Correlative Imaging Reveals Holistic View of Soil Microenvironments

Abstract

The microenvironmental conditions in soil exert a major control on many ecosystem functions of soil. Their investigation in intact soil samples is impaired by methodological challenges in the joint investigation of structural heterogeneity that defines pathways for matter fluxes and biogeochemical heterogeneity that governs reaction patterns and microhabitats. Here we demonstrate how these challenges can be overcome with a novel protocol for correlative imaging based on image registration to combine three-dimensional microstructure analysis of X-ray tomography data with biogeochemical microscopic data of various modalities and scales (light microscopy, fluorescence microscopy, electron microscopy, secondary ion mass spectrometry). Correlative imaging of a microcosm study shows that the majority (75%) of bacteria are located in mesopores (<10 μm). Furthermore, they have a preference to forage near macropore surfaces and near fresh particulate organic matter. Ignoring the structural complexity coming from the third dimension is justified for metrics based on size and distances but leads to a substantial bias for metrics based on continuity. This versatile combination of imaging modalities with freely available software and protocols may open up completely new avenues for the investigation of many important biogeochemical and physical processes in structured soils.

The (Bio)Chemistry of Soil Humus and Humic Substances: Why Is the “New View” Still Considered Novel After More Than 80 Years?

“…Vidal et al (2018) have combined different spectroscopic and microscopic techniques to simultaneously gain information about the distribution of minerals and biomass in the vicinity of roots. More recently, Schlüter et al (2019), using a combination of X-ray µCT, fluorescence microscopy, scanning electron microscopy and nanoSIMS, were 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. This pioneering interdisciplinary research opens the path toward the micro-and mesoscale analysis not just of the dynamics of soil organic matter, and related processes like priming or the storage and protection of carbon, which are eminently relevant in the context of global climate change, but also of other soil-borne processes of great practical importance, like the regulation of soil acidity and the binding of metals, about which various questions have remained unanswered, in spite of a sizeable research effort in the past (e.g., Tipping and Hurley, 1988;Tipping, 2002).…”

Regulation of fungal decomposition at single-cell level

“…A number of techniques have become available over the past few decades that allow detailed studies of the chemical interactions at the interface between microbial cells and their environment, including nanoscale secondary ion mass spectrometry, scanning transmission X-ray microscopy, neutron imaging, X-ray fluorescence spectroscopy, X-ray computed tomography, scanning electron microscopy coupled to energy-dispersive X-ray spectroscopy, IR and Raman spectroscopy and fluorescence spectroscopy [16][17][18][19][20][21][22]. Among these, IR spectroscopy is currently one of the most suitable tools to investigate the chemical interactions between microbial cells and their environments thanks to the detailed spectral information that can be obtained on organic compounds at a micrometer spatial resolution under ambient conditions [42].…”

“…An explanation for the slow progress in characterizing biogeochemical processes at the scale of microorganisms is the lack of appropriate methods. Current analytical techniques that allow microscopic imaging of chemical interactions between microbes and their environment require the sample compartment to be under vacuum and/or provide limited chemical information [16][17][18][19][20][21][22].…”

Combination of Imaging Infrared Spectroscopy and X-ray Computed Microtomography for the Investigation of Bio- and Physicochemical Processes in Structured Soils

“…The combination of different biogeochemical imaging methods, designated as correlative microscopy or correlative imaging, is increasingly used in life sciences (Caplan et al, 2011;Handschuh et al, 2013;Guyader et al, 2018). A few recent applications have demonstrated that there is a great potential for the application of correlative imaging in soil sciences (Hapca et al, 2011;Juyal et al, 2019;Kravchenko et al, 2019;Schlüter et al, 2019). Schlüter et al (2019) highlighted that a combination of different 2D techniques for chemical and microbial imaging, such as scanning electron microscopeenergy dispersive using X-ray (SEM-EDX) analysis and nanoscale secondary ion mass spectrometry (nanoSIMS) or fluorescence microscopy and X-ray µCT, can be used to reveal specific soil microenvironments and thus biogeochemical and physical processes in structured soil.…”