To what extent do uncertainty and sensitivity analyses help unravel the influence of microscale physical and biological drivers in soil carbon dynamics models?

There is still no satisfactory understanding of the factors that enable soil microbial populations to be as highly biodiverse as they are. The present article explores in silico the hypothesis that the heterogeneous distribution of soil organic matter, in addition to the spatial connectivity of the soil moisture, might account for the observed microbial biodiversity in soils. A multi-species, individual-based, pore-scale model is developed and parameterized with data from 3 Arthrobacter sp. strains, known to be, respectively, competitive, versatile, and poorly competitive. In the simulations, bacteria of each strain are distributed in a 3D computed tomography (CT) image of a real soil and three water saturation levels (100, 50, and 25%) and spatial heterogeneity levels (high, intermediate, and low) in the distribution of the soil organic matter are considered. High and intermediate heterogeneity levels assume, respectively, an amount of particulate organic matter (POM) distributed in a single (high heterogeneity) or in four (intermediate heterogeneity) randomly placed fragments. POM is hydrolyzed at a constant rate following a first-order kinetic, and continuously delivers dissolved organic carbon (DOC) into the liquid phase, where it is then taken up by bacteria. The low heterogeneity level assumes that the food source is available from the start as DOC. Unlike the relative abundances of the 3 strains, the total bacterial biomass and respiration are similar under the high and intermediate resource heterogeneity schemes. The key result of the simulations is that spatial heterogeneity in the distribution of organic matter influences the maintenance of bacterial biodiversity. The least competing strain, which does not reach noticeable growth for the low and intermediate spatial heterogeneities of resource distribution, can grow appreciably and even become more abundant than the other strains in the absence of direct competition, if the placement of the resource is favorable. For geodesic distances exceeding 5 mm, microbial colonies cannot grow. These conclusions are conditioned by assumptions made in the model, yet they suggest that microscale factors need to be considered to better understand the root causes of the high biodiversity of soils.

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“…The molecular diffusion coefficient in lattice-Boltzmann units,

, is fixed to 0.5 lu 2 tu -1 ( Vogel et al, 2015 , 2018 ). Since the DOC molecular diffusion coefficient,

, is 6.73 10 -6 cm 2 s -1 ( Weast et al, 1986 ) and 1 lu = 68 μm, the rescaling equation (8) gives 1 tu = 3.44 s.…”

Section: Methodsmentioning

confidence: 99%

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations

et al. 2018

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“…1). The reaction network is an extended adaptation of the carbon dynamics described by Vogel et al (2018), as well as relevant processes in the subsurface as implemented by Manzoni and Porporato (2009). The network accounts for autotrophy and heterotrophy in both aerobic and anaerobic regimes considering four functional groups of microorganisms: aerobic dissolved organic carbon (DOC) degraders, nitrate reducing DOC degraders, ammonium oxidizers, and sulfate reducing DOC degraders.…”

Section: Reaction Networkmentioning

confidence: 99%

Predicting the impact of spatial heterogeneity on microbially mediated nutrient cycling in the subsurface

et al. 2022

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Abstract. The subsurface is a temporally dynamic and spatially heterogeneous compartment of the Earth's critical zone, and biogeochemical transformations taking place in this compartment are crucial for the cycling of nutrients. The impact of spatial heterogeneity on such microbially mediated nutrient cycling is not well known, which imposes a severe challenge in the prediction of in situ biogeochemical transformation rates and further of nutrient loading contributed by the groundwater to the surface water bodies. Therefore, we used a numerical modelling approach to evaluate the sensitivity of groundwater microbial biomass distribution and nutrient cycling to spatial heterogeneity in different scenarios accounting for various residence times. The model results gave us an insight into domain characteristics with respect to the presence of oxic niches in predominantly anoxic zones and vice versa depending on the extent of spatial heterogeneity and the flow regime. The obtained results show that microbial abundance, distribution, and activity are sensitive to the applied flow regime and that the mobile (i.e. observable by groundwater sampling) fraction of microbial biomass is a varying, yet only a small, fraction of the total biomass in a domain. Furthermore, spatial heterogeneity resulted in anaerobic niches in the domain and shifts in microbial biomass between active and inactive states. The lack of consideration of spatial heterogeneity, thus, can result in inaccurate estimation of microbial activity. In most cases this leads to an overestimation of nutrient removal (up to twice the actual amount) along a flow path. We conclude that the governing factors for evaluating this are the residence time of solutes and the Damköhler number (Da) of the biogeochemical reactions in the domain. We propose a relationship to scale the impact of spatial heterogeneity on nutrient removal governed by the log10Da. This relationship may be applied in upscaled descriptions of microbially mediated nutrient cycling dynamics in the subsurface thereby resulting in more accurate predictions of, for example, carbon and nitrogen cycling in groundwater over long periods at the catchment scale.

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“…On the contrary, work in this area, overwhelmingly carried out by soil physicists, mathematicians, and computer scientists, has been extensive over the last decade (e.g., Thullner and Baveye, 2008 ; Heße et al, 2009 ; Gras et al, 2010 , 2011 ; Wang and Or, 2010 ; Gharasoo et al, 2012 ; Ebrahimi and Or, 2014 , 2015 , 2016 , 2017 ; Vogel et al, 2015 ; Tecon and Or, 2017a , b ; Wilmoth et al, 2018 ; Vogel H.J. et al, 2018 ; Vogel L.E. et al, 2018 ).…”

Section: The Microbiological Scenementioning

confidence: 99%

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

et al. 2018

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Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the bulk, macroscopic parameters (e.g., granulometry, pH, soil organic matter, and biomass contents) commonly used to characterize soils provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gasses. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale) that is commensurate with the habitat of many microorganisms. For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. With regard to the microbial aspects, although a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because of the scarcity of relevant experimental data. For significant progress to be made, it is crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead. Fortunately, a number of these challenges may be resolved by brand new measuring equipment that will become commercially available in the very near future.

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To what extent do uncertainty and sensitivity analyses help unravel the influence of microscale physical and biological drivers in soil carbon dynamics models?

Cited by 12 publications

References 35 publications

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations

Microscale Heterogeneity of the Spatial Distribution of Organic Matter Can Promote Bacterial Biodiversity in Soils: Insights From Computer Simulations

Predicting the impact of spatial heterogeneity on microbially mediated nutrient cycling in the subsurface

Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain

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