Microbial Activity In Rhizosphere Research Articles

Soil Rhizosphere pH, Enzymatic and Microbial Activities Under Different Nitrogen and Sulfur Fertilization of Soybean (Glycine max L.)

Soil Rhizosphere pH, Enzymatic and Microbial Activities Under Different Nitrogen and Sulfur Fertilization of Soybean (Glycine max L.)

Treatment of Dairy Farm Runoff in Vegetated Bioretention Systems Amended with Biochar

Nitrogen and fecal indicator bacteria (FIB) in runoff from concentrated animal feeding operations (CAFOs) can impair surface and groundwater quality. Bioretention systems are low impact nature-based technologies that can effectively treat CAFO runoff if modified with an internal water storage zone (IWSZ) or amended with biochar. In this study, the performances of four pilot-scale modified bioretention systems were compared to assess the impacts of (1) amending bioretention media with biochar and (2) planting the systems with Muhlenbergia. The system with both plants and biochar amendment had the best performance, with an average of 5.58 log reduction in E. coli and 98% removal of total nitrogen (TN). All systems treated the first pore volume well as new runoff flushed the treated water from the IWSZ. Biochar improved TN and FIB removal due to its high capacity to adsorb or retain ammonium (NH4+), dissolved organic nitrogen, dissolved organic carbon, and E. coli. Planting improved performance, possibly by increasing rhizosphere microbial activity.

Silicon and selenium alleviate cadmium toxicity in Artemisia selengensis Turcz by regulating the plant-rhizosphere

Soil cadmium (Cd) pollution has emerged as a pressing concern due to its deleterious impacts on both plant physiology and human well-being. Silicon (Si) is renowned for its ability to mitigate excessive Cd accumulation within plant cells and reduce the mobility of Cd in soil, whereas Selenium (Se) augments plant antioxidant capabilities and promotes rhizosphere microbial activity. However, research focusing on the simultaneous utilization of Si and Se to ameliorate plant Cd toxicity through multiple mechanisms within the plant-rhizosphere remains comparatively limited. This study combined hydroponic and pot experiments to investigate the effects of the combined application of Si and Se on Cd absorption and accumulation, as well as the growth and rhizosphere of A. selengensis Turcz under Cd stress. The results revealed that a strong synergistic effect was observed between both Si and Se. The combination of Si and Se significantly increased the activity and content of enzymes and non-enzyme antioxidants within A. selengensis Turcz, reduced Cd accumulation and inhibiting its translocation from roots to shoots. Moreover, Si and Se application improved the levels of reducing sugar, soluble protein, and vitamin C, while reducing nitrite content and Cd bioavailability. Furthermore, the experimental results showed that the combination of Si and Se not only increased the abundance of core rhizosphere microorganisms, but also stimulated the activity of soil enzymes, which effectively limited the migration of Cd in the soil. These findings provided valuable insights into the effective mitigation of soil Cd toxicity to plants and also the potential applications in improving plant quality and safety.

Short-term service crops affect the spatial organization of soil aggregates, microbial C[sbnd]N biomass, and microbial activities in a degraded monoculture system

Service crops are grown to provide ecosystem services, such as the ability to increase soil organic matter and fertility. Also, they reduce erosion processes, weed control, disease regulation, water purification, soil biodiversity, and physical restoration. The physical arrangement of elemental particles in soil aggregates controls many ecosystem functions such as soil stability and carbon sequestration. This study aimed to analyze the short-term effect of including different service crops on the soil aggregate dynamics in a degraded common bean monoculture system and how it influences the rhizospheric microbial activity, carbon, and nitrogen microbial biomass. Here, we measured soil water-stable aggregates, particulate and associated organic carbon, soil microbial biomass, microbial activity, service crop aerial biomass, and cash crop yield in bulk soils during the 2020/2021 and 2021/2022 agricultural cycles. Soil samples from depths of 0–10 cm from five management treatments (annual service crop/common bean) were analyzed under no-tillage: 1) Oat (O) = Avena sativa/common bean; 2) Wheat (W) = Triticale/common bean; 3) Vetch (V) = Vicia villosa/common bean; 4) Melilotus (Me) = Melilotus alba/common bean; 5) common bean monoculture (M) = common bean without service crop. Additionally, two controls were analyzed: 6) Brachiaria perennial (BP) = Brachiaria brizantha perennial; 7) Native vegetation (NV). Service crops significantly increased aggregate stability, mean weight diameter, particulate matter and associated organic carbon, promoting the formation of large macroaggregates (0.25–2 mm and > 2 mm). This led to an increase in carbon stocks. Microbial activity expressed as hydrolysis of fluorescein diacetate and acid phosphatase activity, increased in the largest fraction for all service crops. Vicia improved surface residues; on average all service crops increased the common bean yield by 107.25 %. In summary, Vicia represents the best alternative as a service crop to improve the quality and health of degraded monoculture soils.

Assessing Tropospheric Ozone Influence on Garlic (Allium sativum L.) Rhizosphere Microbial Activity

The study conducted at the Climate Change Observatory, Woodhouse Farm, HRS, Ooty, during 2018-2019 focused on investigating the impact of ozone and ozone protectants on rhizosphere microbial activity in garlic cultivation. Specifically, the experiment evaluated the response of the commercial local variety Ooty-1 garlic to varying ozone levels and ozone protectants. Results from the study demonstrated notable variations in microbial activity, including bacteria, fungi, and actinomycetes, within the rhizosphere of garlic plants under different experimental conditions. Notably, the highest increase in bacterial activity was observed under ambient conditions with panchagavya spray, recording a significant log10 cfu/g of 8.9. Similarly, fungal and actinomycetes activity exhibited higher levels under ambient conditions, with respective log10 cfu/g values of 4.8 and 4.7. Conversely, elevated ozone levels at 150 ppb and 200 ppb led to a decline in bacterial, fungal, and actinomycetes activity within the rhizosphere. The reductions were substantial, with bacterial activity dropping to 2.5 log10 cfu/g and 1.9 log10 cfu/g, fungal activity to 1.1 log10 cfu/g and 0.9 log10 cfu/g, and actinomycetes activity to 2.4 log10 cfu/g and 2.1 log10 cfu/g at the respective ozone levels. However, the application of ozone protectants, including 3% panchagavya, 3% neem oil, and 0.1% ascorbic acid, demonstrated a mitigating effect on the negative impacts of tropospheric ozone on rhizosphere microbial diversity. This finding suggests that escalating concentrations of tropospheric ozone have a detrimental effect on the soil microbial activity of garlic. Still, the use of ozone protectants can significantly alleviate these effects by promoting microbial growth. Overall, the study underscores the importance of understanding the complex interactions between ozone levels, ozone protectants, and rhizosphere microbial activity in garlic cultivation, offering valuable insights for sustainable agricultural practices in the face of climate change challenges.

Exploring Microbial Rhizosphere Communities in Asymptomatic and Symptomatic Apple Trees Using Amplicon Sequencing and Shotgun Metagenomics

The rhizosphere is a dynamic and highly interactive habitat where diverse microbial communities are established, and it plays crucial roles in plant health and disease dynamics. In this study, microbial communities and functional profiles in the rhizosphere of both asymptomatic and symptomatic apple trees were investigated through amplicon sequencing and shotgun metagenomics. The research was conducted at a location in the municipality of Cuauhtemoc, Chihuahua State, Mexico, and a total of 22 samples were collected, comprising 12 for amplicon sequencing and 10 for shotgun metagenomic sequencing. Symptomatic trees were identified based on reddish branches and internal necrosis in the trunk and root, while asymptomatic trees exhibited a healthy physiology. The findings showed that the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Bacteroidetes, with prevalent genera such as Streptomyces, Pseudomonas, and Rhodanobacter. The fungal communities featured Ascomycota, Mortierellomycota, and Basidiomycota, which were dominated by Fusarium, Penicillium, and Mortierella. In the fungal communities, Mortierellomycota, notably abundant in asymptomatic trees, holds potential as a biocontrol agent, as seen in other studies on the suppression of Fusarium wilt disease. The application of shotgun metagenomic sequencing revealed significant differences in alpha and beta diversities in bacterial communities, suggesting a health-dependent change in species composition and abundance. Functional profile analysis highlighted enzymatic activities associated with lipid synthesis/degradation, amino acid biosynthesis, carbohydrate metabolism, and nucleotide synthesis, which have been documented to participate in symbiotic relationships between plants. These insights not only contribute to understanding the dynamics of rhizosphere microbial activity but also provide valuable perspectives on the potential application of microbial communities for tree health and implications for the management of apple orchards.

Leptolyngbya sp. XZMQ and Bacillus XZM co-inoculation reduced sunflower arsenic toxicity by regulating rhizosphere microbial structure and enzyme activity

Microorganisms are of great significance for arsenic (As) toxicity amelioration in plants as soil fertility is directly affected by microbes. In this study, we innovatively explored the effects of indigenous cyanobacteria (Leptolyngbya sp. XZMQ) and plant growth-promoting bacteria (PGPB) (Bacillus XZM) on the growth and As absorption of sunflower plants from As-contaminated soil. Results showed that single inoculation and co-inoculation stimulated the growth of sunflower plants (Helianthus annuus L.), enhanced enzyme activities, and reduced As contents. In comparison to the control group, single innoculation of microalgae and bacteria in the rhizosphere increased extracellular polymeric substances (EPS) by 21.99% and 14.36%, respectively, whereas co-inoculation increased them by 35%. Compared with the non-inoculated group, As concentration in the roots, stems and leaves of sunflower plants decreased by 38%, 70% and 41%, respectively, under co-inoculation conditions. Inoculation of Leptolyngbya sp. XZMQ significantly increased the abundance of nifH in soil, while co-inoculation of cyanobacteria and Bacillus XZM significantly increased the abundance of cbbL, indicating that the coupling of Leptolyngbya sp. XZMQ and Bacillus XZM could stimulate the activity of nitrogen-fixing and carbon-fixing microorganisms and increased soil fertility. Moreover, this co-inoculation increased the enzyme activities (catalase, sucrase, urease) in the rhizosphere soil of sunflower and reduced the toxic effect of As on plant. Among these, the activities of catalase, peroxidase, and superoxide dismutase decreased. Meanwhile, co-inoculation enables cyanobacteria and bacteria to attach and entangle in the root area of the plant and develop as symbiotic association, which reduced As toxicity. Co-inoculation increased the abundance of aioA, arrA, arsC, and arsM genes in soil, especially the abundance of microorganisms with aioA and arsM, which reduced the mobility and bioavailability of As in soil, hence, reduced the absorption of As by plants. This study provides a theoretical basis for soil microbial remediation in mining areas.

Linking the rhizosphere effects of 12 woody species on soil microbial activities with soil and root nitrogen status

The rhizosphere effect depicts the changes in soil physical, chemical, and biological properties due to altered microbial activity in response to root activity, which has important implications for soil carbon and nutrient cycling. However, how the plant-induced changes in rhizosphere soil microbial activity correlate with root and soil nutrient status remains uncertain. Here we targeted 12 woody species of distinct growth forms, i.e., tree vs. shrub, in an urban park on a university campus in Beijing, China. We measured root carbon and nitrogen concentrations and soil properties of paired rhizosphere and bulk soils for each plant. We investigated how the rhizosphere effects on microbial properties, as indicated by microbial biomass and potential activity of soil extracellular hydrolases, varied among the 12 woody species and between trees and shrubs, as well as how they were regulated by bulk soil and root nitrogen status. In general, across the 12 species, root nitrogen content, which is a potential indicator of plant life span and nutrient acquisition strategy, was positively correlated with the rhizosphere effect on potential enzyme activity, while the inverse was true for root carbon: nitrogen ratio, which further verified the role of root functional traits in controlling soil nutrient cycling through the rhizosphere effect. Moreover, soil organic carbon, total nitrogen, and available nitrogen concentrations were all found to be negatively correlated with the rhizosphere effect on microbial properties, which highlighted the stimulation of rhizosphere microbial activity for nitrogen acquisition (the nitrogen-mining hypothesis). Trees and shrubs exhibited no significant differences in their rhizosphere effects, and there was a potential difference in the role of rhizosphere effect in regulating soil nitrogen cycling between legumes and non-legumes. Overall, our study highlights the role of plant nutrient acquisition strategy and soil nutrient status in regulating the rhizosphere effect of woody species on microbial-driven soil processes, which is essential for a better understanding of mechanisms by which plants sustain their nutrient supply.

Differential Response of Rhizosphere Microbial Diversity and Activities to System of Rice Intensification and Conventional Cultivation

Rice holds a vital position among staple crops worldwide, serving as a primary source of essential nutrition for a significant portion of the global population. Rice production is currently plagued by several problems causing a decline in crop yields. System of Rice Intensification (SRI) is a set of farming practices designed to improve the productivity and sustainability of rice cultivation. One of the reasons for the sustainability of SRI has been attributed to enhanced below-ground soil microbial processes around the SRI plant root system. This study assessed the effect of SRI and Normal Transplanting (NTP) cultivation methods on rhizospheric soil microbial populations, phyto-hormones, soil enzyme activities under four different nitrogen (N) treatments under a station trial and in on-farms experiments farmer’s. Rhizosphere soils and root samples of SRI exhibited significantly higher microbial population, microbial diversity, phyto - hormone production, enzyme activities in station trail. Among different levels of nitrogen fertilizer applications, treatments receiving 50% organic + 50% inorganic N forms possessed significantly higher microbiota and their activities. On farm trials also exhibited similar trends as the station trial. In conclusion, the study highlights the positive effects of SRI cultivation combined with a balanced organic and inorganic nitrogen treatment on soil microbial populations and phyto-hormone production and soil enzyme activities which could have an influence of system sustainability.

Correction to: Halophyte functional groups influence seasonal variations in rhizosphere microbial necromass and enzyme activities in an inland saline ecosystem

Correction to: Halophyte functional groups influence seasonal variations in rhizosphere microbial necromass and enzyme activities in an inland saline ecosystem

Halophyte functional groups influence seasonal variations in rhizosphere microbial necromass and enzyme activities in an inland saline ecosystem

Halophyte functional groups influence seasonal variations in rhizosphere microbial necromass and enzyme activities in an inland saline ecosystem

Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis

The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.

Maximizing trace metal phytoextraction through planting methods: Role of rhizosphere fertility and microbial activities

Brownfields are a widespread problem in the world. The poor quality of these soils and the potential presence of contaminants can pose a significant threat to plant establishment and growth. However, it may be possible to improve their establishment with an appropriate agricultural practice. In this paper, the effects of two common planting strategies, seeding and transplanting, on the establishment and growth of the hyperaccumulator species Noccaea caerulescens and on its phytoextraction capacity were investigated. A field experiment was conducted by direct sowing of N. caerulescens seeds on a plot of contaminated Technosols in Jeandelaincourt, France. At the same time, seeds were sown on potting soil under controlled conditions. One month later, the seedlings were transplanted to the field. One year later, the results showed that transplanting improved the establishment and growth of N. caerulescens. This was due to a decrease in soil pH in the rhizosphere, which subsequently increased nutrient availability. This change in rhizosphere properties also appeared to be the key that improved microbial activities in the rhizosphere soil of transplanted plants. The observed improvement in both rhizosphere nutrient availability and microbial activities, in turn, increased auxin concentrations in the rhizosphere and consequently a more developed root system was observed in the transplanted plants. Furthermore, the Cd and Zn phytoextraction yield of transplanted plants is 2.5 and 5 times higher, respectively, than that of sown plants. In conclusion, N. caerulescens transplantation on contaminated sites seems to be an adequate strategy to improve plant growth and enhance trace metal phytoextraction.

Illuminating plant–microbe interaction: How photoperiod affects rhizosphere and pollutant removal in constructed wetland?

Rhizosphere is a crucial area in comprehending the interaction between plants and microorganisms in constructed wetlands (CWs). However, influence of photoperiod, a key factor that regulates photosynthesis and rhizosphere microbial activity, remains largely unknown. This study investigated the effect of photoperiod (9, 12, 15 h/day) on pollutant removal and underlying mechanisms. Results showed that 15-hour photoperiod treatment exhibited the highest removal efficiencies for COD (87.26%), TN (63.32%), and NO3–-N (97.79%). This treatment enhanced photosynthetic pigmentation and root activity, which increased transport of oxygen and soluble organic carbon to rhizosphere, thus promoting microbial nitrification and denitrification. Microbial community analysis revealed a more stable co-occurrence network due to increased complexity and aggregation in the 15-hour photoperiod treatment. Phaselicystis was identified as a key connector, which was responsible for transferring necessary carbon sources, ATP, and electron donors that supported and optimized nitrogen metabolism in the CWs. Structural equation model analysis emphasized the importance of plant–microbe interactions in pollutant removal through increased substance, information, and energy exchange. These findings offer valuable insights for CWs design and operation in various latitudes and rural areas for small-scale decentralized systems.

Interactive effect of biochar and urea addition increases plant growth and rhizosphere microbial activity and decreases N2O emissions

Simultaneous addition of biochar with applied N fertilizer was proposed as useful way how to improve soil fertility and reduce negative effects of nitrogen fertilization. A hypothesis that added N decreases root growth and soil microbial activity and increases N2O emissions while addition of biochar has opposite effect was tested. We further hypothesized that increased microbial activity in biochar-amended soil stimulates growth of subsequently cultivated plants.The supposed interactive effect of biochar and N-fertilizer was studied in pot experiment with cultivation of lettuce in soil amended with urea, biochar and their combination. In each pot, yield of plant biomass was determined and basal respiration, substrate-induced respiration and content of mineral N were determined in soil samples. Soil with roots decomposing after lettuce harvest was also analyzed and subsequently used for the cultivation of wheat plants.Emissions of N2O were measured following N application and measurement continued after harvest. Contrary to the hypothesis, N fertilization stimulated the growth of not only aboveground but also belowground plant biomass. Biochar increased growth of roots in agreement with the hypothesis. The effect of treatments on microbial biomass and respiration was relatively weak in the rhizosphere of growing plants. However, when roots were decomposed, lower Nmin and higher microbial biomass were observed in biochar amended soils. Biochar amendment significantly stimulated the yield of subsequently cultivated wheat. At the beginning of the experiment, N2O emissions were higher in biochar-amended soil. However, at the later phase of the experiment, cumulative emissions were lower in biochar-amended soils. Results suggest that biochar supports more efficient N utilization by plants and increases soil fertility. Biochar also decreases N losses through N2O emissions, even with simultaneous N fertilization.

Hybrid constructed wetlands amended with zeolite/biochar for enhanced landfill leachate treatment

Landfill leachate contains high concentrations of ammonia and recalcitrant organic compounds, which can interfere with wastewater treatment processes. Hybrid constructed wetlands (CWs), consisting of Vertical Flow (VF) CWs followed by Horizontal Flow (HF) CWs, are low cost technologies for onsite leachate treatment. This study investigated the potential of low-cost adsorbent materials, a natural zeolite mineral (clinoptilolite) and biochar, to enhance leachate treatment in hybrid CWs. Two mesocosm hybrid CWs were set up at a Florida (US) landfill. In the Adsorbent-CW 10% (v/v) of zeolite was added to the VF-CW to enhance nitrification and 13% (v/v) biochar was added to the HF-CW to increase microbial activity and plant growth. A Control-CW contained only gravel. Both systems were planted with cattails (Typha latifolia) and cordgrass (Spartina alterniflora) and operated at varying hydraulic loading rates for ~2 years. A HF-CW containing wood chips (Woodchip-CW) was added downstream of the Adsorbent-CW during the final 6-months of operation to enhance denitrification. Results showed that zeolite addition to the VF-CW significantly increased nitrification rates by 16–93% due to cycles of ammonium adsorption and bioregeneration under intermittent loading conditions. Biochar addition increased removal of organic matter (21–26% to 29–44%) and color (1–18% to 7–49%), and improved wetland plant growth and nitrogen removal due to enhanced plant growth and rhizosphere microbial activity. Addition of the Woodchip-CW reduced nitrate accumulation, resulting in total nitrogen removals of up to 79%.

Evaluation of power generation in plant microbial fuel cell using vegetable plants

For exploring the possibility of producing power and food simultaneously, PMFC study was explored. Vegetable plants of Brinjal, Tomato and Chili were studied in triplicates for power generation using plant microbial fuel cell (PMFC) for 27 days. All the plants of Chili and Tomato died on 11th day of study, while the plants of Brinjal survived till 26th day. This suggested that Brinjal plants are more tolerant towards stress arising in the rhizosphere due to presence of electrode. The rise in the magnitude of power from 1 to 200 mW to 300–1300 mW was observed after first 12 days of the study in all PMFC sets. It was due to higher rhizospheric microbial activity as compared to the control sets. This suggests that stressed plants suppressed the rhizospheric microbial activity and resultantly overall power generation in PMFC.

Potassium fulvic acid alleviates salt stress of citrus by regulating rhizosphere microbial community, osmotic substances and enzyme activities.

Salt stress damage to plants has been becoming a global concern for agriculture. The application of potassium fulvic acid (PFA) is a promising strategy to alleviate the damage to plants and improve soil quality. However, the study of PFA on plant growth and rhizosphere microbial community remains limited. In this study, microcosmic experiments were conducted to verify the effect of PFA on citrus. Trifoliate orange (Poncirus trifoliata), the most important citrus rootstock, was used to evaluate the effect of PFA on salt damage. The results showed that PFA significantly increased the contents of chlorophyll a, chlorophyll b and carotenoid by 30.09%, 17.55% and 27.43%, and effectively avoided the yellowing and scorching of leaves under salt stress. Based on the results of two-way ANOVA, the mitigation of salt stress on trifoliate seedlings primarily attributed to the enhancement of protective enzyme activities, K+/Na+ ratio and the contents of soluble sugar, soluble protein and proline. Moreover, PFA enhanced neutral protease (S-NPT), sucrase (S-SC) and urease (S-UE) of rhizosphere soil and improved soil nutrition status. The abundance of Bacillus, a kind of rhizosphere beneficial bacteria, was improved by PFA under salt stress, which was mainly associated with the increased activities of S-NPT, S-SC and S-UE. Overall, the application of PFA showed great potential for the alleviation of salt damage on citrus.

Effect of Drought on the Development of Deschampsia caespitosa (L.) and Selected Soil Parameters during a Three-Year Lysimetric Experiment.

This work presents results from a field experiment which was focused on the impact of the drought period on microbial activities in rhizosphere and non-rhizosphere soil. To demonstrate the effect of drought, the pot experiment lasted from 2012 to 2015. Fifteen lysimeters (plastic containers) were prepared in our area of interest. These lysimeters were filled with the subsoil and topsoil from this area and divided into two groups. The first group consisted of two variants: V1 (control) and V2 (84 kg N/ha), which were not stressed by drought. The second group consisted of three variants, V3 (control), V4 (84 kg N/ha), and V5 (84 kg N/ha + 1.25 L lignohumate/ha), which were stressed by drought every year of the experiment for 30 days. Changes in the soil moisture content caused by drought significantly affect the growth of Deschampsia caespitosa L., the microbial activity, and the soil's capacity to retain nutrients. The measured basal respiration and dehydrogenase activity values confirm the significant effect of drought on microbial activity. These values were demonstrably higher in the period before drought simulation by more than 60%. On the other hand, significant differences between microbial activities in the rhizosphere and non-rhizosphere soil were not found. We did not find a clear effect of drought on the formation of soil water repellency.

Integrated microbiome and metabolomics analysis reveal a closer relationship between soil metabolites and bacterial community than fungal community in pecan plantations

AbstractUnderstanding soil metabolic diversity and the chemical signals that shape rhizosphere microbial activity is important for protecting plants and improving forest productivity. At present, little information is known about the metabolites in the rhizosphere soil of pecan (Carya illinoinensis) plantation. Based on technologies of untargeted metabolomics and high‐throughput sequencing, we investigated differences in the metabolic profiles of rhizosphere and bulk soils and the relationship between metabolites and microorganisms in pecan plantations. The results showed that the abundance of metabolites in rhizosphere soil was significantly higher than that in bulk soil (p < 0.05), especially reflected in plant secondary metabolites and lipids. Orientaloside and marmesin rutinoside were significantly enriched in rhizosphere soil metabolites of pecan at three pecan ages (VIP >1, p < 0.05). The linoleic acid and α‐linolenic acid metabolic pathways were significantly enriched in the differential metabolic set (p < 0.01). In addition, tryptophan metabolism, starch and sucrose metabolism, and galactose metabolism were also important factors affecting the rhizosphere metabolic spectrum. Differential metabolites between bulk and rhizosphere soils were more closely associated with bacteria than with fungal communities, particularly in young pecans. With the increasing age of pecans, new significant enrichment of plant secondary metabolites such as cyanidin, 3‐trans‐caffeoyltormentic acid, N‐(1‐Deoxy‐1‐fructosyl) serine and piperdia emerged in the rhizosphere soil. 3‐trans‐caffeoyltormentic acid was positively related to Saitozyma and Protoglossum. Phenylacetaldehyde was positively correlated with Gaiellaceae, Tausonia, and Tuber. This study provides new insights into the mechanisms of interaction between pecans and microorganisms.