but CCMP1545 and showed highest similarity to Mamiellales and proteobacterial NRTs. NRT2 genes formed a bootstrap-supported clade basal to other green lineage organisms. Several nitrogen-related genes were colocated, forming a nitrogen gene cluster. Overall, RCC299 showed the most divergent suite of nitrogen transporters within the various Mamiellales genomes, and we developed TaqMan quantitative polymerase chain reaction primer-probes targeting a subset of these, as well as housekeeping genes, in RCC299. All those investigated showed expression either under standard growth conditions or under nitrogen depletion. Like other recent publications, our findings show a higher degree of "mixed lineage gene affiliations" among eukaryotes than anticipated, and even the most phylogenetically anomalous versions appear to be functional. Nitrogen is often considered a regulating factor for phytoplankton populations. This study provides a springboard for exploring the use and functional diversification of inorganic nitrogen transporters and related genes in eukaryotic phytoplankton. © 2010 The Author.

The NH4-Digiscan is an in situ analyzer designed for measuring ammonium in estuarine, coastal, and shelf waters at depths of less than 3 m. This wet chemical analyzer uses micro-solenoid pumps to propel sample and reagents, a gas diffusion cell to isolate the analyte from the matrix, and a conductivity detector for analyte detection. Instrument measurements are stable for deployments of at least 30 d. In estuarine and coastal waters, the analyzer is capable of sampling hourly and has a detection limit of 0.2 µM. In shelf waters, the NH4-Digiscan can be configured to have a detection limit of 0.014 µM. The simple chemistry, in situ capability, and high resolution sampling minimizes the use of toxic reagents, minimizes many of the problems plaguing ammonium analyses, and adequately captures the high temporal variability of coastal waters, which is often undersampled. The analyzer has been successfully deployed on coastal moorings, benthic flux chambers, and on a drifter 500 km west of Monterey Bay, California. The system can also be easily configured for laboratory bench top analysis of discrete samples.

An ocean observatory that consists of an array of moored sensor platforms, telemetry, and data collection and dissemination software was designed for monitoring the biogeochemistry and physical dynamics of coastal and estuarine ecosystems. The Land-Ocean Biogeochemical Observatory (LOBO) consists of robust moorings that can withstand tidal currents and weather. The moorings are highly configurable, can be deployed in waters as shallow as 0.5 m, are relatively easy to maintain, and accommodate a complete array of standard and novel sensors. The sensors communicate with an on-board controller which relays data to shore in near-real time. Up to five LOBO moorings have been simultaneously deployed and maintained in Elkhorn Slough, California, since November 2003. Continuous hourly data of biological, chemical, and physical properties are relayed to shore, processed, and disseminated to users through a web interface in near-real time. This article describes the design, implementation, and functionality of the LOBO monitoring system.

In July 2002, a combination of underway mapping and discrete profiles revealed significant along-shore variability in the concentrations of manganese and iron in the vicinity of Monterey Bay, California. Both metals had lower concentrations in surface waters south of Monterey Bay, where the shelf is about 2.5 km wide, than north of Monterey Bay, where the shelf is about 10 km wide. During non-upwelling conditions over the northern broad shelf, dissolvable iron concentrations measured underway in surface waters reached 3.5 nmol L−1 and dissolved manganese reached 25 nmol L−1. In contrast, during non-upwelling conditions over the southern narrow shelf, dissolvable iron concentrations in surface waters were less than 1 nmol L−1 and dissolved manganese concentrations were less than 5 nmol L−1. A pair of vertical profiles at 1000 m water depth collected during an upwelling event showed dissolved manganese concentrations of 10 decreasing to 2 nmol L−1, and dissolvable iron concentrations of 12–20 nmol L−1 in the upper 100 m in the north, compared to 3.5–2 nmol L−1 Mn and ∼0.6 nmol L−1 Fe in the upper 100 m in the south, suggesting the effect of shelf width influences the chemistry of waters beyond the shelf. These observations are consistent with current understanding of the mechanism of iron supply to coastal upwelling systems: Iron from shelf sediments, predominantly associated with particles greater than 20 μm, is brought to the surface during upwelling conditions. We hypothesize that manganese oxides are brought to the surface with upwelling and are then reduced to dissolved manganese, perhaps by photoreduction, following a lag after upwelling. Greater phytoplankton biomass, primary productivity, and nutrient drawdown were observed over the broad shelf, consistent with the greater supply of iron. Incubation experiments conducted 20 km offshore in both regions, during a period of wind relaxation, confirm the potential of these sites to become limited by iron. There was no additional growth response when copper, manganese or cobalt was added in addition to iron. The growth response of surface water incubated with bottom sediment (4 nmol L−1 dissolvable Fe) was slightly greater than in control incubations, but less than in the presence of 4 nmol L−1 dissolved iron. This may indicate that dissolvable iron is not as bioavailable as dissolved iron, although the influence of additional inhibitory elements in the sediment cannot be ruled out.

Nitrite (NO2–) is a substrate for both oxidative and reductive microbial metabolism. NO2– accumulates at the base of the euphotic zone in oxygenated, stratified open ocean water columns, forming a feature known as the primary nitrite maximum (PNM). Potential pathways of NO2– production include the oxidation of ammonia (NH3) by ammonia-oxidizing bacteria or archaea and assimilatory nitrate (NO3–) reduction by phytoplankton or heterotrophic bacteria. Measurements of NH3 oxidation and NO3– reduction to NO2– were conducted at two stations in the central California Current in the eastern North Pacific to determine the relative contributions of these processes to NO2– production in the PNM. Sensitive (< 10 nmol L−1), high-resolution measurements of [NH4+] and [NO2–] indicated a persistent NH4+ maximum overlying the PNM at every station, with concentrations as high as 1.5 μmol L−1. Within and just below the PNM, NH3 oxidation was the dominant NO2– producing process with rates of NH3 oxidation of up to 50 nmol L−1 d−1, coinciding with high abundances of ammonia-oxidizing archaea. Though little NO2– production from NO3– was detected, potentially nitrate-reducing phytoplankton (photosynthetic picoeukaryotes, Synechococcus, and Prochlorococcus) were present at the depth of the PNM. Rates of NO2– production from NO3– were highest within the upper mixed layer (4.6 nmol L−1 d−1) but were either below detection limits or 10 times lower than NH3 oxidation rates around the PNM. One-dimensional modeling of water column NO2– profiles supported direct rate measurements of a net biological sink for NO2– just below the PNM. Residence time estimates of NO2– within the PNM were similar at the mesotrophic and oligotrophic stations and ranged from 150–205 d. Our results suggest the PNM is a dynamic, rather than relict, feature with a source term dominated by ammonia oxidation.

[1] Seven years of observations of surface water iron concentrations in the Monterey Bay region of central California reveal a consistent annual cycle dominated by the injection of high concentrations of particulate iron each spring. A companion study of the water column near the upwelling center at the north end of the bay clearly indicates a sedimentary source for the iron. Local river discharge, during winter storm events, results in the deposition of a fine-grained sediment “fluff” layer along the shelf. The initial rapid shoaling of isotherms at the onset of upwelling in spring brings water from the fluff layer to the surface. Concentrations of iron in both surface and source waters are then quickly diminished although upwelling intensifies, bringing the highest concentration of nitrate to the surface ∼3 months later. The concentration of a number of constituents measured in bottom water samples collected during the companion study strongly suggests that the rapid decrease in surface water iron concentrations is due to the depletion of the fluff layer following initial isotherm shoaling. The decoupling of iron and nitrate supply sets up the potential for iron limitation. However, on the basis of average Fe/NO3 ratios, we conclude that the region is not often iron limited. Iron limitation was apparent only one summer at the offshore station. Summer chlorophyll concentrations are highly correlated to dissolvable (unfiltered) iron concentrations, evidence in support of the role of particulate iron in meeting the ecosystem's iron requirements.

[1] Here we report measurements of iron and aluminum in surface and subsurface waters during late March and late May of 2001 on transects between central California and Hawaii. A large cloud of Asian dust was detected during April 2001, and there was a clear signal in surface water iron due to aerosol deposition on the May transect. Iron and aluminum concentrations increased synchronously by 0.5 and 2 nM along the southern portion of the transect, which includes the Hawaii Ocean Time series (HOT) station, from background values in March (0.1 to 0.2 nM Fe). These changes occurred in a ratio that is close to the crustal abundance ratio of the metals, which indicates a soil aerosol source. A vertical profile of dissolved iron was also measured at the HOT station in late April and this profile also shows a large increase near the surface. Direct observations of aerosol iron concentration at Mauna Loa Observatory on Hawaii indicate that aerosol concentrations were significantly lower than climatological values during this period. Soil aerosol concentrations along the transect were estimated using the real-time Navy Aerosol Analysis and Prediction System (NAAPS). The NAAPS results show a large meridional gradient with maximum concentrations in the boundary layer north of 30°N. However, the deposition of iron and aluminum to surface waters was highest south of 25°N, near Hawaii. There were only weak signals in the ecosystem response to the aerosol deposition.