Combination of techniques to quantify the distribution of bacteria in their soil microhabitats at different spatial scales

Abstract

To address a number of issues of great societal concern at the moment, like the sequestration of carbon, information is direly needed about interactions between soil architecture and microbial dynamics. Unfortunately, soils are extremely complex, heterogeneous systems comprising highly variable and dynamic micro-habitats that have significant impacts on the growth and activity of inhabiting microbiota. Data remain scarce on the influence of soil physical parameters characterizing the pore space on the distribution and diversity of bacteria. In this context, the objective of the research described in this article was to develop a method where X-ray microtomography, to characterize the soil architecture, is combined with fluorescence microscopy to visualize

Spatial Control of Carbon Dynamics in Soil by Microbial Decomposer Communities

“…The simulated spatial patterns in organic matter decomposition are in alignment with experimentally observed patterns of extracellular enzyme activity (Kravchenko et al, 2019). Experimental evidence further suggests that C turnover is strongly determined by pore characteristics (Kravchenko and Guber, 2017;Juyal et al, 2019) and microbial activity is highest in pores between 10 and 300 µm (Kravchenko et al, 2019). Thus, an improved description of microbial C turnover could be gained by integrating realistic descriptions of soil pore structure based on X-ray computed tomography data (see e.g., Portell et al, 2018) in combination with a meaningful correlation structure of substrate and microbial group distribution using evidence-based spatial statistical modeling.…”

“…All parameters were related to the µm-scale. The mean initial density of microbial cells was set to 20 cells mm −2 (close to the lower limit observed by Raynaud and Nunan, 2014;and Juyal et al, 2019). This is equivalent to an average intensity of the…”

“…Their analysis indicated that distributions of bacterial cells in soils are clustered and non-random at the µm-scale, most probably as a result of heterogeneity in soil structure and pore network architecture. Recent experimental evidence from combined X-ray microtomography and fluorescence microscopy at different sampled spatial scales (0.2, 1, 5 mm) indicates that pore characteristics might effectively influence the distribution of bacteria in soil mainly at a spatial scale of ∼5 mm (Juyal et al, 2019). Most rapid decomposition rates were associated with pores of neck diameters of 15-90 µm.…”

“Soil biofilms”: Misleading description of the spatial distribution of microbial biomass in soils

“…Aside from the excessive reliance of soil microbiologists in recent years on metagenomics techniques, which do not require any knowledge of the spatial configuration of soil biomass, a key reason very few people have been talking about soil biofilms in these systems, is simply because experimental evidence that biofilms exist in real soils is virtually non-existent. Starting in the 50s, and especially after the advent of transmission or scanning electron microscopes, as well as, later, of laser scanning microscopes, various soil scientists have accumulated a wealth of visual information about the spatial distribution of bacteria and archaea in soils (e.g., Clark, 1951;Jones and Griffiths, 1964;White et al, 1994;DeLeo et al, 1997;Nunan et al, 2001;Li et al, 2003Li et al, , 2004Eickhorst and Tipköttter, 2008;Raynaud and Nunan, 2014;Watteau et al, 2018;Juyal et al, 2019), including at the interfaces between soil and plant roots (e.g., Danhorn and Fuqua, 2007;Cardinale, 2014;Schmidt et al, 2018). None of the micrographs that were produced with these tools show anything that even vaguely looks like a film, patchy or not.…”

Editorial: Elucidating Microbial Processes in Soils and Sediments: Microscale Measurements and Modeling

“…Using a combination of X-ray µCT, fluorescence microscopy, scanning electron microscopy and nanoSIMS, these authors are able to study the distribution of bacteria in a soil, and to show that they have a preference toward foraging near macropore surfaces and near fresh particulate organic matter. Juyal et al (2019) combined X-ray CT with biological thin sections to elucidate the impact of pore architecture on bacterial distribution in soil. They highlighted that when different methods are being integrated, one needs to consider an "appropriate spatial scale" to understand the factors that regulate the distribution of microbial communities in soils.…”