Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation

Schmidt, Susanne I.; Kreft, Jan‐Ulrich; Mackay, R.; Picioreanu, Cristian; Thullner, Martin

doi:10.1016/j.advwatres.2018.01.013

Cited by 17 publications

(12 citation statements)

References 100 publications

(89 reference statements)

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“…This indicates functional redundancy with respect to C cycling. While there are some first successful attempts to derive mechanistic effective rate laws for specific biogeochemical processes at pedon to landscape scale from pore-scale modeling (e.g., Ebrahimi and Or, 2018;Schmidt et al, 2018), the upscaling of microbial processes and their control from pore scale to macroscopic scales (pedon to landscape), which are practically relevant and accessible to direct observation, remains a largely unresolved research challenge .…”

Section: Introductionmentioning

confidence: 99%

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Pagel

Kriesche

Uksa

et al. 2020

Front. Environ. Sci.

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Trait-based models have improved the understanding and prediction of soil organic matter dynamics in terrestrial ecosystems. Microscopic observations and pore scale models are now increasingly used to quantify and elucidate the effects of soil heterogeneity on microbial processes. Combining both approaches provides a promising way to accurately capture spatial microbial-physicochemical interactions and to predict overall system behavior. The present study aims to quantify controls on carbon (C) turnover in soil due to the mm-scale spatial distribution of microbial decomposer communities in soil. A new spatially explicit trait-based model (SpatC) has been developed that captures the combined dynamics of microbes and soil organic matter (SOM) by taking into account microbial life-history traits and SOM accessibility. Samples of spatial distributions of microbes at µm-scale resolution were generated using a spatial statistical model based on Log Gaussian Cox Processes which was originally used to analyze distributions of bacterial cells in soil thin sections. These µm-scale distribution patterns were then aggregated to derive distributions of microorganisms at mm-scale. We performed Monte-Carlo simulations with microbial distributions that differ in mm-scale spatial heterogeneity and functional community composition (oligotrophs, copiotrophs, and copiotrophic cheaters). Our modeling approach revealed that the spatial distribution of soil microorganisms triggers spatiotemporal patterns of C utilization and microbial succession. Only strong spatial clustering of decomposer communities induces a diffusion limitation of the substrate supply on the microhabitat scale, which significantly reduces the total decomposition of C compounds and the overall microbial growth. However, decomposer communities act as functionally redundant microbial guilds with only slight changes in C utilization. The combined statistical and process-based modeling approach derives distribution patterns of microorganisms at the mm-scale from microbial biogeography at microhabitat scale (µm) and quantifies the emergent macroscopic (cm) microbial and C dynamics. Thus, it effectively links observable process dynamics to the spatial control by microbial communities. Our study highlights a powerful approach that can provide further insights into the biological control of soil organic matter turnover.

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Section: Introductionmentioning

confidence: 99%

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Pagel

Kriesche

Uksa

et al. 2020

Front. Environ. Sci.

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“…Several components like microbial community abundance and distribution, metabolic pathways, chemotactic movement, and alteration of microbial activity (e.g., dormancy) are the essence of biogeochemical modeling (Pett‐Ridge & Firestone, 2005). Unifying major physical, chemical, and biological aspects explicitly into one modeling framework is usually computationally expensive and often not required for a particular problem, which had led to the development of conveniently simple models in the past describing, for example, a single microscale 2D slab only (Hesse, Harms, Attinger, & Thullner, 2010; Heße, Prykhodko, Attinger, & Thullner, 2014; Heße, Radu, Thullner, & Attinger, 2009; Schmidt, Kreft, Mackay, Picioreanu, & Thullner, 2018). Direct numerical simulation has also been used for modeling of microbial growth and the associated biogeochemical reactions in micro‐tomography‐derived pore systems of varying complexity ranging from 2D fully saturated systems (King et al., 2010) to 3D saturated (Peszynska et al., 2016) and unsaturated systems (Yan et al., 2016; Yan et al., 2018).…”

Section: Pore‐scale Modelingmentioning

confidence: 99%

Pore‐scale modeling of microbial activity: What we have and what we need

Golparvar

Kästner

Thullner

2021

Vadose Zone Journal

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Under water-unsaturated conditions, environmental factors (e.g., substrate, nutrients, O 2 , water activity, and porous structure) controlling microbial activity are highly variable in space and time. The physical structure of porous media (pore size distribution and pore arrangements) has been considered to have a significant role in nutrient (either substrate and/or its reaction partners like O 2) fluxes. Understanding what eventually controls microbial activity thus requires a sound description of the physical and chemical conditions in the pore space down to the microscale, as well as knowledge on how microorganisms respond to the energy and matter fluxes in their microscale environment. Microscale modeling has the advantage to resolve the processes down to their fundamental level. In recent years, microscale models describing the physical setting in unsaturated porous media such as soils, as well as growth and functional performance of microorganisms, have become increasingly established and are supported by new experimental techniques resolving the distribution of solid, liquid, and gaseous phases at microscale resolution. Still, integration of these components for simulation of microbial activities in a soil system at the microscale is scarce. This mini-review highlights the available approaches for porescale modeling of flow and transport processes in both saturated and unsaturated porous media, and for modeling the dynamics of microbial activity constrained by different soil boundary conditions. Further, it is discussed what is required in terms of model development and improved modeling concepts to achieve a holistic reactive transport modeling approach describing microbial activity at the pore scale. 1 INTRODUCTION Soil systems and, in general, porous media are interesting domains for many engineering and scientific disciplines (e.g.

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“…Microbial simulation modelling already proved valuable, for example, for analysing bacterial mobility in various environments 22 – 25 , biodegradation efficiency 26 , dynamics during litter decay 27 , microbial dormancy 28 , or bioclogging 29 , 30 .…”

Section: Introductionmentioning

confidence: 99%

Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems

König

Worrich

Banitz

et al. 2018

Sci Rep

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Terrestrial microbial ecosystems are exposed to many types of disturbances varying in their spatial and temporal characteristics. The ability to cope with these disturbances is crucial for maintaining microbial ecosystem functions, especially if disturbances recur regularly. Thus, understanding microbial ecosystem dynamics under recurrent disturbances and identifying drivers of functional stability and thresholds for functional collapse is important. Using a spatially explicit ecological model of bacterial growth, dispersal, and substrate consumption, we simulated spatially heterogeneous recurrent disturbances and investigated the dynamic response of pollutant biodegradation – exemplarily for an important ecosystem function. We found that thresholds for functional collapse are controlled by the combination of disturbance frequency and spatial configuration (spatiotemporal disturbance regime). For rare disturbances, the occurrence of functional collapse is promoted by low spatial disturbance fragmentation. For frequent disturbances, functional collapse is almost inevitable. Moreover, the relevance of bacterial growth and dispersal for functional stability also depends on the spatiotemporal disturbance regime. Under disturbance regimes with moderate severity, microbial properties can strongly affect functional stability and shift the threshold for functional collapse. Similarly, networks facilitating bacterial dispersal can delay functional collapse. Consequently, measures to enhance or sustain bacterial growth/dispersal are promising strategies to prevent functional collapses under moderate disturbance regimes.

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Elucidating the impact of micro-scale heterogeneous bacterial distribution on biodegradation

Cited by 17 publications

References 100 publications

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

Pore‐scale modeling of microbial activity: What we have and what we need

Spatiotemporal disturbance characteristics determine functional stability and collapse risk of simulated microbial ecosystems

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