Colonization on Cucumber Root and Enhancement of Chlorimuron-ethyl Degradation in the Rhizosphere by Hansschlegelia zhihuaiae S113 and Root Exudates

Remediation of isoproturon-contaminated soil by Sphingobium sp. strain YBL2: Bioaugmentation, detoxification and community structure

The widely used phenylurea herbicide isoproturon (IPU) and its residues can inhibit the growth of subsequently planted crops. However, reports on bioremediation of IPU-contaminated soil are scarce. In this study, Sphingobium sp. strain YBL2-gfp (a derivative of the IPU-degrading Sphingobium sp. strain YBL2 isolated by our lab) was constructed to bioremediate IPU-contaminated soil. In pot experiments, strain YBL2-gfp colonized the roots of wheat and eliminated IPU residues in the soil within 21 d, effectively alleviating its toxicity and restoring wheat growth. IPU treatment reduced the richness and diversity of soil bacteria, while inoculation YBL2-gfp mainly affected richness with less impact on diversity. The high concentrations of IPU and inoculation of YBL2-gfp alone reduced the soil microbial community connections, while bioaugmentation treatment enhanced the soil microbial community connections. Additionally, strain YBL2-gfp stimulated the metabolic capacity of the indigenous microbes, promoting the degradation of IPU and reducing the negative impact of high concentrations of IPU on microbial community. Taken together, this study offers relatively comprehensive insights into the practical application of bioaugmentation, demonstrating that strain YBL2 has the potential to remediate IPU-contaminated soils.

Comparative analysis of bacterial populations in sulfonylurea-sensitive and -resistant weeds: insights into community composition and catabolic gene dynamics

This study aimed to compare the impact of iodosulfuron-methyl-sodium and an iodosulfuron-based herbicidal ionic liquid (HIL) on the microbiomes constituting the epiphytes and endophytes of cornflower (Centaurea cyanus L.). The experiment involved biotypes of cornflower susceptible and resistant to acetolactate synthase inhibition, examining potential bacterial involvement in sulfonylurea herbicide detoxification. We focused on microbial communities present on the surface and in the plant tissues of roots and shoots. The research included the synthesis and physicochemical analysis of a novel HIL, evaluation of shifts in bacterial community composition, analysis of the presence of catabolic genes associated with sulfonylurea herbicide degradation and determination of their abundance in all experimental variants. Overall, for the susceptible biotype, the biodiversity of the root microbiome was higher compared to shoot microbiome; however, both decreased notably after herbicide or HIL applications. The herbicide-resistant biotype showed lower degree of biodiversity changes, but shifts in community composition occurred, particularly in case of HIL treatment.

Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health

Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.

The Function of Root Exudates in the Root Colonization by Beneficial Soil Rhizobacteria

Soil-beneficial microbes in the rhizosphere play important roles in improving plant growth and health. Root exudates play key roles in plant-microbe interactions and rhizobacterial colonization. This review describes the factors influencing the dynamic interactions between root exudates and the soil microbiome in the rhizosphere, including plant genotype, plant development, and environmental abiotic and biotic factors. We also discuss the roles of specific metabolic mechanisms, regulators, and signals of beneficial soil bacteria in terms of colonization ability. We highlight the latest research progress on the roles of root exudates in regulating beneficial rhizobacterial colonization. Organic acids, amino acids, sugars, sugar alcohols, flavonoids, phenolic compounds, volatiles, and other secondary metabolites are discussed in detail. Finally, we propose future research objectives that will help us better understand the role of root exudates in root colonization by rhizobacteria and promote the sustainable development of agriculture and forestry.

Root colonization by beneficial rhizobacteria

Rhizosphere microbes play critical roles for plant's growth and health. Among them, the beneficial rhizobacteria have the potential to be developed as the biofertilizer or bioinoculants for sustaining the agricultural development. The efficient rhizosphere colonization of these rhizobacteria is a prerequisite for exerting their plant beneficial functions, but the colonizing process and underlying mechanisms have not been thoroughly reviewed, especially for the nonsymbiotic beneficial rhizobacteria. This review systematically analyzed the root colonizing process of the nonsymbiotic rhizobacteria and compared it with that of the symbiotic and pathogenic bacteria. This review also highlighted the approaches to improve the root colonization efficiency and proposed to study the rhizobacterial colonization from a holistic perspective of the rhizosphere microbiome under more natural conditions.

Remediation of fomesafen contaminated soil by Bacillus sp. Za: Degradation pathway, community structure and bioenhanced remediation

Fomesafen is a diphenyl ether herbicide used to control the growth of broadleaf weeds in bean fields. The persistence, phytotoxicity, and negative impact on crop rotation associated with this herbicide have led to an increasing concern about the buildup of fomesafen residues in agricultural soils. The exigent matter of treatment and remediation of soils contaminated with fomesafen has surfaced. Nevertheless, the degradation pathway of fomesafen in soil remains nebulous. In this study, Bacillus sp. Za was utilized to degrade fomesafen residues in black and yellow brown soils. Fomesafen's degradation rate by strain Za in black soil reached 74.4%, and in yellow brown soil was 69.2% within 30 days. Twelve intermediate metabolites of fomesafen were identified in different soils, with nine metabolites present in black soil and eight found in yellow brown soil. Subsequently, the degradation pathway of fomesafen within these two soils was inferred. The dynamic change process of soil bacterial community structure in the degradation of fomesafen by strain Za was analyzed. The results showed that strain Za potentially facilitate the restoration of bacterial community diversity and richness in soil samples treated with fomesafen, and there were significant differences in species composition at phylum and genus levels between these two soils. However, both soils shared a dominant phylum and genus, Actinobacteriota, Proteoobacteria, Firmicutes and Chloroflexi dominated in two soils, with a high relative abundance of Sphingomonas and Bacillus. Moreover, an intermediate metabolite acetaminophen degrading bacterium, designated as Pseudomonas sp. YXA-1, was isolated from yellow brown soil. When strain YXA-1 was employed in tandem with strain Za to remediate fomesafen contaminated soil, the degradation rate of fomesafen markedly increased. Overall, this study furnishes crucial insights into the degradation pathway of fomesafen in soil, and presents bacterial strain resources potentially beneficial for soil remediation in circumstances of fomesafen contamination.

Development of solid agents of the diphenyl ether herbicide degrading bacterium Bacillus sp. Za based on a mixed organic fertilizer carrier

The long-term and widespread use of diphenyl ether herbicides has caused serious soil residue problems and threatens the agricultural ecological environment. The development of biodegrading agents using high-efficiency degrading strains as pesticide residue remediation materials has been widely recognized. In this study, the strain Bacillus sp. Za was used to prepare solid agents for the remediation of diphenyl ether herbicides-contaminated soil. The ratio of organic fertilizer was 1:3 (pig manure: cow dung), the inoculum amount of Za was 10%, the application amount of solid agents was 7%, and the application mode was mixed application, all of which were the most suitable conditions for solid agents. After the solid agents were stored for 120 days, the amount of Za remained above 10⁸ CFU/g. The degradation rates of the solid agents for lactofen, bifenox, fluoroglycofen, and fomesafen in soil reached 87.40, 82.40, 78.20, and 65.20%, respectively, on the 7th day. The application of solid agents alleviated the toxic effect of lactofen residues on maize seedlings. A confocal laser scanning microscope (CLSM) was used to observe the colonization of Za-gfp on the surface of maize roots treated in the solid agents, and Za-gfp mainly colonized the elongation zone and the mature area of maize root tips, and the colonization time exceeded 21 days. High-throughput sequencing analysis of soil community structural changes in CK, J (solid agents), Y (lactofen), and JY (solid agents + lactofen) groups showed that the addition of solid agents could restore the bacterial community structure in the rhizosphere soil of maize seedlings. The development of solid agents can facilitate the remediation of soil contaminated with diphenyl ether herbicide residues and improve the technical level of the microbial degradation of pesticide residues.

Combined Bioremediation of Bensulfuron-Methyl Contaminated Soils With Arbuscular Mycorrhizal Fungus and Hansschlegelia zhihuaiae S113

Over the past decades, because of large-scale bensulfuron-methyl (BSM) application, environmental residues of BSM have massively increased, causing severe toxicity in rotation-sensitive crops. The removal of BSM from the environment has become essential. In this study, the combined bioremediation of the arbuscular mycorrhizal fungi (AMF) Rhizophagus intraradices and BSM-degrading strain Hansschlegelia zhihuaiae S113 of BSM-polluted soil was investigated. BSM degradation by S113 in the maize rhizosphere could better promote AMF infection in the roots of maize, achieving an infection rate of 86.70% on the 36th day in the AMF + S113 + BSM group. Similarly, AMF enhanced the colonization and survival of S113 in maize rhizosphere, contributing 4.65 × 105 cells/g soil on the 15th day and 3.78 × 104 cells/g soil on the 20th day to a population of colonized-S113 (based possibly on the strong root system established by promoting plant-growth AMF). Both S113 and AMF coexisted in rhizosphere soil. The BSM-degrading strain S113 could completely remove BSM at 3 mg/kg from the maize rhizosphere soil within 12 days. AMF also promoted the growth of maize seedlings. When planted in BSM-contaminated soil, maize roots had a fresh weight of 2.59 ± 0.26 g in group S113 + AMF, 2.54 ± 0.20 g in group S113 + AMF + BSM, 2.02 ± 0.16 g in group S113 + BSM, and 2.61 ± 0.25 g in the AMF group, all of which exceeded weights of the control group on the 36th day except for the S113 + BSM group. Additionally, high-throughput sequencing results indicated that simultaneous inoculation with AMF and strain S113 of BSM-polluted maize root-soil almost left the indigenous bacterial community diversity and richness in maize rhizosphere soil unaltered. This represents a major advantage of bioremediation approaches resulting from the existing vital interactions among local microorganisms and plants in the soil. These findings may provide theoretical guidance for utilizing novel joint-bioremediation technologies, and constitute an important contribution to environmental pollution bioremediation while simultaneously ensuring crop safety and yield.

Biofilm formed by Hansschlegelia zhihuaiae S113 on root surface mitigates the toxicity of bensulfuron-methyl residues to maize

Bensulfuron-methyl (BSM) residues in soil threaten the rotation of BSM-sensitive crops. Microbial biofilms formed on crop roots could improve the ability of microbes to survive and protect crop roots. However, the research on biofilms with the purpose of mitigating or even eliminating BSM damage to sensitive crops is very limited. In this study, one BSM-degrading bacterium, Hansschlegelia zhihuaiae S113, colonized maize roots by forming a biofilm. Root exudates were associated with increased BSM degradation efficiency with strain S113 in rhizosphere soil relative to bulk soil, so the interactions among BSM degradation, root exudates, and biofilms may provide a new approach for the BSM-contaminated soil bioremediation. Root exudates and their constituent organic acids, including fumaric acid, tartaric acid, and l-malic acid, enhanced biofilm formation with 13.0-22.2% increases, owing to the regulation of genes encoding proteins responsible for cell motility/chemotaxis (fla/che cluster) and materials metabolism, thus promoting S113 population increases. Additionally, root exudates were also able to induce exopolysaccharide production to promote mature biofilm formation. Complete BSM degradation and healthy maize growth were found in BSM-contaminated rhizosphere soil treated with wild strain S113, compared to that treated with loss-of-function mutants ΔcheA-S113 (89.3%, without biofilm formation ability) and ΔsulE-S113 (22.1%, without degradation ability) or sterile water (10.7%, control). Furthermore, the biofilm mediated by organic acids, such as l-malic acid, exhibited a more favorable effect on BSM degradation and maize growth. These results showed that root exudates and their components (such as organic acids) can induce the biosynthesis of the biofilm to promote BSM degradation, emphasizing the contribution of root biofilm in reducing BSM damage to maize.

The enhanced mechanisms of Hansschlegelia zhihuaiae S113 degrading bensulfuron-methyl in maize rhizosphere by three organic acids in root exudates

The residues of bensulfuron-methyl (BSM), a sulfonylurea herbicide, in soil have caused serious damage to the rotation of susceptible crops. Many studies have reported that the removal of BSM in soil was achieved by adding degrading bacteria. However, the mechanisms used by bacteria to degrade BSM in the crop rhizosphere remain unclear. In this study, a BSM-degrading bacterium, Hansschlegelia zhihuaiae S113, was applied to investigate the enhancement of effects mediated by organic acids during the bioremediation of BSM-contaminated maize rhizosphere soil. Organic acids, such as L-malic acid, tartaric acid, and fumaric acid, identified in maize root exudates, significantly stimulated the expression of cheA, which encoded the histidine kinase in strain S113 and contributed to the chemotactic response. This process accelerated the accumulation of strain S113 around the maize roots and promoted the colonization process on maize roots. The growth of strain S113 was significantly increased by L-malic acid but not tartaric acid or fumaric acid. After the S113 suspension was root-irrigated to BSM-contaminated soil, the density of strain S113 colonizing root surfaces and in rhizosphere soil reached 1.1 × 10⁴ cells/g for roots and 4.9 × 10⁴ cells/g in dry soil at 15 d, leading to 80.9% BSM degradation efficiency. The treatment with the addition of a mixture of S113 and L-malic acid completely degraded BSM in rhizosphere soil due to the strong attraction and growth promotion of strain S113 by L-malic acid, with a higher efficiency than that with the extra addition of fumaric acid (89.7%) or tartaric acid (87.0%). This paper revealed the enhancement effects of organic acids identified in root exudates for the in situ bioremediation of BSM-contaminated rhizosphere soil.

Genetically Engineered Methanotroph as a Platform for Bioaugmentation of Chemical Pesticide Contaminated Soil

Bioaugmentation is a promising alternative in soil remediation. One challenge of bioaugmentation is that exogenous pollutant-degrading microbes added to soil cannot establish enough biomass to eliminate pollutants. Considering that methanotrophs have a growth advantage in the presence of methane, we hypothesize that genetically engineered methanotrophs could degrade contaminants efficiently in soil with methane. Here, methanotroph Methylomonas sp. LW13, herbicide bensulfuron-methyl (BSM), and two kinds of soil were chosen to confirm this hypothesis. The unmarked gene knock-in method was first developed for strain LW13. Then, BSM hydrolase encoding gene sulE was inserted into the chromosome of strain LW13, conferring it BSM-degrading ability. After inoculation, the cell amount of strain LW13-sulE in soil raised considerably (over 100 fold in 9 days) with methane provision; meanwhile, >90% of BSM in soil was degraded. This study provides a proof of the concept that genetically engineered methanotroph is a potential platform for soil remediation.

Acid resistance of Masson pine (Pinus massoniana Lamb.) families and their root morphology and physiological response to simulated acid deposition

Pinus massoniana Lamb. is one of the most sensitive species to acid deposition among forest woody plants, but differences in acid resistance among pine families still exist. It is of great significance to study the differences in acid resistance of Masson pine families and to analyze the physiological regulation mechanism of their acid resistance. In this study, the 100-day-old seedlings of 16 Masson pine families were treated with the simulated acid rain (SAR) at different pH levels (5.6, 4.5, 3.5 and 2.5) for 100 days to investigate the plant morphology, chlorophyll content, and root physiological responses. Results showed that pine family No. 35 maintained the good morphology, high chlorophyll content and organic acids secretion, and low plasma membrane permeability exposed to SAR, while family No. 79 presented the opposite. SAR not only increased the root plasma membrane permeability, but also induced an exudation of organic acids from the pine roots, and the test parameters changed sharply when the SAR pH was lower than 4.5. The results indicated that Masson pine could resist to acidic environment (pH 4.5–5.6), and family No. 35 had the acid resistance while the family No. 79 was sensitive to acid stress. The acid resistance diversity of different pine families had close relation with the root physiological processes, including the root plasma membrane permeability and organic acids secretion. For the future research, the natural genetic variation of Masson pine in response to acid stress and its acid resistance mechanism should be further studied.

Glutathione-S-transferase (GST) catalyzes the degradation of Chlorimuron-ethyl by Klebsiella jilinsis 2N3

Microbial degradation is one of the most efficient and reliable ways to remove the residues of Chlorimuron-ethyl in the environments such as soil and water. In this study, a glutathione-s-transferase (GST) gene Kj-gst was cloned from the Chlorimuron-ethyl degrading bacterial strain Klebsiella jilinsis 2N3. Results showed that Kj-gst played a key role in the degradation of Chlorimuron-ethyl by strain 2N3. The mutant with gene Kj-gst knocked out showed reduced relative activity up to 70% compared with the wild type in 8 h in culture. After the knockout gene was complemented, the degradation ability of the complement mutant was essentially comparable to that of the wild type. The protein Kj-GST (50 μg) obtained from the gene Kj-gst expressed and purified in E. coli strain BL21(DE3) was capable of degrading Chlorimuron-ethyl with an initial concentration of 50 mg/mL by 42.91% under the optimal conditions (15 °C and pH = 7). Point mutation experiments on a glycine located at position 101 (Glu101) confirmed that the H site of glutathione (GSH) is the key component in Kj-GST for degrading Chlorimuron-ethyl. We conclude that Kj-GST is demonstrated for the first time to degrade Chlorimuron-ethyl with its main functional site identified at the H site of GSH, shedding insight to revealing the molecular mechanisms of degrading Chlorimuron-ethyl by Klebsiella jilinsis 2N3.

The Prevention of Bio-Organic Fertilizer Fermented from Cow Manure Compost by Bacillus sp. XG-1 on Watermelon Continuous Cropping Barrier

The continuous cropping barrier is an important factor leading to the decline of watermelon quality and yield. In this study, we focused on a bio-organic fertilizer prepared with one bacterial strain, Bacillus sp. XG-1, to prevent the occurrence of the continuous cropping barrier. The strain XG-1 was isolated from watermelon rhizosphere soil, and promoted the growth of watermelon by producing phytase (0.19 U/mL), indole-3-acetic acid (IAA, 7.31 mg/L), and gibberellins (GA3, 2.47 mg/L). In addition, the strain also possessed a strong antagonistic effect against the pathogen Fusarium oxysporum f. sp. niveum (Fon) by inhibiting conidia germination with an inhibition ratio of 85.3% and mycelium growth. The bio-organic fertilizer fermented by XG-1, based on cow manure compost and rapeseed meal (85:15, w/w) under optimal conditions, was mixed in soil (watermelon had been planted for two consecutive years). After the cultivation of watermelon for 50 d, a higher density of XG-1 (9.79 × 10⁵ colony-forming units (CFU)/g) and one order of magnitude lower of Fon (1.29 × 10³ copies/g) were detected in the rhizosphere soil compared with soils without bio-organic fertilizer (7.59 × 10⁴ copies/g for Fon), leading to an 86.4% control efficiency of watermelon caused by Fusarium wilt. The application of bio-organic fertilizer enriched soil nutrients, including the organic matter (13.2%), total nitrogen (13.9%), total phosphorus (20.5%), and total potassium (3.77%), adjusted the soil pH from 6.69 to 7.01, and significantly improved the watermelon growth in terms of the seedling height, root length, fresh weight of seedling and root with increase of 78.8%, 72.2%, 84.6%, and 96.4%, respectively. This study regarded the watermelon continuous cropping soil as the research point, and focused on inhibiting Fon, regulating soil properties and enhancing watermelon growth to eliminate the continuous cropping barrier through a combination of compost and functional strains, demonstrating the potential application value in watermelon production.

Carboxylesterase, a de-esterification enzyme, catalyzes the degradation of chlorimuron-ethyl in Rhodococcus erythropolis D310-1

Microbial degradation is considered to be the most acceptable method for degradation of chlorimuron-ethyl, a typical long-term residual sulfonylurea herbicide, but the underlying mechanism at the genetic and biochemical levels is unclear. In this work, the genome sequence of the chlorimuron-ethyl-degrading bacterium Rhodococcus erythropolis D310-1 was completed, and the gene clusters responsible for the degradation of chlorimuron-ethyl in D310-1 were predicted. A carboxylesterase gene, carE, suggested to be responsible for carboxylesterase de-esterification, was cloned from D310-1. CarE was expressed in Escherichia coli BL21 and purified to homogeneity. The active site of the chlorimuron-ethyl-degrading enzyme CarE and the biochemical activities of CarE were elucidated. The results demonstrated that CarE is involved in catalyzing the de-esterification of chlorimuron-ethyl. A carE deletion mutant strain, D310-1ΔcarE, was constructed, and the chlorimuron-ethyl degradation rate in the presence of 100 mg L^-1 chlorimuron-ethyl within 120 h decreased from 86.5 % (wild-type strain D310-1) to 58.2 % (mutant strain D310-1ΔcarE). Introduction of the plasmid pNit-carE restored the ability of the mutant strain to utilize chlorimuron-ethyl. This study is the first to demonstrate that carboxylesterase can catalyze the de-esterification reaction of chlorimuron-ethyl and provides new insights into the mechanism underlying the degradation of sulfonylurea herbicides and a theoretical basis for the utilization of enzyme resources.

Insights Into the Biodegradation of Lindane (γ-Hexachlorocyclohexane) Using a Microbial System

Lindane (γ-hexachlorocyclohexane) is an organochlorine pesticide that has been widely used in agriculture over the last seven decades. The increasing residues of lindane in soil and water environments are toxic to humans and other organisms. Large-scale applications and residual toxicity in the environment require urgent lindane removal. Microbes, particularly Gram-negative bacteria, can transform lindane into non-toxic and environmentally safe metabolites. Aerobic and anaerobic microorganisms follow different metabolic pathways to degrade lindane. A variety of enzymes participate in lindane degradation pathways, including dehydrochlorinase (LinA), dehalogenase (LinB), dehydrogenase (LinC), and reductive dechlorinase (LinD). However, a limited number of reviews have been published regarding the biodegradation and bioremediation of lindane. This review summarizes the current knowledge regarding lindane-degrading microbes along with biodegradation mechanisms, metabolic pathways, and the microbial remediation of lindane-contaminated environments. The prospects of novel bioremediation technologies to provide insight between laboratory cultures and large-scale applications are also discussed. This review provides a theoretical foundation and practical basis to use lindane-degrading microorganisms for bioremediation.