Genetically modified microorganism Spingomonas paucimobilis UT26 for simultaneously degradation of methyl-parathion and γ-hexachlorocyclohexane

Understanding the microbiome-crop rotation nexus in karst agricultural systems: insights from Southwestern China

Understanding how soil properties and microbial communities respond to crop rotation is essential for the sustainability of agroecosystems. However, there has been limited research on how crop rotation alters below-ground microbial communities in soils with serious bacterial wilt within the karst agricultural system. This study investigated the effects of continuous planting of corn, tobacco, and tobacco-corn rotation on soil microbial communities in the karst regions of Southwestern China. High-throughput sequencing was used to evaluate the responses of the soil microbial community structure to crop monoculture and rotation patterns. As expected, the tobacco-corn rotation mitigated the negative effects of continuous cropping and reduced soil acidification. The tobacco-corn rotation also significantly altered the composition of microbial communities and promoted plant growth by fostering a higher abundance of beneficial microorganisms. The predominant bacteria genera Sphingomonas and Gaiella and the predominant fungal genera Mortierella and Saitozyma were identified as discriminant biomarkers that are critical to soil ecosystem health. pH, available potassium (AK), and available phosphorus (AP) were the primary soil factors related to the soil microbiome assembly. This study aimed to demonstrate the association between crop rotation and microbiomes, suggesting that altering cultivation patterns could enhance karst agricultural systems.

Emerging technologies for the removal of pesticides from contaminated soils and their reuse in agriculture

Pesticides are becoming more prevalent in agriculture to protect crops and increase crop yields. However, nearly all pesticides used for this purpose reach non-target crops and remain as residues for extended periods. Contamination of soil by widespread pesticide use, as well as its toxicity to humans and other living organisms, is a global concern. This has prompted us to find solutions and develop alternative remediation technologies for sustainable management. This article reviews recent technological developments for remediating pesticides from contaminated soil, focusing on the following major points: (1) The application of various pesticide types and their properties, the sources of pesticides related to soil pollution, their transport and distribution, their fate, the impact on soil and human health, and the extrinsic and intrinsic factors that affect the remediation process are the main points of focus. (2) Sustainable pesticide degradation mechanisms and various emerging nano- and bioelectrochemical soil remediation technologies. (3) The feasible and long-term sustainable research and development approaches that are required for on-site pesticide removal from soils, as well as prospects for applying them directly in agricultural fields. In this critical analysis, we found that bioremediation technology has the potential for up to 90% pesticide removal from the soil. The complete removal of pesticides through a single biological treatment approach is still a challenging task; however, the combination of electrochemical oxidation and bioelectrochemical system approaches can achieve the complete removal of pesticides from soil. Further research is required to remove pesticides directly from soils in agricultural fields on a large-scale.

Effects of different botanical oil meal mixed with cow manure organic fertilizers on soil microbial community and function and tobacco yield and quality

Introduction

The continuous application of cow manure in soil for many years leads to the accumulation of heavy metals, pathogenic microorganisms, and antibiotic resistance genes. Therefore, in recent years, cow manure has often been mixed with botanical oil meal as organic fertilizer applied to farmland to improve soil and crop quality. However, the effects of various botanical oil meal and cow manure mixed organic fertilizers on soil microbial composition, community structure, and function, tobacco yield, and quality remain unclear.

Methods

Therefore, we prepared organic manure via solid fermentation by mixing cow manure with different oil meals (soybean meal, rape meal, peanut bran, sesame meal). Then, we studied its effects on soil microbial community structure and function, physicochemical properties, enzyme activities, tobacco yield and quality; then we analyzed the correlations between these factors.

Results and discussion

Compared with cow manure alone, the four kinds of mixed botanical oil meal and cow manure improved the yield and quality of flue-cured tobacco to different degrees. Peanut bran, which significantly improved the soil available phosphorus, available potassium, and NO₃^--N, was the best addition. Compared with cow manure alone, soil fungal diversity was significantly decreased when rape meal or peanut bran was combined with cow manure, while soil bacterial and fungal abundance was significantly increased when rape meal was added compared with soybean meal or peanut bran. The addition of different botanical oil meals significantly enriched the subgroup_7 and Spingomonas bacteria and Chaetomium and Penicillium fungi in the soil. The relative abundances of functional genes of xenobiotics biodegradation and metabolism, soil endophytic fungi, and wood saprotroph functional groups increased. In addition, alkaline phosphatase had the greatest effect on soil microorganisms, while NO₃^--N had the least effect on soil microorganisms. In conclusion, the mixed application of cow manure and botanical oil meal increased the available phosphorus and potassium contents in soil; enriched beneficial microorganisms; promoted the metabolic function of soil microorganisms; increased the yield and quality of tobacco; and improved the soil microecology.

Changes in rhizospheric microbiome structure and soil metabolic function in response to continuous cucumber cultivation

With the increasing reliance on intensive arable agriculture, analysis of the problems associated with continuous cropping has become a global research focus. Here, high-throughput sequencing and nontargeted metabolomics were used to evaluate the responses of soil microbial community structure and soil metabolic function to continuous cucumber cultivation (from 1 to 18 years of continuous cultivation) in greenhouses. Continuous cucumber cropping resulted in increased soil nutrient concentrations, but decreased concentrations of available nutrients. The abundance of several bacterial genera associated with nutrient cycling, such as Bacillus and Sphingomonas, was reduced by continuous cucumber cultivation. The abundance of several beneficial fungal genera, including pathogen antagonists (e.g. Chaetomium, Mortierella, Aspergillus, and Penicillium), were found to gradually decrease in response to the increased duration of continuous cropping. 3-amino-2-naphthoic acid and L-valine increased initially and then decreased as the cropping continued, which were related to fatty acid metabolism and amino acid biosynthesis. We also confirmed a close association between microbial community structure and soil metabolites. This study linked the changes in microbial community structure and metabolites in the rhizosphere soil and provided new insights into soil-microbial interactions in continuous cucumber culture systems.

Engineered microbes as effective tools for the remediation of polyaromatic aromatic hydrocarbons and heavy metals

Heavy metals (HMs) and polycyclic aromatic hydrocarbons (PAHs) have become a major concern to human health and the environment due to rapid industrialization and urbanization. Traditional treatment measures for removing toxic substances from the environment have largely failed, and thus development and advancement in newer remediation techniques are of utmost importance. Rising environmental pollution with HMs and PAHs prompted the research on microbes and the development of genetically engineered microbes (GEMs) for reducing pollution via the bioremediation process. The enzymes produced from a variety of microbes can effectively treat a range of pollutants, but evolutionary trends revealed that various emerging pollutants are resistant to microbial or enzymatic degradation. Naturally, existing microbes can be engineered using various techniques including, gene engineering, directed evolution, protein engineering, media engineering, strain engineering, cell wall modifications, rationale hybrid design, and encapsulation or immobilization process. The immobilization of microbes and enzymes using a variety of nanomaterials, membranes, and supports with high specificity toward the emerging pollutants is also an effective strategy to capture and treat the pollutants. The current review focuses on successful bioremediation techniques and approaches that make use of GEMs or engineered enzymes. Such engineered microbes are more potent than natural strains and have greater degradative capacities, as well as rapid adaptation to various pollutants as substrates or co-metabolizers. The future for the implementation of genetic engineering to produce such organisms for the benefit of the environment andpublic health is indeed long and valuable.

Conserved Metabolic and Evolutionary Themes in Microbial Degradation of Carbamate Pesticides

Carbamate pesticides are widely used as insecticides, nematicides, acaricides, herbicides and fungicides in the agriculture, food and public health sector. However, only a minor fraction of the applied quantity reaches the target organisms. The majority of it persists in the environment, impacting the non-target biota, leading to ecological disturbance. The toxicity of these compounds to biota is mediated through cholinergic and non-cholinergic routes, thereby making their clean-up cardinal. Microbes, specifically bacteria, have adapted to the presence of these compounds by evolving degradation pathways and thus play a major role in their removal from the biosphere. Over the past few decades, various genetic, metabolic and biochemical analyses exploring carbamate degradation in bacteria have revealed certain conserved themes in metabolic pathways like the enzymatic hydrolysis of the carbamate ester or amide linkage, funnelling of aryl carbamates into respective dihydroxy aromatic intermediates, C1 metabolism and nitrogen assimilation. Further, genomic and functional analyses have provided insights on mechanisms like horizontal gene transfer and enzyme promiscuity, which drive the evolution of degradation phenotype. Compartmentalisation of metabolic pathway enzymes serves as an additional strategy that further aids in optimising the degradation efficiency. This review highlights and discusses the conclusions drawn from various analyses over the past few decades; and provides a comprehensive view of the environmental fate, toxicity, metabolic routes, related genes and enzymes as well as evolutionary mechanisms associated with the degradation of widely employed carbamate pesticides. Additionally, various strategies like application of consortia for efficient degradation, metabolic engineering and adaptive laboratory evolution, which aid in improvising remediation efficiency and overcoming the challenges associated with in situ bioremediation are discussed.

Effects of Different Continuous Cropping Years on Bacterial Community and Diversity of Cucumber Rhizosphere Soil in Solar-Greenhouse

The rhizosphere soils from 1, 3, 5, and 7 years of cucumber continuous cropping in solar-greenhouse were used as the research objects. The region of bacterial 16S rRNA was analyzed by Illumina MiSeq high-throughput sequencing technology. The effect of continuous cropping years on the microbial community structure and diversity in cucumber soil in the greenhouse was investigated. The physical and chemical properties of soil and the activities of urease and catalase were determined. The results showed that cucumber crop succession for different years affected the community composition of the bacteria at the phylum level, and the abundance of Proteobacteria, Chloroflexi, Gemmatimonadetes, Patescibacteria and Firmicutes gradually increased, while Actinobacteria in the soil significantly decreased. Among the top 15 significantly different genera, with the extension of successive years, the relative abundance of most genera in bacteria decreased after a small increase in year 3. The diversity results indicated that soil samples from continuous cropping for 7 years had the lowest community diversity. PICRUSt analysis showed a decreasing trend in soil bacterial function as the cucumber crop succession age increased. In environmental factor clustering analysis, the soil bacterial community was significantly correlated with pH, available nitrogen (AN), soil urease (SUR) and available phosphorus (AP), and the effect on the bacterial community was expressed as SUR > AP > AN > pH.

Biological approaches practised using genetically engineered microbes for a sustainable environment: A review

Conventional methods used to remediate toxic substances from the environment have failed drastically, and thereby, advancement in newer remediation techniques can be one of the ways to improve the quality of bioremediation. The increased environmental pollution led to the exploration of microorganisms and construction of genetically engineered microbes (GEMs) for pollution abatement through bioremediation. The present review deals with the successful bioremediation techniques and approaches practised using genetically modified or engineered microbes. In the present scenario, physical and chemical strategies have been practised for the remediation of domestic and industrial wastes but these techniques are expensive and toxic to the environment. Involving engineered microbes can provide a much safer and cost effective strategy in comparison with the other techniques. With the aid of biotechnology and genetic engineering, GEMs are designed by transforming microbes with a more potent protein to overexpress the desired character. GEMs such as bacteria, fungi and algae have been used to degrade oil spills, camphor, hexane, naphthalene, toluene, octane, xylene, halobenzoates, trichloroethylene etc. These engineered microbes are more potent than the natural strains and have higher degradative capacities with quick adaptation for various pollutants as substrates or cometabolize. The road ahead for the implementation of genetic engineering to produce such organisms for the welfare of the environment and finally, public health is indeed long and worthwhile.

Biodegradation of α-endosulfan via hydrolysis pathway by Stenotrophomonas maltophilia OG2

Stenotrophomonas maltophilia OG2 was isolated from the intestine of cockroaches that was collected from a cow barn contaminated some pesticides belong to pyrethroid and organochlorine groups. OG2 was able to degrade α-endosulfan in non sulfur medium (NSM) as a sole sulfur source for growth within 10 days of incubation. The effects of some growth parameters on endosulfan biodegradation by OG2 was studied and found that the biodegradation was significantly affected by the endosulfan concentrations, pH and temperature. Experimental results obtained in different conditions show that the optimum concentration of α-endosulfan, pH and temperature were 100 mg/L, 8.0 and 30 °C, respectively. Under these conditions, the bacterium degraded 81.53% of the α-endosulfan after 10 days. The concentration of α-endosulfan and its metabolites was determined by HPLC. Endosulfan ether, endosulfan lactone and endosulfan diol were the main metabolites in culture, but did not produce toxic metabolite, endosulfan sulfate. These results suggested that S. maltophilia OG2 degrades α-endosulfan via a hydrolysis pathway. The present study indicates that strain OG2 may have potential use in the biodegradation of pesticides contaminated environments.

The XylS/Pm regulator/promoter system and its use in fundamental studies of bacterial gene expression, recombinant protein production and metabolic engineering

The XylS/Pm regulator/promoter system originating from the Pseudomonas putida TOL plasmid pWW0 is widely used for regulated low‐ and high‐level recombinant expression of genes and gene clusters in Escherichia coli and other bacteria. Induction of this system can be graded by using different cheap benzoic acid derivatives, which enter cells by passive diffusion, operate in a dose‐dependent manner and are typically not metabolized by the host cells. Combinatorial mutagenesis and selection using the bla gene encoding β‐lactamase as a reporter have demonstrated that the Pm promoter, the DNA sequence corresponding to the 5′ untranslated end of its cognate mRNA and the xylS coding region can be modified and improved relative to various types of applications. By combining such mutant genetic elements, altered and extended expression profiles were achieved. Due to their unique properties, obtained systems serve as a genetic toolbox valuable for heterologous protein production and metabolic engineering, as well as for basic studies aiming at understanding fundamental parameters affecting bacterial gene expression. The approaches used to modify XylS/Pm should be adaptable for similar improvements also of other microbial expression systems. In this review, we summarize constructions, characteristics, refinements and applications of expression tools using the XylS/Pm system.