Spatial control of carbon dynamics in soil by microbial decomposer communities

Abstract

<p>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 modelling 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 modelling 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.</p>

Scenario modelling of carbon mineralization in 3D soil architecture at the microscale: Toward an accessibility coefficient of organic matter for bacteria

“…They attributed this to the closer contact of OM with the soil aggregates where bacteria are located. For a uniform distribution of SOM, Pagel et al (2020) showed that a strong spatial clustering of microbial communities induced diffusionlimited C availability, which translated to lower decomposition degrees of C compounds. Pinheiro et al (2015) found that bacteria could not degrade the solute after a few weeks when initially separated in soil by a distance of 1.7 cm, although they could mineralize it when they were colocalized.…”

“…The distribution of the heterogeneity of minerals, pores, organic matter and microorganisms in soil occurs at fine scales of a few µm (Rawlins et al, 2016, Kravchenko and Guber, 2017. The access of microorganisms to macromolecular soil organic matter is dependent on the hydrolysis of organic molecules by exoenzymes and the diffusive transport of the resulting assimilable carbon in the soil solution from locations of exoenzymatic action to microorganisms (Pagel et al, 2020). The properties of the pore space, such as pore connectivity and tortuosity, affect the water distribution and consequently the diffusion pathways that may control the access of decomposers to organic substrates .…”