Rachel H. R. Stanley

Noble gas constraints on air‐sea gas exchange and bubble fluxes

[1] Air-sea gas exchange is an important part of the biogeochemical cycles of many climatically and biologically relevant gases including CO2 ,O 2, dimethyl sulfide and CH4. Here we use a three year observational time series of five noble gases (He, Ne, Ar, Kr, and Xe) at the Bermuda Atlantic Time series Study (BATS) site in tandem with a onedimensional upper ocean model to develop an improved parameterization for air-sea gas exchange that explicitly includes separate components for diffusive gas exchange and bubble processes. Based on seasonal timescale noble gas data, this parameterization, which has a 1s uncertainty of ±14% for diffusive gas exchange and ±29% for bubble fluxes, is more tightly constrained than previous parameterizations. Although the magnitude of diffusive gas exchange is within errors of that of Wanninkhof (1992), a commonly used parameterization, we find that bubble-mediated exchange, which is not explicitly included by Wanninkhof (1992) or many other formulations, is significant even for soluble gases. If one uses observed saturation anomalies of Ar (a gas with similar characteristics to O2) and a parameterization of gas exchange to calculate gas exchange fluxes, then the calculated fluxes differ by � 240% if the parameterization presented here is used compared to using the Wanninkhof (1992) parameterization. If instead one includes the gas exchange parameterization in a model, then the calculated fluxes differ by � 35% between using this parameterization and that of Wanninkhof (1992). These differences suggest that the bubble component should be explicitly included in a range of marine biogeochemical calculations that incorporate air-sea gas fluxes.

Evaluating triple oxygen isotope estimates of gross primary production at the Hawaii Ocean Time‐series and Bermuda Atlantic Time‐series Study sites

[1]xa0The triple oxygen isotopic composition of dissolved oxygen (17Δ) is a promising tracer of gross oxygen productivity (P) in the ocean. Recent studies have inferred a high and variable ratio of P to 14C net primary productivity (12–24 h incubations) (e.g., P:NPP(14C) of 5–10) using the 17Δ tracer method, which implies a very low efficiency of phytoplankton growth rates relative to gross photosynthetic rates. We added oxygen isotopes to a one-dimensional mixed layer model to assess the role of physical dynamics in potentially biasing estimates ofP using the 17Δ tracer method at the Bermuda Atlantic Time-series Study (BATS) and Hawaii Ocean Time-series (HOT). Model results were compared to multiyear observations at each site. Entrainment of high17Δ thermocline water into the mixed layer was the largest source of error in estimating P from mixed layer 17Δ. At both BATS and HOT, entrainment bias was significant throughout the year and resulted in an annually averaged overestimate of mixed layer P of 60 to 80%. When the entrainment bias is corrected for, P calculated from observed 17Δ and 14C productivity incubations results in a gross:net productivity ratio of 2.6 (+0.9 −0.8) at BATS. At HOT a gross:net ratio decreasing linearly from 3.0 (+1.0 −0.8) at the surface to 1.4 (+0.6 −0.6) at depth best reproduced observations. In the seasonal thermocline at BATS, however, a significantly higher gross:net ratio or large lateral fluxes of 17Δ must be invoked to explain 17Δ field observations.

Prediction of the Export and Fate of Global Ocean Net Primary Production: The EXPORTS Science Plan

Ocean ecosystems play a critical role in the Earth’s carbon cycle and the quantification of their impacts for both present conditions and for predictions into the future remains one of the greatest challenges in oceanography. The goal of the EXport Processes in the Ocean from Remote Sensing (EXPORTS) Science Plan is to develop a predictive understanding of the export and fate of global ocean net primary production (NPP) and its implications for present and future climates. The achievement of this goal requires a quantification of the mechanisms that control the export of carbon from the euphotic zone as well as its fate in the underlying “twilight zone” where some fraction of exported carbon will be sequestered in the ocean’s interior on time scales of months to millennia. Here we present a measurement / synthesis / modeling framework aimed at quantifying the fates of upper ocean NPP and its impacts on the global carbon cycle based upon the EXPORTS Science Plan. The proposed approach will diagnose relationships among the ecological, biogeochemical and physical oceanographic processes that control carbon cycling across a range of ecosystem and carbon cycling states leading to advances in satellite diagnostic and numerical prognostic models. To collect these data, a combination of ship and robotic field sampling, satellite remote sensing and numerical modeling is proposed which enables the sampling of the many pathways of NPP export and fates. This coordinated, process-oriented approach has the potential to foster new insights on ocean carbon cycling that maximizes its societal relevance through the achievement of research goals of many international research agencies and will be a key step towards our understanding of the Earth as an integrated system.

Quantifying seasonal air-sea gas exchange processes using noble gas time-series : a design experiment

A multi-year time-series of measurements of five noble gases (He, Ne, Ar, Kr, and Xe) at a subtropical ocean location may allow quantification of air-sea gas exchange parameters with tighter constraints than is currently available by other methods. We have demonstrated this using a one-dimensional upper ocean model forced by 6-hourly NCEP reanalysis winds and heat flux for the Sargasso Sea near Bermuda. We performed ensemble model runs to characterize the response of the modeled noble gas saturation anomalies to a range of air-sea gas exchange parameters. We then used inverse calculations to quantify the sensitivity of the parameters to hypothetical observations. These calculations show that with currently achievable measurement accuracies, noble gas concentrations in the Sargasso Sea could be used to constrain the magnitude of equilibrium gas exchange to 11%, the magnitude of the total air injection flux to 14%, and the magnitude of net photosynthetic oxygen production to 1.5 mol O2 m -2 y -1 . Additionally, we can use noble gases to quantify the relative contributions of bubbles that are partially dissolved to bubbles that are completely dissolved. These constraints are based on idealized assumptions and may not fully account for some of the uncertainties in the meteorological data, in lateral transport processes, and in the solubilities of the noble gases. As a limited demonstration, we applied this approach to a time series of He, Ne, Ar, and O2 measurements from the Sargasso Sea from 1985 to 1988 (data from Spitzer, 1989). Due to the limited number of gases measured and the lower accuracy of those measurements, the constraints in this example application are weaker than could be achieved with current capabilities.

The triple oxygen isotope tracer of primary productivity in a dynamic ocean model

The triple oxygen isotopic composition of dissolved oxygen (17Δdis) was added to the ocean ecosystem and biogeochemistry component of the Community Earth System Model, version 1.1.1. Model simulations were used to investigate the biological and physical dynamics of 17Δdis and assess its application as a tracer of gross photosynthetic production (gross oxygen production (GOP)) of O2 in the ocean mixed layer. The model reproduced large-scale patterns of 17Δdis found in observational data across diverse biogeographical provinces. Mixed layer model performance was best in the Pacific and had a negative bias in the North Atlantic and a positive bias in the Southern Ocean. Based on model results, the steady state equation commonly used to calculate GOP from tracer values overestimated the globally averaged model GOP by 29%. Vertical entrainment/mixing and the time rate of change of 17Δdis were the two largest sources of bias when applying the steady state method to calculate GOP. Entrainment/mixing resulted in the largest overestimation in midlatitudes and during summer and fall and almost never caused an underestimation of GOP. The tracer time rate of change bias resulted both in underestimation of GOP (e.g., during spring blooms at high latitudes) and overestimation (e.g., during the summer following a bloom). Seasonally, bias was highest in the fall (September-October-November in the Northern Hemisphere, March-April-May in the Southern), overestimating GOP by 62%, globally averaged. Overall, the steady state method was most accurate in equatorial and low-latitude regions where it estimated GOP to within ±10%. Field applicable correction terms are derived for entrainment and mixing that capture 86% of model vertical bias and require only mixed layer depth history and triple oxygen isotope measurements from two depths.

Gross and net production during the spring bloom along the Western Antarctic Peninsula

This study explores some of the physiological mechanisms responsible for high productivity near the shelf in the Western Antarctic Peninsula despite a short growing season and cold temperature. We measured gross and net primary production at Palmer Station during the summer of 2012/2013 via three different techniques: incubation with H2 (18) O; incubation with (14) CO2 ; and in situ measurements of O2 /Ar and triple oxygen isotope. Additional laboratory experiments were performed with the psychrophilic diatom Fragilariopsis cylindrus. During the spring bloom, which accounted for more than half of the seasonal gross production at Palmer Station, the ratio of net-to-gross production reached a maximum greater than c. 60%, among the highest ever reported. The use of multiple techniques showed that these high ratios resulted from low heterotrophic respiration and very low daylight autotrophic respiration. Laboratory experiments revealed a similar ratio of net-to-gross O2 production in F. cylindrus and provided the first experimental evidence for an important level of cyclic electron flow (CEF) in this organism. The low ratio of community respiration to gross primary production observed during the bloom at Palmer Station may be characteristic of high latitude coastal ecosystems and partially supported by a very active CEF in psychrophilic phytoplankton.

Continuous Measurements of Dissolved Ne, Ar, Kr, and Xe Ratios with a Field-deployable Gas Equilibration Mass Spectrometer

Noble gases dissolved in natural waters are useful tracers for quantifying physical processes. Here, we describe a field-deployable gas equilibration mass spectrometer (GEMS) that provides continuous, real-time measurements of Ne, Ar, Kr, and Xe mole ratios in natural waters. Gas is equilibrated with a membrane contactor cartridge and measured with a quadrupole mass spectrometer, after in-line purification with reactive metal alloy getters. We use an electron energy of 35 V for Ne to eliminate isobaric interferences, and a higher electron energy for the other gases to improve sensitivity. The precision is 0.7% or better and 1.0% or better for all mole ratios when the instrument is installed in a temperature-controlled environment and a variable-temperature environment, respectively. In the lab, the accuracy is 0.9% or better for all gas ratios using air as the only calibration standard. In the field (and/or at greater levels of disequilbrium), the accuracy is 0.7% or better for Ne/Kr, Ne/Ar, and Ar/Kr, and 2.5% or better for Ne/Xe, Ar/Xe, and Kr/Xe using air as the only calibration standard. The field accuracy improves to 0.6% or better for Ne/Xe, Ar/Xe, and Kr/Xe when the data is calibrated using discrete water samples run on a laboratory-based mass spectrometer. The e-folding response time is 90-410 s. This instrument enables the collection of a large number of continuous, high-precision and accuracy noble gas measurements at substantially reduced cost and labor compared to traditional methods.

Expansion of tandem repeats and oligomer clustering in coding and noncoding DNA sequences

We review recent studies of distribution of dimeric tandem repeats and short oligomer clustering in DNA sequences. We find that distribution of dimeric tandem repeats in coding DNA is exponential, while in noncoding DNA it often has long power-law tails. We explain this phenomenon using mutation models based on random multiplicative processes. We also develop a clustering measure based on percolation theory that quantifies the degree of clustering of short oligomers. We find that mono-, di-, and tetramers cluster more in noncoding DNA than in coding DNA. However trimers have some degree of clustering in coding DNA and noncoding DNA. We relate this phenomena to modes of tandem repeat expansion.

Clustering of identical oligomers in coding and noncoding DNA sequences.

We develop a quantitative method for analyzing repetitions of identical short oligomers in coding and noncoding DNA sequences. We analyze sequences presently available in the GenBank separately for primate, mammal, vertebrate, rodent, invertebrate and plant taxonomic partitions. We find that some oligomers cluster more than they would if randomly distributed, while other oligomers repel each other. To quantify this degree of clustering, we define clustering measures. We find that (i) clustering significantly differs in coding and noncoding DNA; (ii) in most cases, monomers, dimers and tetramers cluster in noncoding DNA but appear to repel each other in coding DNA. (iii) The degree of clustering for different sources (primates, invertebrates, and plants) is more conserved among these sources in the case of coding DNA than in the case of noncoding DNA. (iv) In contrast to other oligomers, we find that trimers always prefer to cluster. (v) Clustering of each particular oligomer is conserved within the same organism.

Impact of recently upwelled water on productivity investigated using in situ and incubation-based methods in Monterey Bay

Photosynthetic conversion of CO2 to organic carbon and the transport of this carbon from the surface to the deep ocean is an important regulator of atmospheric CO2. To understand the controls on carbon fluxes in a productive region impacted by upwelling, we measured biological productivity via multiple methods during a cruise in Monterey Bay, California. We quantified net community production and gross primary production from measurements of O2/Ar and O2 triple isotopes (17Δ), respectively. We simultaneously conducted incubations measuring the uptake of 14C, 15NO3- and 15NH4+, and nitrification, and deployed sediment traps. At the start of the cruise (Phase 1) the carbon cycle was at steady state and the estimated net community production was 35(10) and 35(8) mmol C m−2 d−1 from O2/Ar and 15N incubations respectively, a remarkably good agreement. During Phase 1, net primary production was 96(27) mmol C m−2 d−1 from C uptake, and gross primary production was 209(17) mmol C m−2 d−1 from 17Δ. Later in the cruise (Phase 2), recently upwelled water with higher nutrient concentrations entered the study area, causing 14C and 15NO3- uptake to increase substantially. Continuous O2/Ar measurements revealed submesoscale variability in water mass structure and likely productivity in Phase 2 that was not evident from the incubations. These data demonstrate that O2/Ar and 15N incubation-based NCP estimates can give equivalent results in an N-limited, coastal system, when the non-steady state O2 fluxes are negligible or can be quantified. This article is protected by copyright. All rights reserved.