Summary: The importance of rhizomicrobiome in plant development, nutrition acquisition and stress tolerance is unquestionable. Relevant plant genes corresponding to the above functions also regulate rhizomicrobiome construction. Deciphering the molecular regulatory network of plant‐microbe interactions could substantially contribute to improving crop yield and quality. Here, the plant gene‐related nutrient uptake, biotic and abiotic stress resistance, which may influence the composition and function of microbial communities, are discussed in this review. In turn, the influence of microbes on the expression of functional plant genes, and thereby plant growth and immunity, is also reviewed. Moreover, we have specifically paid attention to techniques and methods used to link plant functional genes and rhizomicrobiome. Finally, we propose to further explore the molecular mechanisms and signalling pathways of microbe‐host gene interactions, which could potentially be used for managing plant health in agricultural systems.

The beneficial effect of crop residue amendment on soil organic carbon (SOC) stock and stability depends on the functional response of soil microbial communities. Here we synchronized microbial metagenomic analysis, nuclear magnetic resonance and plant-¹⁵N labeling technologies to gain understanding of how microbial metabolic processes affect SOC accumulation in responses to differences in N supply from residues. Residue amendment brought increases in the assemblage of genes involved in C-degradation profiles from labile to recalcitrant C compounds as well as N mineralization. The N mineralization genes were correlated with the C and N accumulation in the particulate and mineral-associated C pools, and plant-derived aliphatic forms of SOC. Thus, the combined C and N metabolic potential of the microbial community transforms residue into persistent organic compounds, thereby increasing C and N sequestration in stable SOC pools. This study emphasizes potential microbially mediated mechanisms by which residue N affects C sequestration in soils.

Background: Understanding how elevated atmospheric CO₂(eCO₂) impacts on phosphorus (P) transformation in plant rhizosphere is critical for maintaining ecological sustainability in response to climate change, especially in agricultural systems where soil P availability is low.Methods: This study used rhizoboxes to physically separate rhizosphere regions (plant root-soil interface) into 1.5-mm segments. Wheat plants were grown in rhizoboxes under eCO₂(800 ppm) and ambient CO₂(400 ppm) in two farming soils, Chromosol and Vertosol, supplemented with phytate (organic P). Photosynthetic carbon flow in the plant-soil continuum was traced with¹³CO₂labeling. Amplicon sequencing was performed on the rhizosphere-associated microbial community in the root-growth zone, and 1.5 mm and 3 mm away from the root.Results: Elevated CO₂accelerated the mineralization of phytate in the rhizosphere zones, which corresponded with increases in plant-derived¹³C enrichment and the relative abundances of discreet phylogenetic clades containing Bacteroidetes and Gemmatimonadetes in the bacterial community, andFunneliformisaffiliated to arbuscular mycorrhizas in the fungal community. Although the amplicon sequence variants (ASVs) associated the stimulation of phytate mineralization under eCO₂differed between the two soils, these ASVs belonged to the same phyla associated with phytase and phosphatase production. The symbiotic mycorrhizas in the rhizosphere of wheat under eCO₂benefited from increased plant C supply and increased P access from soil. Further supportive evidence was the eCO₂-induced increase in the genetic pool expressing the pentose phosphate pathway, which is the central pathway for biosynthesis of RNA/DNA precursors.Conclusions: The results suggested that an increased belowground carbon flow under eCO₂stimulated bacterial growth, changing community composition in favor of phylotypes capable of degrading aromatic P compounds. It is proposed that energy investments by bacteria into anabolic processes increase under eCO₂to level microbial P-use efficiencies and that synergies with symbiotic mycorrhizas further enhance the competition for and mineralization of organic P.

Nitrogen deficiency limits crop performance under elevated CO2 (eCO2), depending on the ability of plant N uptake. However, the dynamics and redistribution of N2 fixation, and fertilizer and soil N use in legumes under eCO2 have been little studied. Such an investigation is essential to improve the adaptability of legumes to climate change. We took advantage of genotype-specific responses of soybean to increased CO2 to test which N-uptake phenotypes are most strongly related to enhanced yield. Eight soybean cultivars were grown in open-top chambers with either 390 ppm (aCO2) or 550 ppm CO2 (eCO2). The plants were supplied with 100 mg N kg-1 soil as 15N-labelled calcium nitrate, and harvested at the initial seed-filling (R5) and full-mature (R8) stages. Increased yield in response to eCO2 correlated highly (r=0.95) with an increase in symbiotically fixed N during the R5 to R8 stage. In contrast, eCO2 only led to small increases in the uptake of fertilizer-derived and soil-derived N during R5 to R8, and these increases did not correlate with enhanced yield. Elevated CO2 also decreased the proportion of seed N redistributed from shoot to seeds, and this decrease strongly correlated with increased yield. Moreover, the total N uptake was associated with increases in fixed-N per nodule in response to eCO2, but not with changes in nodule biomass, nodule density or root length.

The presence of nitrogen inhibits legume nodule formation, but the mechanism of this inhibition is poorly understood. We found that 2.5 mM nitrate and above significantly inhibited nodule initiation but not root hair curling in Medicago trunatula. We analyzed protein abundance in M. truncatula roots after treatment with either 0 or 2.5 mM nitrate in the presence or absence of its symbiont Sinorhizobium meliloti after 1, 2 and 5 days following inoculation. Two-dimensional gel electrophoresis combined with mass spectrometry was used to identify 106 differentially accumulated proteins responding to nitrate addition, inoculation or time point. While flavonoid-related proteins were less abundant in the presence of nitrate, addition of Nod gene-inducing flavonoids to the Sinorhizobium culture did not rescue nodulation. Accumulation of auxin in response to rhizobia, which is also controlled by flavonoids, still occurred in the presence of nitrate, but did not localize to a nodule initiation site. Several of the changes included defense- and redox-related proteins, and visualization of reactive oxygen species indicated that their induction in root hairs following Sinorhizobium inoculation was inhibited by nitrate. In summary, the presence of nitrate appears to inhibit nodulation via multiple pathways, including changes to flavonoid metabolism, defense responses and redox changes.