scholarly journals Supporting hierarchical soil biogeochemical modeling: Version 2 of the Biogeochemical Transport and Reaction model (BeTR-v2)

2021 ◽  
Author(s):  
Jinyun Tang ◽  
William J. Riley ◽  
Qing Zhu
Keyword(s):  
Reactive Transport ◽  
Soil Column ◽  
Numerical Algorithms ◽  
Reaction Model ◽  
Earth System ◽  
Thermal Dynamics ◽  
Generic Structure ◽  
Biogeochemical Modeling ◽  
Soil Biogeochemistry ◽  
Plant Soil

Abstract. Reliable soil biogeochemical modeling is a prerequisite for credible projections of climate change and associated ecosystem feedbacks. This recognition has called for frameworks that can support flexible and efficient development and application of new or alternative soil biogeochemical modules in earth system models (ESMs). The BeTR-v1 code (i.e., CLM4-BeTR) is one such framework designed to accelerate the development and integration of new soil biogeochemistry formulations into ESMs, and to analyze structural uncertainty in ESM simulations. With a generic reactive transport capability, BeTR-v1 can represent multi-phase (e.g., gaseous, aqueous, and solid), multi-tracer (e.g., nitrate and organic carbon), and multi-organism (e.g., plants, bacteria and fungi) dynamics. Here, we describe the new version BeTR-v2, which adopts more robust numerical algorithms and improves on structural design over BeTR-v1. BeTR-v2 better supports different mathematical formulations in a hierarchical manner by allowing the resultant model be run either for a single topsoil layer, a vertically resolved soil column, or fully coupled with the land component of the Energy Exascale Earth System Model (E3SM). We demonstrate the BeTR-v2 capability with benchmark cases and example soil BGC implementations. By taking advantage of BeTR-v2’s generic structure integrated in E3SM, we then found that calibration could not resolve biases introduced by different numerical coupling strategies of plant-soil biogeochemistry. These results highlight the importance of numerically robust implementation of soil biogeochemistry and coupling with hydrology, thermal dynamics, and plants— capabilities that the open-source BeTR-v2 provides.

Evaluating soil biogeochemistry parameterizations in Earth system models with observations

2014 ◽  
Vol 28 (3) ◽  
pp. 211-222 ◽  
Author(s):  
William R. Wieder ◽  
Jennifer Boehnert ◽  
Gordon B. Bonan
Keyword(s):  
Earth System ◽  
Soil Biogeochemistry ◽  
System Models ◽  
Earth System Models

scholarly journals JULES-CN: a coupled terrestrial carbon–nitrogen scheme (JULES vn5.1)

2021 ◽  
Vol 14 (4) ◽  
pp. 2161-2186
Author(s):  
Andrew J. Wiltshire ◽  
Eleanor J. Burke ◽  
Sarah E. Chadburn ◽  
Chris D. Jones ◽  
Peter M. Cox ◽  
...  
Keyword(s):  
Primary Productivity ◽  
Net Primary Productivity ◽  
Natural State ◽  
Earth System ◽  
Terrestrial Carbon ◽  
Soil System ◽  
N Cycle ◽  
Soil Biogeochemistry ◽  
N Limitation ◽  
C Cycle

Abstract. Understanding future changes in the terrestrial carbon cycle is important for reliable projections of climate change and impacts on ecosystems. It is well known that nitrogen (N) could limit plants' response to increased atmospheric carbon dioxide and it is therefore important to include a representation of the N cycle in Earth system models. Here we present the implementation of the terrestrial nitrogen cycle in the Joint UK Land Environment Simulator (JULES) – the land surface scheme of the UK Earth System Model (UKESM). Two configurations are discussed – the first one (JULES-CN) has a bulk soil biogeochemical model and the second one is a development configuration that resolves the soil biogeochemistry with depth (JULES-CNlayer). In JULES the nitrogen (N) cycle is based on the existing carbon (C) cycle and represents all the key terrestrial N processes in a parsimonious way. Biological N fixation is dependent on net primary productivity, and N deposition is specified as an external input. Nitrogen leaves the vegetation and soil system via leaching and a bulk gas loss term. Nutrient limitation reduces carbon-use efficiency (CUE – ratio of net to gross primary productivity) and can slow soil decomposition. We show that ecosystem level N limitation of net primary productivity (quantified in the model by the ratio of the potential amount of C that can be allocated to growth and spreading of the vegetation compared with the actual amount achieved in its natural state) falls at the lower end of the observational estimates in forests (approximately 1.0 in the model compared with 1.01 to 1.38 in the observations). The model shows more N limitation in the tropical savanna and tundra biomes, consistent with the available observations. Simulated C and N pools and fluxes are comparable to the limited available observations and model-derived estimates. The introduction of an N cycle improves the representation of interannual variability of global net ecosystem exchange, which was more pronounced in the C-cycle-only versions of JULES (JULES-C) than shown in estimates from the Global Carbon Project. It also reduces the present-day CUE from a global mean value of 0.45 for JULES-C to 0.41 for JULES-CN and 0.40 for JULES-CNlayer, all of which fall within the observational range. The N cycle also alters the response of the C fluxes over the 20th century and limits the CO2 fertilisation effect, such that the simulated current-day land C sink is reduced by about 0.5 Pg C yr−1 compared to the version with no N limitation. JULES-CNlayer additionally improves the representation of soil biogeochemistry, including turnover times in the northern high latitudes. The inclusion of a prognostic land N scheme marks a step forward in functionality and realism for the JULES and UKESM models.

A new approach to simulate peat accumulation, degradation and stability in a global land surface scheme

2021 ◽  
Author(s):  
Sarah Chadburn ◽  
Eleanor Burke ◽  
Angela Gallego-Sala ◽  
Noah Smith
Keyword(s):  
Carbon Cycle ◽  
Land Surface ◽  
Soil Column ◽  
Organic Matter Content ◽  
Matter Content ◽  
Organic Layer ◽  
Earth System ◽  
Peat Accumulation ◽  
New Approach ◽  
The Uk

<p>Representing peatlands in global Earth System Models (ESMs) is a major challenge, but a crucial one since peatlands represent a significant component of the global carbon cycle.</p><p>Here we present the first ESM implementation of peat accumulation and degradation that integrates both organic and mineral soils in a single formulation, implemented in JULES - the land-surface component of the UK Earth System Model (UKESM). In this scheme, the soil column is able to expand with the addition of new organic material and to subside as this material decomposes, with variable organic layer thickness, which means that peat can appear and disappear within the landscape without a need for a prescribed peatland fraction.</p><p>Thermal and hydraulic characteristics of the soil are dynamically updated depending on the organic matter content and its level of decomposition, using relationships derived from observations. This scheme captures important feedbacks within the soil, such as the way that peatlands - once formed - can be self-sustaining even under conditions where they would not form today. It also captures the loss of carbon and soil structure when peatlands are drained. We demonstrate this behaviour in the model.</p><p>This provides a new approach for improving the simulation of organic and peatland soils, and associated carbon-cycle feedbacks in ESMs.</p><p>The key remaining challenges for simulating global peatlands are to realistically distribute water around the landscape, in order to represent topographically-controlled peatlands, and to develop appropriate peatland vegetation types.</p>

scholarly journals Earth’s Complexity Is Non-Computable: The Limits of Scaling Laws, Nonlinearity and Chaos

Entropy ◽  
2021 ◽  
Vol 23 (7) ◽  
pp. 915
Author(s):  
Sergio Rubin
Keyword(s):  
Complex System ◽  
Scaling Laws ◽  
Climate Models ◽  
Spatial Scales ◽  
Numerical Algorithms ◽  
Earth System ◽  
Response Dynamics ◽  
Planetary Scale ◽  
Gaia Hypothesis ◽  
The Earth

Current physics commonly qualifies the Earth system as ‘complex’ because it includes numerous different processes operating over a large range of spatial scales, often modelled as exhibiting non-linear chaotic response dynamics and power scaling laws. This characterization is based on the fundamental assumption that the Earth’s complexity could, in principle, be modeled by (surrogated by) a numerical algorithm if enough computing power were granted. Yet, similar numerical algorithms also surrogate different systems having the same processes and dynamics, such as Mars or Jupiter, although being qualitatively different from the Earth system. Here, I argue that understanding the Earth as a complex system requires a consideration of the Gaia hypothesis: the Earth is a complex system because it instantiates life—and therefore an autopoietic, metabolic-repair (M,R) organization—at a planetary scale. This implies that the Earth’s complexity has formal equivalence to a self-referential system that inherently is non-algorithmic and, therefore, cannot be surrogated and simulated in a Turing machine. I discuss the consequences of this, with reference to in-silico climate models, tipping points, planetary boundaries, and planetary feedback loops as units of adaptive evolution and selection.

Mathematical model for reactive transport of heavy metals in soil column: Based on PHREEQC and HP1 simulators

2017 ◽  
Vol 6 (1) ◽  
pp. 67-81
Author(s):  
Fatemeh Izadi Tameh ◽  
Gholamreza Asadollahfardi ◽  
Ahmad Khodadadi Darban
Keyword(s):  
Heavy Metals ◽  
Mathematical Model ◽  
Reactive Transport ◽  
Soil Column

scholarly journals Particle-Based Workflow for Modeling Uncertainty of Reactive Transport in 3D Discrete Fracture Networks

Water ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 2502 ◽  
Author(s):  
Phuong Thanh Vu ◽  
Chuen-Fa Ni ◽  
Wei-Ci Li ◽  
I-Hsien Lee ◽  
Chi-Ping Lin
Keyword(s):  
Fractured Rocks ◽  
Reactive Transport ◽  
Fracture Network ◽  
Reaction Model ◽  
Transport Processes ◽  
Fracture Networks ◽  
Flow Paths ◽  
Complex Fracture ◽  
Discrete Fracture Networks ◽  
Discrete Fracture

Fractures are major flow paths for solute transport in fractured rocks. Conducting numerical simulations of reactive transport in fractured rocks is a challenging task because of complex fracture connections and the associated nonuniform flows and chemical reactions. The study presents a computational workflow that can approximately simulate flow and reactive transport in complex fractured media. The workflow involves a series of computational processes. Specifically, the workflow employs a simple particle tracking (PT) algorithm to track flow paths in complex 3D discrete fracture networks (DFNs). The PHREEQC chemical reaction model is then used to simulate the reactive transport along particle traces. The study illustrates the developed workflow with three numerical examples, including a case with a simple fracture connection and two cases with a complex fracture network system. Results show that the integration processes in the workflow successfully model the tetrachloroethylene (PCE) and trichloroethylene (TCE) degradation and transport along particle traces in complex DFNs. The statistics of concentration along particle traces enables the estimations of uncertainty induced by the fracture structures in DFNs. The types of source contaminants can lead to slight variations of particle traces and influence the long term reactive transport. The concentration uncertainty can propagate from parent to daughter compounds and accumulate along with the transport processes.

scholarly journals Carbon-nitrogen feedbacks in the UVic ESCM

2012 ◽  
Vol 5 (5) ◽  
pp. 1137-1160 ◽  
Author(s):  
R. Wania ◽  
K. J. Meissner ◽  
M. Eby ◽  
V. K. Arora ◽  
I. Ross ◽  
...  
Keyword(s):  
Radiative Forcing ◽  
Climate Model ◽  
Gross Primary Production ◽  
N Deposition ◽  
Strong Nonlinearity ◽  
Earth System ◽  
Soil System ◽  
Biological N2 Fixation ◽  
Plant Soil ◽  
Nitrogen Pools

Abstract. A representation of the terrestrial nitrogen cycle is introduced into the UVic Earth System Climate Model (UVic ESCM). The UVic ESCM now contains five terrestrial carbon pools and seven terrestrial nitrogen pools: soil, litter, leaves, stem and roots for both elements and ammonium and nitrate in the soil for nitrogen. Nitrogen cycles through plant tissue, litter, soil and the mineral pools before being taken up again by the plant. Biological N2 fixation and nitrogen deposition represent external inputs to the plant-soil system while losses occur via leaching. Simulated carbon and nitrogen pools and fluxes are in the range of other models and observations. Gross primary production (GPP) for the 1990s in the CN-coupled version is 129.6 Pg C a−1 and net C uptake is 0.83 Pg C a−1, whereas the C-only version results in a GPP of 133.1 Pg C a−1 and a net C uptake of 1.57 Pg C a−1. At the end of a transient experiment for the years 1800–1999, where radiative forcing is held constant but CO2 fertilisation for vegetation is permitted to occur, the CN-coupled version shows an enhanced net C uptake of 1.05 Pg C a−1, whereas in the experiment where CO2 is held constant and temperature is transient the land turns into a C source of 0.60 Pg C a−1 by the 1990s. The arithmetic sum of the temperature and CO2 effects is 0.45 Pg C a−1, 0.38 Pg C a−1 lower than seen in the fully forced model, suggesting a strong nonlinearity in the CN-coupled version. Anthropogenic N deposition has a positive effect on Net Ecosystem Production of 0.35 Pg C a−1. Overall, the UVic CN-coupled version shows similar characteristics to other CN-coupled Earth System Models, as measured by net C balance and sensitivity to changes in climate, CO2 and temperature.

Water table fluctuations and soil biogeochemistry: An experimental approach using an automated soil column system

2014 ◽  
Vol 509 ◽  
pp. 245-256 ◽  
Author(s):  
F. Rezanezhad ◽  
R.-M. Couture ◽  
R. Kovac ◽  
D. O’Connell ◽  
P. Van Cappellen
Keyword(s):  
Water Table ◽  
Experimental Approach ◽  
Soil Column ◽  
Soil Biogeochemistry ◽  
Water Table Fluctuations ◽  
Column System

scholarly journals A soil diffusion-reaction model for surface COS flux: COSSM v1

2015 ◽  
Vol 8 (7) ◽  
pp. 5139-5182 ◽  
Author(s):  
W. Sun ◽  
K. Maseyk ◽  
C. Lett ◽  
U. Seibt
Keyword(s):  
Great Plains ◽  
Dominant Role ◽  
Soil Column ◽  
Carbonyl Sulfide ◽  
Production Capacity ◽  
Terrestrial Ecosystems ◽  
Reaction Model ◽  
Diffusion Reaction ◽  
Wheat Field ◽  
Source Sink

Abstract. Soil exchange of carbonyl sulfide (COS) is the second largest COS flux in terrestrial ecosystems. A novel application of COS is the separation of gross primary productivity (GPP) from concomitant respiration. This method requires that soil COS exchange is relatively small and can be well quantified. Existing models for soil COS flux have incorporated empirical temperature and moisture functions derived from laboratory experiments, but not explicitly resolved diffusion in the soil column. We developed a 1-D diffusion-reaction model for soil COS exchange that accounts for COS uptake and production, relates source-sink terms to environmental variables, and has an option to enable surface litter layers. We evaluated the model with field data from a wheat field (Southern Great Plains (SGP), OK, USA) and an oak woodland (Stunt Ranch Reserve, CA, USA). The model was able to reproduce all observed features of soil COS exchange such as diurnal variations and sink-source transitions. We found that soil COS uptake is strongly diffusion controlled, and limited by low COS concentrations in the soil if there is COS uptake in the litter layer. The model provides novel insights into the balance between soil COS uptake and production: a higher COS production capacity was required despite lower COS emissions during the growing season compared to the post-senescence period at SGP, and unchanged COS uptake capacity despite the dominant role of COS emissions after senescence. Once there is a database of soil COS parameters for key biomes, we expect the model will also be useful to simulate soil COS exchange at regional to global scales.

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