Exogenous application of Bradyrhizobium japonicum AC20 enhances soybean tolerance to atrazine via regulating rhizosphere soil microbial community and amino acid, carbohydrate metabolism related genes expression

Dealkylation metabolites of Atrazine: A previously Neglected Contributor to soybean phytotoxicity within atrazine residue

The phytotoxicity risks of atrazine to crops have received widespread attention, but the toxic effects of its metabolites on plants have been largely overlooked. In this study, the contributions and mechanisms underlying phytotoxicity of the atrazine and its metabolites (DEA and DIA) were systematically investigated in soybean seedlings. Two dealkylation metabolites DEA and DIA caused growth suppression, inhibited photosynthesis, activated the antioxidant system, and induced changes in chloroplast ultrastructure in soybean seedlings. Integrated Biological Response (IBR) analysis indicated that at equivalent environmentally relevant concentrations, the toxicity indices of DEA and DIA were 73.60% and 34.00% of atrazine, respectively. Molecular docking analysis revealed that both DEA and DIA exhibited high binding energies with Photosystem II D1 protein, with their potential target protein in soybean plants being consistent with that of atrazine. Metabolomic analysis further confirmed that the metabolites DEA and DIA disrupt key metabolic pathways, including alpha-linolenic acid metabolism, consistent with the mode of action of atrazine. These effects are associated with the inhibition of the photosynthetic electron transport chain and ROS accumulation. By calculating the environmental risk quotient, the risk of metabolites DEA to succeeding crops is likely to exceed that posed by the parent atrazine. These findings suggested that dealkylation metabolites of atrazine are overlooked contributors to soybean phytotoxicity in atrazine residue, and the risks posed by herbicide metabolites to crops need to be addressed.

Influencing factors on performance of electro-oxidation and UV/electro-oxidation for removal of atrazine: Kinetics, long-term stability and toxicity

Performance of electro-oxidation (EO) and UV/electro-oxidation (UV/EO) on atrazine (ATZ) removal was investigated under various operating factors. Because of synergistic effect on ATZ removal, UV/EO was the most effective process, followed by UV/chlorine, EO, UV irradiation, and chlorination, respectively. Although the energy consumption of UV/EO for 90% removal was similar to that of EO, UV/EO removed ATZ 1.8 times faster than EO. Boron doped diamond (BDD) exhibited greater ATZ removal than dimensionally stable anode (DSA), and performance of BDD was stable for treatment of 50 cycle times (100 h). Performance of EO and UV/EO on ATZ removal increased with higher current density and low pH. ATZ removal by EO and UV/EO was independent to NaCl concentrations (300-1000 mg.L-1). HO• played a major role on ATZ removal, while the role of RCS was minor. The 2nd-order reaction rate constant of HO• with ATZ (kATZ-HO•) was 1.36 × 109 M-1s-1. Although phytotoxicity was a sensitive endpoint to ATZ, different inhibition on germination of Ipomoea aquatica and Oryza sativa L. (Khao Dawk Mali 105) seeds was observed. UV/EO was the most effective process for ATZ detoxication. Germination index of Ipomoea aquatica and Oryza sativa L. (Khao Dawk Mali 105) seeds for samples treated by UV/EO was equivalent or greater than the control sample.

Adaptations of the Genus Bradyrhizobium to Selected Elements, Heavy Metals and Pesticides Present in the Soil Environment

Rhizobial bacteria perform a number of extremely important functions in the soil environment. In addition to fixing molecular nitrogen and transforming it into a form available to plants, they participate in the circulation of elements and the decomposition of complex compounds present in the soil, sometimes toxic to other organisms. This review article describes the molecular mechanisms occurring in the most diverse group of rhizobia, the genus Bradyrhizobium, allowing these bacteria to adapt to selected substances found in the soil. Firstly, the adaptation of bradyrhizobia to low and high concentrations of elements such as iron, phosphorus, sulfur, calcium and manganese was shown. Secondly, the processes activated in their cells in the presence of heavy metals such as lead, mercury and arsenic, as well as radionuclides, were described. Additionally, due to the potential use of Bradyrhziobium as biofertilizers, their response to pesticides commonly used in agriculture, such as glyphosate, sulfentrazone, chlorophenoxy herbicides, flumioxazine, imidazolinone, atrazine, and insecticides and fungicides, was also discussed. The paper shows the great genetic diversity of bradyrhizobia in terms of adapting to variable environmental conditions present in the soil.

Combined Transcriptomics and Metabolomics Uncover the Potential Mechanism of Plant Growth-Promoting Rhizobacteria on the Regrowth of Leymus chinensis After Mowing

Mowing significantly influences nutrient cycling and stimulates metabolic adjustments in plants to promote regrowth. Plant growth-promoting rhizobacteria (PGPR) are crucial for enhancing plant growth, nutrient absorption, and stress resilience; however, whether inoculation with PGPR after mowing can enhance plant regrowth capacity further, as well as its specific regulatory mechanisms, remains unexplored. In this study, PGPR Pantoea eucalyptus (B13) was inoculated into mowed Leymus chinensis to evaluate its effects on phenotypic traits, root nutrient contents, and hormone levels during the regrowth process and to further explore its role in the regrowth of L. chinensis after mowing. The results showed that after mowing, root nutrient and sugar contents decreased significantly, while the signal pathways related to stress hormones were activated. This indicates that after mowing, root resources tend to sacrifice a part of growth and prioritize defense. After mowing, B13 inoculation regulated the plant's internal hormone balance by reducing the levels and signal of JA, SA, and ABA and upregulated the signal transduction of growth hormones in the root, thus optimizing growth and defense in a mowing environment. Transcriptomic and metabolomic analyses indicated that B13 promoted nutrient uptake and transport in L. chinensis root, maintained hormone homeostasis, enhanced metabolic pathways related to carbohydrates, energy, and amino acid metabolism to cope with mowing stress, and promoted root growth and regeneration of shoot. This study reveals the regenerative strategy regulated by B13 in perennial forage grasses, helping optimize resource utilization, increase yield, and enhance grassland stability and resilience.

New insights into the stages of cadmium remediation in ryegrass enhanced by kitchen compost-derived dissolved organic matter: Activation, absorption, and storage

Dissolved organic matter (DOM) regulates plant behavior in both agricultural and environmental fields. However, the regulatory mechanisms by which DOM influences soil-plant system interactions during the phytoremediation of Cd-contaminated soils remain unclear. Therefore, this study investigated the enhanced effect of kitchen compost-derived DOM on the Cd remediation capability of ryegrass across three phases of phytoremediation. The main pathways and mechanisms of DOM-assisted phytoremediation were identified through the analysis of changes in soil microbial communities and metabolism functions. The results revealed that DOM increased the bioavailability of soil Cd and significantly enhanced the Cd enrichment capacity of ryegrass, regardless of the application rate. The application of 20 % DOM to soil with a 20 mg/kg Cd content increased the bioconcentration factors of ryegrass roots and shoots by up to 38.19 and 11.08 times, respectively, compared with the control group. The direct or indirect optimizing effects of DOM on Cd fraction transformation, microbial communities, and their metabolism functions significantly enhanced the Cd enrichment capacity of ryegrass. Notably, DOM exhibited dual effects on ryegrass growth, mainly influenced by changes in soil physicochemical properties, optimization of microbial communities, and alterations in nitrogen metabolic functions. Additionally, the Cd reserves in ryegrass, which serve as a vital indicator of phytoremediation, exhibited a positive response to DOM. This study provides insights into the various reinforcing roles of kitchen compost-derived DOM in Cd-contaminated soil phytoremediation. These findings support the development of effective agronomic strategies for precise Cd regulation.

Effects of Deep Tillage on Rhizosphere Soil and Microorganisms During Wheat Cultivation

The production of wheat is fundamentally interconnected with worldwide food security. The practice of deep tillage (DT) cultivation has shown advantages in terms of soil enhancement and the mitigation of diseases and weed abundance. Nevertheless, the specific mechanisms behind these advantages are unclear. Accordingly, we aimed to clarify the influence of DT on rhizosphere soil (RS) microbial communities and its possible contribution to the improvement of soil quality. Soil fertility was evaluated by analyzing several soil characteristics. High-throughput sequencing techniques were utilized to explore the structure and function of rhizosphere microbial communities. Despite lowered fertility levels in the 0-20 cm DT soil layer, significant variations were noted in the microbial composition of the DT wheat rhizosphere, with Acidobacteria and Proteobacteria being the most prominent. Furthermore, the abundance of Bradyrhizobacteria, a nitrogen-fixing bacteria within the Proteobacteria phylum, was significantly increased. A significant increase in glycoside hydrolases within the DT group was observed, in addition to higher abundances of amino acid and carbohydrate metabolism genes in the COG and KEGG databases. Moreover, DT can enhance soil quality and boost crop productivity by modulating soil microorganisms' carbon and nitrogen fixation capacities.

Nickel oxide nanoparticles decrease the accumulation of atrazine in earthworms

Nickel oxide nanoparticles (NiO-NPs) are common nanomaterials that may be released into the environment, affecting the toxicity of other contaminants. Atrazine (ATZ) is a commonly used herbicide that can harm organisms due to its persistence and bioaccumulation in the environment. Although the toxicity of ATZ to earthworms is well-documented, the risk of co-exposure with NiO-NPs increases as more nanoparticles accumulate in the soil. In this study, we investigated the effects and mechanisms of NiO-NPs on the accumulation of ATZ in earthworms. The results showed that after day 21, the antioxidant system of the cells under ATZ treatment alone was adversely affected, with ROS content 36.05 % higher than that of the control (CK) group. However, the addition of NiO-NPs reduced the ROS contents in the earthworms by 0.6 %- 32.3 %. Moreover, analysis of earthworm intestinal sections indicates that NiO-NPs mitigated cellular and tissue damage caused by ATZ. High-throughput sequencing revealed that NiO-NPs in earthworm intestines increased the abundance of Pseudomonas aeruginosa and Aeromonas aeruginosa. Additionally, the enhanced function of the ABC transport system in the gut resulted in lower accumulation of ATZ in earthworms. In summary, NiO-NPs can reduce the accumulation and thus the toxicity of ATZ in earthworms. Our study contributes to a deeper understanding of the effects of NiO-NPs on co-existing pollutants.

Genome-wide analysis of the common bean (Phaseolus vulgaris) laccase gene family and its functions in response to abiotic stress

BACKGROUND

Laccase (LAC) gene family plays a pivotal role in plant lignin biosynthesis and adaptation to various stresses. Limited research has been conducted on laccase genes in common beans.

RESULTS

29 LAC gene family members were identified within the common bean genome, distributed unevenly in 9 chromosomes. These members were divided into 6 distinct subclades by phylogenetic analysis. Further phylogenetic analyses and synteny analyses indicated that considerable gene duplication and loss presented throughout the evolution of the laccase gene family. Purified selection was shown to be the major evolutionary force through Ka / Ks. Transcriptional changes of PvLAC genes under low temperature and salt stress were observed, emphasizing the regulatory function of these genes in such conditions. Regulation by abscisic acid and gibberellins appears to be the case for PvLAC3, PvLAC4, PvLAC7, PvLAC13, PvLAC14, PvLAC18, PvLAC23, and PvLAC26, as indicated by hormone induction experiments. Additionally, the regulation of PvLAC3, PvLAC4, PvLAC7, and PvLAC14 in response to nicosulfuron and low-temperature stress were identified by virus-induced gene silence, which demonstrated inhibition on growth and development in common beans.

CONCLUSIONS

The research provides valuable genetic resources for improving the resistance of common beans to abiotic stresses and enhance the understanding of the functional roles of the LAC gene family.

A comparative evaluation of biochar and Paenarthrobacter sp. AT5 for reducing atrazine risks to soybeans and bacterial communities in black soil

Application of biochar and inoculation with specific microbial strains offer promising approaches for addressing atrazine contamination in agricultural soils. However, determining the optimal method necessitates a comprehensive understanding of their effects under similar conditions. This study aimed to evaluate the effectiveness of biochar and Paenarthrobacter sp. AT5, a bacterial strain known for its ability to degrade atrazine, in reducing atrazine-related risks to soybean crops and influencing bacterial communities. Both biochar and strain AT5 significantly improved atrazine degradation in both planted and unplanted soils, with the most substantial reduction observed in soils treated with strain AT5. Furthermore, bioaugmentation with strain AT5 outperformed biochar in enhancing soybean growth, photosynthetic pigments, and antioxidant defenses. While biochar promoted higher soil bacterial diversity compared to strain AT5, the latter selectively enriched specific bacterial populations. Additionally, soil inoculated with strain AT5 displayed a notable increase in the abundance of key genes associated with atrazine degradation (trzN, atzB, and atzC), surpassing the effects observed with biochar addition, thus highlighting its effectiveness in mitigating atrazine risks in soil.

Biodegradation of atrazine and nicosulfuron by Streptomyces nigra LM01: Performance, degradative pathway, and possible genes involved

Microbial herbicide degradation is an efficient bioremediation method. In this study, a strain of Streptomyces nigra, LM01, which efficiently degrades atrazine and nicosulfuron, was isolated from a corn field using a direct isolation method. The degradation effects of the identified strain on two herbicides were investigated and optimized using an artificial neural network. The maximum degradation rates of S. nigra LM01 were 58.09 % and 42.97 % for atrazine and nicosulfuron, respectively. The degradation rate of atrazine in the soil reached 67.94 % when the concentration was 108 CFU/g after 5 d and was less effective than that of nicosulfuron. Whole genome sequencing of strain LM01 helped elucidate the possible degradation pathways of atrazine and nicosulfuron. The protein sequences of strain LM01 were aligned with the sequences of the degraded proteins of the two herbicides by using the National Center for Biotechnology Information platform. The sequence (GE005358, GE001556, GE004212, GE005218, GE004846, GE002487) with the highest query cover was retained and docked with the small-molecule ligands of the herbicides. The results revealed a binding energy of - 6.23 kcal/mol between GE005358 and the atrazine ligand and - 6.66 kcal/mol between GE002487 and the nicosulfuron ligand.

Synergistic mitigation of atrazine-induced oxidative stress on soybeans in black soil using biochar and Paenarthrobacter sp. AT5

Atrazine, a widely used herbicide in modern agriculture, can lead to soil contamination and adverse effects on specific crops. To address this, we investigated the efficacy of biochar loaded with Paenarthrobacter sp. AT5 (an atrazine-degrading bacterial strain) in mitigating atrazine's impact on soybeans in black soil. Bacterially loaded biochar (BBC) significantly enhanced atrazine removal rates in both unplanted and planted soil systems. Moreover, BBC application improved soybean biomass, photosynthetic pigments, and antioxidant systems while mitigating alterations in metabolite pathways induced by atrazine exposure. These findings demonstrate the effectiveness of BBC in reducing atrazine-induced oxidative stress on soybeans in black soil, highlighting its potential for sustainable agriculture.

Changes of atrazine dissipation and microbial community under coexistence of graphene oxide in river water

The coexistence of herbicide atrazine (ATZ) and the nanomaterial graphene oxide (GO) in natural water bodies will be an inevitable scenario due to their widespread application and consequent release into aquatic ecosystems. But the dissipation of ATZ with GO and the response of the microbial community to their combination are still not clear. Here, we investigated the dissipation dynamics and transformation of ATZ with and without GO in river water after 21-d incubation. In the presence of GO, ATZ residue significantly decreased by 11%-43%; the transformation of ATZ markedly increased by 11%-17% when ATZ concentrations were not above 1.0 mg∙L-1. The direct adsorption of ATZ on GO, mainly via π-π interactions, proton transfer and hydrogen bonding, contributed 54%-68% of the total increased ATZ dissipation by GO. ATZ and ATZ+GO exerted effects of similar magnitude on microbial OTU numbers with an increase of bacterial diversity. The coexisting GO increased the relative abundance of ATZ-degradation bacteria and Chitinophagales, thus improving ATZ transformation. This work indicated that the coexistence of GO at environmentally relevant concentrations can effectively reduce ATZ residues and promote the transformation of ATZ to degradation products in river water; nevertheless, the potential risk of GO acting as an ATZ carrier should be given more prominence.

Metabolic insights into how multifunctional microbial consortium enhances atrazine removal and phosphorus uptake at low temperature

Agricultural soils in the black soil region of northeast China often face negative stress due to low temperatures, pesticide contamination, and inadequate nutrient supply. In this study, a new cold-tolerant strain of Peribacillus simplex C1 (C1) was selectively isolated from atrazine contaminated soil. The artificially constructed microbial consortium (CPD) [C1, phosphorus-solubilizing bacterium Enterobacter sp. P1, and atrazine-degrading bacterium Acinetobacter lwoffii DNS32] demonstrated the most effective performance in enhancing atrazine degradation and phosphorus-solubilizing capacity when the initial inoculation ratio of 5:1:2 at 15 °C. CPD enhanced energy-related metabolic pathways and increased choline production to regulate bacterial adaptation to temperature decrease. Additionally, the strains could selectively utilize carbon sources (low molecular weight organic acids) or nitrogen sources (some metabolites of atrazine) provided by each other to enhance growth. Furthermore, strain C1 enhanced membrane fluidity through increased expression of the unsaturated fatty acids. Pot experiments demonstrated that CPD assisted soybean seedlings in resisting dual stresses of low temperature and atrazine contamination by inducing the expression of genes related to photosynthesis, membrane permeability, phosphorus response, and cold tolerance.

Triple-transgenic soybean in conjunction with glyphosate drive patterns in the rhizosphere microbial community assembly

Plant roots continuously influence the rhizosphere, which also serves as a recruitment site for microorganisms with desirable functions. The development of genetically engineered (GE) crop varieties has offered unparalleled yield advantages. However, in-depth research on the effects of GE crops on the rhizosphere microbiome is currently insufficient. We used a triple-transgenic soybean cultivar (JD606) that is resistant to insects, glyphosate, and drought, along with its control, ZP661, and JD606 treated with glyphosate (JD606G). Using 16S and ITS rDNA sequencing, their effects on the taxonomy and function of the bacterial and fungal communities in the rhizosphere, surrounding, and bulk soil compartment niches were determined. Alpha diversity demonstrated a strong influence of JD606 and JD606G on bacterial Shannon diversity. Both treatments significantly altered the soil's pH and nitrogen content. Beta diversity identified the soil compartment niche as a key factor with a significant probability of influencing the bacterial and fungal communities associated with soybeans. Further analysis showed that the rhizosphere effect had a considerable impact on bacterial communities in JD606 and JD606G soils but not on fungal communities. Microbacterium, Bradyrhizobium, and Chryseobacterium were found as key rhizobacterial nodes. In addition, the LEfSe analysis identified biomarker taxa with plant-beneficial attributes, demonstrating rhizosphere-driven microbial recruitment. FUNGuild, Bugbase, and FAPROTAX functional predictions showed that ZP661 soils had more plant pathogen-associated microbes, while JD606 and JD606G soils had more stress-tolerance, nitrogen, and carbon cycle-related microbes. Bacterial rhizosphere networks had more intricate topologies than fungal networks. Furthermore, correlation analysis revealed that the bacteria and fungi with higher abundances exhibited varying degrees of positive and negative correlations. Our findings shed new light on the niche partitioning of bacterial and fungal communities in soil. It also indicates that following triple-transgenic soybean cultivation and glyphosate application, plant roots recruit microbes with beneficial taxonomic and functional traits in the rhizosphere.