The Root/Rhizosphere Interface has four major focus areas: Root Biology, Root Imaging, Root Microbiome, and Root Breeding
Roots represent one of the most essential organs in plants and yet are in many cases are least studied and rarely included in breeding efforts. Many current and predicted future limitations to plant productivity, including improved water, nutrient and mineral uptake, are dependent on enhancing root function. The capacity of any plant genotype to acquire minerals and nutrients from soil involves two aspects, ‘nutrient interception’ and the ‘efficiency of uptake’ (Wissuwa et al 2009). Thus, the ability to manipulate root architecture and function has enormous potential for improving crop productivity. One reason roots have been less studied than above ground plant parts is the difficulty in assessing root architecture and function in soil. The simple act of pulling a plant from soil in order to examine its roots results in damage to the roots and destruction of the rhizosphere.
Challenges in the area of root biology include: the ability to visualize and monitor root structure and function real-time in artificial and real soil; the ability to classify root cells as to primary function; determination of the root components directly involved in water uptake; ability to measure and monitor changes in root-shoot communication and subsequent resource and hormone partitioning; carbohydrate storage; root allelopathy; recognition of abiotic (heavy metals, salt, toxins) and biotic (biotrophic, necrotrophic pathogens, insect, nematodes) stressors and activation of defense pathways, including programmed cell death (PCD).
Currently it is not possible to rapidly screen the results of plant breeding for root characteristics directly or rapidly. This is a major limitation to selecting progeny with improved root biology and physiology. Additionally, as soon as the root is removed from soil the natural interaction with the soil is destroyed, interfering with our understanding and making repeat observations impossible. This focus area will develop improved methods for root imaging and quantification using ground penetrating radar and other techniques under development.
The rhizosphere which is directly influenced by the root has a much lower diversity of microorganisms than the surrounding bulk soil. However, these microorganisms are localized within the root, on the root surface, and immediately adjacent to the root. These microorganisms are intricately involved in the molecular, genetic, and ecological components of the root, and they influence plant community composition and soil health. (Rout and Southworth 2013). Plant roots have sophisticated defense responses to guard against colonization by detrimental and pathogenic microorganisms. The root selects for specific subpopulations that provide it with essential ‘ecosystem services.’ These microorganisms that provide multiple benefits to the root and are the “core” root microbiome. Members of the core root microbiome can be altered by the plant during various developmental and stress induced events. Studies on the root microbiome are in their infancy, and primarily focused on model plant systems such as Arabidopsis. We will expand this area of research to agronomically important crops.
Challenges in doing this include: the characterization of core root microbiomes of key plant species; determination of changes in the healthy state microbiome versus stressed state microbiomes; influence of plant genotype on microbiome community composition; patterns of root gene expression modulation by microbiome and determination of core microbiome functions on root performance, nutrient uptake, and activation of plant immune responses; signaling between root cells and microbiome community members; influence of root microbiome on establishment and persistence of mycorrhizal associations; contribution of viruses (including bacteriophages) to the root microbiome composition.
Analogous to studies of the human gut microbiome, these core root microbiome studies are in its infancy, and much research needs to be performed. However, this effort is essential to solving our Grand Challenges and providing sufficient safe and high quality food for the growing world.
The key to this research area is selecting for Roots with Improved Characteristics. The phenotype of a plant (P) is the product of its genotype (G) as influenced by the environment (E). Modern plant breeding approaches have improved our ability to select for crops with improved yield using a number of approaches, including Quantitative Trait Loci (QTLs) and Marker-Assisted Selection (MAS). These approaches are complemented by the ability to measure changes in plant function, size and yield. Root function has largely been overlooked in these studies, especially those focused on yield as the sole parameter. To ensure we have the ability to increase yield under conditions of reduced agronomic inputs and abiotic and biotic stresses, the role of the “functional root” must be addressed. The ‘functional root’ encompasses the root, its associated microbiome, and the ability of this mixed community to enhance water and nutrient uptake. Thus, the Phenotype of the plant is the product of its Genotype as influenced by its Environment in the context of its Microbiome (M).
P = G x E x M
The development of crop genotypes with improved root phenotypes, microbial associations, and root function will require major advances in our ability to characterize root systems in the field. The relationship between Root System Architecture (RSA) and root function in relation to its microbiome is extremely complicated.