Modeling the effect of soil meso- and macropores topology on the biodegradation of a soluble carbon substrate

Soil structure and interactions between biotic and abiotic processes are increasingly recognized as important for explaining the large uncertainties in the outputs of macroscopic SOM decomposition models. We present a numerical analysis to assess the role of meso- and macropore topology on the biodegradation of a soluble carbon substrate in variably water saturated and pure diffusion conditions . Our analysis was built as a complete factorial design and used a new 3D pore-scale model, LBioS, that couples a diffusion Lattice-Boltzmann model and a compartmental biodegradation model. The scenarios combined contrasted modalities of four factors: meso- and macropore space geometry, water saturation, bacterial distribution and physiology. A global sensitivity analysis of these factors highlighted the role of physical factors in the biodegradation kinetics of our scenarios. Bacteria location explained 28% of the total variance in substrate concentration in all scenarios, while the interactions among location, saturation and geometry explained up to 51% of it

Pore-scale monitoring of the effect of microarchitecture on fungal growth in a two-dimensional soil-like micromodel

In spite of the very significant role that fungi are called to play in agricultural production and climate change over the next two decades, very little is known at this point about the parameters that control the spread of fungal hyphae in the pore space of soils. Monitoring of this process in 3 dimensions is not technically feasible at the moment. The use of transparent micromodels simulating the internal geometry of real soils affords an opportunity to approach the problem in 2 dimensions, provided it is confirmed that fungi would actually want to propagate in such artificial systems. In this context, the key objectives of the research described in this article are to ascertain, first, that the fungus Rhizoctonia solani can indeed grow in a micromodel of a sandy loam soil, and, second, to identify and analyze in detail the pattern by which it spreads in the tortuous pores of the micromodel. Experimental observations show that hyphae penetrate easily inside the micromodel, where they bend frequently to adapt to the confinement to which they are subjected, and branch at irregular intervals, unlike in current computer models of the growth of hyphae, which tend to describe them as series of straight tubular segments. A portion of the time, hyphae in the micromodels also exhibit thigmotropism, i.e., tend to follow solid surfaces closely. Sub-apical branching, which in unconfined situations seems to be controlled by the fungus, appears to be closely connected with the bending of the hyphae, resulting from their interactions with surfaces. These different observations not only indicate different directions to follow to modify current mesoscopic models of fungal growth, so they can apply to soils, but they also suggest a wealth of further experiments using the same set-up, involving for example competing fungal hyphae, or the coexistence of fungi and bacteria in the same pore space

Spatial distribution of microbial 2,4-dichlorophenoxy-acetic acid (2,4-D) mineralization from fields to microhabitat scales

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Spatial variability of 2,4-dichlorophenoxyacetic acid (2,4-D) mineralisation potential at a millimetre scale in soil

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2,4-D impact on bacterial communities, and the activity and genetic potential of 2,4-D degrading communities in soil

The key role of telluric microorganisms in pesticide degradation is well recognized but the possible relationships between the biodiversity of soil microbial communities and their functions still remain poorly documented. If microorganisms influence the fate of pesticides, pesticide application may reciprocally affect soil microorganisms. The objective of our work was to estimate the impact of 2,4-D application on the genetic structure of bacterial communities and the 2,4-D-degrading genetic potential in relation to 2,4-D mineralization. Experiments combined isotope measurements with molecular analyses. The impact of 2,4-D on soil bacterial populations was followed with ribosomal intergenic spacer analysis. The 2,4-D degrading genetic potential was estimated by real-time PCR targeted on tfdA sequences coding an enzyme specifically involved in 2,4-D mineralization. The genetic structure of bacterial communities was significantly modified in response to 2,4-D application, but only during the intense phase of 2,4-D biodegradation. This effect disappeared 7 days after the treatment. The 2,4-D degrading genetic potential increased rapidly following 2,4-D application. There was a concomitant increase between the tfdA copy number and the 14C microbial biomass. The maximum of tfdA sequences corresponded to the maximum rate of 2,4-D mineralization. In this soil, 2,4-D degrading microbial communities seem preferentially to use the tfd pathway to degrade 2,4-D

A miniaturised method to quantify microbial mineralisation of C-13-labelled organic compounds in small soil samples

International audienceA miniaturised method developed to measure the mineralisation of C-13-labelled organic compounds in small soil samples is presented. Soil samples (<0.5 g) were placed in wells of microtiter plates with CO2 traps (NaOH-soaked glass microfiber filters) and amended with C-13-labelled-labelled substrate. The microtiter plate was covered with a seal and placed in a microplate clamp system to ensure that each well was airtight. After incubation, the CO2 traps were transferred to tightly sealed glass phials under CO2-free atmosphere and the C-13-labelled-labelled CO2 was released by addition of H3PO4. The CO2 was measured by micro-GC and its isotopic signature was determined using a GC-IRMS. The qualitative and quantitative efficiency of the microplate system was demonstrated by comparison with direct measurement of CO2 in the headspace of phials in which similarly treated soil samples had been incubated. The two methods showed similar mineralisation rates for added C-13-labelled-substrates but the apparent mineralisation of soil organic matter was greater with the microtiter plate method. The microplate system presented here is suitable for studying the mineralisation of different kinds of C-13-labelled-labelled substrates in small soil samples and allows analysis of functional and molecular characteristics on the same micro-samples

Opportunities and limits in imaging microorganisms and their activities in soil microhabitats

International audienceThe soil microhabitat is a heterogeneous and complex environment where local variations can modulate phenomena observed at the plot scale. Most of the current methods used to describe soil functioning are bulk soil analyses which do not account for fine-scale spatial variability and cannot fully account for the processes that occur under the influence of the 3D organisation of soil. A good representation of spatial heterogeneities is necessary for the parametrisation of new models, which aim to represent pore-scale processes that affect microbial activity. The visualization of soil at the scale of the microhabitat can be used to extract descriptors and reveal the nature of the relationships between the fine-scale organisation of soil's constituent parts and soil functioning. However, soil imaging techniques tend to be under-used, possibly due to a lack of awareness of the methods or due to a lack of access to the relevant instruments. In recent years, new methods have been developed, and continuously improved, offering new possibilities to decipher and describe soil physical, chemical and biological features of the soil microhabitat in evermore exquisite detail. 1 This review is structured into several parts in which first imaging methods that are useful for describing the distribution of microorganisms and microbial activities, followed by methods for characterising the physical organisation of the microhabitat and, finally, methods for characterising the distribution of soil chemical features, including soil organic matter, are described. Special attention is given to the preparation steps that are required for the proper use of the methods, either alone or in combination

Impact of soil matric potential on the fine-scale spatial distribution and activity of specific microbial degrader communities

International audienceThe impact of the soil matric potential on the relationship between the relative abundance of degraders and their activity and on the spatial distribution of both at fine scales was determined to understand the role of environmental conditions in the degradation of organic substrates. The mineralization of 13C-glucose and 13C-2,4-dichlorophenoxyacetic acid (2,4-D) was measured at different matric potentials ( 0.001, 0.01 and 0.316 MPa) in 6 9 6 9 6 mm3 cubes excised from soil cores. At the end of the incubation, total bacterial and 2,4-D degrader abundances were determined by quantifying the 16S rRNA and the tfdA genes, respectively. The mineralization of 2,4-D was more sensitive to changes in matric potential than was that of glucose. The amount and spatial structure of 2,4-D mineralization decreased with matric potential, whilst the spatial variability increased. On the other hand, the spatial variation of glucose mineralization was less affected by changes in matric potential. The relationship between the relative abundance of 2,4-D degraders and 2,4-D mineralization was significantly affected by matric potential: the relative abundance of tfdA needed to be higher to reach a given level of 2,4-D mineralization in dryer than in moister conditions. The data show how microbial interactions with their microhabitat can have an impact on soil processes at larger scales

Spatial and temporal evolution of detritusphere hotspots at different soil moistures

International audienceAs a result of the heterogeneous spatial distribution of microorganisms and substrates in soil and their restricted accessibility, biodegradation occurs mainly in hotspots, such as in the detritusphere, induced by decomposing plant residues. Knowing the characteristics of the volume of soil involved in biodegradation of a given organic substrate will facilitate the understanding and prediction of biodegradation. Our objectives were (i) to identify the volume of soil involved in the biodegradation of plant residues and (ii) to determine to what extent this volume is affected by soil moisture under diffusive conditions by monitoring the mineralization and spatio-temporal evolution of residue C and microorganisms in soil at the microbial habitat scale. We incubated repacked soil cores with a central layer of C-13-labelled maize residues at three different matric potentials (0.0031, 0.031 and 0.31 MPa). We monitored C-13 and total C mineralization, and at different dates over 45 days of incubation, we separated soil slices with increasing distances from the residues and analysed C-13 from the residues and the microbial community structure and its activity by PLFA and C-13-PLFA processing. Residue mineralization increased with increasing soil moisture. A detritusphere a few mm thick was rapidly established, with a decreasing gradient of C-13 and total PLFAs and C-13-PLFAs away from the residue layer. Most C-13 from the residues was located in the first 2 mm of the detritusphere and was not dependent on the matric potential. Residue mineralization seemed to take place mainly on the residues themselves, but increasing residue C was transferred to the surrounding soil with increasing soil moisture. Dry conditions slowed residue C transfer and favoured fungi, but residue mineralization was carried out by both bacteria and fungi