Root exudates: from plant to rhizosphere and beyond

Kinetics of uptake, translocation, and metabolism of organophosphate esters in japonica rice (Oryza sativa L.): Hydroponic experiment combined with model

Hydroponics combined with fugacity model was employed to investigate the kinetics of uptake, accumulation, and metabolism of organophosphate esters (OPEs) by japonica rice. The time-dependent process for uptake and accumulation of 5 OPEs and their diester-metabolites in both rice root and shoot fitted well with the pseudo-first-order kinetic model. The peak OPE accumulations in rice root and shoot were significantly positively or negatively correlated with their octanol-water partition coefficient (logKow) respectively, but not for their apparent accumulation rates. Root concentration factors (RCFs) and root-to-shoot translocation factors (TFs) of OPEs were found to be positively and negatively correlated with their logKow, respectively. Triphenyl phosphate with benzene ring substituents showed the highest RCF, but the lowest TF, because of its high potential for root adsorption due to the π electron-rich structures. Sterilized root exudates can hinder the root adsorption and absorption of OPEs from solution probably through competitive adsorption of OPEs with root surface. The first-hand transport and metabolism rates were also obtained by generating these rates to fit the dynamic fugacity model with the measurement values. The simulation indicated that the kinetics of OPE accumulation in rice plants may be controlled by multiple processes and physicochemical properties besides Kow.

Nitrogen fertilization affected microbial carbon use efficiency and microbial resource limitations via root exudates

Root exudation and its mediated nutrient cycling process driven by nitrogen (N) fertilizer can stimulate the plant availability of various soil nutrients, which is essential for microbial nutrient acquisition. However, the response of soil microbial resource limitations to long-term N fertilizer application rates in greenhouse vegetable systems has rarely been investigated. Therefore, we selected a 15-year greenhouse vegetable system, and investigated how N fertilizer application amount impacts on root carbon and nitrogen exudation rates, microbial resource limitations and microbial carbon use efficiency (CUEST). Four N treatments were determined: high (N3), medium (N2), low (N1), and a control without N fertilization (N0). Compared to the control (N0), the results showed that the root C exudation rates decreased significantly by 42.9 %, 57.3 % and 33.6 %, and the root N exudation rates decreased significantly by 29.7 %, 42.6 %, and 24.1 % under N1, N2, and N3 treatments, respectively. Interactions between fertilizer and plant roots altered microbial C, N, P limitations and CUEST; Microbial C and N/P limitations were positively correlated with root C and N exudation rates, negatively correlated with microbial CUEST. Random Forest analysis revealed that the root C and N exudation rates were key factors for soil microbial resource limitations and microbial CUEST. Through the structural equation model (SEM) analysis, soil NH4+ content had significant direct effects on the root exudation rates after long-term N fertilizer application. An increase in root exudation rates led to enhanced microbial resource limitations in the rhizosphere soils, potentially due to increased competition. This enhancement may reduce microbial carbon use efficiency (CUE), that is, microbial C turnover, thereby reducing soil C sequestration. Overall, this study highlights the critical role of root exudation rates in microbial resource limitations and CUE changes in plant-soil systems, and further improves our understanding of plant-microbial interactions.

The effect of rhizosphere pH on removal of naphthenic acid fraction compounds from oil sands process-affected water in a willow hydroponic system

The extraction and processing of bitumen from the oil sands in northern Alberta, Canada generates large volumes of oil sands process-affected water (OSPW). OSPW contains a complex mixture of inorganic and organic compounds, including naphthenic acid fraction compounds (NAFCs) that are of particular concern due to their toxicity to aquatic organisms. Phytoremediation is a cost-effective, scalable approach that has the potential to remove NAFCs from OSPW and reduce OSPW toxicity. Environmental pH influences the chemical form and bioavailability of NAFCs. However, little is known about the influence of pH on the uptake of NAFCs in plant systems. This study sought to elucidate the impact of rhizosphere pH on the uptake of NAFCs using a sandbar willow (Salix interior) hydroponic system. To mimic and maintain the naturally low pH conditions of the root, OSPW solutions in these systems were adjusted to a low pH level (pH 5.0) and their NAFC uptake from solution was compared to that of OSPW at native pH (pH 8.0). Our findings revealed that the lower pH hydroponic systems demonstrated enhanced NAFC removal from solution as determined by LC-MS analysis, where up to 26% of NAFCs were removed from OSPW over 72 h at pH 5.0 compared to 8% removed at pH 8.0. Similarly, analysis of spike-in 13C-labeled NAs demonstrated that the OSPW hydroponic system rapidly removed a relatively labile NA (13C-cyclohexane carboxylic acid) from solution at both pH levels, whereas near complete removal of a recalcitrant NA (13C-1-adamantane carboxylic acid) was observed in pH 5.0 solutions only. These results provide insight into the importance of rhizosphere pH on efficient NAFC uptake by plant root systems. Further research will determine whether OSPW phytoremediation efficiency can be enhanced using field treatment conditions that promote low rhizosphere pH levels.

Organic acids released by submerged macrophytes with damaged leaves alter the denitrification microbial community in rhizosphere

Submerged macrophytes have important impacts on the denitrification and anaerobic ammonia-oxidizing (anammox) processes. Leaf damage in these plants probably changes the rhizosphere environment, affecting organic acid release and denitrifying bacteria. However, there is a lack of comprehensive understanding of the specific changes. This study investigated these changes in the rhizosphere of Potamogeton crispus with four degrees of leaf excision. When 0 %, 30 %, 50 % and 70 % of leaves were excised, the concentrations of total organic acid were 31.45, 32.67, 38.26, and 35.16 mg/L, respectively. The abundances of nirS-type denitrifying bacteria were 2.10 × 1010, 1.59 × 1010, 2.54 × 1010, and 4.67 × 1010 copies/g dry sediment, respectively. The abundances of anammox bacteria were 7.58 × 109, 4.59 × 109, 3.81 × 109, and 3.90 × 109 copies/g dry sediment, respectively. The concentration of total organic acids and the abundance of two denitrification microorganisms in the rhizosphere zone were higher than those in the root zone and non-rhizosphere zone. With increasing leaf damage, the number of OTUs in the Pseudomonas genus of nirS-type denitrifying bacteria first increased and then decreased, while that of the Thauera genus was relatively stable. The overall increase in the OTU number of anammox bacteria indicated that leaf damage promotes root exudates release, thereby leading to an increase in their diversity. The co-occurrence network revealed that the two denitrification microorganisms had about 60.52 % positive connections in rhizosphere while 64.73 % negative connections in non-rhizosphere. The abundance and community composition of both denitrification microorganisms were positively correlated with the concentrations of various substances such as oxalic acid, succinic acid, total organic acids and NO2--N. These findings demonstrate that submerged plant damage has significantly impacts on the structure of denitrification microbial community in the rhizosphere, which may alter the nitrogen cycling process in the deposit sediment. SYNOPSIS: This study reveals leaf damage of macrophyte changed the rhizosphere denitrification microbial community, which is helpful to further understand the process of nitrogen cycle in water.

Evidence of nitrogen inputs affecting soil nitrogen purification by mediating root exudates of salt marsh plants

Salt marsh has an important 'purification' role in coastal ecosystems by removing excess nitrogen that could otherwise harm aquatic life and reduce water quality. Recent studies suggest that salt marsh root exudates might be the 'control centre' for nitrogen transformation, but empirical evidence is lacking. Here we sought to estimate the direction and magnitude of nitrogen purification by salt marsh root exudates and gain a mechanistic understanding of the biogeochemical transformation pathway(s). To achieve this, we used a laboratory incubation to quantify both the root exudates and soil nitrogen purification rates, in addition to the enzyme activities and functional genes under Phragmites australis populations with different nitrogen forms addition (NO3-, NH4+ and urea). We found that NO3- and urea addition significantly stimulate P. australis root exudation of total acids, amino acids, total sugars and total organic carbon, while NH4+ addition only significantly increased total acids, amino acids and total phenol exudation. High total sugars, amino acids and total organic carbon concentrations enlarged nitrogen purification potential by stimulating the nitrogen purifying bacterial activities (including enzyme activities and related genes expression). Potential denitrification rates were not significantly elevated under NH4+ addition in comparison to NO3- and urea addition, which should be ascribed to total phenol self-toxicity and selective inhibition. Further, urea addition stimulated urease and protease activities with providing more NH4+ and NO2- substrates for elevated anaerobic ammonium oxidation rates among the nitrogen addition treatments. Overall, this study revealed that exogenous nitrogen could increase the nitrogen purification-associated bacterial activity through accelerating the root exudate release, which could stimulate the activity of nitrogen transformation, and then improve the nitrogen removal capacity in salt marsh.

Machine learning in soil nutrient dynamics of alpine grasslands

As a terrestrial ecosystem, alpine grasslands feature diverse vegetation types and play key roles in regulating water resources and carbon storage, thus shaping global climate. The dynamics of soil nutrients in this ecosystem, responding to regional climate change, directly impact primary productivity. This review comprehensively explored the effects of climate change on soil nitrogen (N), phosphorus (P), and their balance in the alpine meadows, highlighting the significant roles these nutrients played in plant growth and species diversity. We also shed light on machine learning utilization in soil nutrient evaluation. As global warming continues, alongside shifting precipitation patterns, soil characteristics of grasslands, such as moisture and pH values vary significantly, further altering the availability and composition of soil nutrients. The rising air temperature in alpine regions substantially enhances the activity of soil organisms, accelerating nutrient mineralization and the decomposition of organic materials. Combined with varied nutrient input, such as increased N deposition, plant growth and species composition are changing. With the robust capacity to use and integrate diverse data sources, including satellite imagery, sensor-collected spectral data, camera-captured videos, and common knowledge-based text and audio, machine learning offers rapid and accurate assessments of the changes in soil nutrients and associated determinants, such as soil moisture. When combined with powerful large language models like ChatGPT, these tools provide invaluable insights and strategies for effective grassland management, aiming to foster a sustainable ecosystem that balances high productivity and advanced services with reduced environmental impacts.

Bacterial amino acid chemotaxis: a widespread strategy with multiple physiological and ecological roles

Chemotaxis is the directed, flagellum-based movement of bacteria in chemoeffector gradients. Bacteria respond chemotactically to a wide range of chemoeffectors, including amino, organic, and fatty acids, sugars, polyamines, quaternary amines, purines, pyrimidines, aromatic hydrocarbons, oxygen, inorganic ions, or polysaccharides. Most frequent are chemotactic responses to amino acids (AAs), which were observed in numerous bacteria regardless of their phylogeny and lifestyle. Mostly chemoattraction responses are observed, although a number of bacteria are repelled from certain AAs. Chemoattraction is associated with the important metabolic value of AAs as growth substrates or building blocks of proteins. However, additional studies revealed that AAs are also sensed as environmental cues. Many chemoreceptors are specific for AAs, and signaling is typically initiated by direct ligand binding to their four-helix bundle or dCache ligand-binding domains. Frequently, bacteria possess multiple AA-responsive chemoreceptors that at times possess complementary AA ligand spectra. The identification of sequence motifs in the binding sites at dCache_1 domains has permitted to define an AA-specific family of dCache_1AA chemoreceptors. In addition, AAs are among the ligands recognized by broad ligand range chemoreceptors, and evidence was obtained for chemoreceptor activation by the binding of AA-loaded solute-binding proteins. The biological significance of AA chemotaxis is very ample including in biofilm formation, root and seed colonization by beneficial bacteria, plant entry of phytopathogens, colonization of the intestine, or different virulence-related features in human/animal pathogens. This review provides insights that may be helpful for the study of AA chemotaxis in other uncharacterized bacteria.

Exploring the mechanisms of organic fertilizers on Cd bioavailability in rice fields: Environmental behavior and effect factors

The problem of paddy Cadmium (Cd) contamination is currently the focus of global research. Earlier researches have confirmed that utilization of organic fertilizers regulates Cd chemical fraction distribution by increases organic bound Cd. However, environmental behaviours of organic fertilizers in paddy are still lack exploration. Here, we critical reviewed previous publications and proposed a novel research concept to help us better understand it. Three potential impact pathways of utilization of organic fertilizers on the bioavailability of Cd are presented: (i) use of organic fertilizers changes soil physicochemical properties, which directly affects Cd bioavailability by changing chemical form of Cd(II); (ii) use of organic fertilizers increases soil nutrient content, which indirectly regulates Cd supply and bioaccumulation through ion adsorption and competition for ion-transport channels between nutrients and Cd; and (iii) use of organic fertilizers increases activity of microorganisms and efflux of rice root exudates, which indirectly affects Cd bioavailability of through complexation and sequestration of these organic materials with Cd. Meanwhile, dissolved organic matter (DOM) in the rhizosphere of rice is believed to be the key to revealing the effects of organic fertilizers on Cd. DOM is capable of adsorption and complexation-chelation reactions with Cd and the fractionation of Cd(II) is regulated by DOM. Molecular mass, chemical composition, major functional groups and reaction sequence of DOM determine the formation and solubilization of DOM-Cd complexes.

Characterization of Plant-Growth-Promoting Rhizobacteria for Tea Plant (Camellia sinensis) Development and Soil Nutrient Enrichment

Plant-growth-promoting rhizobacteria (PGPR) play an important role in plant growth and rhizosphere soil. In order to evaluate the effects of PGPR strains on tea plant growth and the rhizosphere soil microenvironment, 38 PGPR strains belonging to the phyla Proteobacteria with different growth-promoting properties were isolated from the rhizosphere soil of tea plants. Among them, two PGPR strains with the best growth-promoting properties were then selected for the root irrigation. The PGPR treatment groups had a higher Chlorophyll (Chl) concentration in the eighth leaf of tea plants and significantly promoted the plant height and major soil elements. There were significant differences in microbial diversity and metabolite profiles in the rhizosphere between different experimental groups. PGPR improved the diversity of beneficial rhizosphere microorganisms and enhanced the root metabolites through the interaction between PGPR and tea plants. The results of this research are helpful for understanding the relationship between PGPR strains, tea plant growing, and rhizosphere soil microenvironment improvement. Moreover, they could be used as guidance to develop environmentally friendly biofertilizers with the selected PGPR instead of chemical fertilizers for tea plants.

Microbial colonisation rewires the composition and content of poplar root exudates, root and shoot metabolomes

BACKGROUND

Trees are associated with a broad range of microorganisms colonising the diverse tissues of their host. However, the early dynamics of the microbiota assembly microbiota from the root to shoot axis and how it is linked to root exudates and metabolite contents of tissues remain unclear. Here, we characterised how fungal and bacterial communities are altering root exudates as well as root and shoot metabolomes in parallel with their establishment in poplar cuttings (Populus tremula x tremuloides clone T89) over 30 days of growth. Sterile poplar cuttings were planted in natural or gamma irradiated soils. Bulk and rhizospheric soils, root and shoot tissues were collected from day 1 to day 30 to track the dynamic changes of fungal and bacterial communities in the different habitats by DNA metabarcoding. Root exudates and root and shoot metabolites were analysed in parallel by gas chromatography-mass spectrometry.

RESULTS

Our study reveals that microbial colonisation triggered rapid and substantial alterations in both the composition and quantity of root exudates, with over 70 metabolites exclusively identified in remarkably high abundances in the absence of microorganisms. Noteworthy among these were lipid-related metabolites and defence compounds. The microbial colonisation of both roots and shoots exhibited a similar dynamic response, initially involving saprophytic microorganisms and later transitioning to endophytes and symbionts. Key constituents of the shoot microbiota were also discernible at earlier time points in the rhizosphere and roots, indicating that the soil constituted a primary source for shoot microbiota. Furthermore, the microbial colonisation of belowground and aerial compartments induced a reconfiguration of plant metabolism. Specifically, microbial colonisation predominantly instigated alterations in primary metabolism in roots, while in shoots, it primarily influenced defence metabolism.

CONCLUSIONS

This study highlighted the profound impact of microbial interactions on metabolic pathways of plants, shedding light on the intricate interplay between plants and their associated microbial communities. Video Abstract.

Phenoxyacetic acid enhances nodulation symbiosis during the rapid growth stage of soybean

Root exudates are known signaling agents that influence legume root nodulation, but the molecular mechanisms for nonflavonoid molecules remain largely unexplored. The number of soybean root nodules during the initial growth phase shows substantial discrepancies at distinct developmental junctures. Using a combination of metabolomics analyses on root exudates and nodulation experiments, we identify a pivotal role for certain root exudates during the rapid growth phase in promoting nodulation. Phenoxyacetic acid (POA) was found to activate the expression of GmGA2ox10 and thereby facilitate rhizobial infection and the formation of infection threads. Furthermore, POA exerts regulatory control on the miR172c-NNC1 module to foster nodule primordia development and consequently increase nodule numbers. These findings collectively highlight the important role of POA in enhancing nodulation during the accelerated growth phase of soybeans.

The impact of kaolin mining activities on bacterial diversity and community structure in the rhizosphere soil of three local plants

Introduction

Thus far, the impact of kaolin mining activities on the surrounding native plants and rhizosphere microecology has not been fully understood.

Methods

In this study, we used 16S rRNA high-throughput sequencing to examine the impact of kaolin mining on the rhizosphere bacterial communities and functions of three local plant species: Conyza bonariensis, Artemisia annua, and Dodonaea viscosa.

Results

The results showed that kaolin mining significantly reduced the diversity of rhizosphere bacteria in these plants, as indicated by the Shannon, Simpson, Chao1, and observed species indices (p < 0.05). Kaolin mining had an impact on the recruitment of three rhizosphere bacteria native to the area: Actinoplanes, RB41, and Mycobacterium. These bacteria were found to be more abundant in the rhizosphere soil of three local plants than in bulk soil, yet the mining of kaolin caused a decrease in their abundance (p < 0.05). Interestingly, Ralstonia was enriched in the rhizosphere of these plants found in kaolin mining areas, suggesting its resilience to environmental stress. Furthermore, the three plants had different dominant rhizosphere bacterial populations in kaolin mining areas, such as Nocardioides, Pseudarthrobacter, and Sphingomonas, likely due to the unique microecology of the plant rhizosphere. Kaolin mining activities also caused a shift in the functional diversity of rhizosphere bacteria in the three local plants, with each plant displaying different functions to cope with kaolin mining-induced stress, such as increased abundance of the GlpM family and glucan-binding domain.

Discussion

This study is the first to investigate the effects of kaolin mining on the rhizosphere microecology of local plants, thus contributing to the establishment of soil microecological health monitoring indicators to better control soil pollution in kaolin mining areas.

Impacts of root exudates on the toxic response of Chrysanthemum coronarium L. to the co-pollution of nanoplastic particles and tetracycline

Nano polystyrene (PS) particles and antibiotics universally co-exist, posing a threat to crop plants and hence human health, nevertheless, there is limited research on their combined toxic effects along with major influential factors, especially root exudates, on crop plants. This study aimed to investigate the response of Chrysanthemum coronarium L. to the co-pollution of nanoplastics and tetracycline (TC), as well as the effect of root exudates on this response. Based on a hydroponic experiment, the biochemical and physiological indices of Chrysanthemum coronarium L. were measured after 7 days of exposure. Results revealed that the co-pollution of TC and PS caused significant oxidative damage to the plants, resulting in reduced biomass. Amongst the two contaminants, TC played a more prominent role. PS could enter the root tissue, and the uptake of TC and PS by plant roots was synergetic. Malic acid, oxalic acid, and formic acid could explain 65.1% of the variation in biochemical parameters and biomass of the roots. These compounds affected the photosynthesis and biomass of Chrysanthemum coronarium L. by gradually lowering root reactive oxygen species (ROS) and leaf ROS. In contrast, the impact of rhizobacteria on the toxic response of the plants was relatively minor. These findings suggested that root exudates could alleviate the toxic response of plants to the co-pollution of TC and PS. This study enhances our understanding of the role of root exudates, providing insights for agricultural management and ensuring food safety.

A systematic review and meta-analysis on the root effects and toxic mechanisms of rare earth elements

Rare earth elements (REEs) have attracted much attention because of their unique physical and chemical properties. The root system is the plant organ most directly in contact with REEs, and it is critical to understand the mechanisms of interaction between the two. This paper investigates the effects of REEs on plant enrichment and fractionation, as well as on various developmental and toxicity indices of the root system. REEs are more likely to be deposited on the root surface under the influence of root secretion. The complexation between the two affects the uptake and fractionation of REEs and the altered pattern of root secretion. The toxicity mechanisms of REEs on plant root cells were lied in: (1) REEs generate reactive oxygen species after entering the plant, leading to oxidative stress and damage to plant cells; (2) REEs with higher charge-to-volume ratios compete for organic ligands with or displace Ca2+, further disrupting the normal function of plant root cells. It was shown that the sensitivity of inter-root microorganisms to REEs varied depending on the content and physicochemical properties of REEs. The paper also concluded with a meta-analysis of phytotoxicity induced by REEs, which showed that REEs affect plant physiological parameters. REEs, as a source of oxidative stress, triggered lipid peroxidation damage in plants and enhanced the activity of antioxidant enzymes, thus revealing the significant toxicity of REEs to plants. The phytotoxic effects of REEs increased with time and concentration. These results help to elucidate the ecotoxicology of rare earth-induced phytotoxicity.

Chemical and physical characteristics of wheat root mucilage influenced by Serendipita indica symbiosis: a comparison among four cultivars

Although there is evidence to suggest that the endophytic fungus Serendipita indica plays a crucial role in enhancing plant tolerance against biotic/abiotic stressors, less is known about the impacts of this symbiosis association on root mucilage chemical composition and its physical functions. The mucilage of inoculated and non-inoculated seedlings of four wheat cultivars (i.e., Roshan, Ghods, Kavir and Pishtaz) were extracted using an aeroponic method. Total solute concentration (TCm), carbon content (Cmucilage), electrical conductivity (EC), pH, fatty acids, surface tension (σm), and viscosity (ηm) of mucilage were measured. Ghods and Kavir had the highest and lowest root colonization percents, respectively. Saturated fatty acids, including palmitic and stearic acids, were dominant over unsaturated fatty acids in wheat root mucilage. However, their compositions were significantly different among wheat cultivars. S. indica colonization, especially for Ghods, increased the TCm, Cmucilage, and palmitic acid. Moreover, root mucilage of S. indica-inoculated Ghods had lower σm and greater ηm. An increased amount of powerful surfactants like palmitic acid in the mucilage of S. indica inoculated treatments led to lower σm and greater ηm. Such studies provide further support for the idea that plant-released mucilage plays a major role in modifying the physical environment of the rhizosphere. This knowledge toward truly understanding the rhizosphere can be potentially used for improving the rhizosphere soil quality and increasing crop growth and yield.

Soil Carbon Dioxide Emissions and Carbon Sequestration with Implementation of Alley Cropping in a Mediterranean Citrus Orchard

Agroecological ecosystems produce significant carbon dioxide fluxes; however, the equilibrium of their carbon sequestration, as well as emission rates, faces considerable uncertainties. Therefore, sustainable cropping practices represent a unique opportunity for carbon sequestration, compensating greenhouse gas emissions. In this research, we evaluated the short-term effect of different management practices in alleys (tillage, no tillage, alley cropping with Rosmarinus officinalis and Thymus hyemalis on soil properties, carbon sequestration, and CO2 emissions in a grapefruit orchard under semiarid climate). For two years every four months, soil sampling campaigns were performed, soil CO2 emissions were measured, and rhizosphere soils were sampled at the end of the experimental period. The results show that alley cropping with Thymus and Rosmarinus contributed to improve soil fertility, increasing soil organic carbon (SOC), total nitrogen, cation exchange capacity, and nutrients. The CO2 emission rates followed the soil temperature/moisture pattern. Tillage did not contribute to higher overall CO2 emissions, and there were no decreased SOC contents. In contrast, alley crops increased CO2 emission rates, especially Rosmarinus; however, the bigger root system and biomass of Rosmarinus contributed to soil carbon sequestration at a greater rate than Thymus. Therefore, Rosmarinus is positioned as a better option than Thymus to be used as an alley crop, although long-term monitoring is required to evaluate if the reported short-term benefits are maintained over time.

Ribulose 1,5-Bisphosphate Carboxylase/Oxygenase Is Required in Bradyrhizobium diazoefficiens for Efficient Soybean Root Colonization and Competition for Nodulation

The Hyphomicrobiales (Rhizobiales) order contains soil bacteria with an irregular distribution of the Calvin-Benson-Bassham cycle (CBB). Key enzymes in the CBB cycle are ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), whose large and small subunits are encoded in cbbL and cbbS, and phosphoribulokinase (PRK), encoded by cbbP. These genes are often found in cbb operons, regulated by the LysR-type regulator CbbR. In Bradyrhizobium, pertaining to this order and bearing photosynthetic and non-photosynthetic species, the number of cbbL and cbbS copies varies, for example: zero in B. manausense, one in B. diazoefficiens, two in B. japonicum, and three in Bradyrhizobium sp. BTAi. Few studies addressed the role of CBB in Bradyrhizobium spp. symbiosis with leguminous plants. To investigate the horizontal transfer of the cbb operon among Hyphomicrobiales, we compared phylogenetic trees for concatenated cbbL-cbbP-cbbR and housekeeping genes (atpD-gyrB-recA-rpoB-rpoD). The distribution was consistent, indicating no horizontal transfer of the cbb operon in Hyphomicrobiales. We constructed a ΔcbbLS mutant in B. diazoefficiens, which lost most of the coding sequence of cbbL and has a frameshift creating a stop codon at the N-terminus of cbbS. This mutant nodulated normally but had reduced competitiveness for nodulation and long-term adhesion to soybean (Glycine max (L.) Merr.) roots, indicating a CBB requirement for colonizing soybean rhizosphere.

Could flooding undermine progress in building climate-resilient crops?

Flooding threatens crop productivity, agricultural sustainability, and global food security. In this article I review the effects of flooding on plants and highlight three important gaps in our understanding: (i) effects of flooding on ecological interactions mediated by plants both below (changing root metabolites and exudates) and aboveground (changing plant quality and metabolites, and weakening the plant immune system), (ii) flooding impacts on soil health and microorganisms that underpin plant and ecosystems health, and (iii) the legacy impacts of flooding. Failure to address these overlooked aspects could derail and undermine the monumental progress made in building climate-resilient crops and soil-microbe-assisted plant resilience. Addressing the outlined knowledge gaps will enhance solutions developed to mitigate flooding and preserve gains made to date.

Variation of root traits and its influences on soil organic carbon stability in response to altered precipitation in an alpine meadow

Soil organic carbon (SOC) dynamics are strongly controlled by plant roots. Yet, how variation of root traits under precipitation change influences SOC stability remains unclear. As part of a 5-year field experiment manipulating precipitation including 90 % (0.1P), 50 % (0.5P), 30 % (0.7P) decrease, and 50 % increase (1.5P), this study was designed to assess the effects of changing precipitation on root traits and production dynamics by minirhizotron and examine how such influences regulate SOC stability in an alpine meadow on the Qinghai-Tibetan Plateau. We found that root length density (RLD), specific root length (SRL), root branching intensity (RBI), and root residue carbon input (RC input) exhibited no significant response, whereas root turnover (RT), root carbon (C), nitrogen (N) concentrations and C/N ratio were altered by precipitation change with nonlinear trends. Absorptive root RT positively correlated to manipulated precipitation within the interannual precipitation range in topsoil, but it showed no significant change under extreme drought treatment. Alpine meadows can maintain the SOC content and density under varied precipitation. However, it showed significant variation in aggregate stability and organic carbon (OC) distribution in aggregates in topsoil, which were mainly due to the strong direct effects of soil moisture and partly related to RLD and RC input of transport roots. Although subsurface soil aggregate stability and OC associated with aggregates were not modified, our results indicated a risk of SOC stability variation in subsurface soil if absorptive root RT and SRL changed. These findings provide vital information to predict responses of SOC dynamics of alpine meadow to future climate change.

Plant growth promoting bacteria (PGPB)-induced plant adaptations to stresses: an updated review

Plants and bacteria are co-evolving and interact with one another in a continuous process. This interaction enables the plant to assimilate the nutrients and acquire protection with the help of beneficial bacteria known as plant growth-promoting bacteria (PGPB). These beneficial bacteria naturally produce bioactive compounds that can assist plants' stress tolerance. Moreover, they employ various direct and indirect processes to induce plant growth and protect plants against pathogens. The direct mechanisms involve phytohormone production, phosphate solubilization, zinc solubilization, potassium solubilization, ammonia production, and nitrogen fixation while, the production of siderophores, lytic enzymes, hydrogen cyanide, and antibiotics are included under indirect mechanisms. This property can be exploited to prepare bioformulants for biofertilizers, biopesticides, and biofungicides, which are convenient alternatives for chemical-based products to achieve sustainable agricultural practices. However, the application and importance of PGPB in sustainable agriculture are still debatable despite its immense diversity and plant growth-supporting activities. Moreover, the performance of PGPB varies greatly and is dictated by the environmental factors affecting plant growth and development. This review emphasizes the role of PGPB in plant growth-promoting activities (stress tolerance, production of bioactive compounds and phytohormones) and summarises new formulations and opportunities.

The Effects of Soil Acidity and Aluminium on the Root Systems and Shoot Growth of Lotus pedunculatus and Lupinus polyphyllus

Lotus pedunculatus (lotus) and Lupinus polyphyllus (Russell lupin) persist in the upland grasslands of New Zealand, where soil acidity and associated aluminium (Al) toxicity impede conventional pasture legumes. This experiment investigated the response of lotus and Russell lupin to soil acidity and Al. The species were sown in 20 cm tall 1.2 L pots of acidic upland soil. A mass of 4.5 or 6.7 g lime (CaCO3)/L was added to either the top or bottom or both soil horizons (0-9 cm and 9-18 cm), resulting in six treatments across six randomised blocks in a glasshouse. The soil pH was 4.4, 4.9, and 5.4; the exchangeable Al concentrations were 24, 2.5, and 1.5 mg/kg for 0, 4.5, and 6.7 g lime/L. At 16 weeks post-sowing, the plants were divided into shoots and roots at 0-9 cm and 9-18 cm. Root morphology, shoot and root dry matter (DM), shoot nitrogen (N), and nodulation were measured. The total plant DM and shoot-to-root DM ratio were higher, and the shoot %N was lower for the lotus plants than the Russell lupin plants for the various lime rates (13.2 vs. 2.9 g plant-1, 5.6 vs. 1.6, and 2.4 vs. 3.3%, p < 0.05). No response to lime in terms of total DM or total root morphology parameters was exhibited in either species (p > 0.05). Root morphology adjustments in response to acidity between soil horizons were not observed. The results indicated that lotus and Russell lupin are tolerant to high soil acidity (pH 4.4-5.4) and exchangeable Al (1.5-24 mg kg-1), highlighting their considerable adaptation to grasslands with acidic soils.

Seasonal drives on potentially toxic elements dynamics in a tropical estuary impacted by mine tailings

This study investigates the impact of seasonality on estuarine soil geochemistry, focusing on redox-sensitive elements, particularly Fe, in a tropical estuary affected by Fe-rich mine tailings. We analyzed soil samples for variations in particle size, pH, redox potential (Eh), and the content of Fe, Mn, Cr, Cu, Ni, and Pb. Additionally, sequential extraction was employed to understand the fate of these elements. Results revealed dynamic changes in the soil geochemical environment, transitioning between near-neutral and suboxic/anoxic conditions in the wet season and slightly acidic to suboxic/oxic conditions in the dry season. During the wet season, fine particle deposition (83%) rich in Fe (50 g kg-1), primarily comprising crystalline Fe oxides, occurred significantly. Conversely, short-range ordered Fe oxides dominated during the dry season. Over consecutive wet/dry seasons, substantial losses of Fe (-55%), Mn (-41%), and other potentially toxic elements (Cr: -44%, Cu: -31%, Ni: -25%, Pb: -9%) were observed. Despite lower pseudo-total PTE contents, exchangeable PTEs associated with carbonate content increased over time (Cu: +188%, Ni: +557%, Pb: +99%). Modeling indicated climatic variables and short-range oxides substantially influenced PTE bioavailability, emphasizing the ephemeral Fe oxide control during the wet season and heightened ecological and health risks during the dry seasons.

Floating treatment wetlands to improve the water quality of the Hang Bang canal, Ho Chi Minh City, Vietnam: Effect of plant species

Floating treatment wetlands (FTWs) are artificial platforms that allow aquatic emergent plants to grow in water. Aquatic macrophytes and microorganisms attached to plant roots contribute to the remediation of the contaminated water through physicochemical and biological processes. The pollutant removal treatment performance is affected by various factors, including the plant species. In this study, several plant species, i.e. Canna generalis, Phragmites australis, Pennisetum purpureum, Cyperus alternifolius rottb, Kyllinga brevifolia rottb, and Cyperus ordoratus were investigated for their potential to clean-up water from the Hang Bang canal in Ho Chi Minh City (Vietnam). Canna generalis, Phragmites australis, and Cyperus alternifolius were found to be suitable for FTWs with the highest performance compared to that of other plant species investigated. The organic and nitrogen removal rates amounted to 48-70 g COD m-3 d-1 and 0.7-1.2 g N m-3 d-1, respectively, whereas the reduction of pathogens was around 1.86-3.00 log. Furthermore, FTW systems bring other benefits such as improving ecosystem functioning and biodiversity, producing value-added products from plant biomass, as well as attracting the attention of communities, thus increasing social acceptance of environmental technology interventions.

Strategies of plants to overcome abiotic and biotic stresses

In their environment, plants are exposed to a multitude of abiotic and biotic stresses that differ in intensity, duration and severity. As sessile organisms, they cannot escape these stresses, but instead have developed strategies to overcome them or to compensate for the consequences of stress exposure. Defence can take place at different levels and the mechanisms involved are thought to differ in efficiency across these levels. To minimise metabolic constraints and to reduce the costs of stress defence, plants prioritise first-line defence strategies in the apoplastic space, involving ascorbate, defensins and small peptides, as well as secondary metabolites, before cellular processes are affected. In addition, a large number of different symplastic mechanisms also provide efficient stress defence, including chemical antioxidants, antioxidative enzymes, secondary metabolites, defensins and other peptides as well as proteins. At both the symplastic and the apoplastic level of stress defence and compensation, a number of specialised transporters are thought to be involved in exchange across membranes that still have not been identified, and information on the regeneration of different defence compounds remains ambiguous. In addition, strategies to overcome and compensate for stress exposure operate not only at the cellular, but also at the organ and whole-plant levels, including stomatal regulation, and hypersensitive and systemic responses to prevent or reduce the spread of stress impacts within the plant. Defence can also take place at the ecosystem level by root exudation of signalling molecules and the emission of volatile organic compounds, either directly or indirectly into the rhizosphere and/or the aboveground atmosphere. The mechanisms by which plants control the production of these compounds and that mediate perception of stressful conditions are still not fully understood. Here we summarise plant defence strategies from the cellular to ecosystem level, discuss their advantages and disadvantages for plant growth and development, elucidate the current state of research on the transport and regeneration capacity of defence metabolites, and outline insufficiently explored questions for further investigation.

Rhizosphere effects and microbial N limitations drive the root N limitations in the rhizosphere during secondary succession in a Pinus tabuliformis forest in North China

Introduction

Rhizosphere effects (REs) have recently been identified as important regulators of root and microbial nutrient acquisition and are positively involved in nutrient cycling of belowground carbon (C), nitrogen (N), and phosphorus (P). Nutrient conditions of the fine roots and soil N are likely to influence REs. Still, it is unclear how REs of soil nutrients themselves variably impact the supply of nutrients to plants in terms of the responses to soil N due to succession.

Methods

In this study, we applied both fine roots and extracellular enzymes for vector analysis and stoichiometry of N:P to explore the metabolic limitations of roots and rhizospheric soil microbes and their relationships with REs across five levels of soil N (0, 5, 10, 15, and 20 kg N m-2 year-1) along successional age classes of 42, 55, and 65 years in a Pinus tabuliformis forest.

Results

Overall, the metabolism of root and rhizospheric soil microbes was mediated by soil N. N limitation of roots initially decreased before increasing, whereas that of microbes demonstrated opposite trends to the N levels owing to competition for inorganic N between them by REs of NO3 --N. However, N limitations of both roots and microbes were alleviated in young stands and increased with succession after the application of N. In addition, root N limitations were manipulated by REs of three different soil N-related indicators, i.e., total N, NH4 +-N, and NO3 --N. Rhizospheric soil microbial N limitation was almost unaffected by REs due to their strong homeostasis but was an important driver in the regulation of root N limitation.

Discussion

Our results indicated that successional age was the most critical driver that directly and indirectly affected root N metabolism. However, the level of N application had a slight effect on root N limitation. Microbial N limitation and variations in the REs of N indicators regulated root N limitation in the rhizosphere. As a result, roots utilized REs to sequester N to alleviate N limitations. These findings contribute to novel mechanistic perspectives on the sustainability of N nutrition by regulating N cycling in a system of plant-soil-microbes in the rhizosphere to adapt to global N deposition or the heterogeneous distribution of bioavailable soil N with succession.

Auxin-mediated regulation of susceptibility to toxic metabolites, c-di-GMP levels, and phage infection in the rhizobacterium Serratia plymuthica

The communication between plants and their microbiota is highly dynamic and involves a complex network of signal molecules. Among them, the auxin indole-3-acetic acid (IAA) is a critical phytohormone that not only regulates plant growth and development, but is emerging as an important inter- and intra-kingdom signal that modulates many bacterial processes that are important during interaction with their plant hosts. However, the corresponding signaling cascades remain largely unknown. Here, we advance our understanding of the largely unknown mechanisms by which IAA carries out its regulatory functions in plant-associated bacteria. We showed that IAA caused important changes in the global transcriptome of the rhizobacterium Serratia plymuthica and multidisciplinary approaches revealed that IAA sensing interferes with the signaling mediated by other pivotal plant-derived signals such as amino acids and 4-hydroxybenzoic acid. Exposure to IAA caused large alterations in the transcript levels of genes involved in amino acid metabolism, resulting in significant metabolic alterations. IAA treatment also increased resistance to toxic aromatic compounds through the induction of the AaeXAB pump, which also confers resistance to IAA. Furthermore, IAA promoted motility and severely inhibited biofilm formation; phenotypes that were associated with decreased c-di-GMP levels and capsule production. IAA increased capsule gene expression and enhanced bacterial sensitivity to a capsule-dependent phage. Additionally, IAA induced the expression of several genes involved in antibiotic resistance and led to changes in the susceptibility and responses to antibiotics with different mechanisms of action. Collectively, our study illustrates the complexity of IAA-mediated signaling in plant-associated bacteria.

IMPORTANCE

Signal sensing plays an important role in bacterial adaptation to ecological niches and hosts. This communication appears to be particularly important in plant-associated bacteria since they possess a large number of signal transduction systems that respond to a wide diversity of chemical, physical, and biological stimuli. IAA is emerging as a key inter- and intra-kingdom signal molecule that regulates a variety of bacterial processes. However, despite the extensive knowledge of the IAA-mediated regulatory mechanisms in plants, IAA signaling in bacteria remains largely unknown. Here, we provide insight into the diversity of mechanisms by which IAA regulates primary and secondary metabolism, biofilm formation, motility, antibiotic susceptibility, and phage sensitivity in a biocontrol rhizobacterium. This work has important implications for our understanding of bacterial ecology in plant environments and for the biotechnological and clinical applications of IAA, as well as related molecules.

Rhizosphere Bacteria Help to Compensate for Pesticide-Induced Stress in Plants

Although exogenous chemicals frequently exhibit a biphasic response in regulating plant growth, characterized by low-dose stimulation and high-dose inhibition, the underlying mechanisms remain elusive. This study demonstrates, for the first time, the compensatory function of rhizosphere microbiota in assisting plants to withstand pesticide stress. It was observed that pak choi plants, in response to foliar-spraying imidacloprid at both low and high doses, could increase the total number of rhizosphere bacteria and enrich numerous beneficial bacteria. These bacteria have capabilities for promoting plant growth and degrading the pesticide, such as Nocardioides, Brevundimonas, and Sphingomonas. The beneficial bacterial communities were recruited by stressed plants through increasing the release of primary metabolites in root exudates, such as amino acids, fatty acids, and lysophosphatidylcholines. At low doses of pesticide application, the microbial compensatory effect overcame pesticide stress, leading to plant growth promotion. However, with high doses of pesticide application, the microbial compensatory effect was insufficient to counteract pesticide stress, resulting in plant growth inhibition. These findings pave the way for designing improved pesticide application strategies and contribute to a better understanding of how rhizosphere microbiota can be used as an eco-friendly approach to mitigate chemical-induced stress in crops.

Mitigating sediment cadmium contamination through combining PGPR Enterobacter ludwigii with the submerged macrophyte Vallisneria natans

Sediment cadmium contamination poses risks to aquatic ecosystems. Phytoremediation is an environmentally sustainable method to mitigate cadmium contamination. Submerged macrophytes are affected by cadmium stress, but plant growth-promoting rhizobacteria (PGPR) can restore the health status of submerged macrophytes. Herein, we aimed to reduce sediment cadmium concentration and reveal the mechanism by which the combined application of the PGPR Enterobacter ludwigii and the submerged macrophyte Vallisneria natans mitigates cadmium contamination. Sediment cadmium concentration decreased by 21.59% after submerged macrophytes were planted with PGPR, probably because the PGPR colonized the rhizosphere and roots of the macrophytes. The PGPR induced a 5.09-fold increase in submerged macrophyte biomass and enhanced plant antioxidant response to cadmium stress, as demonstrated by decreases in oxidative product levels (reactive oxygen species and malondialdehyde), which corresponded to shift in rhizosphere metabolism, notably in antioxidant defence systems (i.e., the peroxidation of linoleic acid into 9-hydroperoxy-10E,12Z-octadecadienoic acid) and in some amino acid metabolism pathways (i.e., arginine and proline). Additionally, PGPR mineralized carbon in the sediment to promote submerged macrophyte growth. Overall, PGPR mitigated sediment cadmium accumulation via a synergistic plantmicrobe mechanism. This work revealed the mechanism by which PGPR and submerged macrophytes control cadmium concentration in contaminated sediment.

Exogenous Sodium Nitroprusside Affects the Redox System of Wheat Roots Differentially Regulating the Activity of Antioxidant Enzymes under Short-Time Osmotic Stress

Nitric oxide (NO) is a multifunctional signalling molecule involved in the regulation of plant ontogenesis and adaptation to different adverse environmental factors, in particular to osmotic stress. Understanding NO-induced plant protection is important for the improvement of plant stress tolerance and crop productivity under global climate changes. The root system is crucial for plant survival in a changeable environment. Damages that it experiences under water deficit conditions during the initial developmental periods seriously affect the viability of the plants. This work was devoted to the comparative analysis of the pretreatment of wheat seedlings through the root system with NO donor sodium nitroprusside (SNP) for 24 h on various parameters of redox homeostasis under exposure to osmotic stress (PEG 6000, 12%) over 0.5-24 h. The active and exhausted solutions of SNP, termed as (SNP/+NO) and (SNP/-NO), respectively, were used in this work at a concentration of 2 × 10-4 M. Using biochemistry and light microscopy methods, it has been revealed that osmotic stress caused oxidative damages and the disruption of membrane cell structures in wheat roots. PEG exposure increased the production of superoxide (O2•-), hydrogen peroxide (H2O2), malondialdehyde (MDA), and the levels of electrolyte leakage (EL) and lipid peroxidation (LPO). Stress treatment enhanced the activities of superoxide dismutase (SOD), ascorbate peroxidase (APX), catalase (CAT), the excretion of proline, and the rate of cell death and inhibited their division. Pretreatment with (SNP/+NO) decreased PEG-induced root damages by differently regulating the antioxidant enzymes under stress conditions. Thus, (SNP/+NO) pretreatment led to SOD, APX, and CAT inhibition during the first 4 h of stress and stimulated their activity after 24 h of PEG exposure when compared to SNP-untreated or (SNP/-NO)-pretreated and stress-subjected plants. Osmotic stress triggered the intense excretion of proline by roots into the external medium. Pretreatment with (SNP/+NO) in contrast with (SNP/-NO) additionally increased stress-induced proline excretion. Our results indicate that NO is able to mitigate the destructive effects of osmotic stress on the roots of wheat seedlings. However, the mechanisms of NO protective action may be different at certain periods of stress exposure.

Facing climate change: plant stress mitigation strategies in agriculture

Climate change poses significant challenges to global agriculture, with rising temperatures, altered precipitation patterns, and increased frequency of extreme weather events threatening crop yields. These changes exceed the adaptability thresholds of many crops, decreasing their yield and threatening food security. At plant physiological levels, climate change-induced stressors disrupt photosynthesis, growth, and reproductive processes, contributing to a reduced productivity. Furthermore, the negative impacts of climate change on agriculture are exacerbated by anthropogenic factors, with agriculture itself contributing significantly to greenhouse gas emissions. To mitigate these challenges, various approaches have been explored. This work reviews the most important physical, chemical, and biological strategies most commonly used in a broad range of agricultural crops. Among physical strategies, increasing water use efficiency without yield reduction through different irrigation strategies, and the use of foliar treatments with reflective properties to mitigate the negative effects of different stresses have been proven to be effective. Concerning chemical approaches, the exogenous treatment of plants with chemicals induces existing molecular and physiological plant defense mechanisms, enhancing abiotic stress tolerance. Regarding biological treatments, plant inoculation with mycorrhiza and plant growth-promoting rhizobacteria (PGPR) can improve enzymatic antioxidant capacity and mineral solubilization, favoring root and plant growth and enhance plant performance under stressful conditions. While these strategies provide valuable short- to medium-term solutions, there is a pressing need for new biotechnological approaches aimed at developing genotypes resistant to stressful conditions. Collaborative efforts among researchers, policymakers, and agricultural stakeholders are essential to ensure global food security in the face of ongoing climate challenges.

Metabolites of blueberry roots at different developmental stages strongly shape microbial community structure and intra-kingdom interactions at the root-soil interface

The rhizosphere microorganisms of blueberry plants have long coexisted with their hosts under distinctively acidic soil conditions, exerting a profound influence on host performance through mutualistic symbiotic interactions. Meanwhile, plants can regulate rhizosphere microorganisms by exerting host effects to meet the functional requirements of plant growth and development. However, it remains unknown how the developmental stages of blueberry plants affect the structure, function, and interactions of the rhizosphere microbial communities. Here, we examined bacterial communities and root metabolites at three developmental stages (flower and leaf bud development stage, fruit growth and development stage, and fruit maturation stage) of blueberry plants. The results revealed that the Shannon and Chao 1 indices as well as community composition varied significantly across all three developmental stages. The relative abundance of Actinobacteria significantly increased by 10 % (p < 0.05) from stage 1 to stage 2, whereas that of Proteobacteria decreased significantly. The co-occurrence network analysis revealed a relatively complex network with 1179 edges and 365 nodes in the stage 2. Niche breadth was highest at stage 2, while niche overlap tended to increase as the plant developed. Furthermore, the untargeted metabolome analysis revealed that the number of differential metabolites of vitamins, nucleic acids, steroids, and lipids increased between stage 1 to stage2 and stage 2 to stage 3, while those for differential metabolites of carbohydrates and peptides decreased. Significant changes in expression levels of levan, L-glutamic acid, indoleacrylic acid, oleoside 11-methyl ester, threo-syringoylglycerol, gingerglycolipid B, and bovinic acid were highly correlated with the bacterial community structure. Collectively, our study reveals that significant alterations in dominant bacterial taxa are strongly correlated with the dynamics of root metabolites. These findings lay the groundwork for developing prebiotic products to enhance the beneficial effects of root microorganisms and boosting blueberry productivity via a sustainable approach.

Molecular Mechanisms of Plant Responses to Copper: From Deficiency to Excess

Copper (Cu) is an essential nutrient for plant growth and development. This metal serves as a constituent element or enzyme cofactor that participates in many biochemical pathways and plays a key role in photosynthesis, respiration, ethylene sensing, and antioxidant systems. The physiological significance of Cu uptake and compartmentalization in plants has been underestimated, despite the importance of Cu in cellular metabolic processes. As a micronutrient, Cu has low cellular requirements in plants. However, its bioavailability may be significantly reduced in alkaline or organic matter-rich soils. Cu deficiency is a severe and widespread nutritional disorder that affects plants. In contrast, excessive levels of available Cu in soil can inhibit plant photosynthesis and induce cellular oxidative stress. This can affect plant productivity and potentially pose serious health risks to humans via bioaccumulation in the food chain. Plants have evolved mechanisms to strictly regulate Cu uptake, transport, and cellular homeostasis during long-term environmental adaptation. This review provides a comprehensive overview of the diverse functions of Cu chelators, chaperones, and transporters involved in Cu homeostasis and their regulatory mechanisms in plant responses to varying Cu availability conditions. Finally, we identified that future research needs to enhance our understanding of the mechanisms regulating Cu deficiency or stress in plants. This will pave the way for improving the Cu utilization efficiency and/or Cu tolerance of crops grown in alkaline or Cu-contaminated soils.

Soil pH, developmental stages and geographical origin differently influence the root metabolomic diversity and root-related microbial diversity of Echium vulgare from native habitats

Improved understanding of the complex interaction between plant metabolism, environmental conditions and the plant-associated microbiome requires an interdisciplinary approach: Our hypothesis in our multiomics study posited that several environmental and biotic factors have modulating effects on the microbiome and metabolome of the roots of wild Echium vulgare plants. Furthermore, we postulated reciprocal interactions between the root metabolome and microbiome. We investigated the metabolic content, the genetic variability, and the prokaryotic microbiome in the root systems of wild E. vulgare plants at rosette and flowering stages across six distinct locations. We incorporated the assessment of soil microbiomes and the measurement of selected soil chemical composition factors. Two distinct genetic clusters were determined based on microsatellite analysis without a consistent alignment with the geographical proximity between the locations. The microbial diversity of both the roots of E. vulgare and the surrounding bulk soil exhibited significant divergence across locations, varying soil pH characteristics, and within the identified plant genetic clusters. Notably, acidophilic bacteria were characteristic inhabitants of both soil and roots under acidic soil conditions, emphasizing the close interconnectedness between these compartments. The metabolome of E. vulgare significantly differed between root samples from different developmental stages, geographical locations, and soil pH levels. The developmental stage was the dominant driver of metabolome changes, with significantly higher concentrations of sugars, pyrrolizidine alkaloids, and some of their precursors in rosette stage plant roots. Our study featured the complex dynamics between soil pH, plant development, geographical locations, plant genetics, plant metabolome and microbiome, shedding light on existing knowledge gaps.

Field-based investigation reveals selective enrichment of companion microbes in vegetables leading to specific accumulation of antibiotic resistance genes

Vegetables capture antibiotic resistance genes (ARGs) from the soil and then pass them on to consumers through the delivery chain and food chain, and are therefore the key node that may increase the risk of human exposure to ARGs. This study investigates the patterns and driving forces behind the transmission of ARGs from soil to vegetables by the commonly planted cash crops in the coastal region of southern China, i.e. broccoli, pumpkin, and broad bean, to investigate. The study used metagenomic data to reveal the microbial and ARGs profiles of various vegetables and the soil they are grown. The results indicate significant differences in the accumulation of ARGs among different vegetables harvested in the same area at the same time frame, and the ARGs accumulation ability of the three vegetables was in the order of broccoli, broad bean, and pumpkin. In addition, broccoli collected the highest number of ARGs in types (n = 14), while pumpkin (n = 13) does not obtain trimethoprim resistance genes and broad beans (n = 10) do not obtain chloramphenicol, fosmidomycin, quinolone, rifamycin, or trimethoprim resistance genes. Host tracking analysis shows a strong positive correlation (|rho| > 0.8, p < 0.05) between enriched ARGs and plant companion microbes. Enrichment analysis of metabolic pathways of companion microbes shows that vegetables exhibit a discernible enrichment of companion microbes, with significant differences among vegetables. This phenomenon is primarily due to the screening of carbohydrate metabolism capabilities among companion microbes and leads varied patterns of ARGs that spread from the soil to vegetables. This offers a novel insight into the intervention of foodborne transmission of ARGs.

Visualizing and quantifying 33P uptake and translocation by maize plants grown in soil

Phosphorus (P) availability severely limits plant growth due to its immobility and inaccessibility in soils. Yet, visualization and measurements of P uptake from different root types or regions in soil are methodologically challenging. Here, we explored the potential of phosphor imaging combined with local injection of radioactive 33P to quantitatively visualize P uptake and translocation along roots of maize grown in soils. Rhizoboxes (20 × 40 × 1 cm) were filled with sandy field soil or quartz sand, with one maize plant per box. Soil compartments were created using a gravel layer to restrict P transfer. After 2 weeks, a compartment with the tip region of a seminal root was labeled with a NaH2 33PO4 solution containing 12 MBq of 33P. Phosphor imaging captured root P distribution at 45 min, 90 min, 135 min, 180 min, and 24 h post-labeling. After harvest, 33P levels in roots and shoots were quantified. 33P uptake exhibited a 50% increase in quartz sand compared to sandy soil, likely attributed to higher P adsorption to the sandy soil matrix than to quartz sand. Notably, only 60% of the absorbed 33P was translocated to the shoot, with the remaining 40% directed to growing root tips of lateral or seminal roots. Phosphor imaging unveiled a continuous rise in 33P signal in the labeled seminal root from immediate post-labeling until 24 h after labeling. The highest 33P activities were concentrated just above the labeled compartment, diminishing in locations farther away. Emerging laterals from the labeled root served as strong sinks for 33P, while a portion was also transported to other seminal roots. Our study quantitatively visualized 33P uptake and translocation dynamics, facilitating future investigations into diverse root regions/types and varying plant growth conditions. This improves our understanding of the significance of different P sources for plant nutrition and potentially enhances models of plant P uptake.

Tradeoffs among root functional traits for phosphorus acquisition in 13 soybean genotypes contrasting in mycorrhizal colonization

BACKGROUND AND AIMS

Plants have adapted to acquire phosphorus (P) primarily through advantageous root morphologies, responsive physiological pathways and associations with mycorrhizal fungi. Yet, to date, little information exists on how variation in arbuscular mycorrhizal (AM) colonization is coordinated with root morphological and physiological traits to enhance P acquisition.

METHODS

Thirteen root functional traits associated with P acquisition were characterized at full bloom stage in pot cultures under low soil P availability conditions for 13 soybean genotypes contrasting in AM colonization.

KEY RESULTS

Significant variation in root functional traits was observed in response to low P stress among the 13 tested soybean genotypes contrasting in AM colonization. Genotypes with low AM colonization exhibited greater root proliferation but with less advantageous root physiological characteristics for P acquisition. In contrast, genotypes with high AM colonization exhibited less root growth but higher phosphatase activities and carboxylate content in the rhizosheath. Root dry weights, and contents of carbon and P were positively correlated with root morphological traits of different root orders and whole root systems, and were negatively correlated with AM colonization of fine roots and whole root systems, as well as rhizosheath phosphatase activities and carboxylate contents. These results taken in combination with a significant positive correlation between plant P content and root morphological traits indicate that root morphological traits play a primary role in soybean P acquisition.

CONCLUSIONS

The results suggest that efficient P acquisition involves tradeoffs among carbon allocation to root proliferation, mycorrhizal symbiosis or P-mobilizing exudation. Complementarity and complexity in the selection of P acquisition strategies was notable among soybean genotypes contrasting in AM colonization, which is closely related to plant C budgeting.

Sulfur enhances iron plaque formation and stress resistance to reduce the transfer of Cd and As in the soil-rice system

Sulfur plays an essential role in agricultural production, but few studies have been reported on how sulfur simultaneously impacts the transformation of cadmium (Cd) and arsenic (As) in the soil-rice system. This research selected two soils co-contaminated with both Cd and As, varying in acidity and alkalinity levels, to study the impacts of elemental sulfur (S) and calcium sulfate (CaSO4) on the migration and accumulation of Cd and As by rice. Results indicated that two types of sulfur had a substantial (P < 0.05) impact on decreasing the contents of Cd (28.3-50.4 %) and As (20.1-38.6 %) in brown rice in acidic and alkaline soils. They also increased rice biomass (29.3-112.8 %) and reduced Cd transport coefficient (27.2-45.6 %) significantly (P < 0.05). Notably, sulfur augmented the generation of iron plaque on rice root surfaces, which increased the fixation of Cd (17.6-61.0 %) and As (14.0-45.9 %). SEM-EDS results also indicated that the rice root surface exhibited significant enrichment of Fe, Cd, and As. The mechanism of simultaneous Cd and As immobilization by sulfur application was mainly ascribed to the contribution of iron plaque. Additionally, sulfur reduced the contents of Cd and As in soil porewater and promoted the transformation of As(III) to As(V) to reduce the toxicity of As. The K-edge XAFS of As in iron plaque also confirmed that sulfur application significantly promoted As(III) oxidation. Sulfur also promoted the activities of antioxidant enzymes and the contents of NPT, GSH, and PCs in rice plants. In general, this study establishes a foundation for sulfur to lower As and Cd bioavailability in paddy soils, enhance iron plaque and rice resistance, and reduce heavy metal accumulation.

Salt marsh nitrogen cycling: where land meets sea

Salt marshes sit at the terrestrial-aquatic interface of oceans around the world. Unique features of salt marshes that differentiate them from their upland or offshore counterparts include high rates of primary production from vascular plants and saturated saline soils that lead to sharp redox gradients and a diversity of electron acceptors and donors. Moreover, the dynamic nature of root oxygen loss and tidal forcing leads to unique biogeochemical conditions that promote nitrogen cycling. Here, we highlight recent advances in our understanding of key nitrogen cycling processes in salt marshes and discuss areas where additional research is needed to better predict how salt marsh N cycling will respond to future environmental change.

Root Exudates Metabolic Profiling Confirms Distinct Defense Mechanisms Between Cultivars and Treatments with Beneficial Microorganisms and Phosphonate Salts Against Verticillium Wilt in Olive Trees

Root exudates play a key role in the life cycle of Verticillium dahliae, the causal agent of Verticillium wilt diseases, because they induce microsclerotia germination to initiate plant infection through the roots. In olive plants, the genotype and the application of biological control agents (BCAs) or phosphonate salts influence the ability of root exudates to decrease V. dahliae viability. Understanding the chemical composition of root exudates could provide new insights into the mechanisms of olive plant defense against V. dahliae. Therefore, the main goal of this study was to analyze the metabolomic profiles of root exudates collected from the olive cultivars Arbequina, Frantoio, and Picual subjected to treatment with BCAs (Aureobasidium pullulans AP08, Bacillus amyloliquefaciens PAB-024) or phosphonate salts (copper phosphite, potassium phosphite). These treatments were selected due to their effectiveness as inducers of resistance against Verticillium wilt in olive plants. Our metabolomic analysis revealed that the olive cultivars exhibited differences in root exudates, which could be related to the different degrees of susceptibility to V. dahliae. The composition of root exudates also changed with the application of BCAs or phosphonate fertilizer, highlighting the complex and dynamic nature of the interactions between olive cultivars and treatments preventing V. dahliae infections. Thus, the identification of genotype-specific metabolic changes and specific metabolites induced by these treatments emphasizes the potential of resistance inducers for enhancing plant defense and promoting the growth of beneficial microorganisms.

Developing stable, simplified, functional consortia from Brachypodium rhizosphere for microbial application in sustainable agriculture

The rhizosphere microbiome plays a crucial role in supporting plant productivity and ecosystem functioning by regulating nutrient cycling, soil integrity, and carbon storage. However, deciphering the intricate interplay between microbial relationships within the rhizosphere is challenging due to the overwhelming taxonomic and functional diversity. Here we present our systematic design framework built on microbial colocalization and microbial interaction, toward successful assembly of multiple rhizosphere-derived Reduced Complexity Consortia (RCC). We enriched co-localized microbes from Brachypodium roots grown in field soil with carbon substrates mimicking Brachypodium root exudates, generating 768 enrichments. By transferring the enrichments every 3 or 7 days for 10 generations, we developed both fast and slow-growing reduced complexity microbial communities. Most carbon substrates led to highly stable RCC just after a few transfers. 16S rRNA gene amplicon analysis revealed distinct community compositions based on inoculum and carbon source, with complex carbon enriching slow growing yet functionally important soil taxa like Acidobacteria and Verrucomicrobia. Network analysis showed that microbial consortia, whether differentiated by growth rate (fast vs. slow) or by succession (across generations), had significantly different network centralities. Besides, the keystone taxa identified within these networks belong to genera with plant growth-promoting traits, underscoring their critical function in shaping rhizospheric microbiome networks. Furthermore, tested consortia demonstrated high stability and reproducibility, assuring successful revival from glycerol stocks for long-term viability and use. Our study represents a significant step toward developing a framework for assembling rhizosphere consortia based on microbial colocalization and interaction, with future implications for sustainable agriculture and environmental management.

Root exudates and rhizosphere microbiota in responding to long-term continuous cropping of tobacco

Soil sickness a severe problem in tobacco production, leading to soil-borne diseases and reduce in tobacco yield. This occurs as a result of the interaction between root exudates and rhizosphere microorganisms, which is however, little studied until now. By combining the field investigation and pot experiment, we found the output yield consistently decreased during the first 10 years of continuous cropping in a tobacco field, but increased at the 15th year (15Y). The root exudate and rhizosphere bacterial community was further analyzed to reveal the underlying mechanism of the suppressive soil formation. Root exudate of 15Y tobacco enriched in amino acids and derivatives, while depleted in the typical autotoxins including phenolic acids and alkaloids. This was correlated to the low microbial diversity in 15Y, but also the changes in community composition and topological properties of the co-occurrence network. Especially, the reduced autotoxins were associated with low Actinobacteria abundance, low network complexity and high network modularity, which significantly correlated with the recovered output yield in 15Y. This study revealed the coevolution of rhizosphere microbiota and root exudate as the soil domesticated by continuous cropping of tobacco, and indicated a potential role of the autotoxins and theirs effect on the microbial community in the formation of suppressive soil.

The rhizosphere microbiome and its influence on the accumulation of metabolites in Bletilla striata (Thunb.) Reichb. f

BACKGROUND

Bletilla striata (Thunb.) Reichb. f. (B. striata) is a perennial herbaceous plant in the Orchidaceae family known for its diverse pharmacological activities, such as promoting wound healing, hemostasis, anti-inflammatory effects, antioxidant properties, and immune regulation. Nevertheless, the microbe-plant-metabolite regulation patterns for B. striata remain largely undetermined, especially in the field of rhizosphere microbes. To elucidate the interrelationships between soil physics and chemistry and rhizosphere microbes and metabolites, a comprehensive approach combining metagenome analysis and targeted metabolomics was employed to investigate the rhizosphere soil and tubers from four provinces and eight production areas in China.

RESULTS

Our study reveals that the core rhizosphere microbiome of B. striata is predominantly comprised of Paraburkholderia, Methylibium, Bradyrhizobium, Chitinophaga, and Mycobacterium. These microbial species are recognized as potentially beneficial for plants health. Comprehensive analysis revealed a significant association between the accumulation of metabolites, such as militarine and polysaccharides in B. striata and the composition of rhizosphere microbes at the genus level. Furthermore, we found that the soil environment indirectly influenced the metabolite profile of B. striata by affecting the composition of rhizosphere microbes. Notably, our research identifies soil organic carbon as a primary driving factor influencing metabolite accumulation in B. striata.

CONCLUSION

Our fndings contribute to an enhanced understanding of the comprehensive regulatory mechanism involving microbe-plant-metabolite interactions. This research provides a theoretical basis for the cultivation of high-quality traditional Chinese medicine B. striata.

Sex Pheromone Receptor Ste2 Orchestrates Chemotropic Growth towards Pine Root Extracts in the Pitch Canker Pathogen Fusarium circinatum

In ascomycetous fungi, sexual mate recognition requires interaction of the Ste2 receptor protein produced by one partner with the α-factor peptide pheromone produced by the other partner. In some fungi, Ste2 is further needed for chemotropism towards plant roots to allow for subsequent infection and colonization. Here, we investigated whether this is also true for the pine pitch canker fungus, Fusarium circinatum, which is a devastating pathogen of pine globally. Ste2 knockout mutants were generated for two opposite mating-type isolates, after which all strains were subjected to chemotropism assays involving exudates from pine seedling roots and synthetic α-factor pheromone, as well as a range of other compounds for comparison. Our data show that Ste2 is not required for chemotropism towards any of these other compounds, but, in both wild-type strains, Ste2 deletion resulted in the loss of chemotropism towards pine root exudate. Also, irrespective of mating type, both wild-type strains displayed positive chemotropism towards α-factor pheromone, which was substantially reduced in the deletion mutants and not the complementation mutants. Taken together, these findings suggest that Ste2 likely has a key role during the infection of pine roots in production nurseries. Our study also provides a strong foundation for exploring the role of self-produced and mate-produced α-factor pheromone in the growth and overall biology of the pitch canker pathogen.

Analysis of small-scale soil CO2 fluxes in an orange orchard under irrigation and soil conservative practices

The quantification of soil carbon dioxide (CO2) flux represents an indicator of the agro-ecosystems sustainability. However, the monitoring of these fluxes is quite challenging due to their high spatially-temporally variability and dependence on environmental variables and soil management practices.In this study, soil CO2 fluxes were measured using a low-cost accumulation chamber, that was realized ad hoc for the surveys, in an orange orchard managed under different soil management (SM, bare versus mulched soils) and water regime (WR, full irrigation versus regulated deficit irrigation) strategies. In particular, the soil CO2 flux measurements were acquired in discontinuous and continuous modes, together with ancillary agrometeorological and soil-related information, and then compared to the agrosystem scale CO2 fluxes measured by the eddy covariance (EC) technique.Overall significant differences were obtained for the soil CO2 discontinuous fluxes as function of the WR (0.16 ± 0.01 and 0.14 ± 0.01 mg m-2 s-1 under full irrigation and regulated deficit irrigation, respectively). For the continuous soil CO2 measurements, the response observed for the SM factor varied from year to year, indicating for the overall reference period 2022-23 higher soil CO2 flux under the mulched soils (0.24 ± 0.01 mg m-2 s-1) than under bare soil conditions (0.15 ± 0.00 mg m-2 s-1). Inter-annual variations were also observed as function of the day-of-year (DOY), the SM and their interactions, resulting in higher soil CO2 flux under the mulched soils (0.24 ± 0.02 mg m-2 s-1) than under bare soil (0.15 ± 0.01 mg m-2 s-1) in certain periods of the years, according to the environmental conditions.

Results

suggest the importance of integrating soil CO2 flux measurements with ancillary variables that explain the variability of the agrosystem and the need to conduct the measurements using different operational modalities, also providing for night-time monitoring of CO2. In addition, the study underlines that the small-scale chamber measurements can be used to estimate soil CO2 fluxes at orchard scale if fluxes are properly scaled.

Metagenomic evaluation of peanut rhizosphere microbiome from the farms of Saurashtra regions of Gujarat, India

The narrow zone of soil around the plant roots with maximum microbial activity termed as rhizosphere. Rhizospheric bacteria promote the plant growth directly or indirectly by providing the nutrients and producing antimicrobial compounds. In this study, the rhizospheric microbiota of peanut plants was characterized from different farms using an Illumina-based partial 16S rRNA gene sequencing to evaluate microbial diversity and identify the core microbiome through culture-independent (CI) approach. Further, all rhizospheric bacteria that could grow on various nutrient media were identified, and the diversity of those microbes through culture-dependent method (CD) was then directly compared with their CI counterparts. The microbial population profiles showed a significant correlation with organic carbon and concentration of phosphate, manganese, and potassium in the rhizospheric soil. Genera like Sphingomicrobium, Actinoplanes, Aureimonas _A, Chryseobacterium, members from Sphingomonadaceae, Burkholderiaceae, Pseudomonadaceae, Enterobacteriaceae family, and Bacilli class were found in the core microbiome of peanut plants. As expected, the current study demonstrated more bacterial diversity in the CI method. However, a higher number of sequence variants were exclusively present in the CD approach compared to the number of sequence variants shared between both approaches. These CD-exclusive variants belonged to organisms that are more typically found in soil. Overall, this study portrayed the changes in the rhizospheric microbiota of peanuts in different rhizospheric soil and environmental conditions and gave an idea about core microbiome of peanut plant and comparative bacterial diversity identified through both approaches.

Acid rain reduced soil carbon emissions and increased the temperature sensitivity of soil respiration: A comprehensive meta-analysis

Soil respiration the second-largest carbon flux in terrestrial ecosystems, has been extensively studied across a wide range of biomes. Surprisingly, no consensus exist on how acid rain (AR) impacts the spatiotemporal pattern of soil respiration. Therefore, we conducted a meta-analysis using 318 soil respiration and 263 soil respiration temperature sensitivity (Q10) data points obtained from 48 studies to assess the impact of AR on soil respiration components and their Q10. The results showed that AR reduced soil total respiration (Rt) and soil autotrophic respiration (Ra) by 7.41 % and 20.75 %, respectively. As the H+ input increased, the response rates of Ra to AR (RR-Ra) and soil heterotrophic respiration (Rh) to AR (RR-Rh) decreased and increased, respectively. With increased AR duration, the RR-Ra increased, whereas the RR-Rh did not change. AR increased the Q10 of Rt (Rt-Q10) and Rh (Rh-Q10) by 1.92 % and 9.47 %, respectively, and decreased the Q10 of Ra (Ra-Q10) by 2.77 %. Increased mean annual temperature, mean annual precipitation, and initial soil organic carbon increased the response rate of Ra-Q10 to AR (RR-Ra-Q10) and decreased the response rate of Rh-Q10 to AR (RR-Rh-Q10). However, as the AR frequency and initial soil pH increased, both RR-Ra-Q10 and RR-Rh-Q10 also increased. In summary, AR decreased Rt but increased Q10, likely due to soil acidification (soil pH decreased by 7.84 %), reducing plant root biomass (decreased by 5.67 %) and soil microbial biomass (decreased by 5.67 %), changing microbial communities (increased fungi to bacteria ratio of 15.91 %), and regulated by climate, vegetation, soil and AR regimes. To the best of our knowledge, this is the first study to reveal the large-scale, varied response patterns of soil respiration components and their Q10 to AR. It highlights the importance of applying the reductionism theory in soil respiration research to enhance our understanding of soil carbon cycling processes with in the context of global climate change.

Rhizosphere metabolic cross-talk from plant-soil-microbe tapping into agricultural sustainability: Current advance and perspectives

Rhizosphere interactions from plant-soil-microbiome occur dynamically all the time in the "black microzone" underground, where we can't see intuitively. Rhizosphere metabolites including root exudates and microbial metabolites act as various chemical signalings involving in rhizosphere interactions, and play vital roles on plant growth, development, disease suppression and resistance to stress conditions as well as proper soil health. Although rhizosphere metabolites are a mixture from plant roots and soil microbes, they often are discussed alone. As a rapid appearance of various omics platforms and analytical methods, it offers possibilities and opportunities for exploring rhizosphere interactions in unprecedented breadth and depth. However, our comprehensive understanding about the fine-tuning mechanisms of rhizosphere interactions mediated by these chemical compounds still remain clear. Thus, this review summarizes recent advances systemically including the features of rhizosphere metabolites and their effects on rhizosphere ecosystem, and looks forward to the future research perspectives, which contributes to facilitating better understanding of biochemical communications belowground and helping identify novel rhizosphere metabolites. We also address challenges for promoting the understanding about the roles of rhizosphere metabolites in different environmental stresses.

Two diversities meet in the rhizosphere: root specialized metabolites and microbiome

Plants serve as rich repositories of diverse chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes, including interactions with various microbes both beneficial and harmful. Considering microbes as bioreactors, the chemical diversity undergoes dynamic changes when root-derived specialized metabolites (RSMs) and microbes encounter each other in the rhizosphere. Recent advancements in sequencing techniques and molecular biology tools have not only accelerated the elucidation of biosynthetic pathways of RSMs but also unveiled the significance of RSMs in plant-microbe interactions. In this review, we provide a comprehensive description of the effects of RSMs on microbe assembly in the rhizosphere and the influence of corresponding microbial changes on plant health, incorporating the most up-to-date information available. Additionally, we highlight open questions that remain for a deeper understanding of and harnessing the potential of RSM-microbe interactions to enhance plant adaptation to the environment. Finally, we propose a pipeline for investigating the intricate associations between root exometabolites and the rhizomicrobiome.

Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress

The root-associated microbiota plays an important role in the response to environmental stress. However, the underlying mechanisms controlling the interaction between salt-stressed plants and microbiota are poorly understood. Here, by focusing on a salt-tolerant plant wild soybean (Glycine soja), we demonstrate that highly conserved microbes dominated by Pseudomonas are enriched in the root and rhizosphere microbiota of salt-stressed plant. Two corresponding Pseudomonas isolates are confirmed to enhance the salt tolerance of wild soybean. Shotgun metagenomic and metatranscriptomic sequencing reveal that motility-associated genes, mainly chemotaxis and flagellar assembly, are significantly enriched and expressed in salt-treated samples. We further find that roots of salt stressed plants secreted purines, especially xanthine, which induce motility of the Pseudomonas isolates. Moreover, exogenous application for xanthine to non-stressed plants results in Pseudomonas enrichment, reproducing the microbiota shift in salt-stressed root. Finally, Pseudomonas mutant analysis shows that the motility related gene cheW is required for chemotaxis toward xanthine and for enhancing plant salt tolerance. Our study proposes that wild soybean recruits beneficial Pseudomonas species by exudating key metabolites (i.e., purine) against salt stress.

The characteristics of fungal responses to uranium mining activities and analysis of their tolerance to uranium

The influence of uranium (U) mining on the fungal diversity (FD) and communities (FC) structure was investigated in this work. Our results revealed that soil FC richness and FD indicators obviously decreased due to U, such as Chao1, observed OTUs and Shannon index (P<0.05). Moreover, the abundances of Mortierella, Gibberella, and Tetracladium were notably reduced in soil samples owing to U mining activities (P<0.05). In contrast, the abundances of Cadophora, Pseudogymnoascus, Mucor, and Sporormiella increased in all soil samples after U mining (P<0.05). Furthermore, U mining not only dramatically influenced the Plant_Pathogen guild and Saprotroph and Pathotroph modes (P<0.05), but also induced the differentiation of soil FC and the enrichment of the Animal_Pathogen-Soil_Saprotroph and Endophyte guilds and Symbiotroph and Pathotroph Saprotroph trophic modes. In addition, various fungal populations and guilds were enriched to deal with the external stresses caused by U mining in different U mining areas and soil depths (P<0.05). Finally, nine U-tolerant fungi were isolated and identified with a minimum inhibitory concentration range of 400-600 mg/L, and their adsorption efficiency for U ranged from 11.6% to 37.9%. This study provides insights into the impact of U mining on soil fungal stability and the response of fungi to U mining activities, as well as aids in the screening of fungal strains that can be used to promote remediation of U mining sites on plateaus.