Comparison of methods for mapping rhizosphere processes in the context of their surrounding root and soil environments

The rhizosphere embodies a complex biogeochemical zone with enhanced rates of nutrient exchange between plants, soil, and microbial communities. Understanding controls on rhizosphere dynamics is critical to support emerging concepts including rhizosphere engineering and reduced dependence on chemical fertilizers which have direct application to food production, increased biofuel generation, and habitat restoration efforts. Yet, its fine spatial scale and complex interactions between geochemical and microbial processes within complex spatiotemporal gradients make the rhizosphere notoriously difficult to study. Emerging instrumentation and methodologies, however, are providing improved resolution to rhizosphere measurements and helping to address critical knowledge gaps in rhizosphere function, ecology, and establishment. Here, we examine recent advances in analysis techniques and the resulting potential for improved understanding of rhizosphere function.

Smart soils to observe hidden rhizosphere processes

Agriculture must reduce green-house gas emission and pollution, produce safer and healthier food, closer to home, reducing waste whilst delivering more diverse diets to a growing world population. Soils could enable this transformation, but unfortunately, they have a hugely complex and opaque structure and studies of its myriad of mechanisms are difficult. Here, the fabrication of smart soils for the screening of below-ground bio-processes is demonstrated. Particles were generated from fluoropolymer waste with functionalisation converting them into sensors able to report on key chemical dynamics. Tailored functionalization was obtained by radical terpolymerisation to improve growth conditions and sensing capabilities. The study demonstrates the potential for the development of accelerated genetic or agrochemical screens and could pave the way for controlled indoor soil bio-production systems.

Linking rhizosphere processes across scales: Opinion

Purpose Simultaneously interacting small-scale rhizosphere processes determine emergent plant-scale behaviour, including growth, transpiration, nutrient uptake, soil carbon storage and transformation by microorganisms. Current advances in modelling and experimental methods open the path to unravel and link those processes. Methods We present a series of examples of state-of-the art simulations addressing this multi-scale, multi-process problem from a modelling point of view, as well as from the point of view of integrating newly available rhizosphere data and images. Results Each example includes a model that links scales and experimental data to set-up simulations that explain and predict spatial and temporal distribution of rhizodeposition as driven by root architecture development, soil structure, presence of root hairs, soil water content and distribution of soil water. Furthermore, two models explicitly simulate the impact of the rhizodeposits on plant nutrient uptake and soil microbial activity, respectively. This exemplifies the currently available state of the art modelling tools in this field: image-based modelling, pore-scale modelling, continuum scale modelling and functional-structural plant modelling. We further show how to link the pore scale to the continuum scale by homogenisation or by deriving effective physical parameters like viscosity from nano-scale chemical properties. Conclusion Modelling allows to integrate and make use of new experimental data across different rhizosphere processes (and thus across different disciplines) and scales. Described models are tools to test hypotheses and consequently improve our mechanistic understanding of how rhizosphere processes impact plant-scale behaviour. Linking multiple scales and processes is the logical next step for future research.

Distinct and Dynamic Distributions of Multiple Elements and Their Species in the Rice Rhizosphere

AimsThe biogeochemical cycles of elements from soils to plants are mainly governed by their rhizosphere processes. Understanding these processes is challenging and remains largely unresolved due to the complex interrelationships among different elements and due to a lack of appropriate techniques for simultaneous spatiotemporal monitoring.MethodsThis study employed an In-situ Porewater Iterative (IPI) sampler array (0-22 mm measurement distance every 1.7 mm, with a time interval of 3 to 10 days) to capture the in situ spatiotemporal dynamics of ten elements (Fe, Mn, As, P, S, Cr, Co, Zn, Sb and Cd) in the paddy rhizosphere to examine their covarying changes in time and space dimensions.ResultsThe findings revealed that the solute-phase concentration of most elements, other than Sb and Cd, increased to a peak after 30 days of paddy soil flooding and then decreased. Additionally, Sb and Cd continuously decreased during flooding. Fe (-52%), Mn (-17%), P (-43%), Co (-11%), and As species (-74%) were substantially immobilized within a 10 mm zone around the roots, while Zn (28%) and Cd (41%) increased. The greater immobilization of As and re-mobilization of Cd, in the rhizosphere, are stimulated by biotic oxidation of arsenite to arsenate with root oxygen loss and the pH decrease, respectively.ConclusionsOur study showed most sampled elements covaried with Fe both in time and space in the rhizosphere, but the elements are temporally and spatially determined by multiple biogeochemical processes in soils as well as exudates from plant roots.

Specialized Plant Growth Chamber Designs to Study Complex Rhizosphere Interactions

The rhizosphere is a dynamic ecosystem shaped by complex interactions between plant roots, soil, microbial communities and other micro- and macro-fauna. Although studied for decades, critical gaps exist in the study of plant roots, the rhizosphere microbiome and the soil system surrounding roots, partly due to the challenges associated with measuring and parsing these spatiotemporal interactions in complex heterogeneous systems such as soil. To overcome the challenges associated with in situ study of rhizosphere interactions, specialized plant growth chamber systems have been developed that mimic the natural growth environment. This review discusses the currently available lab-based systems ranging from widely known rhizotrons to other emerging devices designed to allow continuous monitoring and non-destructive sampling of the rhizosphere ecosystems in real-time throughout the developmental stages of a plant. We categorize them based on the major rhizosphere processes it addresses and identify their unique challenges as well as advantages. We find that while some design elements are shared among different systems (e.g., size exclusion membranes), most of the systems are bespoke and speaks to the intricacies and specialization involved in unraveling the details of rhizosphere processes. We also discuss what we describe as the next generation of growth chamber employing the latest technology as well as the current barriers they face. We conclude with a perspective on the current knowledge gaps in the rhizosphere which can be filled by innovative chamber designs.

High-Resolution Chemical Mapping and Identifying Spatial Distribution of Microbes in the Zea mays Rhizosphere using Correlative Microscopy

<p>Studying the spatial distribution of bacteria and characterizing the soil chemistry (i.e., elemental, isotopic and molecular composition) underpins the comprehensive understanding of rhizosphere associated processes. During the past decades, several stand-alone methods have been developed to investigate soil chemistry, nutrient cycling and plant nutrition. However, individual approaches as stand-alone are not capable of providing an overall rhizosphere processes involving soil, root and microbes in a spatial context, as there is no common sample preparation method available to satisfy individual needs of each technique. Here, we present i) a sample preparation method, which includes soil embedding, sectioning and ii) a correlative imaging and image registration workflow, which allows for characterization of minerals, roots and microbes by different high-resolution imaging and microanalytical techniques. This allows for conducting rhizosphere studies on different scales, focusing on root-soil-microbe interfaces with spatial resolution of nano-meter scale. Hydrophilic, immunohistochemistry compatible, low viscosity LR White resin was used to embed and stabilize the soil and make it ultra-high vacuum compatible. We employed water-jet cutting as a novel approach to slice the embedded samples, and, by doing so, avoided polishing of the surface which often leads to translocation of sample material (smearing). The quality of this embedding was analyzed by and Helium Ion Microscopy (HIM). Epifluorescence microscopy in combination with Catalyzed Reporter Deposition-Fluorescence in-situ Hybridization (CARD-FISH) was employed to accurately identify and determine the spatial distribution of bacteria in the embedded sample, thus avoiding ambiguities from high levels of auto-fluorescence emitted by soil particles and organic matter. Chemical mapping of the rhizosphere was acquired by SEM/EDX, ToF-SIMS, nanoSIMS for elemental, molecular and isotopic characterization, respectively, and µ-Raman microscopy for specific identification of minerals.</p><p>In summary, we demonstrate that LR White embedding and water-jet cutting of soil in combination with CARD-FISH and a correlative microscopic workflow, allows for a comprehensive characterization of biotic and abiotic components in the rhizosphere. The developed sample preparation method can facilitate the various requirements of involved microscopy techniques and individual workflows for imaging and image registration to analyze data. We foresee that this approach will establish an excellent platform to study various soil processes and synergistic understanding of complex rhizosphere processes.</p>