Background Plant roots sense and respond to changes in their soil environment, but conversely contribute to rhizosphere organization through chemical, mechanical and biotic interactions. Transcriptomic profiling of plant roots can be used to assess how the plant adjusts its gene expression in relation to environment, genotype and rhizosphere processes; thus enabling us to achieve a better understanding of root-soil interactions. Methods We used a standardized soil column experimental platform to investigate the impact of soil texture (loam, sand) and root hair formation (wildtype, root hair defective rth3 mutant) in a spatial context (three sampling depths) and assessed maize root transcriptomic profiles using next-generation RNA sequencing. Results Substrate induced the largest changes in root gene expression patterns, affecting gene functions related to immunity, stress, growth and water uptake. Genes with column depth-related expression levels were associated with growth and plant defense. The influence of root hairs mainly manifested in differential expression of epidermal cell differentiation and cell wall organization, and defense response-related genes. Substrate type strongly modified the transcriptomic patterns related to column depth and root hair elongation, highlighting the strong impact of soil texture. Conclusions Our results demonstrate that substrate, sampling depth and plant genotype interactively affect maize gene expression, and suggest feedback processes between the plant, the soil and the microbiome. The obtained results form a foundational basis for the integration and interpretation of future experiments utilizing the same experimental platform.

Aims: Root hairs are important for uptake, especially for nutrients with low mobility in soils with high sorption capacity. Yet, this has rarely been demonstrated in the field during a whole growing season. Mutants with defective root hairs are expected to have lower nutrient uptake, unless they compensate with more root growth. Since root hairs can also contribute to the plant's water uptake their importance could change over the course of a growing season. Methods: The root hair mutant rth3 of Zea mays and the corresponding wild-type were grown for two years under field conditions on sand and loam.Results: Shoot growth and P and K uptake of the plants were promoted by the presence of hairs at all growth stages. Differences between genotypes were greater on loam than on sand until tassel emergence, because additional exploitation by hairs is more relevant in loam. Compensation for the absence of root hairs by increased root growth was not observed in absolute terms. The root to shoot ratio was higher for rth3 than for wild-type. Root traits showed high plasticity in response to texture, the most salient being a greater mean root diameter in sand, irrespective of genotype. The mechanism causing the increase in mean root diameter is still unknown. Root length density was higher in sand, which can be explained by a greater need for exploration than exploitation in this substrate. Conclusion: The greater investment in root growth on sand compared to loam is expected to alter the long-term carbon balance.

Non-invasive X-ray computed tomography (XRCT) is increasingly used in rhizosphere research to visualize development of soil–root interfaces in situ. However, exposing living systems to X-rays can potentially impact their processes and metabolites. In order to evaluate these effects, we assessed the responses of rhizosphere processes 1 and 24 h after a low X-ray exposure (0.81 Gy). Changes in root gene expression patterns occurred 1 h after exposure with down-regulation of cell wall-, lipid metabolism-, and cell stress-related genes, but no differences remained after 24 h. At either time point, XRCT did not affect either root antioxidative enzyme activities or the composition of the rhizosphere bacterial microbiome and microbial growth parameters. The potential activities of leucine aminopeptidase and phosphomonoesterase were lower at 1 h, but did not differ from the control 24 h after exposure. A time delay of 24 h after a low X-ray exposure (0.81 Gy) was sufficient to reverse any effects on the observed rhizosphere systems. Our data suggest that before implementing novel experimental designs involving XRCT, a study on its impact on the investigated processes should be conducted.

Preservation of the phytostimulatory functions of plant growth-promoting bacteria relies on the adaptation of their community to the rhizosphere environment. Here, an amplicon sequencing approach was implemented to specifically target microorganisms with 1-aminocyclopropane-1-carboxylate deaminase activity, carrying the acdS gene. We stated the hypothesis that the relative phylogenetic distribution of acdS carrying microorganisms is affected by the presence or absence of root hairs, soil type, and depth. To this end, a standardized soil column experiment was conducted with maize wild type and root hair defective rth3 mutant in the substrates loam and sand, and harvest was implemented from three depths. Most acdS sequences (99%) were affiliated to Actinobacteria and Proteobacteria, and the strongest influence on the relative abundances of sequences were exerted by the substrate. Variovorax, Acidovorax, and Ralstonia sequences dominated in loam, whereas Streptomyces and Agromyces were more abundant in sand. Soil depth caused strong variations in acdS sequence distribution, with differential levels in the relative abundances of acdS sequences affiliated to Tetrasphaera, Amycolatopsis, and Streptomyces in loam, but Burkholderia, Paraburkholderia, and Variovorax in sand. Maize genotype influenced the distribution of acdS sequences mainly in loam and only in the uppermost depth. Variovorax acdS sequences were more abundant in WT, but Streptomyces, Microbacterium, and Modestobacter in rth3 rhizosphere. Substrate and soil depth were strong and plant genotype a further significant single and interacting drivers of acdS carrying microbial community composition in the rhizosphere of maize. This suggests that maize rhizosphere acdS carrying bacterial community establishes according to the environmental constraints, and that root hairs possess a minor but significant impact on acdS carrying bacterial populations.

Aims Root hairs are important for uptake, especially for nutrients with low mobility in soils with high sorption capacity. Mutants with defective root hairs are expected to have lower nutrient uptake, unless they compensate with more root growth. Since root hairs can also contribute to the plant's water uptake their importance could change over the course of a growing season. It was our objective to investigate the role of root hairs under field conditions. Methods The root hair mutant rth3 of Zea mays and the corresponding wild-type were grown for two years under field conditions on sand and loam. Results Shoot growth and P and K uptake of the plants were promoted by the presence of hairs at all growth stages. Differences between genotypes were greater on loam than on sand until tassel emergence, presumably as additional exploitation by hairs is more relevant in loam. Compensation for the absence of root hairs by increased root growth was not observed in absolute terms. The root to shoot ratio was higher for rth3 than for wild-type. Root traits showed high plasticity in response to texture, the most salient being a greater mean root diameter in sand, irrespective of genotype. The mechanism causing the increase in mean root diameter is still unknown. Root length density was higher in sand, which can be explained by a greater need for exploration than exploitation in this substrate. Conclusion The role of hairs for nutrient uptake could be confirmed under field conditions. The large impact of texture on root growth and consequences for carbon balance require further investigations.