Strategies and methods for studying the rhizosphere—the plant science toolbox

Abstract

This review summarizes and discusses methodological approaches for studies on the impact of plant roots on the surrounding rhizosphere and for elucidation of the related mechanisms, covering a range from simple model experiments up to the field scale. A section on rhizosphere sampling describes tools and culture systems employed for analysis of root growth, root morphology, vitality testing and for monitoring of root activity with respect to nutrient uptake, water, ion and carbon flows in the rhizosphere. The second section on rhizosphere probing covers techniques to detect physicochemical changes in the rhizosphere as a consequence of root activity. This comprises compartment systems to obtain rhizosphere samples, visualisation techniques, reporter gene approaches and remote sensing technologies for monitoring the conditions in the rhizosphere.Approaches for the experimental manipulation of the rhizosphere by use of molecular and genetic methods as tools to study rhizosphere processes are discussed in a third section. Finally it is concluded that in spite of a wide array of methodological approaches developed in the recent past for studying processes and interactions in the rhizosphere mainly under simplified conditions in model experiments, there is still an obvious lack of methods to test the relevance of these findings under real field conditions or even on the scale of ecosystems. This also limits reliable data input and validation in current rhizosphere modelling approaches. Possible interactions between different environmental factors or plantmicrobial interactions (e.g. mycorrhizae) are frequently not considered in model experiments. Moreover, most of the available knowledge arises from investigations with a very limited number of plant species, mainly crops and studies considering also intraspecific genotypic differences or the variability within wild plant species are just emerging.

Challenges in imaging and predictive modeling of rhizosphere processes

“…In addition to simple field studies that compare chemical concentrations between bulk soil and rhizosphere soil, compartment-system approaches with a known position of the root-soil interface have contributed tremendously to process understanding (Neumann et al 2009). The latter approach has been used based either on destructive sampling and application of conventional soil analysis using different extractants, or by using radio-labelled nutrients or stable isotopes.…”

“…Compartment systems provide only a linear geometry instead of the true radial geometry around a root and do not allow processes to be resolved along a developing root from the tip to more basal parts. Such resolution is possible using a rhizobox or root windows, wherein roots grow in the soil along a transparent plate which is either perforated to allow installation of sensors at certain positions along a root (Neumann et al 2009), or which can be removed to allow direct contact of the visible root-soil interface with an imaging device (Dinkelaker et al 1993). These chemical mapping systems always require a soil matrix whose texture enables good contact between the imaging device and the root-soil interface.…”

“…These chemical mapping systems always require a soil matrix whose texture enables good contact between the imaging device and the root-soil interface. This is important, because whether the device is a gel (agar, agarose, polyacrylamide), glass-fiber or paper filter, membrane, ion-exchange resin or foil, the species from the root-soil interface are brought into contact with the imaging device via diffusion (Neumann et al 2009). A key advantage of these techniques is that one can image whole root systems, or at least large parts of root systems, in 2D.…”

“…2D-imaging in rhizoboxes has been applied to study release of carbon or specific organic compounds by 14 C application and/or chemical analyses of spatial resolved collected exudates with HPLC, HPLC-MS, capillary electrophoreses or GC-MS (Dessureault-Rompré et al 2006;Haase et al 2007;Neumann et al 2009). Enzyme activity (acid phosphatase) was imaged based on dyeimpregnated filter paper as early as 1992 by Dinkelaker and Marschner (1992).…”

Root distributions in a laboratory box evaluated using two different techniques (gravimetric and image processing) and their impact on root water uptake simulated with HYDRUS

“…depends on the plant species and its interaction with soil conditions (Bengough et al, 2011;Hallett et al, 2013;Loades et al, 2013;Nikodem et al, 2013). Root distribution can be studied directly in the field or in differently designed laboratory boxes using various techniques (Maeght et al, 2013;Neumann et al, 2009). Field root development analysis can be performed using nondestructive methods, i.e.…”