BackgroundTraditional agro-systems in arid areas are a bulwark for preserving soil stability and fertility, in the sight of “reverse desertification”. Nevertheless, the impact of desert farming practices on the diversity and abundance of the plant associated microbiome is poorly characterized, including its functional role in supporting plant development under drought stress.Methodology/Principal FindingsWe assessed the structure of the microbiome associated to the drought-sensitive pepper plant (Capsicum annuum L.) cultivated in a traditional Egyptian farm, focusing on microbe contribution to a crucial ecosystem service, i.e. plant growth under water deficit. The root system was dissected by sampling root/soil with a different degree of association to the plant: the endosphere, the rhizosphere and the root surrounding soil that were compared to the uncultivated soil. Bacterial community structure and diversity, determined by using Denaturing Gradient Gel Electrophoresis, differed according to the microhabitat, indicating a selective pressure determined by the plant activity. Similarly, culturable bacteria genera showed different distribution in the three root system fractions. Bacillus spp. (68% of the isolates) were mainly recovered from the endosphere, while rhizosphere and the root surrounding soil fractions were dominated by Klebsiella spp. (61% and 44% respectively). Most of the isolates (95%) presented in vitro multiple plant growth promoting (PGP) activities and stress resistance capabilities, but their distribution was different among the root system fractions analyzed, with enhanced abilities for Bacillus and the rhizobacteria strains. We show that the C. annuum rhizosphere under desert farming enriched populations of PGP bacteria capable of enhancing plant photosynthetic activity and biomass synthesis (up to 40%) under drought stress.Conclusions/SignificanceCrop cultivation provides critical ecosystem services in arid lands with the plant root system acting as a “resource island” able to attract and select microbial communities endowed with multiple PGP traits that sustain plant development under water limiting conditions.

Although drought is an increasing problem in agriculture, the contribution of the root-associated bacterial microbiome to plant adaptation to water stress is poorly studied. We investigated if the culturable bacterial microbiome associated with five grapevine rootstocks and the grapevine cultivar Barbera may enhance plant growth under drought stress. Eight isolates, over 510 strains, were tested in vivo for their capacity to support grapevine growth under water stress. The selected strains exhibited a vast array of plant growth promoting (PGP) traits, and confocal microscopy observation of gfp-labelled Acinetobacter and Pseudomonas isolates showed their ability to adhere and colonize both the Arabidopsis and grapevine rhizoplane. Tests on pepper plants fertilized with the selected strains, under both optimal irrigation and drought conditions, showed that PGP activity was a stress-dependent and not a per se feature of the strains. The isolates were capable of increasing shoot and leaf biomass, shoot length, and photosynthetic activity of drought-challenged grapevines, with an enhanced effect in drought-sensitive rootstock. Three isolates were further assayed for PGP capacity under outdoor conditions, exhibiting the ability to increase grapevine root biomass. Overall, the results indicate that PGP bacteria contribute to improve plant adaptation to drought through a water stress-induced promotion ability.

Poor iron (Fe) availability in soil represents one of the most important limiting factors of agricultural production and is closely linked to physical, chemical and biological processes within the rhizosphere as a result of soil–microorganism–plant interactions. Iron shortage induces several mechanisms in soil organisms, resulting in an enhanced release of inorganic (such as protons) and organic (organic acids, carbohydrates, amino acids, phytosiderophores, siderophores, phenolics and enzymes) compounds to increase the solubility of poorly available Fe pools. However, rhizospheric organic compounds (ROCs) have short half-lives because of the large microbial activity at the soil–root interface, which might limit their effects on Fe mobility and acquisition. In addition, ROCs also have a selective effect on the microbial community present in the rhizosphere. This review aims therefore to unravel these complex dynamics with the objective of providing an overview of the rhizosphere processes involved in Fe acquisition by soil organisms (plants and microorganisms). In particular, the review provides information on (i) Fe availability in soils, including mineral weathering and Fe mobilization from soil minerals, ligand and element competition and plant-microbe competition; (ii) microbe–plant interactions, focusing on beneficial microbial communities and their association with plants, which in turn influences plant mineral nutrition; (iii) plant–soil interactions involving the metabolic changes triggered by Fe deficiency and the processes involved in exudate release from roots; and (iv) the influence of agrochemicals commonly used in agricultural production systems on rhizosphere processes related to Fe availability and acquisition by crops

Summary• In Strategy-I-plants, iron (Fe) deficiency induces processes leading to increased Fe solubilization in the rhizosphere, including reduction by ferric reductases and active proton extrusion. These processes require active respiration to function. In this work we investigated the effect of Fe deficiency on respiratory activities of cucumber (Cucumis sativus) roots.• We compared oxygen consumption rate and the activities of the respiratory chain complexes on purified mitochondria from roots grown in the presence or absence of Fe using biochemical and molecular approaches.• Oxygen consumption rate in apex roots was increased under Fe deficiency that was mostly resistant to KCN and salycilichydroxamic acid (SHAM) inhibitors, indicating other oxygen-consuming reactions could be present. Indeed, enzyme assays revealed that lack of Fe induced a decrease in the activities of respiratory complexes that was proportional to the number of Fe atoms in each complex. A decrease of cyt c, Rieske and NAD9 proteins was also observed. Transmission electron microscopy (TEM) analysis showed that mitochondria undergo structural changes under Fe deficiency.• Our data show that mitochondria and the electron transport chain are an important target of Fe limitation and that mitochondria modify their function to meet higher demands for organic acids while restricting the activity of enzymes with Fe cofactors.

BackgroundIron deficiency induces in Strategy I plants physiological, biochemical and molecular modifications capable to increase iron uptake from the rhizosphere. This effort needs a reorganization of metabolic pathways to efficiently sustain activities linked to the acquisition of iron; in fact, carbohydrates and the energetic metabolism has been shown to be involved in these responses. The aim of this work was to find both a confirmation of the already expected change in the enzyme concentrations induced in cucumber root tissue in response to iron deficiency as well as to find new insights on the involvement of other pathways.ResultsThe proteome pattern of soluble cytosolic proteins extracted from roots was obtained by 2-DE. Of about two thousand spots found, only those showing at least a two-fold increase or decrease in the concentration were considered for subsequent identification by mass spectrometry. Fifty-seven proteins showed significant changes, and 44 of them were identified. Twenty-one of them were increased in quantity, whereas 23 were decreased in quantity. Most of the increased proteins belong to glycolysis and nitrogen metabolism in agreement with the biochemical evidence. On the other hand, the proteins being decreased belong to the metabolism of sucrose and complex structural carbohydrates and to structural proteins.ConclusionsThe new available techniques allow to cast new light on the mechanisms involved in the changes occurring in plants under iron deficiency. The data obtained from this proteomic study confirm the metabolic changes occurring in cucumber as a response to Fe deficiency. Two main conclusions may be drawn. The first one is the confirmation of the increase in the glycolytic flux and in the anaerobic metabolism to sustain the energetic effort the Fe-deficient plants must undertake. The second conclusion is, on one hand, the decrease in the amount of enzymes linked to the biosynthesis of complex carbohydrates of the cell wall, and, on the other hand, the increase in enzymes linked to the turnover of proteins.