In Situ X-Ray Tomography Imaging of Soil Water and Cyanobacteria From Biological Soil Crusts Undergoing Desiccation

Abstract

Biological soil crusts (biocrusts) are millimeter-sized microbial communities developing on the topsoils of arid lands that cover some 12% of Earth's continental area. Biocrusts consist of an assemblage of mineral soil particles consolidated into a crust by microbial organic polymeric substances that are mainly produced by filamentous bundle-forming cyanobacteria, among which Microcoleus vaginatus is perhaps the most widespread. This cyanobacterium is the primary producer for, and main architect of biocrusts in many arid soils, sustaining the development of a diverse microbial community. Biocrusts are only active when wet, and spend most of their time in a state of desiccated quiescence, from which they can quickly recover upon wetting. Despite their ecological importance for arid ecosystems, little is known about the mechanisms that allow biocrust organisms to endure long periods of dryness while remaining viable for rapid resuscitation upon wetting. We had previously observed the persistence of significant rates of light-dependent carbon fixation in apparently dry biocrusts dominated by M. vaginatus, indicating that it may be able to remain hydrated against a background soil of very low water potential. One potential explanation for this may be that the abundant exopolysaccharide sheaths of M. vaginatus can preferentially retain moisture thus slowing the water equilibration with the surrounding soil allowing for extended activity periods. In order to test this hypothesis we aimed to develop methodologies to visualize and quantify the water dynamics within an undisturbed biocrust undergoing desiccation. We used synchrotron based X-ray microtomography and were able to resolve the distribution of air, liquid water, mineral particles and cyanobacterial bundles at the microscale. We could demonstrate the formation of steep, decreasing gradients of water content from the cyanobacterial bundle surface outward, while the bundle volume remained stable, as the local bulk water content decreased linearly, hence demonstrating a preferential retention of water in the microbes. Our data also suggest a transfer of hydration water from the EPS sheath material into the cyanobacterial filament as Couradeau et al. X-Ray Microtomography of a Biocrust Undergoing Desiccation desiccation progresses. This work demonstrates the value of X-ray tomography as a tool to study microbe-scale water redistribution in biocrusts.

Distribution of Mixotrophy and Desiccation Survival Mechanisms across Microbial Genomes in an Arid Biological Soil Crust Community

“…6 ) as water and organic C availability decreases, it is unclear if the low soil water content during the dry period allows any ongoing enzyme activity. While pockets of increased humidity have been proposed to exist in dry soil ( 5 , 66 ), a study applying in situ X-ray tomography to BSCs from the Moab Desert suggested the absence of such pockets after complete desiccation ( 78 ). However, even the near complete absence of water does not have to be fatal for a microbial cell.…”

Microhydrological Niches in Soils: How Mucilage and EPS Alter the Biophysical Properties of the Rhizosphere and Other Biological Hotspots

“… Examples of polymeric structures formed by mucilage and extracellular polymeric substances (EPS) in porous media: (a) light microscope image of threads of mucilage (mucilage content = 4.5 mg g −1 [mg dry mucilage per g of particles]) formed across a large pore during drying; (b) light microscope image of cylinder formed between neighboring glass beads (1.7–2 mm in diameter) at intermediate mucilage content (0.7 mg g −1 ); (c) two‐dimensional EPS‐based structures joining quartz grains in intact biocrusts imaged with synchrotron‐based X‐ray tomographic microscopy (Couradeau et al, 2018), where high EPS content resulted in the formation of characteristic structures (red arrows) comparable with those formed by maize mucilage (the blue arrow marks a cyanobacterial bundle with the EPS sheath surrounding the trichomes of Microcoleus vaginatus ); (d) cross‐section through a synchrotron‐based X‐ray tomographic microscopy volume of dry maize mucilage structures in glass beads (bright circles) (mucilage content = 8 mg g −1 ; glass bead diameter = 0.1– 0.2 mm); and (e) three‐dimensional segmentation of dry mucilage structures (red) from (d) that formed interconnected surfaces of ∼1‐μm thickness within the pore space of glass beads (blue). Additional images of mucilage in porous media can be found in Supplemental Fig.…”

“…The resulting voxel edge length was 1.3 μm. A more detailed description of the procedure can be found elsewhere (Couradeau et al, 2018).…”

“…Similar to the effect of mucilage, extracellular polymeric substances (EPS) produced by microorganism buffers fluctuations in soil moisture in hotspots of high biological activity, like the rhizosphere (Kuzyakov and Blagodatskaya, 2015), microbial colonies (Or et al, 2007; Zheng et al, 2018) and biocrusts (Chamizo et al, 2016; Couradeau et al, 2018; Rossi et al, 2018). Biocrusts stand out as an example, arguably the most extended biofilm on the planet (Elbert et al, 2012; Rodriguez‐Caballero et al, 2018).…”

Testing Contrast Agents to Improve Micro Computerized Tomography (μCT) for Spatial Location of Organic Matter and Biological Material in Soil

“…Among the diverse techniques that are currently used (for details see the review from Baveye et al, 2018), one of the more promising techniques entails microcomputerized X-ray tomography (µCT). It serves as a powerful tool to analyze soil structure, including aggregates and porosity (Zabler et al, 2008;Peth et al, 2014;Couradeau et al, 2018;Quigley et al, 2018;Totsche et al, 2018). The µCT technique may also be used as a non-destructive method to analyze the soil biota, for example, detecting fine roots and micro-fauna (Mooney et al, 2012;Guimarães et al, 2017).…”