Smith, S. R., Briggs, K., Bourassa, M. A., Elya, J., & Paver, C. R. (2018). Shipboard automated meteorological and oceanographic system data archive: 2005-2017. Geosci Data J , 5 (2), 73–86.
Abstract: Since 2005, the Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative has been collecting, quality-evaluating, distributing, and archiving underway navigational, meteorological, and oceanographic observations from research vessels. Herein we describe the procedures for acquiring ship and instrumental metadata and the one-minute interval observations from 44 research vessels that have contributed to the SAMOS initiative from 2005 to 2017. The overall data processing workflow and quality control procedures are documented along with data file formats and version control procedures. The SAMOS data are disseminated to the user community via web, FTP, and Thematic Real-time Environmental Distributed Data Services from both the Marine Data Center at the Florida State University and the National Centers for Environmental Information, which serves as the long-term archive for the SAMOS initiative. They have been used to address topics ranging from air-sea interaction studies, the calibration, evaluation, and development of satellite observational products, the evaluation of numerical atmospheric and ocean models, and the development of new tools and techniques for geospatial data analysis in the informatics community. Maps provide users the geospatial coverage within the SAMOS dataset, with a focus on the Essential Climate/Ocean Variables, and recommendations are made regarding which versions of the dataset should be accessed by different user communities.
Steffen, J., & Bourassa, M. (2018). Barrier Layer Development Local to Tropical Cyclones based on Argo Float Observations. J. Phys. Oceanogr. , 48 (9), 1951–1968.
Abstract: The objective of this study is to quantify barrier layer development due to tropical cyclone (TC) passage using Argo float observations of temperature and salinity. To accomplish this objective, a climatology of Argo float measurements is developed from 2001 to 2014 for the Atlantic, eastern Pacific, and central Pacific basins. Each Argo float sample consists of a prestorm and poststorm temperature and salinity profile pair. In addition, a no-TC Argo pair dataset is derived for comparison to account for natural ocean state variability and instrument sensitivity. The Atlantic basin shows a statistically significant increase in barrier layer thickness (BLT) and barrier layer potential energy (BLPE) that is largely attributable to an increase of 2.6 m in the post-TC isothermal layer depth (ITLD). The eastern Pacific basin shows no significant changes to any barrier layer characteristic, likely due to a shallow and highly stratified pycnocline. However, the near-surface layer freshens in the upper 30 m after TC passage, which increases static stability. Finally, the central Pacific has a statistically significant freshening in the upper 20-30 m that increases upper-ocean stratification by similar to 35%. The mechanisms responsible for increases in BLPE vary between the Atlantic and both Pacific basins; the Atlantic is sensitive to ITLD deepening, while the Pacific basins show near-surface freshening to be more important in barrier layer development. In addition, Argo data subsets are used to investigate the physical relationships between the barrier layer and TC intensity, TC translation speed, radial distance from TC center, and time after TC passage.
Stukel, M. R., & Barbeau, K. A. (2020). Investigating the Nutrient Landscape in a Coastal Upwelling Region and Its Relationship to the Biological Carbon Pump. Geophys. Res. Lett. , 47 (6), e2020GL087351.
Abstract: We investigated nutrient patterns and their relationship to vertical carbon export using results from 38 Lagrangian experiments in the California Current Ecosystem. The dominant mode of variability reflected onshore-offshore nutrient gradients. A secondary mode of variability was correlated with silica excess and dissolved iron and likely reflects regional patterns of iron-limitation. The biological carbon pump was enhanced in high nutrient and Fe-stressed regions. Patterns in the nutrient landscape proved to be better predictors of the vertical flux of sinking particles than contemporaneous measurements of net primary production. Our results suggest an important role for Fe-stressed diatoms in vertical carbon flux. They also suggest that either preferential recycling of N or non-Redfieldian nutrient uptake by diatoms may lead to high PO:NO and Si(OH):NO ratios, following export of P- and Si-enriched organic matter. Increased export following Fe-stress may partially explain inverse relationships between net primary productivity and export efficiency.
Stukel, M. R., & Kelly, T. B. The carbon: 234Thorium ratios of sinking particles in the California current ecosystem 2: Examination of a thorium sorption, desorption, and particle transport model. Marine Chemistry , .
Stukel, M. R., & Kelly, T. B. (2019). The carbon: (234) Thorium ratios of sinking particles in the California current ecosystem 2: Examination of a thorium sorption, desorption, and particle transport model. Marine Chemistry , 212 , 1–15.
Abstract: Thorium-234 (234Th) is a powerful tracer of particle dynamics and the biological pump in the surface ocean; however, variability in carbon: thorium ratios of sinking particles adds substantial uncertainty to estimates of organic carbon export. We coupled a mechanistic thorium sorption and desorption model to a one-dimensional particle sinking model that uses realistic particle settling velocity spectra. The model generates estimates of 238U234Th disequilibrium, particulate organic carbon concentration, and the C:234Th ratio of sinking particles, which are then compared to in situ measurements from quasi-Lagrangian studies conducted on six cruises in the California Current Ecosystem. Broad patterns observed in in situ measurements, including decreasing C:234Th ratios with depth and a strong correlation between sinking C:234Th and the ratio of vertically-integrated particulate organic carbon (POC) to vertically-integrated total water column 234Th, were accurately recovered by models assuming either a power law distribution of sinking speeds or a double log normal distribution of sinking speeds. Simulations suggested that the observed decrease in C:234Th with depth may be driven by preferential remineralization of carbon by particle-attached microbes. However, an alternate model structure featuring complete consumption and/or disaggregation of particles by mesozooplankton (e.g. no preferential remineralization of carbon) was also able to simulate decreasing C:234Th with depth (although the decrease was weaker), driven by 234Th adsorption onto slowly sinking particles. Model results also suggest that during bloom decays C:234Th ratios of sinking particles should be higher than expected (based on contemporaneous water column POC), because high settling velocities minimize carbon remineralization during sinking.
Stukel, M. R., Biard, T., Krause, J. W., & Ohman, M. D. (2018). Large Phaeodaria in the twilight zone: Their role in the carbon cycle. Association for the Sciences of Limnology and Oceanography , .
Abstract: Advances in in situ imaging allow enumeration of abundant populations of large Rhizarians that compose a substantial proportion of total mesozooplankton biovolume. Using a quasi-Lagrangian sampling scheme, we quantified the abundance, vertical distributions, and sinking‐related mortality of Aulosphaeridae, an abundant family of Phaeodaria in the California Current Ecosystem. Inter‐cruise variability was high, with average concentrations at the depth of maximum abundance ranging from < 10 to > 300 cells m−3, with seasonal and interannual variability associated with temperature‐preferences and regional shoaling of the 10°C isotherm. Vertical profiles showed that these organisms were consistently most abundant at 100�150 m depth. Average turnover times with respect to sinking were 4.7�10.9 d, equating to minimum in situ population growth rates of ~ 0.1�0.2 d−1. Using simultaneous measurements of sinking organic carbon, we find that these organisms could only meet their carbon demand if their carbon : volume ratio were ~ 1 μg C mm−3. This value is substantially lower than previously used in global estimates of rhizarian biomass, but is reasonable for organisms that use large siliceous tests to inflate their cross‐sectional area without a concomitant increase in biomass. We found that Aulosphaeridae alone can intercept > 20% of sinking particles produced in the euphotic zone before these particles reach a depth of 300 m. Our results suggest that the local (and likely global) carbon biomass of Aulosphaeridae, and probably the large Rhizaria overall, needs to be revised downwards, but that these organisms nevertheless play a major role in carbon flux attenuation in the twilight zone.
Stukel, M. R., Decima, M., & Kelly, T. B. (2018). A new approach for incorporating 15N isotopic data into linear inverse ecosystem models with Markov Chain Monte Carlo sampling. PLoS One , 13 (6), e0199123.
Abstract: Oceanographic field programs often use delta15N biogeochemical measurements and in situ rate measurements to investigate nitrogen cycling and planktonic ecosystem structure. However, integrative modeling approaches capable of synthesizing these distinct measurement types are lacking. We develop a novel approach for incorporating delta15N isotopic data into existing Markov Chain Monte Carlo (MCMC) random walk methods for solving linear inverse ecosystem models. We test the ability of this approach to recover food web indices (nitrate uptake, nitrogen fixation, zooplankton trophic level, and secondary production) derived from forward models simulating the planktonic ecosystems of the California Current and Amazon River Plume. We show that the MCMC with delta15N approach typically does a better job of recovering ecosystem structure than the standard MCMC or L2 minimum norm (L2MN) approaches, and also outperforms an L2MN with delta15N approach. Furthermore, we find that the MCMC with delta15N approach is robust to the removal of input equations and hence is well suited to typical pelagic ecosystem studies for which the system is usually vastly under-constrained. Our approach is easily extendable for use with delta13C isotopic measurements or variable carbon:nitrogen stoichiometry.
Stukel, M. R., Décima, M., Landry, M. R., & Selph, K. E. (2018). Nitrogen and isotope flows through the Costa Rica Dome upwelling ecosystem: The crucial mesozooplankton role in export flux. Global Biogeochemical Cycles , 32 (12), 1815–1832.
Abstract: The Costa Rica Dome (CRD) is an open-ocean upwelling ecosystem, with high biomasses of picophytoplankton (especially Synechococcus), mesozooplankton, and higher trophic levels. To elucidate the food web pathways supporting the trophic structure and carbon export in this unique ecosystem, we used Markov Chain Monte Carlo techniques to assimilate data from four independent realizations of δ15N and planktonic rate measurements from the CRD into steady state, multicompartment ecosystem box models (linear inverse models). Model results present well-constrained snapshots of ecosystem nitrogen and stable isotope fluxes. New production is supported by upwelled nitrate, not nitrogen fixation. Protistivory (rather than herbivory) was the most important feeding mode for mesozooplankton, which rely heavily on microzooplankton prey. Mesozooplankton play a central role in vertical nitrogen export, primarily through active transport of nitrogen consumed in the surface layer and excreted at depth, which comprised an average 36-46% of total export. Detritus or aggregate feeding is also an important mode of resource acquisition by mesozooplankton and regeneration of nutrients within the euphotic zone. As a consequence, the ratio of passively sinking particle export to phytoplankton production is very low in the CRD. Comparisons to similar models constrained with data from the nearby equatorial Pacific demonstrate that the dominant role of vertical migrators to the biological pump is a unique feature of the CRD. However, both regions show efficient nitrogen transfer from mesozooplankton to higher trophic levels (as expected for regions with large fish, cetacean, and seabird populations) despite the dominance of protists as major grazers of phytoplankton.
Stukel, M. R., Ohman, M. D., Kelly, T. B., & Biard, T. (2019). The Roles of Suspension-Feeding and Flux-Feeding Zooplankton as Gatekeepers of Particle Flux Into the Mesopelagic Ocean in the Northeast Pacific. Front. Mar. Sci. , 6 .
Abstract: Zooplankton are important consumers of sinking particles in the ocean's twilight zone. However, the impact of different taxa depends on their feeding mode. In contrast to typical suspension-feeding zooplankton, flux-feeding taxa preferentially consume rapidly sinking particles that would otherwise penetrate into the deep ocean. To quantify the potential impact of two flux-feeding zooplankton taxa [Aulosphaeridae (Rhizaria), and Limacina helicina (euthecosome pteropod)] and the total suspension-feeding zooplankton community, we measured depth-stratified abundances of these organisms during six cruises in the California Current Ecosystem. Using allometric-scaling relationships, we computed the percentage of carbon flux intercepted by flux feeders and suspension feeders. These estimates were compared to direct measurements of carbon flux attenuation (CFA) made using drifting sediment traps and U-238-Th-234 disequilibrium. We found that CFA in the shallow twilight zone typically ranged from 500 to 1000 m mol organic C flux remineralized per 10-m vertical depth bin. This equated to approximately 6-10% of carbon flux remineralized/10 m. The two flux-feeding taxa considered in this study could account for a substantial proportion of this flux near the base of the euphotic zone. The mean flux attenuation attributable to Aulosphaeridae was 0.69%/10 m (median = 0.21%/10 m, interquartile range = 0.04-0.81%) at their depth of maximum abundance (similar to 100 m), which would equate to similar to 10% of total flux attenuation in this depth range. The maximum flux attenuation attributable to Aulosphaeridae reached 4.2%/10 m when these protists were most abundant. L. helicina, meanwhile, could intercept 0.45-1.6% of carbon flux/10 m, which was slightly greater (on average) than the Aulosphaeridae. In contrast, suspension-feeding zooplankton in the mesopelagic (including copepods, euphausiids, appendicularians, and ostracods) had combined clearance rates of 2-81 L m(-3) day(-1) (mean of 19.6 L m(-3) day(-1)). This implies a substantial impact on slowly sinking particles, but a negligible impact on the presumably rapidly sinking fecal pellets that comprised the majority of the material collected in sediment traps. Our results highlight the need for a greater research focus on the many taxa that potentially act as flux feeders in the oceanic twilight zone.
Sun, J., & Wu, Z. (2019). Isolating spatiotemporally local mixed Rossby-gravity waves using multi-dimensional ensemble empirical mode decomposition. Clim Dyn , (3-4), 1383–1405.
Abstract: Tropical waves have relatively large amplitudes in and near convective systems, attenuating as they propagate away from the area where they are generated due to the dissipative nature of the atmosphere. Traditionally, nonlocal analysis methods, such as those based on the Fourier transform, are applied to identify tropical waves. However, these methods have the potential to lead to the misidentification of local wavenumbers and spatial locations of local wave activities. To address this problem, we propose a new method for analyzing tropical waves, with particular focus placed on equatorial mixed Rossby-gravity (MRG) waves. The new tropical wave analysis method is based on the multi-dimensional ensemble empirical mode decomposition and a novel spectral representation based on spatiotemporally local wavenumber, frequency, and amplitude of waves. We first apply this new method to synthetic data to demonstrate the advantages of the method in revealing characteristics of MRG waves. We further apply the method to reanalysis data (1) to identify and isolate the spatiotemporally heterogeneous MRG waves event by event, and (2) to quantify the spatial inhomogeneity of these waves in a wavenumber-frequency-energy diagram. In this way, we reveal the climatology of spatiotemporal inhomogeneity of MRG waves and summarize it in wavenumber-frequency domain: The Indian Ocean is dominated by MRG waves in the period range of 8–12 days; the western Pacific Ocean consists of almost equal energy distribution of MRG waves in the period ranges of 3–6 and 8–12 days, respectively; and the eastern tropical Pacific Ocean and the tropical Atlantic Ocean are dominated by MRG waves in the period range of 3–6 days. The zonal wavenumbers mostly fall within the band of 4–15, with Indian Ocean has larger portion of higher wavenumber (smaller wavelength components) MRG waves.
