Notably, the distinct exudation of clay-grown plants disappeared when exudates were collected in vitro, indicating that the differences observed resulted from the presence of clay, and not from an altered exudation of compounds by B. distachyon. About 20% of compounds were distinct between hydroponic and clay exudates, and most of these compounds were reduced in abundance in the presence of clay. Among these compounds were organic acids, amino acids, and nucleosides. When clay was incubated with a defined medium, 75% of compounds were reduced in abundance, among them negatively and positively charged compounds, as well as neutral compounds. The higher metabolite retention by clay in the defined medium experiment compared with the plant experiment might be due to several factors: The clay was incubated for two hours with the defined medium, but for three weeks with plants producing exudates. Although exudates were also collected for two hours in the plant experiment, the clay was likely already saturated to some degree with exudates. The quantification of exudate amounts at different plant developmental stages in future studies would enable a better estimation of the total amount of compounds exuded and would correct for the difference in the two experimental setups. The reduction of metabolite abundance in the presence of clay is most likely due to its high ion exchange capacity,indoor vertical farming compared with quartz-based particles such as sand or glass beads . Previous studies investigating sorption of bacterial lysates to ferrihydrite found a depletion of more than half of the metabolites .

Similarly, incubation of bacterial lysates with a soil consisting of 51% sand, 28% silt, and 21% clay resulted in low metabolite recovery rates . These findings are consistent with our data. Interestingly, two nitrogenous metabolites were higher in abundance in exudates of in situ clay-grown plants, . These compounds were not detected in clay negative controls, or in in vitro exudates of clay-grown plants, making it likely that the presence of plants leads to the release of these compounds from clay. Multiple examples exist in literature that describe a release of compounds from minerals by specific exudates. For example, plant-derived organic acids such as malate and citrate solubilize mineral-bound phosphate , and plant-derived oxalate releases organic compounds bound to minerals, making them available to microbial metabolism . Altered exudation depending on the growth substrate was also described for tomato, cucumber, and sweet pepper growing in stone wool, with higher exuded levels of organic acids and sugars compared with glass bead-grown plants . The authors suggest that the presence of aluminum ions in stone wool might be responsible for the altered exudation observed. As the authors did not investigate in vitro-collected exudates of stone wool grown plants, it is unclear to which degree the observed effect was due to changes in plant metabolism or due to the presence of stone wool. In soils, metabolite sorption to minerals can lower decomposition rates . Also, the amount of clay in soil is correlated with retention of labeled carbon in soils . In clay-dominated soils, the size of clay particles shapes how much carbon can be retained: large clay aggregates were found to adsorb more carbon than smaller aggregates . Here, we only investigated one size of clay particles. Thus, it would be prudent to investigate the sorption behavior of clays with different particle sizes, and the ability of microbes to subsequently desorb these compounds.

In natural systems, the presence of large amounts of clay with a specific particle size likely results in the sorption of plant-derived compounds to particles, changing the direct availability of these compounds to heterotroph organisms and, thus, altering soil processes.Microbes can release sorbed compounds from minerals, and they likely preferentially colonize minerals that are associated with compounds missing from the environment . The rhizobacterium Pseudomonas fluorescens utilized in this study was indeed able to desorb metabolites from clay, utilizing them as a carbon source for growth . In soils, root exudation creates zones with high metabolite concentrations. The released exudates can either be directly taken up by root-associated microbes or sorbed to minerals. Although P. fluorescens was able to grow on particles conditioned with exudates, it did not grow on the effluent of the washed particles. This suggests that the organism is able to release mineral-bound metabolites as an additional source for growth—a trait that supports competitiveness and survival in the rhizosphere. Root-associated bacteria have distinct exudate substrate preferences from bulk soil bacteria , which might also define the kind of compounds bacteria are able to release from minerals . Our results are further evidence that minerals play an important role in plant–microbe interactions by sorbing root exudates, which can later be solubilized by microbes for growth. We conclude that alteration in particle size affects root morphology in B. distachyon. Root exudation was constant per root fresh weight, and the exudate metabolite profiles were similar across root morphologies. Mass spectrometry imaging detected ion abundances across various regions of the root system, suggesting involvement of different tissues in exudation.

Exudates were strongly sorbed by clay, significantly reducing the availability of free metabolites. Some of the clay-bound metabolites however could be utilized by a rhizobacterium for growth. Soil clay content thus is likely an important factor to consider when investigating root exudates or plant–microbe interactions in natural environments.Phosphorus is an essential element for plant growth and fecundity . Crop plants require P in large amounts, and acquire it from the rhizosphere solution as phosphate . Because of the low solubility product of Pi salts, Pi concentrations in soil solutions are extremely low , which restricts the diffusion and mass flow of P to the rhizosphere . For this reason, Pi-fertilisers are applied to young crops to support their P demands. The use of Pi-fertilisers can incur both financial and environmental costs. For example, in the UK the volatile price of inorganic Pi-fertilisers fluctuated over fourfold between 2007 and early 2009 , and it is estimated that 11,800 tonnes of the P reaching the surface waters of Great Britain arises from agriculture . In addition, commercially viable reserves of phosphate rock for the production of Pi-fertilisers could be exhausted within the next 100 to 400 years at current rates of consumption . Potatoes have a high demand for P fertilisers. For example,best indoor vertical garden system this crop occupied about 3.1% of the cultivated arable land in Great Britain in 2004, but consumed about 9.4% of the inorganic Pifertiliser applied to all arable crops .These include Pi-fertiliser placement and the optimization of the amounts and timing of Pi-fertiliser applications through informed recommendations . Recommendations for Pi-fertiliser applications are often based on analyses of soil solution and/or plant P concentrations, and/or the occurrence of visible P-deficiency symptoms in crops . However, these methods are subject to methodological vagaries and cannot rectify production losses due to P-deficiency during the growing season. This paper describes a novel method to monitor the physiological status of a potato crop in the field, which could allow remedial Pi-fertilization to prevent losses of yield due to P-deficiency. The method is based on global gene expression patterns in diagnostic leaves.Nitrogen is the mineral element that most often limits plant growth and primary productivity in natural and agricultural systems. Plants usually acquire N from the soil in the forms of ammonium and nitrate , and management of these forms is vital to agriculture. Wheat can utilize either form alone , but mixed N nutrition typically produces the best grain yields and quality in hydroponically grown and field-grown plants . Ammonium and nitrate affect crops differently when either is supplied as the sole N source . Ammonium requires less energy to assimilate into organic compounds , but can prove toxic if it accumulates to high concentrations within plant tissues . Nitrate is generally the predominant form available in aerated, temperate agricultural soils , and may accumulate within plant tissues to high concentrations without toxicity . In wheat, the N form supplied has been found to influence many physiological parameters profoundly including biomass , leaf area , tillering , seed mass , protein content , and mineral nutrient acquisition and distribution , although such differences can vary among cultivars .

The presence of NH4 + , as either a sole N source or in mixed N nutrition, increased organic N concentration in shoots, roots, and grain and decreased partitioning of dry matter to the roots in wheat . Decreased cation uptake has been found in wheat under NH4 + nutrition , although results varied among cultivars . For example, NH4 + nutrition decreased whole plant and shoot accumulations of K, Cu, Ca, Mg, Fe, Mn, and Zn . Nutrient allocation to plant tissues also varied between N forms. NH4 + -fed plants distributed a smaller percentage of total P, K, Cu, and B to roots relative to NO3 + -fed plants . Also, a greater percentage of reduced N was allocated to the shoots in NH4 + -fed plants . Elevated atmospheric concentrations of CO2 alter growth and N dynamics of wheat and other C3 plants. Under elevated CO2, wheat has lower protein and N concentrations , and lower macro- and micro-nutrients concentrations . Grain phytate concentrations are also thought to increase or remain the same under elevated CO2,and in conjunction with decreased concentrations of micro-nutrients, bio-available Zn and Fe are expected to decrease even further under elevated CO2 , as these micro-nutrients form indigestible complexes with phytate. By contrast, wheat yields , harvest index , whole plant biomass , shoot biomass , and root biomass typically increase under CO2 enrichment. In addition, elevated CO2 concentration can increase tillering , nitrogen use efficiency , and micro/macro-nutrient use efficiencies . The influence of elevated CO2 on many of these characteristics may vary among cultivars and research protocols . Wheat grown under CO2 enrichment behaves differently under NO− 3 and NH4 + nutrition. Exposure to elevated CO2 inhibits NO− 3 photo assimilation in wheat as well as in all other C3 and C3– C4 intermediate plants tested . At elevated CO2, NH4 + -fed plants showed greater increases in leaf area and smaller decreases in shoot protein concentration than NO− 3 -fed plants , which could have consequences for human nutrition. Vegetative plants receiving NH4 + had greater shoot, stem, and root biomass at elevated CO2 . Wheat receiving NO− 3 grew slower at elevated CO2 than at ambient CO2 . Shoot NO− 3 concentrations in NH4 + -fed plants were undetectable while those in NO− 3 -fed plants increased by 62% with CO2 enrichment . This increase was associated with an inhibition in NO− 3 and NO− 2 reductase activities under elevated CO2 . The interaction between atmospheric CO2 concentration and inorganic N form and how it influences plant growth and nutrient concentrations has not been examined in wheat or any other crop species grown to senescence. Here, we grew wheat hydroponically in controlled environment chambers and measured mineral nutrition, biomass, and nutrient allocation in response to three concentrations of atmospheric CO2 and two forms of N nutrition . We tested the following hypotheses: plant nutrient concentrations and allocation patterns will respond differently to CO2 enrichment under the two N forms, and NO− 3 -fed plants will show a smaller biomass and yield enhancement in response to CO2 enrichment than NH4 + -fed plants as a result of CO2 inhibition of shoot NO− 3 assimilation. Also, we observed both differences in the Zn concentration between plants grown on NH4 + and NO− 3 and a strong dependence of Zn absorption on Zn and phytate concentration, indicating that phytate and bio-available Zn are affected by N form and CO2. Therefore, we used the well supported Miller equation to estimate how N and CO2 might impact a hypothetical human population. Iron, another important micro-nutrient that forms complexes with phytate, was not analyzed because we observed no significant differences in iron concentrations between the N forms and because how best to estimate Fe absorption in humans is still uncertain .Wheat seeds were surface sterilized for one minute in 2.6% sodium hypochlorite solution and thoroughly rinsed with DDI water. The seeds were then rolled up in germination paper saturated with 10 mM CaSO4.