L3_CNP-ECA-Root_Leaf_Traits Design Doc
- William Riley (Unlicensed)
- Qing Zhu
- Renata McCoy
Owned by William Riley (Unlicensed)
The Design Document page provides a description of the algorithms, implementation and planned testing including unit, verification, validation and performance testing.
Design Document
In the table below, 4.Equ means Equations and Algorithms, 5.Ver means Verification, 6.Perf - Performance, 7. Val - Validation, 
- completed, 
- in progress, 
- not done
Overview table for the owner and an approver of this feature
1.Description | CNP model with root uptake kinetics, leaf level physiology, soil nutrient competition, N-P interactions through N2 fixation and phosphatase activity |
| 2.Owner | |
| 3.Created | |
| 4.Equ | |
| 5.Ver | |
| 6.Perf | |
| 7.Val | |
| 8.Approver | |
| 9.Approved Date | |
| V1.0 | Accepted |
Title: Nutrient COMpetition (N-COM): a mechanistic treatment of plant-soil nutrient interactions
Requirements and Design
ACME Land Group
Date: 8/28/2015
Summary
The ECA kinetics (Tang and Riley 2013; 2015) is being integrated into the ACME Land Model v1 (ALMv1) to represent multiple nutrient (i.e., nitrogen and phosphorus in v1) interactions and competition between multiple consumers (microbes, abiotic surfaces, and plants). This work has followed the original proposed tasks, primarily under M3.10 and M3.14. The code is being integrated in such a way as to allow for straightforward testing of different competition hypotheses.
References for this document:
- Ghimire, B., W. J. Riley, and C. D. Koven (2016), Representing leaf and root physiology in CLM results in improved global carbon and nitrogen cycling predictions, DOI: 10.1002/2015MS000538, JAMES.
- Tang, J. Y., and W. J. Riley (2015), Weaker soil carbon-climate feedbacks resulting from microbial and abiotic interactions, Nature Climate Change, 5,WOS:00034651390001956-60.
- Zhu, Q., and W. J. Riley (2015), Improved modeling of soil nitrogen losses, Nature Climate Change, 5, doi:10.1038/nclimate2696, 705-706.
- Zhu, Q., W. J. Riley, J. Y. Tang, and C. D. Koven (2016), Multiple soil nutrient competition between plants, microbes, and mineral surfaces: Model development, parameterization, and example applications in several tropical forests, Biogeosciences, 13, 341-363.
- Tang, J. Y., and W. J. Riley (2013), A total quasi-steady-state formulation of substrate uptake kinetics in complex networks and an example application to microbial litter decomposition, Biogeosciences, 10,WOS:000329054600033, Doi 10.5194/Bg-10-8329-2013, 8329-8351.
Requirements
Requirement: Implement ECA kinetics to represent coupled N and P controls on carbon cycle processes
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
Implementing ECA kinetics to represent coupled N and P controls on carbon cycle processes requires the following code developments:
(1) Add nutrient competition through ECA kinetics: root, decomposing microbes, nitrate compete for NH4; root, decomposing microbes, denitrifier compete for NO3; root, decomposing microbes compete for POx
(2) Add root nutrient uptake kinetics to facilitate ECA kinetics implementation
(3) Predict the nutrient uptake profile based on ECA kinetics
(4) Link photosynthesis capacity with leaf nitrogen and phosphorus levels to facilitate ECA kinetics implementation
(5) Impelement dynamic allocation scheme considering nutrient, water, and light resource supplies
(6) Modify N2 fixation, mechanistically implement N2 fixation and its interaction with nitrogen and phosphorus availability to allow ECA kinetics framework to uniformly treat competition
(7) Mechanistically implement phosphatase activity and its interaction with nitrogen and phosphorus availability in the ECA kinetics framework
Algorithmic Formulations
Design solution: New modules are added to facilitate ECA kinetics and multi-nutrient competition
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
Two competition algorithms are implemented (Zhu et al. 2015, 2016):
- Soil microbes outcompete plants
UPmic = min(Nav, UPmic)
UPplant = min(max(Nav - UPmic,0), UPplant)
UPmic and UPplant are microbial decomposer and plant nutrient uptake rate. Nav is soil available nutrient pool size - Plant-microbe competition is scaled by functional traits (e.g., biomass density) through ECA formulation
UPmic = VMAXmic * [Emic]*[Nav]/(KMmic + [Nav] + [Emic] + [Eplant]*KMmic/KMplant)
UPplant = VMAXplant * [Eplant]*[Nav]/(KMplant + [Nav] + [Eplant] + [Emic]*KMplant/KMmic)
VMAX and KM are kinetics parameters, Emic and Eplant are nutrient carrier enzyme abundance for decomposing microbes and plants
The ECA kinetics integration requires:
- Leaf level physiology: how N (Ghimire et al. 2016) and P leaf levels affect GPP
- VCMAX = f(leafN, leafP); JMAX = f(leafN, leafP)
- VCMAX and JMAX are maximum carboxylation and electron transport rate for photosynthesis.
- Their relationships with leaf level N/P concentration are derived form the TRY database.
- N2 fixation = f(carbon cost of root nitrogen uptake, carbon cost of N2 fixation, plant phosphorus status)
- N2 fixation occurs only when roots are not able to acquire enough nitrogen. N2 fixation rate could be limited by plant phosphorus shortage.
- Phosphatase activity = f(nitrogen cost, plant nitrogen status, plant phosphorus status)
- Phosphatase activity is nitrogen expensive. It occur only when the benefit is larger than the cost.
Design and Implementation
Implementation: Offline test with MATLAB codes plus online test within ACME Land Model (ALM)
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
- Initial prototype of the N-COM model has been developed, tested, and published (Zhu et al. 2015, 2016).
- The N-COM model is being integrated in ACME following the Algorithmic Formulations described above.
Planned Verification and Unit Testing
Verification and Unit Testing: Benchmarking
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
Once integrated with Master, we will perform the offline simulations described below (Planned Validation Testing) as a first cut at Verification. Unit testing of model subcomponents will be designed and implemented over the 6 months following code freeze (Nov. 1, 2015)
Planned Validation Testing
Validation Testing: Model validate with global, regional, and site-level datasets
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
The ECA representation of nutrient competition is being, and will continue to be, tested against site-level, regional syntheses, and global remote-sensed and meta-analyses products:
- ACME with N-COM integration have been (N components; Ghimire et al. 2016), and will be, evaluated and validated using the International Land Model Benchmarking (ILAMB) package.
- ACME with N-COM integration will be validated against global scale nitrogen and phosphorus fertilization experiments, across multiple ecosystems. We plan to integrate this meta-analysis into the ILAMB package.
Planned Performance Testing
Date last modified:
Contributors: Qing Zhu, William Riley (Unlicensed)
- The ACME Land Model N-COM code will be tested with historical 1850 simulations timing, and compared to baseline ALMv0 performance timing.
- Preliminary results indicate no decrease in computational performance with integration of N-COM, but substantial increase in model simulation quality compared to observations
- Computational performance will be evaluated for offline and coupled global simulations using the ACME timing tools.