scholarly journals Sensitivity analysis of six soil organic matter models applied to the decomposition of animal manures and crop residues

2016 ◽  
Vol 11 ◽  
Author(s):  
Daniele Cavalli ◽  
Pietro Marino Gallina ◽  
Luca Bechini
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Organic Matter Decomposition ◽  
Model Parameters ◽  
Monod Kinetics ◽  
Decomposition Rates ◽  
Mineral N ◽  
First Order ◽  
Inhibition Hypothesis ◽  
C Decomposition

Two features distinguishing soil organic matter simulation models are the type of kinetics used to calculate pool decomposition rates, and the algorithm used to handle the effects of N shortage on C decomposition. Compared to widely used first-order kinetics, Monod kinetics more realistically represent organic matter decomposition, because they relate decomposition to both substrate and decomposer size. Most models impose a fixed C to N ratio for microbial biomass. When N required by microbial biomass to decompose a given amount of substrate- C is larger than soil available N, carbon decomposition rates are limited proportionally to N deficit (N inhibition hypothesis). Alternatively, C-overflow was proposed as a way of getting rid of excess C, by allocating it to a storage pool of polysaccharides. We built six models to compare the combinations of three decomposition kinetics (first-order, Monod, and reverse Monod), and two ways to simulate the effect of N shortage on C decomposition (N inhibition and C-overflow). We conducted sensitivity analysis to identify model parameters that mostly affected CO<sub>2</sub> emissions and soil mineral N during a simulated 189-day laboratory incubation assuming constant water content and temperature. We evaluated model outputs sensitivity at different stages of organic matter decomposition in a soil amended with three inputs of increasing C to N ratio: liquid manure, solid manure, and low-N crop residue. Only few model parameters and their interactions were responsible for consistent variations of CO<sub>2</sub> and soil mineral N. These parameters were mostly related to microbial biomass and to the partitioning of applied C among input pools, as well as their decomposition constants. In addition, in models with Monod kinetics, CO<sub>2</sub> was also sensitive to a variation of the halfsaturation constants. C-overflow enhanced pool decomposition compared to N inhibition hypothesis when N shortage occurred. Accumulated C in the polysaccharides pool decomposed slowly; therefore model outputs were not sensitive to a variation of its decay constant. Six-month organic matter decomposition was generally higher for models implementing classical Monod kinetics, followed by models with first-order and reverse Monod kinetics, due to the effect of soil microbial biomass growth on decomposition rates. Moreover, models implementing Monod kinetics predicted positive priming effects of native organic matter after soil amendment, according to co-metabolism theory. Thus, priming was proportional to the increase of the microbial biomass and in turn to the decomposability of applied organic matter. We conclude that model calibration should focus only on the few important parameters.

scholarly journals SHIMMER (1.0): a novel mathematical model for microbial and biogeochemical dynamics in glacier forefield ecosystems

2015 ◽  
Vol 8 (10) ◽  
pp. 3441-3470 ◽  
Author(s):  
J. A. Bradley ◽  
A. M. Anesio ◽  
J. S. Singarayer ◽  
M. R. Heath ◽  
S. Arndt
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Microbial Growth ◽  
Model Development ◽  
Biogeochemical Cycling ◽  
Biogeochemical Model ◽  
Model Parameters ◽  
Glacier Forefield ◽  
Unconstrained Model

Abstract. SHIMMER (Soil biogeocHemIcal Model for Microbial Ecosystem Response) is a new numerical modelling framework designed to simulate microbial dynamics and biogeochemical cycling during initial ecosystem development in glacier forefield soils. However, it is also transferable to other extreme ecosystem types (such as desert soils or the surface of glaciers). The rationale for model development arises from decades of empirical observations in glacier forefields, and enables a quantitative and process focussed approach. Here, we provide a detailed description of SHIMMER, test its performance in two case study forefields: the Damma Glacier (Switzerland) and the Athabasca Glacier (Canada) and analyse sensitivity to identify the most sensitive and unconstrained model parameters. Results show that the accumulation of microbial biomass is highly dependent on variation in microbial growth and death rate constants, Q10 values, the active fraction of microbial biomass and the reactivity of organic matter. The model correctly predicts the rapid accumulation of microbial biomass observed during the initial stages of succession in the forefields of both the case study systems. Primary production is responsible for the initial build-up of labile substrate that subsequently supports heterotrophic growth. However, allochthonous contributions of organic matter, and nitrogen fixation, are important in sustaining this productivity. The development and application of SHIMMER also highlights aspects of these systems that require further empirical research: quantifying nutrient budgets and biogeochemical rates, exploring seasonality and microbial growth and cell death. This will lead to increased understanding of how glacier forefields contribute to global biogeochemical cycling and climate under future ice retreat.

Mountain lakes increase organic matter decomposition rates in streams

2010 ◽  
Vol 29 (2) ◽  
pp. 521-529 ◽  
Author(s):  
Keli J. Goodman ◽  
Michelle A. Baker ◽  
Wayne A. Wurtsbaugh
Keyword(s):  
Organic Matter ◽  
Mountain Lakes ◽  
Organic Matter Decomposition ◽  
Decomposition Rates

Modeling Biodegradation of Subsurface Oil in Sand Beaches Polluted with Oil

2014 ◽  
Vol 2014 (1) ◽  
pp. 1113-1125
Author(s):  
Xiaolong Geng ◽  
Michel C. Boufadel
Keyword(s):  
Microbial Biomass ◽  
Galvanized Steel ◽  
Sensitivity Analyses ◽  
Parameter Estimates ◽  
Model Parameters ◽  
Zone Model ◽  
Residual Oil ◽  
Monod Kinetics ◽  
Microbial Biomass Nitrogen ◽  
Total N

ABSTRACT In April 2010, the explosion of the Deepwater Horizon (DWH) drilling platform led to the release of nearly 4.9 million barrels of crude oil into the Gulf of Mexico. The oil was brought to the supratidal zone of beaches (landward of the high tide line) by waves during storms, and was buried during subsequent storms. The objective of this paper is to investigate the biodegradation of subsurface oil in a tidally influenced sand beach located at Bon Secour National Wildlife Refuge and polluted by the DWH oil spill. Two transects were installed perpendicular to the shoreline within the supratidal zone of the beach. One transect had four galvanized steel piezometer wells to measure the water level. The other transect had four stainless steel multiport sampling wells that were used to collect pore water samples below the beach surface. The samples were analyzed for dissolved oxygen (DO), nitrogen, and redox conditions. Sediment samples were also collected at different depths to measure residual oil concentrations and microbial biomass. As the biodegradation of hydrocarbons was of interest, a biological model based on Monod kinetics was developed and coupled to the transport model MARUN, which is a two dimensional (vertical slice) finite element model for water flow and solute transport in tidally influenced beaches. The resulting coupled model, BIOMARUN, was used to simulate the biodegradation of total n-alkanes and polycyclic aromatic hydrocarbons (PAHs) trapped as residual oil in the unsaturated zone. Model parameter estimates were constrained by published Monod kinetics parameters. The field measurements, such as the concentrations of the oil, microbial biomass, nitrogen, and DO, were used as inputs for the simulations. The biodegradation of alkanes and PAHs was predicted in the simulation, and sensitivity analyses were conducted to assess the effect of the model parameters on the modeling results. Simulation results indicated that n-alkanes and PAHs would be biodegraded by 80% after 2 ± 0.5 years and 3.5 ± 0.5 years, respectively.

scholarly journals Plant functional traits determined the latitudinal variations in soil microbial functions: evidence from a forest transect in China

2019 ◽  
Author(s):  
Zhiwei Xu ◽  
Guirui Yu ◽  
Xinyu Zhang ◽  
Ruili Wang ◽  
Ning Zhao ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Community ◽  
Soil Organic Matter ◽  
Microbial Biomass ◽  
Functional Traits ◽  
Plant Functional Traits ◽  
Decomposition Rates ◽  
Substrate Use ◽  
Soil Microbial ◽  
Carbon Concentrations

Abstract. Plant functional traits have increasingly been studied as determinants of ecosystem properties, especially for soil biogeochemical processes. While the relationships between biological community structures and ecological functions are a central issue in ecological theory, these relationships remain poorly understood at the large scale. We selected nine forests along the North–South Transect of Eastern China (NSTEC) to determine how plant functional traits influence the latitudinal pattern of soil microbial functions, and how soil microbial communities and functions are linked at the regional scale. We found that there was considerable variation in the profiles of different substrate use along the NSTEC. Soil microorganisms from temperate forests mainly metabolized high-energy substrates, while those from subtropical forests used all the substrates equally. The soil silt content and plant functional traits together shaped the biogeographical pattern of the soil microbial substrate use. Soil organic matter decomposition rates were significantly higher in temperate forests than in subtropical and tropical forests, which was consistent with the pattern of soil microbial biomass carbon concentrations. Soil organic matter decomposition rates were also significantly and negatively related to soil dissolved organic carbon concentrations, and carboxylic acid, polymer, and miscellaneous substrates. The soil microbial community structures and functions were significantly correlated along the NSTEC. Soil carbohydrate and polymer substrate use were mainly related to soil G+ bacterial and actinomycetes biomass, while the use of amine and miscellaneous substrates were related to soil G− bacteria, fungal biomass, and the F/B ratio. The contributions of different groups of microbial biomass to the production of soil enzyme activities differed. The relationship between soil microbial community structure and functions supported that there was functional dissimilarity.

scholarly journals Modelling organic matter dynamics in different soils.

1990 ◽  
Vol 38 (3A) ◽  
pp. 221-238 ◽  
Author(s):  
E.L.J. Verberne ◽  
J. Hassink ◽  
P. de Willigen ◽  
J.J.R. Groot ◽  
J.A. van Veen
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Microbial Biomass ◽  
Soil Microbial Biomass ◽  
State Level ◽  
N Cycling ◽  
First Order ◽  
Soil Microbial ◽  
First Order Kinetics ◽  
Different Soils

A mathematical model was developed to describe carbon (C) and nitrogen (N) cycling in different soil types, e.g. clay and sandy soils. Transformation rates were described by first-order kinetics. Soil organic matter is divided into four fractions (including microbial biomass pool) and three fractions of residues. The fraction of active soil organic matter was assumed to be affected by the extent of physical protection within the soil, as was the soil microbial biomass. The extent of protection influenced the steady state level of the model, and, hence, the mineralization rates. The mineralization rate in fine-textured soils is lower than in coarse-textured soils; in fine-textured soils a larger proportion of the soil organic matter may be physically protected. The availability of organic materials as a substrate for microorganisms is not only determined by their chemical composition, but also by their spatial distribution in the soil. (Abstract retrieved from CAB Abstracts by CABI’s permission)

scholarly journals Labile Soil Organic Matter Pools Are Influenced by 45 Years of Applied Farmyard Manure and Mineral Nitrogen in the Wheat—Pearl Millet Cropping System in the Sub-Tropical Condition

Agronomy ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 2190
Author(s):  
Ranjan Laik ◽  
B. H. Kumara ◽  
Biswajit Pramanick ◽  
Santosh Kumar Singh ◽  
Nidhi ◽  
...  
Keyword(s):  
Organic Matter ◽  
Microbial Biomass ◽  
Management Practices ◽  
Microbial Biomass Carbon ◽  
Cropping Systems ◽  
Farmyard Manure ◽  
Mineral N ◽  
N Application ◽  
Tropical Climates

Labile soil organic matter pools (LSOMp) are believed to be the most sensitive indicator of soil quality when it is changed rapidly with varied management practices. In sub-tropical climates, the turnover period of labile pools is quicker than in temperate climates. Organic amendments are of importance in improve the LSOMp for a temperate climate and may be helpful in sub-tropical climates as well. Hence, the status of LSOMp was studied in long term farmyard manure (FYM) amended soils under wheat (Triticum aestivum L.) and pearl millet (Pennisetum glaucum L.) cropping systems in sub-tropical arid conditions. At the same time, we also attempt to determine the impact of mineral nitrogen (N) application in these pools. In this study, dissolved organic matter (DOM), microbial biomass (MB), and light fraction (LF) were isolated in the management practices involving different modes and rates of FYM applications along with the application of nitrogenous fertilizer. C and N contents of the labile pools were analyzed in the soil samples at different periods after FYM applications. Among the different pools, microbial biomass carbon (MBC) and dissolved organic carbon (DOC) were changed significantly with different rates and modes of FYM application and mineral N application. Application of FYM at 15 Mg ha−1 in both the seasons + 120 kg ha−1 mineral N resulted in significantly higher MBC and DOC as compared to all of the other treatments. This treatment also resulted in 13.75% and 5.8% more MBC and DOC, respectively, as compared to the amount of MBC and DOC content in the control plot where FYM and mineral N were not applied. Comparing the labile organic matter pools of 45 years of FYM amendment with initial values, it was found that the dissolved organic carbon, microbial biomass carbon, and light fraction carbon were increased up to the maximum extent of about 600, 1200, and 700 times, respectively. The maximum amount of DOM (562 mg kg−1 of DOC and 70.1 mg kg−1 of DON), MB (999 mg kg−1 of MBC and 158.4 mg kg−1 of MBN), LF (2.61 g kg−1 of LFC and 154.6 g kg−1 of LFN) were found in case of both season applied FYM as compared to either summer or winter applied FYM. Concerning the different rates of FYM application, 15 Mg ha−1 FYM also resulted in a significantly higher amount of DOM, MB, and LF as compared to other FYM rates (i.e., 5 Mg ha−1 and 10 Mg ha−1). Amongst different pools, MB was found to be the most sensitive to management practices in this study. From this study, it was found that the long-term FYM amendment in sub-tropical soil along with mineral N application can improve the LSOMp of the soil. Thus, it can be recommended that the application of FYM at 15 Mg ha−1 in summer and winter with +120 kg ha−1 mineral N can improve SOC and its labile pools in subtropical arid soils. Future studies on LSOMp can be carried out by considering different cropping systems of subtropical climate.

Forest floor characteristics and soil nitrogen availability on slash-burned sites in coastal British Columbia

1991 ◽  
Vol 21 (10) ◽  
pp. 1516-1522 ◽  
Author(s):  
J. W. Fyles ◽  
I. H. Fyles ◽  
W. J. Beese ◽  
M. C. Feller
Keyword(s):  
Organic Matter ◽  
N Mineralization ◽  
Forest Floor ◽  
Nitrogen Availability ◽  
Model Parameters ◽  
N Availability ◽  
Order Kinetic ◽  
Fire Weather Index ◽  
First Order ◽  
Morphological Criteria

Organic forest floor materials were surveyed on spring and fall slash-burned sites in the Sproat Lake region of Vancouver Island 2 years after burning. Dominant organic matter types, distinguished according to morphological criteria, were sampled and incubated in the laboratory for 26 weeks with periodic leaching and measurement of mineral N. Mineralization data closely fit a first-order kinetic model. Field mineralization, estimated using mass of each organic matter type in the field and first-order model parameters corrected for local temperature, ranged from 2 to 6 g N•m−2•year−1, depending on burn severity, suggesting that slash burning did not reduce N availability below levels required to support early plantation growth, except in situations of severe burns on coarse-textured soils. Differential consumption of forest floor organic matter types increased spatial variability in N mineralization and resulted, at the most severely burned site, in 50% of mineralizable N being derived from materials covering only 5% of the site. Significant correlation between N mineralization and codes and indices of the Canadian Forest Fire Weather Index System indicated that predictions of slash-burn impacts on site fertility may be made from weather conditions prior to and during burning.

scholarly journals Models of soil organic matter decomposition: the SOILR package, version 1.0

2012 ◽  
Vol 5 (2) ◽  
pp. 993-1039 ◽  
Author(s):  
C. A. Sierra ◽  
M. Müller ◽  
S. E. Trumbore
Keyword(s):  
Organic Matter ◽  
Soil Organic Matter ◽  
Organic Matter Decomposition ◽  
Important Process ◽  
Decomposition Rates ◽  
Modeling Framework ◽  
Soil Organic Matter Decomposition ◽  
The Earth ◽  
Decomposition Models ◽  
Model Structures

Abstract. Organic matter decomposition is a very important process within the Earth System because it controls the rates of mineralization of carbon and other biogeochemical elements, determining their flux to the atmosphere and the hydrosphere. SOILR is a modeling framework that contains a library of functions and tools for modeling soil organic matter decomposition under the R environment for computing. It implements a variety of model structures and tools to represent carbon storage and release from soil organic matter. In SOILR organic matter decomposition is represented as a linear system of ordinary differential equations that generalizes the structure of most compartment-based decomposition models. A variety of functions is also available to represent environmental effects on decomposition rates. This document presents the conceptual basis for the functions implemented in the package. It is complementary to the help pages released with the software.

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