Cadmium phytoavailability from 1976 through 2016: Changes in soil amended with phosphate fertilizer and compost

The interplay between antimicrobial resistance, heavy metal pollution, and the role of microplastics

Environmental pollution with heavy metals (HMs) and microplastics (MPs) could enhance the global health challenge antimicrobial resistance (AMR). Herein, we explore the complicated mechanics of how HMs, MPs, and AMR are interlinked within microbial ecosystems, as well as the co-selection and cross-resistance mechanisms. Unlike antibiotics, HMs have influenced microbial evolution for billions of years, promoting resistance mechanisms that predate antibiotic resistance genes (ARGs). At the same time, this conundrum is further complicated by the pervasive spread of MPs in the aquatic and terrestrial environments, acting as substrates for bacterial pathogenic biofilms and accelerates the horizontal gene transfer (HGT) of ARGs and heavy metal resistance genes (MRGs). This review highlights that HMs such as lead (Pb), mercury (Hg), arsenic (As), chromium (Cr), cadmium (Cd), and nickel (Ni) have persistently selected for resistance traits through efflux systems and genetic co-regulation. Together, these interactions are amplified by MPs that create genetic exchange hotspots due to biofilm formation. These dynamics are modulated by organic matter, which serves both as a nutrient source and a mediator of HM bioavailability, directly influencing ARG abundance. Soil and water ecosystems, including riverine systems and landfill leachate, are reservoirs for ARGs and ARG-MRG combinations, with notable contributions originating from anthropogenic activities. This review also emphasizes the urgent need for integrated environmental and public health strategies to mitigate pollutant-driven AMR. This work seeks to approach HMs and MPs as synergistic drivers of AMR such that both HMs and MPs are upstream (causes) levers, a foundation from which future research on sustainable environmental management practices and health policy (One Health Approach), aimed at curbing the spread of resistance determinants can proceed.

Transcriptomic and metabolomic analysis of recalcitrant phosphorus solubilization mechanisms in Trametes gibbosa

Introduction

Phosphorus (P) is a crucial growth-limiting nutrient in soil, much of which remains challenging for plants to absorb and use. Unlike chemical phosphate fertilizers, phosphate-solubilizing microorganisms (PSMs) offer a means to address available phosphorus deficiency without causing environmental harm. PSMs possess multiple mechanisms for phosphorus solubilization. Although the phosphorus-solubilizing mechanisms of phosphate-solubilizing bacteria (PSB) have been well characterized, the mechanisms utilized by phosphate-solubilizing fungi (PSF) remain largely unexplored.

Methods

This study isolated a PSF strain, Trametes gibbosa T-41, from soil and evaluated its phosphorus solubilizing capacity with organic (calcium phytin; Phytin-P) and inorganic (tricalcium phosphate; Ca-P) phosphorus sources. The phosphorus solubilization, enzyme activity, and organic acid production of T-41 were measured. And the P-solubilizing mechanism conducted by transcriptomic and metabolomic analyses.

Results and discussion

T-41 exhibited varying phosphorus solubilizing capacity when grown with organic (calcium phytin; Phytin-P) and inorganic (tricalcium phosphate; Ca-P) phosphorus sources (109.80 ± 8.9 mg/L vs. 57.5 ± 7.9 mg/L, p < 0.05). Compared with the Ca-P treatment, T-41 demonstrated a stronger alkaline phosphatase (ALP) production capacity under Phytin-P treatment (34.5 ± 1.2 μmol/L/h vs. 19.8 ± 0.8 μmol/L/h, p < 0.05). Meanwhile, the production of oxalic acid, maleic acid, and succinic acid was higher under Phytin-P treatment (p < 0.05). Transcriptomic and metabolomic analysis revealed that different phosphorus sources altered metabolic pathways such as galactose metabolism, glyoxylate and dicarboxylic acid metabolism, and ascorbate and aldolate metabolism. Key metabolites like myo-inositol, 2-oxoglutarate, and pyruvate were found to impact the performance of T. gibbosa T-41 differently under the two P sources. Notably, synthesis in Ca-P vs. Pytin-P, T-41 upregulated genes involved in myo-inositol synthesis, potentially enhancing its P-solubilizing ability. These results provide new insights into the molecular mechanisms of PSF at the transcriptomic and metabolomic levels, laying a theoretical foundation for the broader application of PSF as bio-phosphorus fertilizers in the future.

Unveiling the Rising Threat of Cadmium Pollution and Alarming Health Risks Associated with the Consumption of 15 Commercially Important Fish Species in the Middle Stretch of River Ganga, at Patna, India

Among environmental contaminants, the rising level of cadmium in freshwater ecosystems is one of the most significant global concerns. The study addresses the current pollution status of cadmium in the middle stretch of River Ganga and explores the potential hazard associated with the consumption of 15 commercially important fish species by the inhabitants. Together 72 water and sediment samples were analyzed from the four representative sampling sites of River Ganga after the surveillance of major anthropogenic stressors. The concentration of cadmium ranges from 0.003 to 0.011 mg/l and 0.2 to 3.48 mg/kg in water and sediment respectively in 2022. The average concentration of cadmium was recorded to be the highest in Channa punctatus (1.35 mg/kg), followed by Rita rita = Johnius coitor (1.15 mg/kg), and the lowest in Labeo bata (0.2 mg/kg). The finding highlights greater exposure duration and feeding preferences of fish species have played a significant role in the bioaccumulation of the metal in the riverine system. Notably, the domestic effluents, agricultural runoffs, and pollutants brought along by the tributaries of River Ganga are identified as the main anthropogenic stressors for the moderate to considerably polluted status of the River Ganga. The target hazard quotient (THQ) and target carcinogenic risk (TCR) have revealed a higher susceptibility to cadmium contamination in children followed by females, and males. In addition, hierarchical cluster analysis (HCA) has noted intake of Rita rita, Channa punctata, Puntius sophore, and Johnius coitor could be more detrimental to children's health than adults.

Arsenic, cadmium, and chromium concentrations in contrasting phosphate fertilizers and their bioaccumulation by crops: Towards a green label?

Potentially toxic elements such as arsenic (As), cadmium (Cd), and chromium (Cr) are severely regulated in fertilizers and deserve continuous investigation. Phosphate-derived Cd has been a stepping-stone toward achieving sustainable and safe worldwide food production, especially after a new regulation aiming for reduced limits of Cd in P fertilizers (EU, 2019/1009). Three pot experiments were conducted to assess the variability of As, Cd, and Cr concentrations - with a particular focus on Cd - from monoammonium phosphates (MAP 1, MAP 2, and MAP 3 from different geographic origins) and their accumulation in limed and unlimed soils, and contrasting crops, representing staple food and significant sources of these elements for humans (i.e., potato, tobacco, and rice). A diverse array of sensitive techniques for trace elements determination were used to reveal the highest level of Cd of MAP 3 (20.71 mg kg-1 MAP), which loaded the highest amounts of this element to the soil matrix and solution, plant shoots, and xylem sap, contrasting with results for MAP 1 (0.87 mg kg-1 MAP), which has almost ten times less Cd than that required for low-Cd labeling of P fertilizers (≤20 mg Cd kg-1 P2O5). MAP 3 also had the highest Cr concentration (139.3 mg kg-1 MAP). Among crops, rice accumulated 16-fold less Cd than potato plants. Liming decreased Cd in tobacco and potato shoots up to 35%. Moreover, reductions of about 20% were also observed for Cd accumulation in tubers and sap. Conversely, Cd from MAP 3 was always much more accumulated in soil solution, achieving up to 20 μg L-1, while values < 5 μg L-1 (i.e., a groundwater limit) were obtained from MAP 1. Our findings may be used as a reference in developing green labels for fertilizers in scenarios where Cd accumulation represents a potential risk for soil and human health.

Effect of long-term application of pig slurry and NPK fertilizers on trace metal content in the soil

One of the goals of sustainable agricultural production is to avoid soil contamination by elements defined as trace metals (TMs). The aim of this study was to assess the long-term impact of the use of pig slurry (PS) and NPK mineral fertilizers on the soil content of cadmium (Cd), copper (Cu), lead (Pb) and zinc (Zn). In a 9-year crop rotation, PS was used three times only before root crops. The same four levels of NPK doses (N0P0K0, N1P1K1, N3P2K2, N4P2K2) were applied to both plots with and without PS. Soil samples were collected in early spring from topsoil (0-0.3 m) and subsoil (0.3-0.6 m). Three forms of TMs were determined in the soil: pseudo-total (Aqua regia); bioavailable (Mehlich 3 method) and readily bioavailable (mobile) forms (1 M NH4NO3). The tested factors did not have a significant impact on the Cd, Cu and Pb content, regardless of the form analyzed and the soil depth. PS application significantly increased the content of bioavailable forms of Zn regardless of the year, and the content of pseudo-total Zn only in the sugar beet year, i.e. after manure application. Increasing NPK doses increased the content of mobile Zn in the topsoil, especially in PS plots. A tendency to accumulate mobile forms of Cd and Pb was also observed on NPK-fertilized plots. Thus, long-term application of high NPK doses may increase the risk of contamination of the food chain with these metals. The content of mobile Cd and Zn was positively related to the content of total nitrogen in the soil and negatively related to pH.

The Level of Selected Metals in Made Tea and Tea Infusion from the Roadside Tea Plants and Health Risk Assessment

The effects of human activities are becoming clearer every year, with multiple reports of struggling and eroded ecosystems resulting in new threats of plant and animal extinctions throughout the world. It has been speculated that roadside tea-growing soils impact on metal dynamics from soil to tea plants and subsequently to tea infusion which may be threatened by increasingly unpredictable and dangerous surroundings. Furthermore, heavy metals released from vehicles on the national highway (NH) could be a source of metal contamination in roadside tea soils and tea plants. This study was articulated to realize the effect of NH on a buildup of selected metals (Cu, Cd, Fe, Mn, Ni, and Zn) in made tea along with repeated tea infusion. In general, metal concentration was found significantly higher in made tea prepared from the young shoots collected from the vicinity of NH. The results also showed that distance from the NH and infusion process significantly influenced to content of the analysed metal in tea infusions. The mean average daily intake (ADI) and hazard quotient (HQ) values of analysed tea samples were found in the orderMn˃Fe˃Zn˃Cu˃Ni˃Cd and Mn˃Cu˃Zn˃Fe˃Ni˃Cd, respectively. The HQ values of all analysed metals were found << 1, indicating that ingestion of tea infusion with analysed heavy metals should not cause a danger to human health. However, this study further demonstrates the consumption of tea infusion prepared from made tea around the vicinity of NH may contribute to a significantly higher quantity of metal intake in the human body. From the hierarchical cluster analysis, it has been observed that there are three homogenous groups of analysed heavy metals.

In silico identification and expression analyses of peroxidases in Tenebrio molitor

Human advancements in agriculture, urbanization, and industrialization have led to various forms of environmental pollution, including heavy metal pollution. Insects, as highly adaptable organisms, can survive under various environmental stresses, which induce oxidative damage and impair antioxidant systems. To investigate the peroxidase (POX) family in Tenebrio molitor, we characterized two POXs, namely TmPOX-iso1 and TmPOX-iso2. The full-length cDNA sequences of TmPox-iso1 and TmPox-iso2 respectively consisted of an open reading frame of 1815 bp encoding 605 amino acids and an open reading frame of 2229 bp encoding 743 amino acids. TmPOX-iso1 and TmPOX-iso2 homologs were found in five distinct insect orders. In the phylogenetic tree analysis, TmPOX-iso1 was clustered with the predicted POX protein of T. castaneum, and TmPOX-iso2 was clustered with the POX precursor protein of T. castaneum. During development, the highest expression level of TmPox-iso1 was observed in the pre-pupal stage, while that of TmPox-iso2 expression were observed in the pre-pupal and 4-day pupal stages. TmPox-iso1 was primarily expressed in the early and late larval gut, while TmPox-iso2 mRNA expression was higher in the fat bodies and Malpighian tubules. In response to cadmium chloride treatment, TmPox-iso1 expression increased at 3 hours and then declined until 24 hours, while in the zinc chloride-treated group, TmPox-iso1 expression peaked 24 hours after the treatment. Both treated groups showed increases in TmPox-iso2 expression 24 hours after the treatments.

Spatial and variety distributions, risk assessment, and prediction model for heavy metals in rice grains in China

In this study, 6229 brown rice grains from three major rice-producing regions were collected to investigate the spatial and variety distributions of heavy metals in rice grains in China. The potential sources of heavy metals in rice grains were identified using the Pearson correlation matrix and principal component analysis, and the health risks of dietary exposure to heavy metals via rice consumption were assessed using the hazard index (HI) and total carcinogenic risk (TCR) method, respectively. Moreover, 48 paired soil and rice samples from 11 cities were collected to construct a predicting model for Cd accumulation in rice grains using the multiple linear stepwise regression analysis. The results indicated that Cd and Ni were the main heavy metal pollutants in rice grains in China, with approximately 10% of samples exceeding their corresponding maximum allowable limits. The Yangtze River basin had heavier pollution of heavy metals than the Southeast Coastal Region and Northeast Plain, and the indica rice varieties had higher heavy metal accumulation abilities compared with the japonica rice. The Cu, Pb, and Cd mainly originated from anthropogenic sources, while As, Hg, Cr, and Ni originated from both natural and anthropogenic sources. The mean HI and TCR values of dietary exposure to heavy metals via rice consumption ranged from 2.92 to 4.31 and 9.74 × 10-3 to 1.44 × 10-2, respectively, much higher than the acceptable range, and As and Ni were the main contributor to the HI and TCR for Chinese adults and children, respectively. The available Si (ASi), total Cd (TCd), available Mo (AMo), and available S (AS) were the main soil factors determining grain Cd accumulation. A multiple linear stepwise regression model was constructed based on ASi, TCd, AMo, and AS in soils with good accuracy and precision, which could be applied to predict Cd accumulation in rice grains and guide safe rice production in contaminated paddy fields.

Investigation of the incidence of heavy metals contamination in commonly used fertilizers applied to vegetables, fish ponds, and human health risk assessments

Overuse of fertilizers on agricultural lands and fish ponds may result in serious pollution problems, such as heavy metals that can enter the food chain and pose serious health problems. Due to this, the present study investigates the incidence of heavy metals in commonly used fertilizers and its association with heavy metals in vegetables, soil, fish species, and pond water. Samples were collected from different sites (fields and ponds) in district Kohat, where the application of fertilizers was common and control groups (no fertilizers used). Heavy metal analysis was carried out through a spectrophotometer. Results showed higher Cd and Cr concentrations in triple superphosphate (TSP), Cu and Pb in nitrogen, phosphorus, and potassium (NPK), while lower concentrations were found in gypsum. In vegetables (onion, tomato, brinjal, and potato) and associated soil, most of the heavy metals concentrations were significantly higher (P < 0.05) in fertilizer-applied sites than in the control. Also, the Cd concentration in potatoes and Pb level in all vegetables obtained from sites were greater than the WHO/FAO standard limit. In the case of fish species (Hypophthalmichthys molitrix and Cyprinus carpio) muscles and their habitat (water), all the understudy heavy metals were notably higher (P < 0.05) in fertilizer-applied sites (ponds) than the control group. Collectively, in all vegetables and muscles of fish species, the bioaccumulation factor was higher in sites compared to the control. The estimated daily intake (EDI) and target hazard quotient (THQ) values were also higher in fertilizer-applied sites (fields and ponds) than control. The health index (HI) value was > 1 in vegetables (onion, tomato, and potato) and fish muscles collected from different sites compared to the control. Thus, there is the possibility of severe health risks. The use of fertilizers must be carefully monitored in order to ensure that humans and animals are safe from exposure to heavy metals.

A combined passivator of zeolite and calcium magnesium phosphate fertilizer: Passivation behavior and mechanism for Cd (II) in composting

Passivation of heavy metals is one of the most efficient techniques to improve the quality of compost. Many studies confirmed the passivation effect of passivators (e.g., zeolite and calcium magnesium phosphate fertilizer) on cadmium (Cd), but passivators with single component could not effectively passivate Cd in the long-term operation of composting. In the present study, a combined passivator of zeolite and calcium magnesium phosphate fertilizer (ZCP) was used to explore its impacts of adding at different composting periods (heating period, thermophilic period, cooling period) on the Cd control, compost quality (e.g., temperature, moisture content and humification), microbial community structure as well as the compost available forms of Cd and addition strategy of ZCP. Results showed that Cd passivation rate could be increased by 35.70-47.92% under all treatments in comparison to the control treatment. By altering bacterial community structure, reducing Cd bioavailability and improving the chemical properties of the compost, the combined inorganic passivator could achieve high efficiency for Cd passivation. To sum up, the addition of ZCP at different composting periods has effects on the process and quality of composting, which could provide ideas for the optimization of the passivators addition strategy.

Exogenous TiO2 Nanoparticles Alleviate Cd Toxicity by Reducing Cd Uptake and Regulating Plant Physiological Activity and Antioxidant Defense Systems in Rice (Oryza sativa L.)

Cadmium (Cd) is a potentially hazardous element with significant biological toxicity, negatively affecting plant growth and physio-biochemical metabolism. Thus, it is necessary to examine practical and eco-friendly approaches to reduce Cd toxicity. Titanium dioxide nanoparticles (TiO2-NPs) are growth regulators that help in nutrient uptake and improve plant defense systems against abiotic and biological stress. A pot experiment was performed in the late rice-growing season (July-November) 2022 to explore the role of TiO2-NPs in relieving Cd toxicity on leaf physiological activity, biochemical attributes, and plant antioxidant defense systems of two different fragrant rice cultivars, i.e., Xiangyaxiangzhan (XGZ) and Meixiangzhan-2 (MXZ-2). Both cultivars were cultivated under normal and Cd-stress conditions. Different doses of TiO2-NPs with and without Cd-stress conditions were studied. The treatment combinations were: Cd-, 0 mg/kg CdCl2·2.5 H2O; Cd+, 50 mg/kg CdCl2·2.5 H2O; Cd + NP1, 50 mg/kg Cd + 50 TiO2-NPs mg/L; Cd + NP2, 50 mg/kg Cd + 100 TiO2-NPs mg/L; Cd + NP3, 50 mg/kg Cd + 200 TiO2-NPs mg/L; Cd + NP4, 50 mg/kg Cd + 400 TiO2-NPs mg/L. Our results showed that the Cd stress significantly (p < 0.05) decreased leaf photosynthetic efficiency, stomatal traits, antioxidant enzyme activities, and the expression of their encoding genes and protein content. Moreover, Cd toxicity destabilized plant metabolism owing to greater accretion of hydrogen peroxide (H2O2) and malondialdehyde (MDA) levels at vegetative and reproductive stages. However, TiO2-NPs application improved leaf photosynthetic efficacy, stomatal traits, and protein and antioxidant enzyme activities under Cd toxicity. Application of TiO2-NPs decreased the uptake and accumulation of Cd in plants and levels of H2O2 and MDA, thereby helping to relieve Cd-induced peroxidation damage of leaf membrane lipids by enhancing the activities of different enzymes like ascorbate peroxidase (APX), catalase (CAT), peroxidase (POS), and superoxide dismutase (SOD). Average increases in SOD, APX, CAT, and POS activities of 120.5 and 110.4%, 116.2 and 123.4%, 41.4 and 43.8%, and 36.6 and 34.2% in MXZ-2 and XGZ, respectively, were noted in Cd + NP3 treatment across the growth stages as compared with Cd-stressed plants without NPs. Moreover, the correlation analysis revealed that the leaf net photosynthetic rate is strongly associated with leaf proline and soluble protein content, suggesting that a higher net photosynthetic rate results in higher leaf proline and soluble protein content. Of the treatments, the Cd + NP3 (50 mg/kg Cd + 200 mg/L TiO2-NPs) performed the best for both fragrant rice cultivars under Cd toxicity. Our results showed that TiO2-NPs strengthened rice metabolism through an enhanced antioxidant defense system across the growth stages, thereby improving plant physiological activity and biochemical characteristics under Cd toxicity.

Co-application of combined amendment (limestone and sepiolite) and Si fertilizer reduces rice Cd uptake and transport through Cd immobilization and Si-Cd antagonism

Limestone and sepiolite combined amendment (LS) and silicon (Si) fertilizers are commonly applied for the remediation of Cd-polluted paddy soil. However, it is difficult to further decrease cadmium (Cd) accumulation in rice grains by the individual application of LS or Si fertilizer to heavily Cd-polluted paddy fields. Two seasons of continuous field experiments were conducted in heavily Cd-polluted soil to study how the co-application of LS and Si fertilizer (namely soil-applied Si and foliar-sprayed Si) influences Cd and Si bioavailability in soil and Cd uptake and transport in rice. The results indicated that LS co-applied with soil-applied Si fertilizer treatments can enhance pH, cation exchange capacity (CEC), and available Si content in soil by 0.56-1.26 units, 19.3%-57.2%, and 14.7%-58.9% (p < 0.05), respectively, and reduce the toxicity characteristic leaching procedure (TCLP) extractable Cd content in soil by 26.5%-49.8% (p < 0.05) relative to the control. Furthermore, the co-application of LS and soil and foliar-sprayed Si fertilizer treatments reduced the Cd content in brown rice by 18.8%-70.6% (p < 0.05) compared with the control. Particularly, the brown rice Cd content under the co-application treatment (4500 kg/ha of soil applied LS, 90 kg/ha of Si fertilizer, and 0.4 g/L of foliar-sprayed Si fertilizer) was below 0.20 mg/kg in both seasons. Meanwhile, the Si content in rice was considerably enhanced by LS co-applied with Si fertilizer and negatively (p < 0.05) correlated with the rice Cd content. Therefore, the reduction of Cd bioavailability in soil and the antagonistic effect between Cd and Si in rice might be the key factors regulating Cd accumulation in rice via the co-application of LS and Si fertilizer.

Deciphering Interactions between Phosphorus Status and Toxic Metal Exposure in Plants and Rhizospheres to Improve Crops Reared on Acid Soil

Acid soils are characterized by deficiencies in essential nutrient elements, oftentimes phosphorus (P), along with toxicities of metal elements, such as aluminum (Al), manganese (Mn), and cadmium (Cd), each of which significantly limits crop production. In recent years, impressive progress has been made in revealing mechanisms underlying tolerance to high concentrations of Al, Mn, and Cd. Phosphorus is an essential nutrient element that can alleviate exposure to potentially toxic levels of Al, Mn, and Cd. In this review, recent advances in elucidating the genes responsible for the uptake, translocation, and redistribution of Al, Mn, and Cd in plants are first summarized, as are descriptions of the mechanisms conferring resistance to these toxicities. Then, literature highlights information on interactions of P nutrition with Al, Mn, and Cd toxicities, particularly possible mechanisms driving P alleviation of these toxicities, along with potential applications for crop improvement on acid soils. The roles of plant phosphate (Pi) signaling and associated gene regulatory networks relevant for coping with Al, Mn, and Cd toxicities, are also discussed. To develop varieties adapted to acid soils, future work needs to further decipher involved signaling pathways and key regulatory elements, including roles fulfilled by intracellular Pi signaling. The development of new strategies for remediation of acid soils should integrate the mechanisms of these interactions between limiting factors in acid soils.

The high-dimensional geographic dataset revealed significant differences in the migration ability of cadmium from various sources in paddy fields

Cadmium (Cd) contamination in paddy fields and its subsequent transfer in soil-rice systems are of particular concern. Significant discrepancies exist in the transfer process of Cd pollution sources from soil to rice. Here, we proposed a novel hybrid framework to reveal the priority of controlling Cd pollution sources in soil-rice systems, based on a high-dimensional geographical database. We further defined transfer potential (TP) to describe the ability of Cd from soil to rice (TPr = Cdr/Cds) and activated status (TPa = Cda/Cds), respectively, to reveal the priority sources of Cd pollution at the regional scale. The mining source has both high levels of TPr and TPa, which should be a controlled priority. Followed by traffic sources with a higher value of TPr, showing the risk to rice rather than the soil. The activated and enriched capacities of soil Cd are unequal in different sources that we attribute to the disparities of Cd transport in soil-rice systems. Cd contamination shows a significant spatial heterogeneity due to the difference in its transport performance. Our findings provide support for designing site-specific and pollution-targeted control priorities for suitable Cd pollution mitigation strategies at the regional scale.

Contributions of Beneficial Microorganisms in Soil Remediation and Quality Improvement of Medicinal Plants

Medicinal plants (MPs) are important resources widely used in the treatment and prevention of diseases and have attracted much attention owing to their significant antiviral, anti-inflammatory, antioxidant and other activities. However, soil degradation, caused by continuous cropping, excessive chemical fertilizers and pesticide residues and heavy metal contamination, seriously restricts the growth and quality formation of MPs. Microorganisms, as the major biota in soil, play a critical role in the restoration of the land ecosystem. Rhizosphere microecology directly or indirectly affects the growth and development, metabolic regulation and active ingredient accumulation of MPs. Microbial resources, with the advantages of economic efficiency, harmless to environment and non-toxic to organisms, have been recommended as a promising alternative to conventional fertilizers and pesticides. The introduction of beneficial microbes promotes the adaptability of MPs to adversity stress by enhancing soil fertility, inhibiting pathogens and inducing systemic resistance. On the other hand, it can improve the medicinal quality by removing soil pollutants, reducing the absorption and accumulation of harmful substances and regulating the synthesis of secondary metabolites. The ecological and economic benefits of the soil microbiome in agricultural practices are increasingly recognized, but the current understanding of the interaction between soil conditions, root exudates and microbial communities and the mechanism of rhizosphere microecology affecting the secondary metabolism of MPs is still quite limited. More research is needed to investigate the effects of the microbiome on the growth and quality of different medicinal species. Therefore, the present review summarizes the main soil issues in medicinal plant cultivation, the functions of microbes in soil remediation and plant growth promotion and the potential mechanism to further guide the use of microbial resources to promote the ecological cultivation and sustainable development of MPs.

Transcriptome Profiling Analysis of Phosphate-Solubilizing Mechanism of Pseudomonas Strain W134

Phosphate-solubilizing bacteria (PSB) can alleviate available phosphorus deficiency without causing environmental pollution, unlike chemical phosphate fertilizers. However, the phosphate solubilization mechanisms of PSB are still unclear. Transcriptome sequencing was used to analyze the expression patterns of differential expressed genes (DEGs) of the phosphate-solubilizing bacterium W134 under the conditions of soluble phosphorus (group A), insoluble phosphorus (group B), and lacking phosphorus (group C). Nine DEGs in three different groups were detected by quantitative real-time polymerase chain reaction (qRT-PCR). Then, high performance liquid chromatography (HPLC) was applied to detect the concentrations and composition of organic acids. Compared with group A, Gene Ontology (GO) annotation showed that the cluster of W134 DEGs in groups B and C were basically the same. Besides, the results of enrichment Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway indicated that genes in the Citrate cycle (TCA cycle) pathway closely related to organic acid production were significantly upregulated. The qRT-PCR results were almost consistent with the expression trends of the transcriptome data. The HPLC results showed that the formic acid, ascorbic acid, acetic acid, citric acid, and succinic acid concentrations were significantly increased in group B and C (p < 0.05), while the contents of lactic acid and malic acid were significantly increased in group B (p < 0.05). The above results provided further validation that the upregulated genes should be related to W134 secretion of organic acids. Our study revealed several potential candidate genes and tried to explain phosphate solubilization mechanisms. This provides a new insight for calcareous reclaimed soil, and it will reduce the need of chemical phosphate fertilizers to promote environmentally friendly agriculture.

Dynamic Changes in Soil Phosphorus Accumulation and Bioavailability in Phosphorus-Contaminated Protected Fields

Soil phosphorus accumulation resulting in a high risk of phosphorus pollution is due to high multiple vegetable cropping indexes and excessive fertilizer input in protected fields. Therefore, this study explored the bioavailability of soil-accumulated phosphorus to improve fertilization and reduce the risk of soil phosphorus contamination in protected fields. A field trial was performed in Yanbian Prefecture, China to study the phosphorus bioavailability after continuous spinach planting without phosphate fertilizer applications. Results indicated that with increasing numbers of planting stubbles, soil inorganic phosphorus and occluded phosphorus changed little, while water-soluble and loose phosphorus, aluminum-phosphate, iron-phosphate, and calcium-phosphorus decreased first and then increased. Soil available phosphorus declined linearly. For planting spinach in protected fields, the threshold of soil phosphorus deficiency is 200 mg kg^-1. A soil phosphorus supply potential model was established between x (the soil available phosphorus) and y (the numbers of planting stubbles): y = 6.759 + 0.027x, R = 0.99, which can be used to predict how planting stubbles are needed to raise the soil available phosphorus above the critical value of phosphorus deficiency for spinach. These results will provide the theoretical guidance for rational phosphorus fertilizer applications and control agricultural, non-point pollution sources in protected fields.

Phosphorus Regulates the Level of Signaling Molecules in Rice to Reduce Cadmium Toxicity

Phosphorus treatment can reduce Cd accumulation and Cd toxicity in rice, but alterations in the internal regulatory network of rice during this process have rarely been reported. We have removed the effect of cadmium phosphate precipitation from the hydroponic system, treated a pair of different Cd-response rice varieties with different levels of phosphorus and cadmium and examined the changes in physiological indicators and regulatory networks. The results demonstrated that phosphorus treatment significantly reduced Cd accumulation in both types of rice, although the antioxidant systems within the two types of rice produced opposite responses. Overall, 3 mM phosphorus treatment to Cd-N decreased the expression of OsIAA17 and OsACO1 by 32% and 37%, respectively, while increasing the expression of OsNR2 by 83%; these three genes regulate the synthesis of auxin, ethylene, and nitric oxide in rice. IAA and NO levels in rice shoots increased by 24% and 96%, respectively, and these changes contribute to Cd detoxification. The cadmium transporter genes OsHMA2, OsIRT1, and OsABCC1 were significantly down-regulated in Cd-N roots after triple phosphorus treatment. These data suggest that phosphorus treatment can reduce Cd accumulation and enhance Cd resistance in rice by affecting the expression of signaling molecules.

Consistent inter-annual reduction of rice cadmium in 5-year biannual organic amendment

Organic fertilizers may contain cadmium (Cd) and the transformation of organic materials in soil also has a role in soil-plant Cd distribution, both of which lead to Cd accumulation in plant edible parts. However, the advisability of applying organic fertilizer to remediate soils that are moderately and slightly contaminated with Cd has not been clarified. In this study, we investigated the impacts of an organic amendment (chicken manure) on the Cd concentration in rice grains (Cd_R) and the soil chemical properties over a five year period (10 rice seasons) within a slightly contaminated paddy soil in Hunan Province, subtropical China. We found that the Cd_R was reduced by 28%-56% as a result of the organic amendment. The within-year reduction in Cd_R was higher in late rice (43%-56%, averaging 51%) than in early rice (28%-45%, averaging 38%); however, the inter-annual reduction in Cd_R was fairly stable (40%-49%), which suggests that chicken manure amendment has a long-term and persistent remediation potential. The concentrations of DTPA-extractable Cd and exchangeable plus water-soluble Cd fractions in soil were reduced, whereas soil pH and the concentrations of soil organic C and its labile fractions increased. These results indicate a lower apparent phytoavailability of Cd in soil following organic amendment. A two-variable empirical model using DTPA-Cd extracted from the soil at the full heading stage of rice and a climatic factor (total precipitation during the rice growing season) showed great potential in effectively predicting Cd_R. Our study suggests that Cd phytoavailability in soil (indexed by DTPA-extractable and exchangeable Cd) and climatic factors (such as temperature and precipitation) may control inter-annual reductions in Cd_R following organic amendment in slightly contaminated paddy soils.

Inter-annual reduction in rice Cd and its eco-environmental controls in 6-year biannual mineral amendment in subtropical double-rice cropping ecosystems

The alkaline mineral amendment is a practical means of alleviating Cd concentration in rice grain (Cd_R) in the short-term; however, the long-term remediation effect of mineral amendment on the Cd_R and the eco-environmental controls remains unknown. Here a mineral (Si-Ca-Mg) amendment, calcined primarily from molybdenum tailings and dolomite, was applied biannually over 6 years (12 seasons) to acidic and moderately Cd-contaminated double-rice cropping ecosystems. This study investigated the inter-annual variation of Cd in the rice-soil ecosystem and the eco-environmental controls in subtropical rice ecosystems. Cd_R was reduced by 50%-86% following mineral amendment. The within-year reduction in Cd_R was similar between early rice (50%-86%, mean of 68%) and late rice (68%-85%, mean of 74%), leading to Cd_R in all early rice and in 83% of late rice samples below the upper limit (0.2 mg kg^-1) of the China National Food Safety Standards. In contrast, the inter-annual reduction in Cd_R was moderately variable, showing a greater Cd_R reduction in the later 3 years (73%-86%) than in the former 3 years (54%-79%). Three years continuous mineral amendment was required to guarantee the safety rice production. The concentrations of DTPA-extractable and exchangeable Cd fractions in soil were reduced, while the concentration of oxides-bound Cd was increased. In addition, the soil pH, concentrations of Olsen-P and exchangeable Ca and Mg were elevated. These imply a lower apparent phytoavailability of Cd in the soil following mineral amendment. An empirical model of the 3-variable using soil DTPA-Cd, soil Olsen-P, and a climatic factor (precipitation) effectively predicted temporal changes in Cd_R. Our study demonstrates that Cd phytoavailability in soil (indexed by DTPA-extractable Cd) and climatic factors (e.g., temperature and precipitation) may directly/indirectly control the inter-annual reduction in Cd_R following mineral amendment in slightly and moderately Cd-contaminated paddy ecosystems.

Assessing the leaching of cadmium in an irrigated and grazed pasture soil

To decrease the concentration of the toxic metal cadmium (Cd) in topsoil, and the human food chain, many countries have limited the Cd concentration allowed in phosphorus (P) fertilisers. However, to inform those limits we need accurate estimates of Cd leaching from established farming systems. Different soil layers were sampled to 2000 mm depth of a long-term trial that had applied 22.5 kg P ha^-1 yr^-1 for 67 years to grazed pastures that received either no irrigation or were irrigated when soil moisture fell below 10 or 20%. The annual yield of Cd leaching from the top 150 mm of soil to the 151-250 mm layer was between 1.1 and 1.8 g ha^-1 with Cd leaching increasing with the frequency of irrigation. The rate of Cd accumulation measured to 2000 mm was within the mean and standard error estimated for treatments using a mass balance approach. Estimates of annual Cd leaching loss were like those established from field trials measuring leaching events over a year (0.3-1.8 g ha^-1) with a similar rate of P application (9-24 kg P ha^-1 yr^-1). Using a Cd leaching rate of 1.8 g ha^-1 yr^-1 and P applications rates of 22.5 kg P ha^-1, topsoil Cd concentrations may stop increasing if Cd concentrations in P fertiliser can be maintained at < 72 mg Cd kg^-1 P.

Multi-Omics Reveal the Efficient Phosphate-Solubilizing Mechanism of Bacteria on Rocky Soil

Phosphate-solubilizing bacteria (PSB) can alleviate available phosphorus (AP)-deficiency without causing environmental pollution like chemical phosphate fertilizers. However, the research and application of PSB on the barren rocky soil is very rare. We screened six PSB from sweetpotato rhizosphere rocky soil. Among them, Ochrobactrum haematophilum FP12 showed the highest P-solubilizing ability of 1,085.00 mg/L at 7 days, which was higher than that of the most reported PSB. The assembled genome of PSB FP12 was 4.92 Mb with P-solubilizing and plant growth-promoting genes. In an AP-deficient environment, according to transcriptome and metabolomics analysis, PSB FP12 upregulated genes involved in gluconic acid synthesis and the tricarboxylic acid cycle, and increased the concentration of gluconic acid and malic acid, which would result in the enhanced P-solubilizing ability. Moreover, a series of experiments in the laboratory and field confirmed the efficient role of the screened PSB on significantly increasing AP in the barren rocky soil and promoting sweetpotato yield. So, in this study, we screened highly efficient PSB, especially suitable for the barren rocky soil, and explored the P-solubilizing mechanism. The research will reduce the demand for chemical phosphate fertilizers and promote the environment-friendly agricultural development.

Azospirillum brasilense Az39 restricts cadmium entrance into wheat plants and mitigates cadmium stress

In this work, we tested if inoculation with the plant growth-promoting rhizobacteria Azospirillum brasilense strain Az39 alleviates Cd²⁺ stress in wheat seedlings grown under controlled conditions. Growth, total N, N-related metabolites/enzymes, and oxidative stress parameters were measured. Additionally, the usefulness of a real-time PCR protocol to screen the preferred colonization site of the introduced microorganism was evaluated. Inoculated plants demonstrated mitigation of cadmium-induced adverse effects on plant growth and less reactive oxygen species accumulation in their roots by the end of the experiment, 28 days after sowing. Cd addition resulted in lower NO₃^- content in the leaves and higher NO₃^- content in the roots, and a significant rise in NH₄⁺ concentration in both organs in uninoculated plants; in inoculated plants, NH₄⁺ content in the roots did not vary. A. brasilense Az39 enhanced NO levels in wheat root tips, and more adventitious roots and root hairs were observed in inoculated plants. Despite having a more developed root system, inoculated plants showed lower Cd levels in their roots compared to non-inoculated plants. Inoculation with this PGPR favored ion homeostasis in the roots of metal-exposed plants, decreasing Cd/Fe ratio. We corroborated A. brasilense Az39 preference for wheat exorhizosphere using a real-time PCR-based method targeting the nifA gene.

Effects of straw return with N fertilizer reduction on crop yield, plant diseases and pests and potential heavy metal risk in a Chinese rice paddy: A field study of 2 consecutive wheat-rice cycles

Understanding the comprehensive effect on crop production and quality, soil acidification, and Cd accumulation and distribution for wheat-rice rotation under N fertilization and continuous straw return is important for proper contaminated agricultural soil management. A 2-year paddy field experiment was conducted to study the effects of above factors change in the Zhejiang province, China. Fertilization treatments included: conventional N fertilizer application (N3), 20% reduction of N application (N2), 40% reduction of N application (N1), combined with three portions of straw incorporation: all straws retention (N3), half of the straws into the fields (S2), 20% straws retention(S1). The N1 treatments significantly decreased crop yields compared to N2 and N3 treatments. Except for C2-wheat, soil pH generally decreased with increasing N fertilizer input in the order of N1>N2>N3, regardless of how many straws was amended. Moreover, we found that straw addition plus N fertilization had a intersystem impacts on Cd accumulation, distribution and availability. Although total Cd had different trends among 4 experimental seasons, when the N reduced 20% applied, the DTPA-Cd contents were lowest among 3 out of four experimental seasons, except for that of C2-wheat, where N2 treatments ranked the second lower contents. For most seasons, Cd contents in straws were higher than soils and lowest in grains, and S2N2 treatment performed an intermediate value among all treatments. Furthermore, our study demonstrated that S2 or N2 treatments or S2N2 reduced the potential risk of plant diseases and pests with lower disease index, disease cluster rate. Notably, the relative outbreak of pests was remarkably suppressed under S2 treatments, especially S2N2. Thus, these findings demonstrated that in wheat-rice rotation reducing 20% N fertilization with 50% straw returning may be a win-win practice in this region for the equilibrium between agricultural productivity, quality and low Cd polluted risk.

Novel QTL Associated with Shoot Branching Identified in Doubled Haploid Rice (Oryza sativa L.) under Low Nitrogen Cultivation

Shoot branching is considered as an important trait for the architecture of plants and contributes to their growth and productivity. In cereal crops, such as rice, shoot branching is controlled by many factors, including phytohormones signaling networks, operating either in synergy or antagonizing each other. In rice, shoot branching indicates the ability to produce more tillers that are essential for achieving high productivity and yield potential. In the present study, we evaluated the growth and development, and yield components of a doubled haploid population derived from a cross between 93-11 (P1, indica) and Milyang352 (P2, japonica), grown under normal nitrogen and low nitrogen cultivation open field conditions. The results of the phenotypic evaluation indicated that parental lines 93-11 (P1, a high tillering indica cultivar) and Milyang352 (P2, a low tillering japonica cultivar) showed distinctive phenotypic responses, also reflected in their derived population. In addition, the linkage mapping and quantitative trait locus (QTL) analysis detected three QTLs associated with tiller number on chromosome 2 (qTNN2-1, 130 cM, logarithm of the odds (LOD) 4.14, PVE 14.5%; and qTNL2-1, 134 cM, LOD: 6.05, PVE: 20.5%) and chromosome 4 (qTN4-1, 134 cM, LOD 3.92, PVE 14.5%), with qTNL2-1 having the highest phenotypic variation explained, and the only QTL associated with tiller number under low nitrogen cultivation conditions, using Kompetitive Allele-Specific PCR (KASP) and Fluidigm markers. The additive effect (1.81) of qTNL2-1 indicates that the allele from 93-11 (P1) contributed to the observed phenotypic variation for tiller number under low nitrogen cultivation. The breakthrough is that the majority of the candidate genes harbored by the QTLs qTNL2-1 and qTNN4-1 (here associated with the control of shoot branching under low and normal nitrogen cultivation, respectively), were also proposed to be involved in plant stress signaling or response mechanisms, with regard to their annotations and previous reports. Therefore, put together, these results would suggest that a possible crosstalk exists between the control of plant growth and development and the stress response in rice.