New Methods To Unravel Rhizosphere Processes

Abstract

Root-triggered processes (growth, uptake and release of solutes) vary in space and time, and interact with heterogeneous soil microenvironments that provide habitats for (micro)biota on various scales. Despite tremendous progress in method development in the past decades, finding a suitable experimental set-up to investigate processes occurring at the dynamic conjunction of biosphere, hydrosphere, and pedosphere in the close vicinity of active plant roots still represents a major challenge. We discuss recent methodological developments in rhizosphere research with a focus on imaging techniques. We further review established concepts that have been updated with novel techniques, highlighting the need for combinatorial approaches to disentangle rhizosphere processes on relevant scales.

Maintaining connectivity: understanding the role of root order and mycelial networks in fine root decomposition of woody plants

“…Fortunately, new technologies have emerged and are beginning to be applied to rhizosphere processes that might make such an understanding possible in the not-to-distant future. For instance, advances in high throughput sequencing, combined with pipelines for managing the large volumes of data produced, now make it feasible to characterize the microbial community composition associated with different root orders through the course of decomposition using a metagenomics approach (Oburger and Schmidt 2016). Metatranscriptomics, metaproteomics, and metabolomics are rapidly developing techniques that make it possible to screen for changes in gene expression, characterize protein profiles, and understand activity of key metabolic pathways at the scale of the whole rhizosphere community associated with roots of different developmental orders (Oburger and Schmidt 2016;van Dam and Bouwmeester 2016).…”

“…Related techniques that can be used to track the movement of isotopic tracers from fine root pools into microbes and eventually into various SOM fractions include nanoSIMS (nano secondary ion mass spectrometry), and synchrotron-based spectromicroscopy (STXM; Keiluweit et al 2012). Details on the potential of these techniques for unraveling the mysteries of fine root decomposition have been discussed in a number of recent publications (Ohno et al 2010;Behrens et al 2012;Keiluweit et al 2012;van Dam and Bouwmeester 2016;Oburger and Schmidt 2016).…”

Linking 3D Soil Structure and Plant-Microbe-Soil Carbon Transfer in the Rhizosphere

“…The complexity of biogeochemical processes occurring in the rhizosphere requires observations at process-relevant scales, i.e., at the interface of root cells, microorganisms, and soil Oburger and Schmidt, 2016). The microscopic observation of intact soil structures as embedded thin sections has been applied since the 1930s (Kubiena, 1938;Alexander and Jackson, 1954) and has enabled the observation of the rhizosphere at the scale of organism interactions (Martin and Foster, 1985).…”

Molecular and Microscopic Insights into the Formation of Soil Organic Matter in a Red Pine Rhizosphere

“…The challenges of characterizing the SOM pool need to be addressed through the development of high spatial, chemical, and molecular resolution techniques. A comprehensive review by Oburger and Schmidt [18] discusses approaches for research on C input in soils. Mikutta et al [19] and Pett-Ridge and Firestone [20] present stable isotope-enabled capabilities for tracing dynamic processes of organic molecules from roots and microorganisms in SOM.…”