Potential effects of Rhodococcus qingshengii strain djl-6 on the bioremediation of carbendazim-contaminated soil and the assembly of its microbiome

Advances in actinobacteria-based bioremediation: mechanistic insights, genetic regulation, and emerging technologies

Untreated wastewater from sewage, industries, and agriculture contaminates ecosystems due to rapid population growth and industrialization. It introduces hazardous pollutants, including pesticides, polycyclic aromatic hydrocarbons (PAHs), and heavy metals, which pose serious health risks such as cancer, lung disorders, and kidney damage, threatening both environmental and human well-being. Using microorganisms for bioremediation is thought to be safer and more effective. Compared to other approaches, bioremediation is the most effective way to absorb heavy metals. Due to the high cost and unreliability of traditional remediation techniques, such as chemical and physical treatments, interest in bioremediation as an environmentally benign substitute has grown. Through the use of microorganisms, bioremediation successfully removes heavy metals and breaks down organic contaminants from contaminated circumstances. Actinobacteria are unique among these microbes because of their flexibility in metabolism and capacity to endure severe environments. They create secondary metabolites, such as enzymes, that help break down a variety of pollutants. Actinobacteria also produce siderophores and extracellular polymeric substances (EPS), which aid in trapping organic contaminants and immobilizing heavy metals. This review explores the diverse applications of actinobacteria in bioremediation, with a focus on their mechanisms for breaking down and neutralizing pollutants. We highlighted the advancements in bioremediation strategies, including the use of mixed microbial cultures, biosurfactants, nanoparticles and immobilized cell technologies which enhance the efficiency and sustainability of pollutant removal. The integration of omics technologies such as metagenomics, meta-transcriptomics, and meta-proteomics provides deeper insights into the genetic and metabolic pathways involved in bioremediation, suggesting the way for the development of genetically optimized strains with enhanced degradation capabilities. By leveraging these emerging technologies and microbial strategies, actinobacteria-mediated bioremediation presents a highly promising approach for mitigating environmental pollution. Ongoing research and technological advancements in this field can further enhance the scalability and applicability of bioremediation techniques, offering sustainable solutions for restoring contaminated ecosystems and protecting human health.

Acid-modified corn straw biochar immobilized Pseudomonas hibiscus CN-1 facilitated the bioremediation of carbendazim-contaminated soil

Carbendazim application in agroecosystems has posed potential threats to ecosystems and human health. The utilization of biochar-based materials for immobilizing microorganisms offers a sustainable strategy for effective bioremediation. In this study, a novel highly efficient carbendazim-degrading bacterium Pseudomonas hibiscus CN-1 was isolated and immobilized using corn straw-based biochar as a carrier. The effects of degrading strain CN-1, biochar materials, and biochar-CN-1 composite on carbendazim degradation, soil enzyme activities, and community structure diversity were investigated. Under the optimal conditions (pH 6.6, 31 °C, and 6.5% inoculum volume), strain CN-1 metabolized carbendazim into benzimidazole-2-carbamic acid and 2-hydroxybenzimidazole, indicating that demethylation was a major metabolic pathway. Among the biochar materials, acid-modified biochar pyrolyzed at 700 °C proved to be the most effective carrier for strain CN-1 immobilization and efficient removal of carbendazim, achieving a removal rate of 78.7% in water. Compared to the control, the degradation half-lives of carbendazim in the soil with biochar, strain CN-1, and the biochar-strain CN-1 composite were reduced from 30.97 to 23.23, 19.46, and 10.99 days, respectively. Soil enzyme activities and bacterial community diversity results demonstrated that the biochar-strain CN-1 composite not only mitigated the adverse effects of carbendazim on soil enzyme activities but also had the most positive impact on soil microbial richness and diversity. This study highlights the importance of selecting appropriate biochar materials and offers insights into an environmentally friendly method for the efficient bioremediation of soils contaminated with carbendazim.

Response of earthworm enzyme activity and gut microbial functional diversity to carbendazim in the manured soil

The effect of pesticide pollution on environmental microorganisms in soil has become the focus of widespread concern in society today. The response of earthworm gut and surrounding soil microbial functional diversity and enzyme activity to carbendazim (CBD) was studied in a soil-earthworm ecosystem amended with manure. In the experiment, CBD was added to the manured soil (MS). Meanwhile, the pesticide treatment without manure and the control treatment without pesticides were also set up. The activities of catalase (CAT) and acetylcholinesterase (AChE) were measured to evaluate the toxicity of CBD. The Biolog method was used to assess the functional diversity of the microbial community. In the 2 mg/kg CBD treatment, earthworm AChE activity decreased significantly in the MS after 14 d, which occurred earlier than in the un-manured soil (NS). The changes of earthworm CAT activity in the pesticide treatments showed a trend of initially increasing and then maintaining at a high activity level. However, the CAT activities at 28 d in the manured soils were clearly lower than that at 7 d for both the CBD treatments, while they remained stable in the control treatments. The carbon source utilization, Simpson index, Shannon index, and McIntosh index of soil microorganisms in the MS treatments were significantly higher than those in the NS treatments. The overall activity of earthworm gut microorganisms in the MS treated with 2 mg/kg CBD was higher than that in the control. Also, CBD treatment (2 mg/kg) increased significantly the Simpson index and McIntosh index of earthworm gut microorganisms. The results indicated that the enzyme activities in the manured soils increased before 7 d for the pesticide treatments. Furthermore, exposure to CBD at a high concentration in the MS not only led to the earlier inhibition of earthworm enzyme activity but also significantly improved the overall activity of earthworm gut microorganisms and microbial functional diversity. This study revealed the ecotoxicological effects of earthworms in response to pesticide stress following the use of organic fertilizers under facility environmental conditions, which can provide a theoretical basis for the remediation of pesticide pollution in soil in the future.

A promising alternative for sustainable remediation of carbendazim in aquatic environments

The treatment of carbendazim-contaminated effluents is a challenge because of its complex composition and toxicity. A promising solution lies in biodegradation and the fungus Actinomucor elegans LBM 290 shows significant potential in this regard. Thus, the aim of this study was to biodegrade MBC by A. elegans LBM 290 in a liquid medium addressing the changes in the fungal morphology and protein production. The fungus A. elegans LBM 290 efficiently remove the fungicide carbendazim, with 86.6% removal within 8 days. This degradation is a combination of biodegradation (24.54%) and adsorption (62.08%). Exposure to carbendazim negatively affected the fungus, causing a decrease in biomass and morphological changes. Proteomic analysis revealed the fungal response to carbendazim stress through increased production of Cu-Zn superoxide dismutase, an antioxidant enzyme that combats oxidative stress, and the presence of a G protein subunit, suggesting participation in stress signaling pathways. These findings contribute to understanding the strategies of A. elegans LBM 290 to cope with carbendazim exposure in aquatic environments.

Microbes as carbendazim degraders: opportunity and challenge

Carbendazim (methyl benzimidazol-2-ylcarbamate, CBZ) is a systemic benzimidazole carbamate fungicide and can be used to control a wide range of fungal diseases caused by Ascomycetes, Basidiomycetes and Deuteromycetes. It is widely used in horticulture, forestry, agriculture, preservation and gardening due to its broad spectrum and leads to its accumulation in soil and water environmental systems, which may eventually pose a potential threat to non-target organisms through the ecological chain. Therefore, the removal of carbendazim residues from the environment is an urgent problem. Currently, a number of physical and chemical treatments are effective in degrading carbendazim. As a green and efficient strategy, microbial technology has the potential to degrade carbendazim into non-toxic and environmentally acceptable metabolites, which in turn can dissipate carbendazim from the contaminated environment. To date, a number of carbendazim-degrading microbes have been isolated and reported, including, but not limited to, Bacillus, Pseudomonas, Rhodococcus, Sphingomonas, and Aeromonas. Notably, the common degradation property shared by all strains was their ability to hydrolyze carbendazim to 2-aminobenzimidazole (2-AB). The complete mineralization of the degradation products is mainly dependent on the cleavage of the imidazole and benzene rings. Additionally, the currently reported genes for carbendazim degradation are MheI and CbmA, which are responsible for breaking the ester and amide bonds, respectively. This paper reviews the toxicity, microbial degradation of carbendazim, and bioremediation techniques for carbendazim-contaminated environments. This not only summarizes and enriches the theoretical basis of microbial degradation of carbendazim, but also provides practical guidance for bioremediation of carbendazim-contaminated residues in the environment.

Reducing the accumulation of cadmium and phenanthrene in rice by optimizing planting spacing: Role of low-abundance but core rhizobacterial communities

Optimizing planting spacing is a common agricultural practice for enhancing rice growth. However, its effect on the accumulation of cadmium (Cd) and phenanthrene (Phen) in soil-rice systems and the response mechanisms of rhizobacteria to co-contaminants remain unclear. This study found that reducing rice planting spacing to 5 cm and 10 cm significantly decreased the bioavailability of Cd (by 7.9 %-29.5 %) and Phen (by 12.9 %-47.6 %) in the rhizosphere soil by converting them into insoluble forms. The increased accumulation of Cd and Phen in roots and iron plaques (IPs) ultimately led to decreased Cd (by 32.2 %-39.9 %) and Phen (by 4.2 %-17.3 %) levels in brown rice, and also significantly affected the composition of rhizobacteria. Specifically, reducing rice planting spacing increased the abundance of low-abundance but core rhizobacteria in the rhizosphere soil and IPs, including Bacillus, Clostridium, Sphingomonas, Paenibacillus, and Leifsonia. These low-abundance but core rhizobacteria exhibited enhanced metabolic capacities for Cd and Phen, accompanied by increased abundances of Cd-resistance genes (e.g., czcC and czcB) and Phen-degradation genes (e.g., pahE4 and pahE1) within the rhizosphere soil and IPs. Reduced planting spacing had no noticeable impact on rice biomass. These findings provide new insights into the role of low-abundance but core rhizobacterial communities in Cd and Phen uptake by rice, highlighting the potential of reduced planting spacing as an eco-friendly strategy for ensuring the safety of rice production on contaminated paddy soils.

Mechanisms of benzene and benzo[a]pyrene biodegradation in the individually and mixed contaminated soils

There is a lack of knowledge on the biodegradation mechanisms of benzene and benzo [a]pyrene (BaP), representative compounds of polycyclic aromatic hydrocarbons (PAHs), and benzene, toluene, ethylbenzene, and xylene (BTEX), under individually and mixed contaminated soils. Therefore, a set of microcosm experiments were conducted to explore the influence of benzene and BaP on biodegradation under individual and mixed contaminated condition, and their subsequent influence on native microbial consortium. The results revealed that the total mass loss of benzene was 56.0% under benzene and BaP mixed contamination, which was less than that of individual benzene contamination (78.3%). On the other hand, the mass loss of BaP was slightly boosted to 17.6% under the condition of benzene mixed contamination with BaP from that of individual BaP contamination (14.4%). The significant differences between the microbial and biocide treatments for both benzene and BaP removal demonstrated that microbial degradation played a crucial role in the mass loss for both contaminants. In addition, the microbial analyses revealed that the contamination of benzene played a major role in the fluctuations of microbial compositions under co-contaminated conditions. Rhodococcus, Nocardioides, Gailla, and norank_c_Gitt-GS-136 performed a major role in benzene biodegradation under individual and mixed contaminated conditions while Rhodococcus, Noviherbaspirillum, and Phenylobacterium were highly involved in BaP biodegradation. Moreover, binary benzene and BaP contamination highly reduced the Rhodococcus abundance, indicating the toxic influence of co-contamination on the functional key genus. Enzymatic activities revealed that catalase, lipase, and dehydrogenase activities proliferated while polyphenol oxidase was reduced with contamination compared to the control treatment. These results provided the fundamental information to facilitate the development of more efficient bioremediation strategies, which can be tailored to specific remediation of different contamination scenarios.

Probiotics reshape the coral microbiome in situ without detectable off-target effects in the surrounding environment

Beneficial microorganisms for corals (BMCs), or probiotics, can enhance coral resilience against stressors in laboratory trials. However, the ability of probiotics to restructure the coral microbiome in situ is yet to be determined. As a first step to elucidate this, we inoculated putative probiotic bacteria (pBMCs) on healthy colonies of Pocillopora verrucosa in situ in the Red Sea, three times per week, during 3 months. pBMCs significantly influenced the coral microbiome, while bacteria of the surrounding seawater and sediment remained unchanged. The inoculated genera Halomonas, Pseudoalteromonas, and Bacillus were significantly enriched in probiotic-treated corals. Furthermore, the probiotic treatment also correlated with an increase in other beneficial groups (e.g., Ruegeria and Limosilactobacillus), and a decrease in potential coral pathogens, such as Vibrio. As all corals (treated and non-treated) remained healthy throughout the experiment, we could not track health improvements or protection against stress. Our data indicate that healthy, and therefore stable, coral microbiomes can be restructured in situ, although repeated and continuous inoculations may be required in these cases. Further, our study provides supporting evidence that, at the studied scale, pBMCs have no detectable off-target effects on the surrounding microbiomes of seawater and sediment near inoculated corals.

Characterization and low-temperature biodegradation mechanism of 17β-estradiol-degrading bacterial strain Rhodococcus sp. RCBS9

Steroidal estrogens residues in the environment can be a serious hazard to humans and animals and has been listed as group 1 carcinogens by World Health Organization (WHO). Microbial degradation is one of the effective strategies for the removal of such contaminants. In this study, a low-temperature degrading bacterial strain (Rhodococcus sp. RCBS9) was isolated from the soil of a dairy farm for 17β-estradiol (E2) degradation. The strain RCBS9 exhibited an efficient degradation potential at low temperatures. To lean how different factors influence E2 degradation, we have found a major role of intracellular enzymes in E2 degradation. Genomic and metabolomic analyses have suggested potential degradation genes and four metabolic pathways. These findings provide valuable strain resources for the low temperature bioremediation of E2 contamination and insights into E2 biodegradation mechanism.

Insight into functional mechanisms of percarbamide and nitrification inhibitors in degrading fungicide residues and shaping microbial communities in soil-plant systems

Fungicides and nitrogen (N) fertilizers are essential to maintain plant yield in current intensive agriculture. Percarbamide is a novel type of N fertilizer with strong oxidizing property, and the nitrification inhibitor is widely used in agricultural production. It may be feasible to apply percarbamide and nitrification inhibitor as N management to promote fungicide dissipations in soil-plant system. This study quantified the effects of percarbamide and nitrification inhibitor dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP) on carbendazim residues, and microbial communities of soil-plant systems, and relationships among carbendazim residues, soil and endophytic microbial communities and plant yields were also comprehensively quantified. Compared with the control, the percarbamide significantly reduced soil carbendazim residues by 29.4% but enhanced the lettuce yield by 28.0%. Soil carbendazim residues were significantly and negatively correlated with the soil total N and NO3--N contents. Soil microbial community structures and co-occurrence networks were more sensitive to N management than their endophytic counterparts. In comparison to the percarbamide alone, the DCD significantly increased the nodes of soil fungal community co-occurrence network which were positively correlated with the plant yield. The DCD outweighed DMPP in increasing the lettuce yield and soil fungal community stability and reshaping soil bacterial community structure. Our study suggested that soil microbial communities were more sensitive to percarbamide and nitrification inhibitor applications than their endophytic counterparts under fungicide pressure and that the DCD outweighed DMPP in reshaping microbial communities. The integrated applications of percarbamide and nitrification inhibitors were promising soil N management strategies to promote fungicide removal and stimulate microbial community in the soil-plant systems.

Biotransformation of carbendazim in cowpea pickling process

Carbendazim, a systemic fungicide, is one of the most commonly detected pesticides in cowpeas. Pickled cowpea is a fermented vegetable product with unique flavor favored in China. The dissipation and degradation of carbendazim were investigated in the pickled process. The degradation rate constant of carbendazim in pickled cowpeas was 0.9945 and the half-life of the carbendazim was 14.06 ± 0.82 d. Seven transformation products (TPs) were identified in the pickled process. Furthermore, the toxicity of some TPs show more harmful to three aquatic organisms (TP134) and rats (all the identified TPs) than carbendazim. And most of the TPs posed more development toxicity and mutagenicity than carbendazim. 4 out of 7 TPs were discovered in the real pickled cowpea samples. These results shed light on the degradation and biotransformation of the carbendazim in the pickled process, to better understand the potential health risk of pickled food and evaluate the environmental pollution.

Stenotrophomonas pavanii DJL-M3 inoculated biochar stabilizes the rhizosphere soil homeostasis of carbendazim-stressed rice

Plant-microbe interactions have been effectively used in phytoremediation to reduce agrochemical contamination of crops and soils, but little information is available regarding the general effect of such association on rhizosphere soil homeostasis. In this study, we immobilized Stenotrophomonas pavanii DJL-M3, a carbendazim (CBZ)-degrading endophyte, in rice husk-derived biochar to control fungicide residue in the rice microenvironment. The influence of biochar inoculated with strain DJL-M3 on rhizobacterial communities was also investigated, including activity and fundamental function predictions. An adsorption kinetics test showed that strain DJL-M3 slowed the adsorption rate slightly without sacrificing the adsorption capacity of rice-husk biochar on CBZ. Immobilization in biochar helped S. pavanii DJL-M3 to establish an ecological niche in rhizosphere soils. This process significantly reduced CBZ levels in rice and rhizosphere soil while maintaining stable heterotrophic microbial respiration and carbon (C) metabolic activity. Soil amendment with the strain DJL-M3-biochar composite resulted in relatively little disturbance of fundamental soil functions, such as nitrogen (N) and sulfur (S) cycling, which explained the better plant growth and higher soil fertility observed with CBZ contamination. Overall, the combination of biochar and S. pavanii DJL-M3 demonstrated the potential to safeguard the microbiological environment of rice.

The win-win effects of nitrification inhibitors on soil-crop systems: Decreasing carbendazim residues but promoting soil bacterial community diversities and stabilities and crop yields

Applying nitrogen (N)-cycling inhibitors is an effective measure to improve N fertilizer utilization efficiency, but the effects of N-cycling inhibitors on fungicide residues in soil-crop systems are unclear. In this study, nitrification inhibitors dicyandiamide (DCD) and 3, 4-dimethylpyrazole phosphate (DMPP) and urease inhibitor N-(n-butyl) thiophosphoric triamide (NBPT) were applied into agricultural soils with fungicide carbendazim applications. The soil abiotic properties, carrot yields, carbendazim residues, bacterial communities and their comprehensive relationships were also quantified. Compared to the control treatment, the DCD and DMPP significantly decreased soil carbendazim residues by 96.2% and 96.0%, and the DMPP and NBPT significantly reduced carrot carbendazim residues by 74.3% and 60.3%, respectively. The nitrification inhibitor applications also generated significant and positive effects on carrot yields and soil bacterial community diversities. The DCD application significantly stimulated soil Bacteroidota and endophytic Myxococcota and modified soil and endophytic bacterial communities. Meanwhile, the DCD and DMPP applications also positively stimulated the co-occurrence network edges of soil bacterial communities by 32.6% and 35.2%, respectively. The linear correlation coefficients between soil carbendazim residues and pH, ETSA and NH₄⁺-N contents were - 0.84, - 0.57 and - 0.80, respectively. The nitrification inhibitor applications generated win-win effects on the soil-crop systems by decreasing carbendazim residues but promoting soil bacterial community diversities and stabilities and crop yields.

Combined effects of spent mushroom substrate and dicyandiamide on carbendazim dissipation in soils: Double-edged sword effects and potential risk controls

Repeated and high-dose carbendazim applications have caused serious soil carbendazim contamination, and eco-friendly and economical approaches have been suggested to promote carbendazim removal in agricultural soil. Spent mushroom substrate (SMS) is a special recycled resource after harvesting mushrooms and can be utilized in contaminated soil amendment. The SMS application into agricultural soil might increase antibiotic resistance gene abundances, and the health risks of SMS application might be reduced with reasonable management to adjust the related electron transport of soil nitrification or denitrification. In this study, the SMS and nitrification inhibitor dicyandiamide were used to remediate agricultural soil contaminated with the carbendazim, and the carbendazim contents, soil microbial biomass, activities and community and human disease genes were determined. Compared to the control treatment, the combined applications of SMS and dicyandiamide significantly decreased soil carbendazim content by 38.14% but significantly enhanced soil β-glucosidase, chitinase, arylsulfatase, urease and electron transfer system activities. The relative abundances of Proteobacteria and Actinobacteria were increased by 11.0% and 8.2% with the SMS application, respectively. The carbendazim residues were negatively correlated with the soil pH, electron transfer system activities and relative abundances of Proteobacteria and Actinobacteria. The relative abundances of human disease genes were also dramatically increased with the SMS application, but compared to the SMS alone, extra dicyandiamide application significantly reduced the relative abundances of human disease genes in soils. The SMS applications into fungicide-contaminated soils could generate double-edged sword effects of facilitating fungicide dissipation but leading to potential health risk increase, while applying the dicyandiamide with SMS might be an effective strategy to decrease the negative effect of health risk.

Revealing the driving synergistic degradation mechanism of Rhodococcus sp. B2 on the bioremediation of pretilachlor-contaminated soil

The pretilachlor has been widely used worldwide and has contaminated the environment for many years. The environmental fate of pretilachlor and its residues removal from the contaminated environment have attracted great concern. Reportedly, pretilachlor could partly be transformed to HECDEPA by Rhodococcus sp. B2. However, the effects of pretilachlor on soil bacterial communities and its complete metabolic pathway remain unknown. Herein, we investigated the mechanism of driving synergistic degradation of pretilachlor by strain B2 in the soil. The results revealed that pretilachlor showed a negative effect on bacterial communities and caused significant variations in the community structure. Strain B2 showed the ability to remediate the pretilachlor-contaminated soils and network analysis revealed that it may drive the enrichment of potential pretilachlor-degrading bacteria from the soil. The soil pretilachlor degradation may be facilitated by the members of the keystone families Comamonadaceae, Caulobacteraceae, Rhodospirillaceae, Chitinophagaceae, and Sphingomonadaceae. Meanwhile, Sphingomonas sp. M6, a member of the Sphingomonadaceae family, has been isolated from the strain B2 inoculation sample soil. The co-culture, comprising strain M6 and B2, could synergistic degrade pretilachlor within 30 h, which is the highest degradation rate. Strain M6 could completely degrade the HECDEPA via CDEPA and DEA. In the soil, a comparable pretilachlor degradation pathway may exist. This study suggested that strain B2 had the potential to drive the remediation of pretilachlor-contaminated soils.

In situ bioremediation of petroleum hydrocarbon–contaminated soil: isolation and application of a Rhodococcus strain

Due to low consumption and high efficiency, in situ microbial remediation of petroleum hydrocarbons (PHs)-contaminated sites in in-service petrochemical enterprises has attracted more and more attention. In this study, a degrading strain was isolated from oil depot-contaminated soil with soil extract (PHs) as the sole carbon source, identified and named Rhodococcus sp. OBD-3. Strain OBD-3 exhibited wide adaptability and degradability over a wide range of temperatures (15-37 °C), pH (6.0-9.0), and salinities (1-7% NaCl) to degrade 60.6-86.6% of PHs. Under extreme conditions (15 °C and 3-7% salinity), PHs were degraded by 60.6 ± 8.2% and more than 82.1% respectively. In OBD-3, the alkane monooxygenase genes alkB1 and alkB2 (GenBank accession numbers: MZ688386 and MZ688387) were found, which belonged to Rhodococcus by sequence alignment. Moreover, strain OBD-3 was used in lab scale remediation in which the contaminated soil with OBD-3 was isolated as the remediation object. The PHs were removed at 2,809 ± 597 mg/kg within 2 months, and the relative abundances of Sphingobium and Pseudomonas in soil increased more than fivefold. This study not only established a system for the isolation and identification of indigenous degrading strains that could efficiently degrade pollutants in the isolated environment but also enabled the isolated degrading strains to have potential application prospects in the in situ bioremediation of PHs-contaminated soils.

Rhodococcus: A promising genus of actinomycetes for the bioremediation of organic and inorganic contaminants

Rhodococcus is a genus of actinomycetes that has been explored by the scientific community for different purposes, especially for bioremediation uses. However, the mechanisms governing Rhodococcus-mediated bioremediation processes are far from being fully elucidated. In this sense, this work aimed to compile the recent advances in the use of Rhodococcus for the bioremediation of organic and inorganic contaminants present in different environmental compartments. We reviewed the bioremediation capacity and mechanisms of Rhodococcus spp. in the treatment of polycyclic aromatic hydrocarbons, phenolic substances, emerging contaminants, heavy metals, and dyes given their human health risks and environmental concern. Different bioremediation techniques were discussed, including experimental conditions, treatment efficiencies, mechanisms, and degradation pathways. The use of Rhodococcus strains in the bioremediation of several compounds is a promising approach due to their features, primarily the presence of appropriate enzyme systems, which result in high decontamination efficiencies; but that vary according to experimental conditions. Besides, the genus Rhodococcus contains a small number of opportunistic species and pathogens, representing an advantage from the point of view of safety. Advances in analytical detection techniques and Molecular Biology have been collaborating to improve the understanding of the mechanisms and pathways involved in bioremediation processes. In the context of using Rhodococcus spp. as bioremediation agents, there is a need for more studies that 1) evaluate the role of these actinomycetes on a pilot and field scale; 2) use genetic engineering tools and consortia with other microorganisms to improve the bioremediation efficiency; and 3) isolate new Rhodococcus strains from environments with extreme and/or contaminated conditions aiming to explore their adaptive capabilities for bioremediation purposes.

Bioremediation of hazardous pollutants from agricultural soils: A sustainable approach for waste management towards urban sustainability

Soil contamination is perhaps the most hazardous issue all over the world; these emerging pollutants ought to be treated to confirm the safety of our living environment. Fast industrialization and anthropogenic exercises have resulted in different ecological contamination and caused serious dangerous health effects to humans and animals. Agro wastes are exceptionally directed because of their high biodegradability. Effluents from the agro-industry are a possibly high environmental risk that requires suitable, low-cost, and extensive treatment. Soil treatment using a bioremediation method is considered an eco-accommodating and reasonable strategy for removing toxic pollutants from agricultural fields. The present review was led to survey bioremediation treatability of agro soil by microbes, decide functional consequences for microbial performance and assess potential systems to diminish over potentials. The presence of hazardous pollutants in agricultural soil and sources, and toxic health effects on humans has been addressed in this review. The present review emphasizes an outline of bioremediation for the effective removal of toxic contaminants in the agro field. In addition, factors influencing recent advancements in the bioremediation process have been discussed. The review further highlights the roles and mechanisms of micro-organisms in the bioremediation of agricultural fields.

Use of soil actinomycetes for pharmaceutical, food, agricultural, and environmental purposes

In this article, we reviewed the international scientific production of the last years on actinomycetes isolated from soil aiming to report recent advances in using these microorganisms for different applications. The most promising genera, isolation conditions and procedures, pH, temperature, and NaCl tolerance of these bacteria were reported. Based on the content analysis of the articles, most studies have focused on the isolation and taxonomic description of new species of actinomycetes. Regarding the applications, the antimicrobial potential (antibacterial and antifungal) prevailed among the articles, followed by the production of enzymes (cellulases and chitinases, etc.), agricultural uses (plant growth promotion and phytopathogen control), bioremediation (organic and inorganic contaminants), among others. Furthermore, a wide range of growth capacity was verified, including temperatures from 4 to 60 °C (optimum: 28 °C), pH from 3 to 13 (optimum: 7), and NaCl tolerance up to 32% (optimum: 0-1%), which evidence a great tolerance for actinomycetes cultivation. Streptomyces was the genus with the highest incidence among the soil actinomycetes and the most exploited for different uses. Besides, the interest in isolating actinomycetes from soils in extreme environments (Antarctica and deserts, for example) is growing to explore the adaptive capacities of new strains and the secondary metabolites produced by these microorganisms for different industrial interests, especially for pharmaceutical, food, agricultural, and environmental purposes.

High tolerance and degradation of fungicides by fungal strains isolated from contaminated soils

The aim of this work was to isolate fungal strains from phytotoxic agricultural soils, screen them, categorize the most tolerant fungi to three fungicides, and identify them by a molecular approach. In this study, 28 fungal strains were isolated from phytotoxic agricultural soil with intensive use of pesticides. The capacity of fungi to resist and degrade different concentrations of carbendazim, captan, and zineb was determined by an exploratory multivariate analysis. Actinomucor elegans LBM 239 was identified as the most tolerant fungus to these fungicides, degrading a 86.62% of carbendazim after 7 days of treatment. In conclusion, A. elegans LBM 239 demonstrated the highest tolerance and capacity to biodegrade carbendazim, becoming a potential candidate for bioremediation of contaminated soils with carbendazim, captan, or zineb.

Rapid Detection of Carbendazim Residue in Apple Using Surface-Enhanced Raman Scattering and Coupled Chemometric Algorithm

In order to achieve rapid and precise quantification detection of carbendazim residues, surface-enhanced Raman spectroscopy (SERS) combined with variable selected regression methods were developed. A higher sensitivity and greater density of "hot spots" in three-dimensional (3D) SERS substrates based on silver nanoparticles compound polyacrylonitrile (Ag-NPs @PAN) nanohump arrays were fabricated to capture and amplify the SERS signal of carbendazim. Four Raman spectral variable selection regression models were established and comparatively assessed. The results showed that the bootstrapping soft shrinkage-partial least squares (BOSS-PLS) method achieved the best predictive capacity after variable selection, and the final BOSS-PLS model has the correlation coefficient (R_P) of 0.992. Then, this method used to detect the carbendazim residue in apple samples; the recoveries were 86~116%, and relative standard deviation (RSD) is less than 10%. The 3D SERS substrates combined with the BOSS-PLS algorithm can deliver a simple and accurate method for trace detection of carbendazim residues in apples.

Enhanced bioremediation of sediment contaminated with polycyclic aromatic hydrocarbons by combined stimulation with sodium acetate/phthalic acid

In this study, four groups of laboratory scale experiments were performed by adding sodium acetate (SA), phthalic acid (PA), and SA-PA to river sediment to observe the microbial response and biodegradation efficiency of polycyclic aromatic hydrocarbons (PAHs). The results showed that the amount of total organic carbon consumed and the amount of sulfate reduction were both positively correlated (p < 0.01) with the biodegradation efficiency of the sum (∑) PAHs (∼40.5%). The lower the number of rings, the more PAHs were biodegraded, with an efficiency of 63.0% for ∑ (2 + 3) ring PAHs. Based on high-throughput sequencing and molecular ecological network analysis, it was found that the combined stimulation of SA and PA not only increased the relative abundance of PAHs-degrading bacterial (eg., Proteobacteria, Desulfobacterota, Campilobacterota and Firmicutes), but also had a strengthening effect on microbes in sediments. The altered microbial structure caused a variation in metabolic functions, which increased the amino acid metabolism to 12.2%, thus increasing the positive correlations among genera and improving the connectivity of the microbial network (p < 0.01). These changes may be responsible for the enhanced biodegradation of PAHs under SA-PA dosing in comparison to SA or PA dosing alone. This study revealed that the microbial community was stimulated by the combined addition of SA and PA, and indicated its role in enhancing biodegradation of PAHs in contaminated river sediments.

A Competitive Assay Based on Dual-Mode Au@Pt-DNA Biosensors for On-Site Sensitive Determination of Carbendazim Fungicide in Agricultural Products

Carbendazim (CBZ), a systemic, broad-spectrum benzimidazole fungicide, is widely used to control fungal diseases in agricultural products. Its residues might pose risks to human health and the environment. Therefore, it is warranted to establish a rapid and reliable method for its residual quantification. Herein, we proposed a competitive assay that combined aptamer (DNA) specific recognition and bimetallic nanozyme gold@platinum (Au@Pt) catalysis to trace the CBZ residue. The DNA was labeled onto bimetallic nanozyme Au@Pt surface to produce Au@Pt probes (Au@Pt-DNA). The magnetic Fe₃O₄ was functionalized with a complementary strand of DNA (C-DNA) to form Fe₃O₄ probes (Fe₃O₄-C-DNA). Subsequently, the CBZ and the Fe₃O₄ probes competitively react with Au@Pt probes to form two Au@Pt-DNA biosensors (Au@Pt-ssDNA-CBZ and Au@Pt-dsDNA-Fe₃O₄). The Au@Pt-ssDNA-CBZ biosensor was designed for qualitative analysis through a naked-eye visualization strategy in the presence of CBZ. Meanwhile, Au@Pt-dsDNA-Fe₃O₄ biosensor was developed to quantitatively analyze CBZ using a multifunctional microplate reader. A competitive assay based on the dual-mode Au@Pt-DNA biosensors was established for onsite sensitive determination of CBZ. The limit of detection (LOD) and recoveries of the developed assay were 0.038 ng/mg and 71.88-110.11%, with relative standard deviations (RSDs) ranging between 3.15 and 10.91%. The assay demonstrated a good correlation with data acquired from liquid chromatography coupled with mass spectrometry/mass spectrometry analysis. In summary, the proposed competitive assay based on dual-mode Au@Pt-DNA biosensors might have a great potential for onsite sensitive detection of pesticides in agro-products.

Diversity of rice rhizosphere microorganisms under different fertilization modes of slow-release fertilizer

The application of slow-release fertilizer is an effective way to satisfy the demand for nutrients of crops. The objective of present study was to investigate the microbial community characteristics in rice rhizosphere soil under different fertilization modes of slow-release fertilizer. Three fertilization modes of slow-release fertilizer, i.e., (CK) manually broadcasted on the soil surface at 300 kg·ha⁻¹ before transplanting and then same fertilizer rate was applied at the same way one week after transplanting; (SF) 10 cm depth mechanized placement at 600 kg·ha⁻¹ during the transplanting; (DSF) 10 cm depth mechanized placement at 480 kg·ha⁻¹ during the transplanting, were adopt in the field experiment. The results showed that SF and DSF treatments promoted richness (ACE and Chao1 values) and diversity (Shannon value) of rice rhizosphere microorganisms compared with CK treatment. Compared with CK, SF treatment increased relative abundances of Planctomycetes and decreased relative abundance of Nitrospirae, DSF treatments increased relative abundances of Deltaproteobacteria. Moreover, higher relative abundances of Paenibacillus and Sphingomonas were recorded in DSF treatment than CK. In addition, the partial factor productivity (PFP) deep placement of slow-release fertilizer treatment was significantly higher than that of CK treatment. DSF treatment increased the yield by 16.61% compared with CK treatment while reducing fertilizer input by 20%. In conclusion, compared with broadcasting, deep placement of slow-release fertilizer could improve the structure, distribution, and diversity of the microbial community in rice rhizosphere soil, and increase the utilization rate of fertilizers, and increase rice yield.

Different performance of pyrene biodegradation on metal-modified montmorillonite: Role of surface metal ions from a bioelectrochemical perspective

Microbial extracellular electron transfer (EET) at microbe-mineral interface has been reported to play a significant role in pollutant biotransformation. Different metals often co-exist with organic pollutants and are immobilized on mineral surfaces. However, little is known about the influence of mineral surface metal ions on organic pollutant biodegradation and the involved electron transfer mechanism. To address this knowledge gap, pyrene was used as a model compound to investigate the biodegradation of polycyclic aromatic hydrocarbon on montmorillonite mineral saturated with metal ions (Na(I), Ni(II), Co(II), Cu(II) and Fe(III)) by Mycobacteria strain NJS-1. Further, the possible underlying electron transfer mechanism by electrochemical approaches was investigated. The results show that pyrene biodegradation on montmorillonite was markedly influenced by surface metal ions, with degradation efficiency following the order Fe(III) > Na(I) ≈ Co(II) > Ni(II) ≈ Cu(II). Bioelectrochemical analysis showed that electron transfer activities (i.e., electron donating capacity and electron transport system activity) varied in different metal-modified montmorillonites and were closely related to pyrene biodegradation. Fe(III) modification greatly stimulated degrading enzyme activities (i.e., peroxidase and dioxygenase) and electron transfer activities resulting in enhanced pyrene biodegradation, which highlights its potential as a technique for pollutant bioremediation. The bacterial extracellular protein and humic substances played important roles in EET processes. Membrane-bound cytochrome C protein and extracellular riboflavin were identified as the electron shuttles responsible for transmembrane and cross extracellular matrix electron transfer, respectively. Additions of exogenetic electron mediators of riboflavin, humic acid and potassium ferricyanide accelerated pyrene biodegradation which further verified the critical role of EET in PAH transformation at bacteria-mineral interfaces. These results support the development of clay mineral based advanced bioremediation techniques through regulating the electron transfer processes at the microbe-mineral interfaces by mineral surface modification.

Actinobacteria: An eco-friendly and promising technology for the bioaugmentation of contaminants

Over the past two decades, various eco-friendly approaches utilizing microbial species to clean up contaminated environments have surfaced. In this aspect, actinobacteria have demonstrated their potential in contaminant degradation. The members of actinobacteria phylum exhibits a cosmopolitan distribution, which means that they can be found widely in both aquatic and terrestrial ecosystems. Actinobacteria play important ecological roles in the environment, such as degrading complex polymers, recycling compounds, and producing bioactive molecules. Hence, using actinobacteria to clean up contaminants is an attractive method in the field of biotechnology. This can be achieved through the green technology of bioaugmentation, whereby the degradative capacity of contaminated areas can be greatly improved through the introduction of specific microorganisms. This review describes actinobacteria as an eco-friendly and a promising technology for the bioaugmentation of contaminants, with focus on pesticides and heavy metals.