177 research outputs found
jamesrco/LipidPhotoOxBox: LipidPhotoOxBox v1.0.0
No full textInitial release of data and code in LipidPhotoOxBox to support Collins, J. R., H. F. Fredricks, J. M. Diaz, J. S. Bowman, C. P. Ward, C. Moreno, K. Longnecker, A. Marchetti, C. M. Hansel, H. W. Ducklow, and B. A. S. Van Mooy (2017), The diverse products and biogeochemical significance of lipid photooxidation in coastal surface waters of West Antarctica
Microbial loop carbon cycling in ocean environments studied using a simple steady-state model
No full textA simple steady-state model is used to examine the microbial loop as a pathway for organic C in marine systems, constrained by observed estimates of bacterial to primary production ratio (BP:PP) and bacterial growth efficiency (BGE). Carbon sources (primary production including extracellular release of dissolved organic carbon, DOC), cycling via zooplankton grazing and viral lysis, and sinks (bacterial and zooplankton respiration) are represented. Model solutions indicate that, at least under near steady-state conditions, recent estimates of BP:PP of about 0.1 to 0.15 are consistent with reasonable scenarios of C cycling (low BGE and phytoplankton extracellular release) at open ocean sites such as the Sargasso Sea and subarctic North Pacific. The finding that bacteria are a major (50%) sink for primary production is shown to be consistent with the best estimates of BGE and dissolved organic matter (DOM) production by zooplankton and phytoplankton. Zooplankton-related processes are predicted to provide the greatest supply of DOC for bacterial consumption. The bacterial contribution to C flow in the microbial loop, via bacterivory and viral lysis, is generally low, as a consequence of low BGE. Both BP and BGE are hard to quantify accurately. By indicating acceptable combinations of parameter values for given BP:PP, the model provides a simple tool for examining the reliability of BP and BGE estimates
Long-term studies of the marine ecosystem along the west Antarctic Peninsula
No full textAuthor Posting. © The Author(s), 2008. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Deep Sea Research Part II: Topical Studies in Oceanography 55 (2008): 1945-1948, doi:10.1016/j.dsr2.2008.05.014.Articles in this volume focus on longer-term studies of the marine ecosystem of the
continental shelf west of the Antarctic Peninsula, principally by the Palmer, Antarctica Long-
Term Ecological Research project (Ross et al., 1996; Ducklow et al., 2007). There is a rich
history of oceanographic and ecological research in the Bellingshausen Sea region and on the
continental shelf dating back to the 19th and early 20th centuries (El-Sayed, 1996). The modern
era of scientific research started with the British Discovery Investigations of 1925-37 (Hardy,
1967), and included classic studies of phytoplankton (Hart, 1934) and krill (Marr, 1962). Hart’s
report presciently suggested primary producers could be limited by iron availability. El-Sayed
(1996) dissects the subsequent history of oceanographic research up to the advent of the
Southern Ocean GLOBEC (Hofmann et al., 2001; Hofmann et al., 2004) and JGOFS (Anderson
and Smith Jr., 2001) programs. The period from the 1970’s to the mid-90’s was dominated by
expeditionary and process-level studies of particular regions and processes extending over a few
seasons to a few years at most. The Research on Antarctic Coastal Ecosystem Rates (RACER)
Program (Huntley et al., 1991; Karl, 1991) is the outstanding example of this mode of research,
having focused on determination of key rate processes as a new approach to understanding
ecosystem dynamics (Karl et al., 1991a; Karl et al., 1991b). RACER was a direct predecessor
and major influence on Palmer LTER, GLOBEC and JGOFS. What was lacking in Antarctic
waters, as in most other regions and ocean provinces were sustained, long-term observations of a
variety of ocean properties and rates, conducted in the context of hypothesis-driven,
experimental science (Ducklow et al., 2008a). The creation of the US LTER Network in 1980
(Magnuson, 1990) made this possible.Observations reported in this volume were supported by NSF Grants OPP-90-11927 and OPP-
96-32763 to the University of California-Santa Barbara and OPP-02-17282 to the Virginia
Institute of Marine Science
Estimation of bacterial respiration and growth efficiency in the Ross Sea, Antarctica
No full textSeawater cultures were conducted in large volume (36 1) gas impermeable tri-laminate bags for the purpose of empirically deriving bacterial growth efficiency (BGE) and carbon conversion factors (CCF) in the south central Ross Sea. This experimental design allowed for concomitant measurements of metabolic reactants (loss of total and dissolved organic carbon [TOC and DOC]) and products (gain of total carbon dioxide [TCOz] and bacterial biomass) to be made from a single incubation vessel. Some previous studies have relied on proxy measurements (e.g. 02, 3H-thymidine incorporation and cell abundance) to determine BGE and CCF rather than direct carbon measurements. Our experimental design enabled a complete carbon budget to be constructed and eliminated variability associated with normally employed parallel bottle incubations. Uhlization of TOC was well balanced by the production of TC02, in 7 of 8 experiments, validating the use of tri-laminate bags for measuring microbial respiration. In 3 experiments, where TOC, DOC, TCOz and bacterial biovolume were directly measured, carbon mass balance yielded BGE estimates of 12, 32 and 38% and bacterial CCF of 77, 95 and 134 fg C pm-3. In experiments where independent DOC measurements were not made we used our empirically derived CCF values to determine bacterial carbon production and calculated DOC concentrations and BGE for these remaining experiments. The BGE derived from all the bag experiments conducted throughout the austral spring and summer 1995-1997 ranged from 9 to 38%. Our experimental design and carbon mass balance approach could be applied to other aquatic systems to empirically derive the BGE and CCF, factors essential for determining carbon flux through bacterioplankton
The magnitude of spring bacterial production in the North Atlantic Ocean
No full textDissolved organic carbon (DOC), a major reservoir in the ocean carbon cycle, is produced by a profusion of plankton sources and processes but is consumed mainly by bacterioplankton. Thus bacterial metabolism regulates the entry of DOC into the longer scale global carbon cycle. Bacterial production (BP) is the routinely measured quantity for evaluating the roles of bacteria in carbon cycling. However BP cannot be measured directly and instead is estimated from related metabolic processes requiring the use of poorly constrained conversion factors. BP and thus the total carbon utilization, are potentially uncertain by a factor of two or more. In the North Atlantic Bloom Experiment (NABE), BP was estimated to be about 30% of the simultaneous particulate primary production (PP), with some daily estimates exceeding 50%. Here we reassess these estimates, synthesizing knowledge and understanding of plankton dynamics gained since the 1989 NABE study. Daily BP derived from six different conversion factors averaged 20% of PP but ranged from 3 to 68%. The coupling of BP to PP was not consistent with either short-term cycling of labile DOC (hours) nor with much longer term cycling of semilabile DOC (seasons). Trophodynamic processes, including release of DOC from phytoplankton, by themselves could have maintained BP at about 15% of PP. Use of decomposing POC or previously accumulated semilabile DOC could each have supported some additional increment of BP for brief periods. Both reconsideration of observations and model results indicated that higher estimates of BP exceeding 20% of PP could not be supported without extraordinary and prolonged inputs of allochthonous carbon. Recent assertions of high BP in the tropics and other oceanic regimes should be considered carefully, especially if external subsidies are not obvious.Virginia Institute of Marine Scienc
WAP-1D-VAR v1.0: A One-Dimensional Variational Data Assimilation Model for the West Antarctic Peninsula
No full textWAP-1D-VAR (v1.0) is a variational data assimilation 1-D marine ecosystem model combining the forward model simulation and the backward model simulation for model optimization. The backward model simulation is a tangent linear adjoint version of the forward model and is used in a variational adjoint method that optimizes model parameters to adjust model outputs towards observations.
The variational adjoint method requires four components for data assimilation that WAP-1D-VAR provides within: 1) a forward model simulated by physical forcings and initial (initial conditions and model parameter guesses) and boundary conditions; 2) a cost function to evaluate misfits between the forward model results and the assimilated observations; 3) a tangent linear adjoint version of the forward model to compute the gradient of the cost function with respect to model parameters; and 4) an optimization procedure (M1QN3 3.1) to determine the direction and the optimal step size by which the model parameters should be modified to reduce the cost function based on the cost function gradient from 3). These four components are iterated sequentially to determine a set of the adjusted model parameters until present criteria are satisfied (e.g., low gradients), which then serves as an optimal numerical solution (equations with the optimized model parameters) for the final model outputs.
The model development and validation for version v1.0 of the model for Palmer Station, Antarctica, is presented in: Kim, H. H., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., Doney, S. C (2021). WAP-1D-VAR v1.0: Development and Evaluation of a One-Dimensional Variational Data Assimilation Model for the Marine Ecosystem Along the West Antarctic Peninsula, Geoscientific Model Development, Under Review. The Kim et al. manuscript describes in more detail the variables and model equations used in the forward model, physical forcing data sets used for Palmer Station, and the resulting optimized model parameters
Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits
No full text© The Author(s), 2022. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Kim, H. H., Bowman, J. S., Luo, Y.-W., Ducklow, H. W., Schofield, O. M., Steinberg, D. K., & Doney, S. C. Modeling polar marine ecosystem functions guided by bacterial physiological and taxonomic traits. Biogeosciences, 19(1), (2022): 117–136, https://doi.org/10.5194/bg-19-117-2022.Heterotrophic marine bacteria utilize organic carbon for growth and biomass synthesis. Thus, their physiological variability is key to the balance between the production and consumption of organic matter and ultimately particle export in the ocean. Here we investigate a potential link between bacterial traits and ecosystem functions in the rapidly warming West Antarctic Peninsula (WAP) region based on a bacteria-oriented ecosystem model. Using a data assimilation scheme, we utilize the observations of bacterial groups with different physiological traits to constrain the group-specific bacterial ecosystem functions in the model. We then examine the association of the modeled bacterial and other key ecosystem functions with eight recurrent modes representative of different bacterial taxonomic traits. Both taxonomic and physiological traits reflect the variability in bacterial carbon demand, net primary production, and particle sinking flux. Numerical experiments under perturbed climate conditions demonstrate a potential shift from low nucleic acid bacteria to high nucleic acid bacteria-dominated communities in the coastal WAP. Our study suggests that bacterial diversity via different taxonomic and physiological traits can guide the modeling of the polar marine ecosystem functions under climate change.This research has been supported by the NASA (grant no. NNX14AL86G) and the NSF (grant no. PLR-1440435)
jamesrco/LipidPhotoOxBox: LipidPhotoOxBox v2.0.0
No full text<p>Final release of data and code in LipidPhotoOxBox to support Collins, J. R., H. F. Fredricks, J. S. Bowman, C. P. Ward, C. Moreno, K. Longnecker, A. Marchetti, C. M. Hansel, H. W. Ducklow, and B. A. S. Van Mooy (2018), The molecular products and biogeochemical significance of lipid photooxidation in West Antarctic surface waters.</p>
Temporal and vertical dynamics in picoplankton photoheterotrophic production in the subtropical North Pacific Ocean
No full textHeterotrophic microbial production is a fundamental determinant in the flow of bioelements and energy within the pelagic ecosystems of the open ocean. To characterize the temporal dynamics in rates of heterotrophic picoplankton production (HPP), we examined vertical profiles of H-3-leucine (H-3-leu) and [methyl-H-3]-thymidine (H-3-TdR) incorporation at Stn ALOHA (22 degrees 45'N, 158 degrees W) in the oligotrophic North Pacific Ocean. Euphotic zone rates of H-3-leu and H-3-TdR incorporation were measured in situ under light and dark conditions on cruises to Stn ALOHA between April 2000 and August 2005. Rates of H-3-leu and H-3-TdR incorporation were elevated in the well-lit upper euphotic zone ( 0.05). Both H-3-leu and H-3-TdR displayed similar temporal variability, but neither proxy for HPP was correlated to measured rates of primary production. These observations provide the first examination of the temporal dynamics in HPP at Stn ALOHA, and lend insight into the potential importance of photoheterotrophic growth by Prochlorococcus spp, Although organic matter utilization by Prochlorococcus spp. has been documented previously, this is the first study to evaluate their potential role in secondary production of the oceanic ecosystem.Virginia Institute of Marine Scienc
- …
