Assessment of skill and portability in regional marine biogeochemical models: Role of multiple planktonic groups

Friedrichs, Marjorie A. M.; Dusenberry, Jeffrey A.; Anderson, L.; Armstrong, Robert A.; Chai, Fei; Christian, James R.; Doney, Scott C.; Dunne, John; Fujii, Masahiko; Hood, Raleigh R.; McGillicuddy, Dennis J.; Moore, J. Keith; Schartau, Markus; Spitz, Yvette H.; Wiggert, Jerry D.

doi:10.1029/2006jc003852

Cited by 239 publications

(256 citation statements)

References 83 publications

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“…This complexity creates a problem when trying to understand and model DOM cycling because complex models, with many state variables and parameters, often do not perform better than simpler ones (Anderson, 2005;Arhonditsis et al, 2006;Freidrichs et al, 2007;Hood et al, 2006). However, since the cycling of DOM is so complex, it cannot be adequately described using the simple modeling approach of aggregating species into all-encompassing functional groups (as in NPZ models) and adding a DOM pool.…”

Section: Model Formulationmentioning

confidence: 99%

Modeling the seasonal autochthonous sources of dissolved organic carbon and nitrogen in the upper Chesapeake Bay

Keller

Hood

2011

Ecological Modelling

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a b s t r a c tIn this paper we investigate the seasonal autochthonous sources of dissolved organic carbon (DOC) and nitrogen (DON) in the euphotic zone at a station in the upper Chesapeake Bay using a new mass-based ecosystem model. Important features of the model are: (1) carbon and nitrogen are incorporated by means of a set of fixed and varying C:N ratios; (2) dissolved organic matter (DOM) is separated into labile, semi-labile, and refractory pools for both C and N; (3) the production and consumption of DOM is treated in detail; and (4) seasonal observations of light, temperature, nutrients, and surface layer circulation are used to physically force the model. The model reasonably reproduces the mean observed seasonal concentrations of nutrients, DOM, plankton biomass, and chlorophyll a. The results suggest that estuarine DOM production is intricately tied to the biomass concentration, ratio, and productivity of phytoplankton, zooplankton, viruses, and bacteria. During peak spring productivity phytoplankton exudation and zooplankton sloppy feeding are the most important autochthonous sources of DOM. In the summer when productivity peaks again, autochthonous sources of DOM are more diverse and, in addition to phytoplankton exudation, important ones include viral lysis and the decay of detritus. The potential importance of viral decay as a source of bioavailable DOM from within the bulk DOM pool is also discussed. The results also highlight the importance of some poorly constrained processes and parameters. Some potential improvements and remedies are suggested. Sensitivity studies on selected parameters are also reported and discussed.

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Section: Model Formulationmentioning

confidence: 99%

Modeling the seasonal autochthonous sources of dissolved organic carbon and nitrogen in the upper Chesapeake Bay

Keller

Hood

2011

Ecological Modelling

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“…The weight gives the variables approximately equal influence on the overall cost, at least initially. The weighting approach is common in parameter optimization studies (see, e.g., Friedrichs, 2001;Schartau and Oschlies, 2003;Friedrichs et al, 2007;Kane et al, 2011). To avoid biasing the cost calculation toward the NH + 4 profiles, we computed an average cost per profile.…”

Section: Parameter Optimizationmentioning

confidence: 99%

Parameterization of biogeochemical sediment–water fluxes using in situ measurements and a diagenetic model

et al. 2016

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Abstract. Diagenetic processes are important drivers of water column biogeochemistry in coastal areas. For example, sediment oxygen consumption can be a significant contributor to oxygen depletion in hypoxic systems, and sedimentwater nutrient fluxes support primary productivity in the overlying water column. Moreover, nonlinearities develop between bottom water conditions and sediment-water fluxes due to loss of oxygen-dependent processes in the sediment as oxygen becomes depleted in bottom waters. Yet, sedimentwater fluxes of chemical species are often parameterized crudely in coupled physical-biogeochemical models, using simple linear parameterizations that are only poorly constrained by observations. Diagenetic models that represent sediment biogeochemistry are available, but rarely are coupled to water column biogeochemical models because they are computationally expensive. Here, we apply a method that efficiently parameterizes sediment-water fluxes of oxygen, nitrate and ammonium by combining in situ measurements, a diagenetic model and a parameter optimization method. As a proof of concept, we apply this method to the Louisiana Shelf where high primary production, stimulated by excessive nutrient loads from the Mississippi-Atchafalaya River system, promotes the development of hypoxic bottom waters in summer. The parameterized sediment-water fluxes represent nonlinear feedbacks between water column and sediment processes at low bottom water oxygen concentrations, which may persist for long periods (weeks to months) in hypoxic systems such as the Louisiana Shelf. This method can be applied to other systems and is particularly relevant for shallow coastal and estuarine waters where the interaction between sediment and water column is strong and hypoxia is prone to occur due to land-based nutrient loads.

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“…One approach is the combination of flexiblestoichiometry, multielement (C, N, P) models of plankton biogeochemistry (Y. Luo & H. Ducklow unpubl. ), with data assimilation (Friedrichs 2001, Friedrichs et al 2007). Without objective means of model-data comparison and parameter adjustment, the estimates of carbon fluxes generated by models are unconstrained and provide no measure of the overall agreement between modeled and observed fluxes.…”

Section: Modeling Carbon Flow Through Oceanic Bacteriamentioning

confidence: 99%

Towards a better understanding of microbial carbon flux in the sea*

Gasol¹,

Pinhassi²,

Alonso‐Sáez³

et al. 2008

Aquat. Microb. Ecol.

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We now have a relatively good idea of how bulk microbial processes shape the cycling of organic matter and nutrients in the sea. The advent of the molecular biology era in microbial ecology has resulted in advanced knowledge about the diversity of marine microorganisms, suggesting that we might have reached a high level of understanding of carbon fluxes in the oceans. However, it is becoming increasingly clear that there are large gaps in the understanding of the role of bacteria in regulating carbon fluxes. These gaps may result from methodological as well as conceptual limitations. For example, should bacterial production be measured in the light? Can bacterial production conversion factors be predicted, and how are they affected by loss of tracers through respiration? Is it true that respiration is relatively constant compared to production? How can accurate measures of bacterial growth efficiency be obtained? In this paper, we discuss whether such questions could (or should) be addressed. Ongoing genome analyses are rapidly widening our understanding of possible metabolic pathways and cellular adaptations used by marine bacteria in their quest for resources and struggle for survival (e.g. utilization of light, acquisition of nutrients, predator avoidance, etc.). Further, analyses of the identity of bacteria using molecular markers (e.g. subgroups of Bacteria and Archaea) combined with activity tracers might bring knowledge to a higher level. Since bacterial growth (and thereby consumption of DOC and inorganic nutrients) is likely regulated differently in different bacteria, it will be critical to learn about the life strategies of the key bacterial species to achieve a comprehensive understanding of bacterial regulation of C fluxes. Finally, some processes known to occur in the microbial food web are hardly ever characterized and are not represented in current food web models. We discuss these issues and offer specific comments and advice for future research agendas.

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Assessment of skill and portability in regional marine biogeochemical models: Role of multiple planktonic groups

Cited by 239 publications

References 83 publications

Modeling the seasonal autochthonous sources of dissolved organic carbon and nitrogen in the upper Chesapeake Bay

Modeling the seasonal autochthonous sources of dissolved organic carbon and nitrogen in the upper Chesapeake Bay

Parameterization of biogeochemical sediment–water fluxes using in situ measurements and a diagenetic model

Towards a better understanding of microbial carbon flux in the sea*

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