Silicon (Si) forms a defensive barrier in roots of Si-accumulators such as rice, blocking the absorption of toxic metals and salt, but many dicotyledons do not accumulate Si, limiting the Si application in agriculture. This may be related to differences in their cell walls: mixed-linkage glucan (MLG) exists in cell walls of monocotyledons but is absent in dicotyledons. In vivo and in vitro experiments, material characterization, and genetic modification approaches were employed to investigate the structural roles of MLG in root Si barriers and its effects on plant stress resistance. Both the roots of Si transporter Lsi2 (low silicon rice 2) defective rice mutants and dead rice continued to accumulate Si, showing root Si deposition is controlled by cell wall components, but not transporters. MLG-induced Si polymerization in vitro and CslF6 (encoding an MLG synthase) controlled root MLG and Si concentrations. Overexpression of rice CslF6 in Arabidopsis, an Si non-accumulator, enabled them to form Si barriers, enhancing resistance to cadmium, chromium, and salt stress. These findings suggest that MLG serves as a structural basis for root Si barriers and that genetic modification combined with Si supply is a promising strategy to endow Si non-accumulators with Si-mediated stress resistance.

Soil health reflects the sustained capacity of soil to function as a vital living ecosystem, ensuring support for all forms of life. The evaluation of soil health relies heavily on physicochemical indicators. However, it remains unclear whether and how microbial traits are related to soil health in soil with long-term organic manure amendment. This study aims to examine how detrimental and beneficial microbial traits change with soil health based on physicochemical indicators. This research measures the effects of 9-year manure supplementation on soil health using multiomics techniques. We found that, compared to 100% chemical fertilizers, the soil health index increased by 5.2%, 19.3%, and 72.6% with 25%, 50%, and 100% organic fertilizer amendments, respectively. Correspondingly, the abundance of beneficial microorganisms, including Actinomadura, Actinoplanes, Aeromicrobium, Agromyces, Azospira, Cryobacterium, Dactylosporangium, Devosia, Hyphomicrobium, Kribbella, and Lentzea, increased progressively, while the abundance of the pathogenic fungus Fusarium decreased with the organic manure application rate. In addition, the application of organic manure significantly increased the concentrations of soil metabolites, such as sugars (raffinose, trehalose, maltose, and maltotriose) and lithocholic acid, which promoted plant growth and soil aggregation. Moreover, the abundances of pathogens and beneficial microorganisms and the concentrations of beneficial soil metabolites were significantly correlated with the soil health index based on physicochemical indicators. We conclude that organic fertilizer can enhance soil health by promoting the increase in beneficial microorganisms while suppressing detrimental microorganisms, which can serve as potential indicators for assessing soil health. In agricultural production, substituting 25–50% of chemical fertilizers with organic fertilizers significantly helps improve soil health and promotes crop growth.

Engineering root microbiomes holds great promise to enhance plant health. Enhanced plant resistance via breeding or genetic modification can promote recruiting beneficial microbes, but is challenging to achieve. Here we showed that calcium (Ca) addition caused significant changes in tomato physiology, resulting in enhanced immunity towards the pathogen Ralstonia solanacearum along with increased levels of salicylic acid (SA), sugar content, and defense enzyme activities in roots. High Ca levels significantly altered the root microbiomes, enriching sixteen bacterial genera, including Dyella japonica, Rhodanobacter glycinis, Paenibacillus polymyxa, and Pseudomonas aeruginosa, with the mostly enriched genus showing a 16.5-fold increase in the relative abundance compared to no Ca addition. Associated with the enhancement of these bacterial genera, tomato wilt incidence was reduced from 80 to 0

The soil microbiome plays an important role in carbon (C) and nitrogen (N) processing and storage and is influenced by rare earth elements (REEs), which can have both direct and indirect effects on plant metabolic processes. Using conventional physicochemical methods and metagenomic-based analyses, we investigated REEs effects on soil respiration, soil mineral N, soil microbial community structure and functional genes related to C and N metabolism. High doses of cerium (0.16 and 0.32 mmol kg- 1 soil) increased CO2 net production rate by 59 and 42%, and N2O net production rate by 255 and 609%, respectively, compared to no REEs. Similarly, high doses of lanthanum (0.16 and 0.32 mmol kg- 1 soil) increased CO2 net production rate by 47 and 39%, and N2O net production rate by 105 and 187%, respectively. Increased soil respiration from altered relative abundances of key soil microorganisms associated with soil N cycling and organic matter degradation and functional genes encoding enzymes involved in C and N metabolism, accelerated N mineralization. Elevated REEs levels substantially increased the relative abundances of functional genes related to cellulose, chitin, glucans, hemicellulose, lignin, and peptidoglycan degradation. REEs also influenced multiple functional genes associated with the N cycle. The abundance of genes responsible for organic N degradation and synthesis, such as asnB, gdh_K15371, glsA, and gs, increased with elevated cerium and lanthanum concentrations. Similarly, the abundances of denitrification genes, including narl, narJ, narZ, and nosZ, also rose with increasing amounts of cerium and lanthanum. However, the decrease in narB and nirB gene abundance with increasing REE concentrations was attributed to the reduction of nitrate to amino groups. Our findings highlight the influence of REEs on key soil microorganisms associated with soil N cycling and organic matter degradation and key functional genes in soil C and N metabolism, with implications for agriculture, environmental protection, and human health.

Manure application is a global approach for enhancing soil organic carbon (SOC) sequestration. However, the response of SOC decomposition in manure-applied soil to abrupt warming, often occurring during diurnal temperature fluctuations, remains poorly understood. We examined the effects of long-term (23 years) continuous application of manure on SOC chemical composition, soil respiration, and microbial communities under temperature shifts (15 vs 25 °C) in the presence of plant residues. Compared to soil without fertilizer, manure application reduced SOC recalcitrance indexes (i.e., aliphaticity and aromaticity) by 17.45 and 21.77%, and also reduced temperature sensitivity (Q10) of native SOC decomposition, plant residue decomposition, and priming effect by 12.98, 15.98, and 52.83%, respectively. The relative abundances of warm-stimulated chemoheterotrophic bacteria and fungi were lower in the manure-applied soil, whereas those of chemoautotrophic Thaumarchaeota were higher. In addition, the microbial network of the manure-applied soil was more interconnected, with more negative connections with the warm-stimulated taxa than soils without fertilizer or with chemical fertilizer applied. In conclusion, our study demonstrated that the reduced loss of SOC to abrupt warming by manure application arises from C chemistry modification, less warm-stimulated microorganisms, a more complex microbial community, and the higher CO2 intercepting capability by Thaumarchaeota.

Understanding root uptake mechanisms for various elements is crucial for optimizing heavy metal remediation strategies and enhancing plant-nutrient interactions. However, simple and effective methods to differentiate the contributions of specific root segments in element uptake are lacking. Here, we developed a layered culture device consisting of a culture box and a plant suspension mechanism, which isolates different root segments through solid media and waterproof coating. Then, we used the device to investigate the roles of distinct root segments (0-1 cm and 1-2 cm from the tip) in heavy metal chromium (Cr) and beneficial element silicon (Si) uptake in rice. The results indicated that the 0-1 cm root segment contributed approximately 58% of leaf Cr(VI), with higher efflux compared to the 1-2 cm segment. Conversely, the 1-2 cm root segment served as the primary source of leaf Si and Cr(III), accounting for 62% and 54%, respectively. The translocation factors for Cr(VI) were similar for both segments (0.039 and 0.032), while the Cr(III) translocation factor for the 0-1 cm root segment (0.061) was 2.8 times that of the 1-2 cm segment. Notably, Si application to the 0-1 cm segment most effectively alleviated Cr (III) and Cr (VI) stress, boosting shoot length, fresh weight, and chlorophyll concentration and reducing Cr concentrations in roots and leaves by 24.7%-65.7%. In contrast, Si application to the 1-2 cm segment had minimal impact on rice growth or Cr uptake. These results suggest a deep Si application strategy for remediating Cr-contaminated soil. The innovative device provides a scientific foundation for distinguishing element uptake contributions of different root segments and enhancing the utilization efficiency of remediation materials and nutrient management in agriculture.

The fate of soil biogenic silica (BSi) in coastal salt marshes is of global importance because of its role in providing both available silicon (Si) for the growth of plants and diatoms and in sequestering carbon (C) (blue C) in soils and sediments. However, the accumulation of BSi and BSi-occluded C (BSiOC) under different vegetation habitats in coastal ecosystems, particularly in response to relative sea-level rise (RSLR), remains poorly understood. Here we established a paired waterlogging-control system and collected the soil samples under both waterlogged and non-waterlogged conditions from three vegetation habitats (single Phragmites australis, a mixture of P. australis and Suaeda salsa, and single S. salsa) corresponding to a gradient of distance from the coastline in three independent salt marshes. Our findings indicated that RSLR decreased average BSi content, especially in the 0-20 cm soil layer of the single P. australis and the mixed P. australis and S. salsa community. Although RSLR increased soil organic C (SOC) content, it generally decreased soil BSiOC content and its contribution to SOC. Consequently, RSLR resulted in lower soil BSi and BSiOC densities, particularly in the salt marsh dominated by the Si accumulator P. australis. Here, BSi and BSiOC densities at depths of 0-80 cm decreased by an average of 19% and 18% following waterlogging, respectively. The BSi pool was dominated by phytoliths in nonwaterlogged soils, while both diatoms and phytoliths were present in soils subjected to RSLR. Soil physicochemical properties including SOC, electrical conductivity and dissolved Si were influenced by RSLR. These factors, along with erosion were suggested as key influencers for BSi and its C sequestration in coastal salt marshes. Our results provide a scientific basis for elucidating biogeochemical Si cycles and predicting changes in BSiOC sequestration to optimize its storage.

Microbial communities have been demonstrated to be essential for healthy and productive soil ecosystems. However, an understanding of the relationship between soil microbial community and soil productivity levels is remarkably limited. In this study, bulk soil (BS), rhizosphere soil (RS), and root (R) samples from the historical high-productive (H) and low-productive (L) soil types of wheat in Hebei province of China were collected and analyzed by high-throughput sequencing. The study highlighted the richness, diversity, and structure of bacterial communities, along with the correlation networks among different bacterial genera. Significant differences in the bacterial community structure between samples of different soil types were observed. Compared with the low-productive soil type, the bacterial communities of samples from the high-productive soil type possessed high species richness, low species diversity, complex and stable networks, and a higher relative abundance of beneficial microbes, such as Pseudoxanthomonas, unclassified Vicinamibacteraceae, Lysobacter, Massilia, Pseudomonas, and Bacillus. Further analysis indicated that the differences were mainly driven by soil organic matter (SOM), available nitrogen (AN), and electrical conductivity (EC). Overall, the soil bacterial community is an important factor affecting soil health and crop production, which provides a theoretical basis for the targeted regulation of microbes in low-productivity soil types.

Rare earth is physiologically active elements,which can affect the growth and development of plants,and plant roots can respond to exogenous plant growth regulators and regulate plant growth.Using tomato seedings as materials,the effects of lanthanum and cerium on the growth and root exudates of tomato seedlings were analyzed by hydroponic experiment. The results showed that the application concentration of rare earth elements at 0.05 mmol/kg promoted the increase of tomato plant height and leaf area,but inhibit them when the concentration reached 0.1 mmol/kg.The application of rare earth elements inhibited the growth of plant roots.The components and contents of tomato root exudates were identified and analyzed.There were 110 metabolites with significant difference between rare earth treatment and blank group,belonging to 10 secondary classifications and 38 tertiary classifications,among which the differences among Fatty acyls class ification,Carboxylic acids and derivatives class ification and Organoxygen compounds class ification were the most significant.However,the effect mechanism of various root exudates on tomato growth still needs to be further studied.

Lignin and cellulose are the most important component of crop straw entering arable soil. The decomposition of lignin and cellulose are related to carbon sequestration and soil fertility. The keystone microbes decomposing lignin and cellulose in cropland and their impact on agricultural management, however, remains largely unclear. In this study, we traced the carbon (C) from highly enriched 13C-labeled (atom% 13C = 99 %) lignin and cellulose to functional keystone microbes in soils of a 26-year fertilization field experiment with stable isotope probing (SIP). 13C-cellulose and 13C-lignin decomposition were significantly accelerated with the long-term application of fertilization, especially with the combination of organic and chemical fertilization (NPKM). The 13C was mainly assimilated by bacteria Acidobacteria (i.e. GP1, GP3, GP6), Proteobacteria (i.e. unidentified gamaproteobactiera, Bradyrhizobium), and fungi Ascomycota (i.e. Talaromyces and Fusarium, etc.). The keystone bacteria taxa decomposing cellulose and lignin were large overlapped, but substantially shaped by fertilization. For instance, GP3 was the dominant bacterium that decomposed both cellulose and lignin in no fertilizer control (CK), while GP1 and GP6 were the ones in chemical fertilization (NPK) and NPKM, respectively. The decomposition rates of cellulose in different fertilizations were majorly predicted by soil total phosphorus (TP), functional fungi abundance, total nitrogen (TN), whereas functional bacterial and fungal abundance, TP, and community structure of functional fungi manipulated the decomposing rate of lignin. Together, we demonstrate that keystone functional microbes decomposing cellulose and lignin were largely concurring and significantly altered by long-term resources enrichment, which drives the similar patterns of decomposition rates of these two substrates along the resource enrichment gradient.

As a potent greenhouse gas, soil nitrous oxide (N2O) is strongly stimulated by rising temperature, triggering a positive feedback effect of global warming. However, its temperature sensitivity varies greatly among soils with different physical and chemical characteristics, while associated mechanisms remain unknown. Here we performed a meta-analysis of the effect of warming on N2O emission and found distinctions in the response of N2O to temperature increase in soils with different textures. Then, we conducted an incubation experiment on 11 arable soils with varying textures sampled across China. The results show that the temperature sensitivity of N2O emissions was lower as soil texture became more clayey and was consistent with the outcome of meta-analysis. Further analysis was conducted by classifying the soils into clay and loam subgroups. As shown in the clay soil subgroup, N2O emission was significantly correlated with both inorganic nitrogen contents and potential denitrification and nitrification activities. Correlation analysis and partial least square (PLS) path model revealed that temperature mediated N2O emission by regulating nosZ gene abundance indirectly. In loam soils, however, the indirect effect of temperature on N2O production was achieved mainly through nirS gene abundance. Additionally, soil DON content strongly correlated with N2O emission in both subgroups and affected N2O emissions by influencing the abundance of denitrifiers under warming conditions. Our findings suggest that (i) soil texture was an important factor affecting temperature sensitivity of N2O emission and (ii) variable efficacy of warming in soil N2O production might originate from the enriching DON and nitrate content and its different indirect effects on nirS- or nosZ-type denitrifiers.

为验证新型复合肥在大桃上的应用效果,为该产品的大面积推广提供一定的研究基础,本研究在北京市平谷区金海湖镇胡庄村设立试验点进行研究.通过测定施肥前后桃园的土壤有机质、碱解氮、速效磷、有效钾含量和pH,以及不施肥、农户常规处理和新型复合肥处理后的单果重、单株留果数、产量、果实硬度、可溶性固形物含量、可滴定酸含量、投入产出比等指标,分析新型复合肥在大桃上的应用肥效.研究发现,施用新型复合肥(N 14％、P2O59％、K2O 26％)颗粒后,显著提高大桃的果实单果重、 留果量和产量,提高桃果实硬度、可溶性固形物含量,显著降低桃可滴定酸含量,显著提高果实固酸比,显著改善果实的口感.施用新型复合肥能够显著提高农民的经济效益,建议大面积推广使用.

Microbial immobilization of fertilizer nitrogen (N) can effectively reduce N losses in soil. However, the effects of crop residue on microbial assimilation of fertilizer-N and the underlying microbial mechanisms in upland soils are unclear. We evaluated the influence of maize residue (13C) addition on the microbial assimilation of ammonium-N (15N) in DNA from fertilizer, and quantified the bacterial 13C or 15N assimilation by quantitative stable isotope probing (DNA-qSIP). We found that the straw addition did increase total microbial assimilation of ammonium from fertilizer during the 2-week incubation. However, bacterial taxa varied in their responses to straw addition: Bacteriodetes and Proteobacteria accounted for large fractions of ammonium assimilation and their N assimilations were increased, while N assimilations of Acidobacteria were decreased. We revealed that highly 13C-labeled taxa were the main contributors of N assimilation under straw addition. The straw primarily enhanced the contributions of bacterial taxa to ammonium assimilation through increasing the extent of N assimilation, or enhancing the abundance of the N-assimilating bacterial taxa. Overall, our study elucidated an interaction between microbial assimilation of fertilizer-N and straw-C, showing a close element coupling of the keystone functional microbial taxa in N immobilization driven by organic carbon.

Phytolith carbon (C) sequestration plays a key role in mitigating global climate change at a centennial to millennial time scale. However, previous estimates of phytolith‐occluded carbon (PhytOC) storage and potential in China's grasslands have large uncertainties mainly due to multiple data sources. This contributes to the uncertainty in predicting long‐term C sequestration in terrestrial ecosystems using Earth System Models. In this study, we carried out an intensive field investigation (79 sites, 237 soil profiles [0–100 cm], and 61 vegetation assessments) to quantify PhytOC storage in China's grasslands and to better explore the biogeographical patterns and influencing factors. Generally, PhytOC production flux and soil PhytOC density in both the Tibetan Plateau and the Inner Mongolian Plateau had a decreasing trend from the Northeast to the Southwest. The aboveground PhytOC production rate in China's grassland was 0.48 × 106 t CO2 a–1, and the soil PhytOC storage was 383 × 106 t CO2. About 45% of soil PhytOC was stored in the deep soil layers (50–100 cm), highlighting the importance of deep soil layers for C stock assessments. Importantly, the Tibetan Plateau had the greatest contribution (more than 70%) to the PhytOC storage in China's grasslands. The results of multiple regression analysis indicated that altitude and soil texture significantly influenced the spatial distribution of soil PhytOC, explaining 78.1% of the total variation. Soil phytolith turnover time in China's grasslands was mainly controlled by climatic conditions, with the turnover time on the Tibetan Plateau being significantly longer than that on the Inner Mongolian Plateau. Our results offer more accurate estimates of the potential for phytolith C sequestration from ecological restoration projects in degraded grassland ecosystems. These estimates are essential to parameterizing and validating global C models.

为了探索不同磷形态处理下土壤、水稻根际和根内环境中细菌群落组成、结构、多样性,从而挖掘不同磷形态下水稻根际中介导植物-微生物相互作用的细菌群落特征.以籼稻(kasalath)为试验材料,采集南京的低磷土壤进行为期8周的水稻盆栽试验,采用高通量测序方法(16S rDNA Illumina测序),并结合土壤有效磷浓度和水稻生物学指标,分别比较不同磷形态处理下水稻生长和根际土、根内细菌微生物群落结构组成和多样性.研究发现,有机磷和无机磷处理显著提高了土壤有效磷含量和磷酸酶活性,其中与不加磷对照相比,无机磷处理显著提高了植株全磷含量,有机磷处理与无机磷处理无显著性差异;在根际土和根内细菌中,有机磷和对照处理植株细菌多样性均显著高于无机磷处理;不同磷形态下水稻的根系细菌多样性和丰富度均显著(P<0.001)低于根际和非根际土壤细菌多样性和丰富度指数.不同处理中主要细菌包括:厚壁菌门(Firmicutes)、变形菌门(Proteobacteria)、放线菌门(Actinobacteria)、酸杆菌门(Acidobacteria)、Ignavibacteriae、绿弯菌门(Chloroflexi).无机磷处理与对照、有机磷处理相比较,在根际土壤和根内细菌中微杆菌科(Microbacteriaceae)、链霉菌科(Streptomycetaceae)相对丰度较低,高温放线菌科(Thermoactinomycetace-ae)、Ignavibacteriaceae显著高于对照和有机磷处理,其中芽孢杆菌科(Bacillaceae)在根际、非根际土壤及根系相对丰度均低于对照和有机磷处理.根际土细菌多样性与植株全磷呈极显著负相关;根系细菌多样性与地上部生物量呈极显著负相关(P<0.01),与有效磷和磷酸酶活性呈显著负相关(P<0.05);根系细菌丰富度与有效磷呈显著负相关:非根际土壤细菌多样性与有效磷呈极显著负相关,与磷酸酶活性和植株全磷呈显著负相关;非根际土壤细菌多样性和丰富度均与有效磷呈极显著负相关,与磷酸酶活性和植株全磷呈显著负相关.本研究结果表明,不同磷形态对水稻根系微生物存在显著差异,无机磷比有机磷的作用更强,为理解磷形态-植物-微生物的相互关系提供了科学依据.

Nitrogen (N) is an essential element for plant growth and development. N levels in soil may also impact plant disease occurrence. However, the physiological and microbial mechanisms between N levels in soil and plant disease occurrence are not quite clear at present. In this study, we examined the impact of seven urea levels (0 to 800 mg kg(-1) soil) on the physiology of tomato (Lycopersicon esculentum) and fungal disease occurrence. Our results showed that the disease incidence and index caused by a tomato early blight pathogen (Alternaria alternata) increased with increasing N levels. The disease index and percentage of disease incidence were positively correlated with N content, indole-3-acetic acid (IAA) and salicylic acid (SA) in plants, but negatively correlated with fungal community diversity. In addition to pathogens (A. alternata) that cause known early blight, 39 other fungal taxa were also identified as plant pathogens in tomato roots, leaves, and soil, the dominant putative pathogens included Ceratobasidiaceae sp., Fusarium oxysporum, Macrophomina phaseolina, Nectriaceae sp., Podosphaera fusca and Trichoderma viride. N levels affected the distribution and dynamics of the fungal pathogen community, such as the abundance of Fusarium oxysporum increased by 33% on roots from days 25 to 35. Our results demonstrated that plants undergo complex disease risk from different pathogens under different N levels, highlighting a need for proper N management, and integration of nutrient management as a disease control approach for sustainable agricultural production.

There are many kinds of soil amendments that consist of different materials. The soil amendment is usually of benefit to plant health. However, the effects of the soil amendments on plant disease have rarely been compared and the involved mechanisms are largely unknown. In the present study, we investigated the influences of five contrasting soil amendments (i.e., potassium silicate (PS), calcium silicate (CS), biochar (BC), calcium silicate humic acid (SCHA), and bio-organic fertilizer (BOF)) on tomato bacterial wilt. In addition, we dissected the mechanism with high-throughput sequencing. The results showed that BC, SCHA, and BOF significantly reduced the incidence and delayed the disease, while BOF significantly reduced the incidence of bacterial wilt disease in the whole tomato growing period. In the early stage of the disease, BC, SCHA, and BOF significantly reduced the soil pH compared to CK. However, the contents of soil NH4+-N and NO3−-N were significantly increased. Some beneficial bacteria genera (Burkholderia, Mortierella, and Trichoderma) had a certain correlation with the incidence. Burkholderia and Mortierella were negatively associated with morbidity, but Trichoderma was positively associated with morbidity. Particularly, the Spearman correlation and the least partial squares path analysis indicated that Trichoderma was significantly positively correlated with the disease incidence, the soil physicochemical properties, and the numbers of soil pathogens (NSP) were significantly positively correlated with the number of root pathogens (NRP) and the physicochemical properties of plants were negatively correlated with the disease incidence. Moreover, BOF had better inhibitory effect on the occurrence of tomato bacterial wilt. Our results have implications for the better integrated management of tomato bacterial wilt.

Rare earth elements (REE) are extensively exploited in the agricultural ecosystems due to their various beneficial roles on plant growth. However, the ecotoxicological effects and environmental risk of REE are poorly assessed. Here, we investigated the effects of lanthanum and cerium nitrate on soil prokaryote and viral metal resistance genes (MRGs) and antibiotics resistance genes (ARGs) using a metagenomic-based approach. We found that relative abundances of prokaryote phyla Bacteroidetes and Chloroflexi decreased with increasing of both REE compounds. In addition, low level REE nitrate (0.05 and 0.1 mmol kg-1 soil) inhibited the viral family Phycodanaviridae, Rudiviridae, Schitoviridae, whereas high level (0.16 and 0.32 mmol kg-1 soil) REE nitrate suppressed the viral family Herelleviridae, Iridoviridae, Podoviridae. ARGs were not significantly affected by low level of REE nitrate. However, high level of both REEs nitrate increased the abundances of dominant prokaryote genes resisting to most of the drug classes, such as aminoglycoside, elfamycin, fluoroquinolone, macrolide, rifamycin. Abundance of MRGs in prokaryote did not change consistently with REE nitrate compound type and input rate. MRGs were only partially detected in the virome in some of the treatments, while ARGs was not detected in virome. Together, we demonstrated that overuse of REE nitrate in agriculture would increase the risk of dissemination of ARGs through prokaryotes but not virus, although viral community was substantially shifted.

Phytohormones are a group of signal compounds that regulate plant growth, development, health and plant-soil interactions. We aimed to investigate the distribution and controlling factors of a diverse set of phytohormones found in the plant-soil continuum. Twenty phytohormones belonging to seven categories were studied in maize roots, rhizosphere and bulk soil with ultra-high-performance liquid chromatography–tandem mass spectrometry. In addition, the microbiomes shaped by gamma-sterilization and reinoculation were analyzed using high throughput sequencing. We found three major distribution patterns of the 17 phytohormones detected along the root-soil continuum. In the first of these, the phytohormones were predominant in roots, followed by rhizosphere and then by bulk soil. In the second pattern, concentrations of the phytohormones were smallest in the rhizosphere. While, in the third pattern, concentrations of the phytohormones were greatest in the rhizosphere. The concentrations of the phytohormones were closely related to those of root phytohormone or roots biomass as well as relative abundances of wide range of microbial taxa. The results indicated that the distribution patterns of six categories of phytohormones in the root-soil continuum are driven by a balance between the production and uptake by the roots and the production, utilization and degradation by the soil microbiome in a phytohormone-specific manner.