scholarly journals Bottom RedOx Model (BROM v.1.1): a coupled benthic–pelagic model for simulation of water and sediment biogeochemistry

2017 ◽  
Vol 10 (1) ◽  
pp. 453-482 ◽  
Author(s):  
Evgeniy V. Yakushev ◽  
Elizaveta A. Protsenko ◽  
Jorn Bruggeman ◽  
Philip Wallhead ◽  
Svetlana V. Pakhomova ◽  
...  
Keyword(s):  
Organic Matter ◽  
Redox State ◽  
Nutrient Loading ◽  
Chemical Elements ◽  
Bottom Layer ◽  
Saturation State ◽  
Biogeochemical Models ◽  
Sediment Biogeochemistry ◽  
Marine Carbonate ◽  
Mineralization Of Organic Matter

Abstract. Interactions between seawater and benthic systems play an important role in global biogeochemical cycling. Benthic fluxes of some chemical elements (e.g., C, N, P, O, Si, Fe, Mn, S) alter the redox state and marine carbonate system (i.e., pH and carbonate saturation state), which in turn modulate the functioning of benthic and pelagic ecosystems. The redox state of the near-bottom layer in many regions can change with time, responding to the supply of organic matter, physical regime, and coastal discharge. We developed a model (BROM) to represent key biogeochemical processes in the water and sediments and to simulate changes occurring in the bottom boundary layer. BROM consists of a transport module (BROM-transport) and several biogeochemical modules that are fully compatible with the Framework for the Aquatic Biogeochemical Models, allowing independent coupling to hydrophysical models in 1-D, 2-D, or 3-D. We demonstrate that BROM is capable of simulating the seasonality in production and mineralization of organic matter as well as the mixing that leads to variations in redox conditions. BROM can be used for analyzing and interpreting data on sediment–water exchange, and for simulating the consequences of forcings such as climate change, external nutrient loading, ocean acidification, carbon storage leakage, and point-source metal pollution.

scholarly journals Bottom RedOx Model (BROM, v.1.0): a coupled benthic-pelagic model for simulation of seasonal anoxia and its impact

2016 ◽  
Author(s):  
E. V. Yakushev ◽  
E. A. Protsenko ◽  
J. Bruggeman ◽  
R. G. J. Bellerby ◽  
S. V. Pakhomova ◽  
...  
Keyword(s):  
Boundary Layer ◽  
Organic Matter ◽  
Redox State ◽  
Nutrient Loading ◽  
Chemical Elements ◽  
Bottom Layer ◽  
Redox Conditions ◽  
Bottom Boundary Layer ◽  
Bottom Boundary ◽  
Benthic Sediments

Abstract. Interaction between seawater and benthic sediments plays an important role in global biogeochemical cycling. Benthic fluxes of chemical elements (C, N, P, O, Si, Fe, Mn, S) directly affect redox state and acidification (i.e. pH and carbonate saturation), which in turn determine the functioning of the benthic and pelagic ecosystems. The redox state of the near bottom layer can change and oscillate in many regions responding to the supply of organic matter, physical regime and coastal discharge. The goal of this work was to develop a model that captures key biogeochemical processes occurring at the bottom boundary layer and sediment–water interface and analyze the changes that result from seasonal variability in redox conditions in the water column. We used a modular approach allowing the model to be coupled to existing hydrophysical models in 1-D, 2-D or 3-D. The model is capable to simulate seasonality in production and respiration of organic matter as well as in mixing, that leads to variation of redox conditions in the bottom boundary layer. Production and reduction of organic matter and varying redox conditions in the bottom boundary layer affect the carbonate system and lead to changes in pH and alkalinity. Bacteria play a significant role in the fate of organic matter due to chemosynthesis (autotrophs) and consumption of organic matter (heterotrophs). Changes in the bottom boundary layer redox conditions modify the distribution of nutrients (N and P) and redox metals (Mn and Fe). The model can be used for analyzing and interpreting data on sediment-water exchange, and estimating the consequences of forcing such as climate change, external nutrient loading, ocean acidification, carbon storage leakages, and point-source metal pollution.

scholarly journals Mineralization of organic matter in boreal lake sediments: rates, pathways, and nature of the fermenting substrates

2020 ◽  
Vol 17 (18) ◽  
pp. 4571-4589
Author(s):  
François Clayer ◽  
Yves Gélinas ◽  
André Tessier ◽  
Charles Gobeil
Keyword(s):  
Organic Matter ◽  
Lake Sediments ◽  
Dissolved Inorganic Carbon ◽  
Biogeochemical Models ◽  
Mineralization Of Organic Matter ◽  
Carbohydrate Fermentation ◽  
Mass Balancing ◽  
Reaction Transport ◽  
Lake Basins

Abstract. The complexity of organic matter (OM) degradation mechanisms represents a significant challenge for developing biogeochemical models to quantify the role of aquatic sediments in the climate system. The common representation of OM by carbohydrates formulated as CH2O in models comes with the assumption that its degradation by fermentation produces equimolar amounts of methane (CH4) and dissolved inorganic carbon (DIC). To test the validity of this assumption, we modelled using reaction-transport equation vertical profiles of the concentration and isotopic composition (δ13C) of CH4 and DIC in the top 25 cm of the sediment column from two lake basins, one whose hypolimnion is perennially oxygenated and one with seasonal anoxia. Furthermore, we modelled solute porewater profiles reported in the literature for four other seasonally anoxic lake basins. A total of 17 independent porewater datasets are analyzed. CH4 and DIC production rates associated with methanogenesis at the five seasonally anoxic sites collectively show that the fermenting OM has a mean (± SD) carbon oxidation state (COS) value of -1.4±0.3. This value is much lower than the value of zero expected from carbohydrate fermentation. We conclude that carbohydrates do not adequately represent the fermenting OM in hypolimnetic sediments and propose to include the COS in the formulation of OM fermentation in models applied to lake sediments to better quantify sediment CH4 outflux. This study highlights the potential of mass balancing the products of OM mineralization to characterize labile substrates undergoing fermentation in sediments.

scholarly journals Mineralization of organic matter in boreal lake sediments: Rates, pathways and nature of the fermenting substrates

2020 ◽  
Author(s):  
François Clayer ◽  
Yves Gélinas ◽  
André Tessier ◽  
Charles Gobeil
Keyword(s):  
Organic Matter ◽  
Lake Sediments ◽  
Environmental Changes ◽  
Dissolved Inorganic Carbon ◽  
Biogeochemical Models ◽  
Mineralization Of Organic Matter ◽  
The Common ◽  
Reaction Transport ◽  
Lake Basins

Abstract. The complexity of organic matter (OM) degradation mechanisms represents a significant challenge for developing biogeochemical models to quantify the role of aquatic sediments in the climate system. The common representation of OM by carbohydrates formulated as CH2O in models comes with the assumption that its degradation by fermentation produces equimolar amounts of methane (CH4) and dissolved inorganic carbon (DIC). To test the validity of this assumption, we modeled using reaction-transport equations vertical profiles of the concentration and isotopic composition (δ13C) of CH4 and DIC in the top 25 cm of the sediment column from two lake basins, one whose hypolimnion is perennially oxygenated and one with seasonal anoxia. Our results reveal that methanogenesis only occurs via hydrogenotrophy in both basins. Furthermore, we calculate, from CH4 and DIC production rates associated with methanogenesis, that the fermenting OM has an average carbon oxidation state (COS) below −0.9. Modeling solute porewater profiles reported in the literature for four other seasonally anoxic lake basins also yields negative COS values. Collectively, the mean (±SD) COS value of −1.4 ± 0.3 for all the seasonally anoxic sites is much lower than the value of zero expected from carbohydrates fermentation. We conclude that carbohydrates do not adequately represent the fermenting OM and that the COS should be included in the formulation of OM fermentation in models applied to lake sediments. This study highlights the need to better characterize the labile OM undergoing mineralization to interpret present-day greenhouse gases cycling and predict its alteration under environmental changes.

scholarly journals Coastal hypoxia and sediment biogeochemistry

2009 ◽  
Vol 6 (7) ◽  
pp. 1273-1293 ◽  
Author(s):  
J. J. Middelburg ◽  
L. A. Levin
Keyword(s):  
Organic Matter ◽  
Bottom Water ◽  
Water Exchange ◽  
Transport Processes ◽  
Ecosystem Dynamics ◽  
Ecosystem Functions ◽  
Oxygen Levels ◽  
Concise Review ◽  
Water Oxygen ◽  
Sediment Biogeochemistry

Abstract. The intensity, duration and frequency of coastal hypoxia (oxygen concentration <63 μM) are increasing due to human alteration of coastal ecosystems and changes in oceanographic conditions due to global warming. Here we provide a concise review of the consequences of coastal hypoxia for sediment biogeochemistry. Changes in bottom-water oxygen levels have consequences for early diagenetic pathways (more anaerobic at expense of aerobic pathways), the efficiency of re-oxidation of reduced metabolites and the nature, direction and magnitude of sediment-water exchange fluxes. Hypoxia may also lead to more organic matter accumulation and burial and the organic matter eventually buried is also of higher quality, i.e. less degraded. Bottom-water oxygen levels also affect the organisms involved in organic matter processing with the contribution of metazoans decreasing as oxygen levels drop. Hypoxia has a significant effect on benthic animals with the consequences that ecosystem functions related to macrofauna such as bio-irrigation and bioturbation are significantly affected by hypoxia as well. Since many microbes and microbial-mediated biogeochemical processes depend on animal-induced transport processes (e.g. re-oxidation of particulate reduced sulphur and denitrification), there are indirect hypoxia effects on biogeochemistry via the benthos. Severe long-lasting hypoxia and anoxia may result in the accumulation of reduced compounds in sediments and elimination of macrobenthic communities with the consequences that biogeochemical properties during trajectories of decreasing and increasing oxygen may be different (hysteresis) with consequences for coastal ecosystem dynamics.

Dissolved organic matter accumulation, reactivity, and redox state in ground water of a recharge wetland

Wetlands ◽  
2008 ◽  
Vol 28 (3) ◽  
pp. 747-759 ◽  
Author(s):  
Natalie Mladenov ◽  
Philippa Huntsman-Mapila ◽  
Piotr Wolski ◽  
Wellington R. L. Masamba ◽  
Diane M. McKnight
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Ground Water ◽  
Redox State ◽  
Organic Matter Accumulation

Mineralization of organic matter and the carbon sequestration capacity of zonal soils

2008 ◽  
Vol 41 (7) ◽  
pp. 717-730 ◽  
Author(s):  
V. M. Semenov ◽  
L. A. Ivannikova ◽  
T. V. Kuznetsova ◽  
N. A. Semenova ◽  
A. S. Tulina
Keyword(s):  
Organic Matter ◽  
Carbon Sequestration ◽  
Mineralization Of Organic Matter ◽  
Zonal Soils

scholarly journals Surfactant control of gas transfer velocity along an offshore coastal transect: results from a laboratory gas exchange tank

2016 ◽  
Vol 13 (13) ◽  
pp. 3981-3989 ◽  
Author(s):  
R. Pereira ◽  
K. Schneider-Zapp ◽  
R. C. Upstill-Goddard
Keyword(s):  
Organic Matter ◽  
Gas Exchange ◽  
Trace Gas ◽  
Gas Transfer ◽  
Transfer Velocity ◽  
Chl A ◽  
Gas Transfer Velocity ◽  
Biogeochemical Models ◽  
Sea Surface Microlayer ◽  
Laboratory Water

Abstract. Understanding the physical and biogeochemical controls of air–sea gas exchange is necessary for establishing biogeochemical models for predicting regional- and global-scale trace gas fluxes and feedbacks. To this end we report the results of experiments designed to constrain the effect of surfactants in the sea surface microlayer (SML) on the gas transfer velocity (kw; cm h−1), seasonally (2012–2013) along a 20 km coastal transect (North East UK). We measured total surfactant activity (SA), chromophoric dissolved organic matter (CDOM) and chlorophyll a (Chl a) in the SML and in sub-surface water (SSW) and we evaluated corresponding kw values using a custom-designed air–sea gas exchange tank. Temporal SA variability exceeded its spatial variability. Overall, SA varied 5-fold between all samples (0.08 to 0.38 mg L−1 T-X-100), being highest in the SML during summer. SML SA enrichment factors (EFs) relative to SSW were  ∼  1.0 to 1.9, except for two values (0.75; 0.89: February 2013). The range in corresponding k660 (kw for CO2 in seawater at 20 °C) was 6.8 to 22.0 cm h−1. The film factor R660 (the ratio of k660 for seawater to k660 for “clean”, i.e. surfactant-free, laboratory water) was strongly correlated with SML SA (r ≥ 0.70, p ≤ 0.002, each n = 16). High SML SA typically corresponded to k660 suppressions  ∼  14 to 51 % relative to clean laboratory water, highlighting strong spatiotemporal gradients in gas exchange due to varying surfactant in these coastal waters. Such variability should be taken account of when evaluating marine trace gas sources and sinks. Total CDOM absorbance (250 to 450 nm), the CDOM spectral slope ratio (SR = S275 − 295∕S350 − 400), the 250 : 365 nm CDOM absorption ratio (E2 : E3), and Chl a all indicated spatial and temporal signals in the quantity and composition of organic matter in the SML and SSW. This prompts us to hypothesise that spatiotemporal variation in R660 and its relationship with SA is a consequence of compositional differences in the surfactant fraction of the SML DOM pool that warrants further investigation.

scholarly journals Simulating measurable ecosystem carbon and nitrogen dynamics with the mechanistically-defined MEMS 2.0 model

2021 ◽  
Author(s):  
Yao Zhang ◽  
Jocelyn M. Lavallee ◽  
Andy D. Robertson ◽  
Rebecca Even ◽  
Stephen M. Ogle ◽  
...  
Keyword(s):  
Organic Matter ◽  
Soil Water ◽  
Root Zone ◽  
Ecosystem Respiration ◽  
Gross Primary Production ◽  
Total N ◽  
Calibration And Validation ◽  
Biogeochemical Models ◽  
Lower Accuracy ◽  
C Stocks

Abstract. For decades, predominant soil biogeochemical models have used conceptual soil organic matter (SOM) pools and only simulated them to a shallow depth in soil. Efforts to overcome these limitations have prompted the development of new generation SOM models, including MEMS 1.0, which represents measurable biophysical SOM fractions, over the entire root zone, and embodies recent understanding of the processes that govern SOM dynamics. Here we present the result of continued development of the MEMS model, version 2.0. MEMS 2.0 is a full ecosystem model with modules simulating plant growth with above and below-ground inputs, soil water, and temperature by layer, decomposition of plant inputs and SOM, and mineralization and immobilization of nitrogen (N). The model simulates two commonly measured SOM pools – particulate and mineral-associated organic matter (POM and MAOM), respectively. We present results of calibration and validation of the model with several grassland sites in the U.S. MEMS 2.0 generally captured the soil carbon (C) stocks (R2 of 0.89 and 0.6 for calibration and validation, respectively) and their distributions between POM and MAOM throughout the entire soil profile. The simulated soil N matches measurements but with lower accuracy (R2 of 0.73 and 0.31 for calibration and validation of total N in SOM, respectively) than for soil C. Simulated soil water and temperature were compared with measurements and the accuracy is comparable to the other commonly used models. The seasonal variation in gross primary production (GPP; R2 = 0.83), ecosystem respiration (ER; R2 = 0.89), net ecosystem exchange (NEE; R2 = 0.67), and evapotranspiration (ET; R2 = 0.71) were well captured by the model. We will further develop the model to represent forest and agricultural systems and improve it to incorporate new understanding of SOM decomposition.

scholarly journals Average annual background quantity of chemical elements and organic matter in the streams of the "River" environment flowing into Lake Baikal reservoirs

2020 ◽  
Vol 5 (4) ◽  
pp. 433-447
Author(s):  
Olga Yu. Astrakhantseva ◽  
◽  
Oleg Yu. Palkin ◽  
Keyword(s):  
Organic Matter ◽  
Lake Baikal ◽  
Chemical Elements ◽  
The South ◽  
River Flows ◽  
Chemical Balance ◽  
Biogenic Components ◽  
Annual Amount ◽  
Natural Component

The aim of the article is to assess the average long-term background hydrochemical input of chemical elements and organic matter from the flows of the natural component of the environment "Rivers" flowing into the South, Selenginsky, Middle and North reservoirs of Lake. Baikal. The results of calculation of the average annual amount (g/year) of chemical elements and organic matter (Na+, K+, Ca2+, Mg2+, Al, Si, Mn2+, Feобщ , SO42-, HCO3-, Cl-, NO3-, PO43-, Cr, Cu, Cd, Hg, Pb, Sr, Zn, Co, U, V, Mo, Cорг, Nорг, Pорг, Sорг, CO2, Ti) in the streams of the natural component of the environment "Rivers" flowing into the South, Selenginsky, Sredniy, Severny reservoirs of Lake Baikal are presented. The scale of the river chemical input into the reservoirs and the contribution of the "River" flows to the chemical balances of these reservoirs have been determined. It has been established that only in the Selenga reservoir the rivers carry a significant amount of matter (about 3%). The contribution of river flows to the chemical balance of the reservoir is 3.54; 5.4; 17.5 and 21.5% in the South, Selenga, Middle and North reservoirs, respectively. The rivers flowing into the Selenga reservoir carry 70.6% of the total amount of matter brought by the rivers into the lake. Whereas the rivers of the Northern, Middle and Southern reservoirs carry 14.0; 11.6 and 3.8% of the matter. Only in the Selenga and Northern reservoirs, the rivers (tributaries) are the main sources of macrocomponents (K+, Na+, Ca2+, SO42-, CO3-, Cl-), a number of microcomponents (Rb, Mo, Hg, Sr, and Cu and Zn in the Selenga river-), organic matter (Corgг, Norg, Porg), and biogenic components in the Selenga reservoir (NO3-).

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