Root exudation is an important process determining plant interactions with the soil environment. Many studies have linked this process to soil nutrient mobilization. Yet, it remains unresolved how exudation is controlled and how exactly and under what circumstances plants benefit from exudation. The majority of root exudates including primary metabolites (sugars, amino acids, and organic acids) are believed to be passively lost from the root and used by rhizosphere-dwelling microbes. In this review, we synthetize recent advances in ecology and plant biology to explain and propose mechanisms by which root exudation of primary metabolites is controlled, and what role their exudation plays in plant nutrient acquisition strategies. Specifically, we propose a novel conceptual framework for root exudates. This framework is built upon two main concepts: (1) root exudation of primary metabolites is driven by diffusion, with plants and microbes both modulating concentration gradients and therefore diffusion rates to soil depending on their nutritional status; (2) exuded metabolite concentrations can be sensed at the root tip and signals are translated to modify root architecture. The flux of primary metabolites through root exudation is mostly located at the root tip, where the lack of cell differentiation favors diffusion of metabolites to the soil. We show examples of how the root tip senses concentration changes of exuded metabolites and translates that into signals to modify root growth. Plants can modify the concentration of metabolites either by controlling source/sink processes or by expressing and regulating efflux carriers, therefore challenging the idea of root exudation as a purely unregulated passive process. Through root exudate flux, plants can locally enhance concentrations of many common metabolites, which can serve as sensors and integrators of the plant nutritional status and of the nutrient availability in the surrounding environment. Plant-associated micro-organisms also constitute a strong sink for plant carbon, thereby increasing concentration gradients of metabolites and affecting root exudation. Understanding the mechanisms of and the effects that environmental stimuli have on the magnitude and type of root exudation will ultimately improve our knowledge of processes determining soil CO2 emissions, ecosystem functioning, and how to improve the sustainability of agricultural production.

Root Exudation of Primary Metabolites: Mechanisms and Their Roles in Plant Responses to Environmental Stimuli.

Over the last 60 years, soil microbiologists have accumulated a wealth of experimental data showing that the usual bulk, macroscopic parameters used to characterize soils (e.g., granulometry, pH, soil organic matter and biomass contents) provide insufficient information to describe quantitatively the activity of soil microorganisms and some of its outcomes, like the emission of greenhouse gases. Clearly, new, more appropriate macroscopic parameters are needed, which reflect better the spatial heterogeneity of soils at the microscale (i.e., the pore scale). For a long time, spectroscopic and microscopic tools were lacking to quantify processes at that scale, but major technological advances over the last 15 years have made suitable equipment available to researchers. In this context, the objective of the present article is to review progress achieved to date in the significant research program that has ensued. This program can be rationalized as a sequence of steps, namely the quantification and modeling of the physical-, (bio)chemical-, and microbiological properties of soils, the integration of these different perspectives into a unified theory, its upscaling to the macroscopic scale, and, eventually, the development of new approaches to measure macroscopic soil characteristics. At this stage, significant progress has been achieved on the physical front, and to a lesser extent on the (bio)chemical one as well, both in terms of experiments and modeling. In terms of microbial aspects, whereas a lot of work has been devoted to the modeling of bacterial and fungal activity in soils at the pore scale, the appropriateness of model assumptions cannot be readily assessed because relevant experimental data are extremely scarce. For the overall research to move forward, it will be crucial to make sure that research on the microbial components of soil systems does not keep lagging behind the work on the physical and (bio)chemical characteristics. Concerning the subsequent steps in the program, very little integration of the various disciplinary perspectives has occurred so far, and, as a result, researchers have not yet been able to tackle the scaling up to the macroscopic level. Many challenges, some of them daunting, remain on the path ahead.

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Emergent Properties of Microbial Activity in Heterogeneous Soil Microenvironments: Different Research Approaches Are Slowly Converging, Yet Major Challenges Remain.

The largest terrestrial organic carbon pool, carbon in soils, is regulated by an intricate connection between plant carbon inputs, microbial activity, and the soil matrix. This is manifested by how microorganisms, the key players in transforming plant-derived carbon into soil organic carbon, are controlled by the physical arrangement of organic and inorganic soil particles. Here we conduct an incubation of isotopically labelled litter to study effects of soil structure on the fate of litter-derived organic matter. While microbial activity and fungal growth is enhanced in the coarser-textured soil, we show that occlusion of organic matter into aggregates and formation of organo-mineral associations occur concurrently on fresh litter surfaces regardless of soil structure. These two mechanisms-the two most prominent processes contributing to the persistence of organic matter-occur directly at plant-soil interfaces, where surfaces of litter constitute a nucleus in the build-up of soil carbon persistence. We extend the notion of plant litter, i.e., particulate organic matter, from solely an easily available and labile carbon substrate, to a functional component at which persistence of soil carbon is directly determined.

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Particulate organic matter as a functional soil component for persistent soil organic carbon.

The Glomeromycota: A Species List With New Families and New Gener

Spatially Resolved Mass Spectrometry at the Single Cell: Recent Innovations in Proteomics and Metabolomics.

Plant roots are major transmitters of atmospheric carbon into soil. The rhizosphere, the soil volume around living roots influenced by root activities, represents hotspots for organic carbon inputs, microbial activity, and carbon turnover. Rhizosphere processes remain poorly understood and the observation of key mechanisms for carbon transfer and protection in intact rhizosphere microenvironments are challenging. We deciphered the fate of photosynthesis-derived organic carbon (OC) in intact wheat rhizosphere, combining stable isotope labeling at field scale with high-resolution 3D-imaging. We used nano-scale secondary ion mass spectrometry and focus ion beam-scanning electron microscopy to generate insights into rhizosphere processes at nanometer scale. In immature wheat roots, the carbon circulated through the apoplastic pathway, via cell walls, from the stele to the cortex. The carbon was transferred to substantial microbial communuties, mainly represented by bacteria surrounding peripheral root cells. Iron oxides formed bridges between roots and bigger mineral particles, such as quartz, and surrounded bacteria in microaggregates close to the root surface. Some microaggregates were also intimately associated with the fungal hyphae surface. Based on these results, we propose a conceptual model depicting the fate of carbon at biogeochemical interfaces in the rhizosphere, at the forefront of growing roots. We observed complex interplays between vectors (roots, fungi, bacteria), transferring plant-derived OC into root-free soil and stabilizing agents (iron oxides, root and microorganism products), potentially protecting plant-derived OC within microaggregates in the rhizosphere.

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

Rice straw amendment ameliorates harmful effect of salinity and increases nitrogen availability in a saline paddy soil

Mycorrhizae can enhance plant growth and phosphorus (P) use efficiency in horticultural plants. This research evaluated the effectiveness of mycorrhizae on increasing growth and yield of nine horti...

Mycorrhizae enhances horticultural plant yield and nutrient uptake under phosphorus deficient field soil condition

Biochar is a pyrolyzed biomass produced under limited oxygen or oxygen absent conditions. Few investigations have been conducted to determine the combined effect of biochar with chemical fe...

Rice straw biochar amended soil improves wheat productivity and accumulated phosphorus in grain

My previous experimental findings suggested that phosphorus (P) enhances aluminium (Al) tolerance in both Al-tolerant and Al-sensitive wheat seedlings. However, the role of P in the amelioration of Al toxicity within plant tissue is still unclear. Therefore, a soil culture horizontal split-root system was used to quantify whether or not translocated P alleviates Al toxicity within the plant tissue. Different level of Al and P were added in two compartments in various combinations for separate root halves. Constrasting Al-tolerant (ET8) and Al-sensitive (ES8) wheat genotypes were used as a testing plant. The limitation of root growth was independent to Al-toxicity in one root half. However, root proliferation occurred as a compensatory growth on the other root half that has no Al-toxicity. Where half of the roots were given 60 mg P/kg, plant did not translocated P in the other part of the root system that grown in Al toxic soil. When 40 mg P/kg were mixed with 60 mg AlCl3/kg within one root half combinations, root dry weight of both ET8 and ES8 increased markedly in that root half. In contrast, root dry weight of both ET8 and ES8 decreased noticeably only 60 mg AlCl3/kg treated root half. The shoot P and Al uptake in both ET8 and ES8 was lower in combined 40 mg P/kg and 60 mg AlCl3/kg addition as compared to other combination with same P and Al level. Result from this study confirm that addition of P to Al toxic acid soil played dual role like amelioration of Al-toxicity in soil and utilize P as nutrition for plant growth and development. Findings also attributed that added P was reduced by precipitation with added Al. However, evidence found that translocated P was not able to alleviate Al toxicity within plant tissue of both ES8 and ET8.

Toufiq Iqbal

Papers

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

Rice straw amendment ameliorates harmful effect of salinity and increases nitrogen availability in a saline paddy soil

Mycorrhizae enhances horticultural plant yield and nutrient uptake under phosphorus deficient field soil condition

Rice straw biochar amended soil improves wheat productivity and accumulated phosphorus in grain

A split-root experiment shows that translocated phosphorus does not alleviate aluminium toxicity within plant tissue