Genetically modified Pseudomonas biosensing biodegraders to detect PCB and chlorobenzoate bioavailability and biodegradation in contaminated soils

Bioengineered Microbes for Soil Health Restoration - Present Status and Future

According to the United Nations Environment Programme (UNEP), soil health is declining over the decades and it has an adverse impact on human health and food security. Hence, soil health restoration is a need of the hour. It is known that microorganisms play a vital role in remediation of soil pollutants like heavy metals, pesticides, hydrocarbons, etc. However, the indigenous microbes have a limited capacity to degrade these pollutants and it will be a slow process. Genetically modified organisms (GMOs) can catalyze the degradation process as their altered metabolic pathways lead to hypersecretions of various biomolecules that favor the bioremediation process. This review provides an overview on the application of bioengineered microorganisms for the restoration of soil health by degradation of various pollutants. It also sheds light on the challenges of using GMOs in environmental application as their introduction may affect the normal microbial community in soil. Since soil health also refers to the potential of native organisms to survive, the possible changes in the native microbial community with the introduction of GMOs are also discussed. Finally, the future prospects of using bioengineered microorganisms in environmental engineering applications to make the soil fertile and healthy have been deciphered. With the alarming rates of soil health loss, the treatment of soil and soil health restoration need to be fastened to a greater pace and the combinatorial efforts unifying GMOs, plant growth-promoting rhizobacteria, and other soil amendments will provide an effective solution to soil heath restoration ten years ahead.

A method for detecting perfluorooctanoic acid and perfluorooctane sulfonate in water samples using genetically engineered bacterial biosensor

A simple, reagent and pre-treatment (i.e. dilution, sample purification and pH adjustment) free approach based genetically engineered bacterial biosensor is developed and demonstrated for the detection of perfluorinated compounds in water samples. The bacterial biosensor was developed by integrating two genes called regulatory (defluorinase gene) and reporter gene (green fluorescence gene) through genetic engineering techniques. The as-developed bacterial biosensor was employed to detect perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) in water samples upon induction of regulatory gene and expression of green fluorescence protein. The induced fluorescence emission by the biosensor was visualized using fluorescence microscopic images. The specificity of biosensor was evaluated with different types of organic pollutants such as chlorinated compounds, polyaromatic hydrocarbons and pesticides etc., in both presence and absence of PFOA and PFOS. The biosensor was employed to detect the perfluorinated compounds at nano gram level in both standard solutions and natural water samples like river water, wastewater and drinking water with an analysis time of 24 h. The detection of PFOA and PFOS by the developed-bacterial sensor is validated by liquid chromatography coupled with mass spectrometer. The developed biosensor has demonstrated a rapid and sensitive detection of PFOA and PFOS in various water samples.

Microbial and enzymatic degradation of PCBs from e-waste-contaminated sites: a review

Electronic waste is termed as e-waste and on recycling it produces environmental pollution. Among these e-waste pollutants, polychlorinated biphenyls (PCBs) are significantly important due to ubiquitous, organic in nature and serious health and environmental hazards. PCBs are used in different electrical equipment such as in transformers and capacitors for the purposes of exchange of heat and hydraulic fluids. Bioremediation is a reassuring technology for the elimination of the PCBs from the environment. In spite of their chemical stability, there are several microbes which can bio-transform or mineralize the PCBs aerobically or anaerobically. In this review paper, our objective was to summarize the information regarding PCB-degrading enzymes and microbes. The review suggested that the most proficient PCB degraders during anaerobic condition are Dehalobacter, Dehalococcoides, and Desulfitobacterium and in aerobic condition are Burkholderia, Achromobacter, Comamonas, Ralstonia, Pseudomonas, Bacillus, and Alcaligenes etc., showing the broadest substrate among bacterial strains. Enzymes found in soil such as dehydrogenases and fluorescein diacetate (FDA) esterases have the capability to breakdown PCBs. Biphenyl upper pathway involves four enzymes: dehydrogenase (bphB), multicomponent dioxygenase (bphA, E, F, and G), second dioxygenase (bphC), hydrolase, and (bphD). Biphenyl dioxygenase is considered as the foremost enzyme used for aerobic degradation of PCBs in metabolic pathway. It has been proved that several micro-organisms are responsible for the PCB metabolization. The review provides novel strategies for e-waste-contaminated soil management.

Transcriptional regulation of organohalide pollutant utilisation in bacteria

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds. Such bacteria are of potential high interest for bioremediation of contaminated sites. Dehalogenase genes are often part of gene clusters that may include regulators, accessory genes and genes for transporters and other enzymes of organohalide degradation pathways. Organohalides and their degradation products affect the activity of regulatory factors, and extensive genome-wide modulation of gene expression helps dehalogenating bacteria to cope with stresses associated with dehalogenation, such as intracellular increase of halides, dehalogenase-dependent acid production, organohalide toxicity and misrouting and bottlenecks in metabolic fluxes. This review focuses on transcriptional regulation of gene clusters for dehalogenation in bacteria, as studied in laboratory experiments and in situ. The diversity in gene content, organization and regulation of such gene clusters is highlighted for representative organohalide-degrading bacteria. Selected examples illustrate a key, overlooked role of regulatory processes, often strain-specific, for efficient dehalogenation and productive growth in presence of organohalides.

Rhizoremediation of Cu(II) ions from contaminated soil using plant growth promoting bacteria: an outlook on pyrolysis conditions on plant residues for methylene orange dye biosorption

Rhizoremediation is one of the most accepted, cost-effective bioremediation techniques focusing on the application of rhizospheric microorganisms in combination with plants for the remediation of organic and inorganic pollutants from the contaminated sites. This work focuses on isolation and identification of metal resistant bacteria to grow on medium with the copper ion concentration of 1500 mg/L. The resistant isolate was identified as Pantoea dispersa by a 16S rRNA sequencing. The bioaccumulation of Cu(II) ions in plant is high at the concentration of Cu(II) ion is 125 mg/L in soil. In Sphaeranthus indicus the Cu(II) ion translocation factor has expanded with an expansion of grouping of Cu(II) ion in the soil and the most extreme TF factor was acquired at the centralization of Cu(II) ion is 150 mg/L in soil. Surface morphology of biochar was characterized by Scanning Electron Microscopy (SEM) analysis. The adsorption performance of biochar (Sphaeranthus indicus biomass) and mechanism for the removal of Cu(II) ion were investigated. This study resolves that pyrolysis is promising technology for the conversion of metal ion contaminated plant residues from phytoremediation into valuable products.

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.

A whole-cell bioreporter approach for the genotoxicity assessment of bioavailability of toxic compounds in contaminated soil in China

A whole-cell bacterial bioreporter Acinetobacter baylyi strain ADP1_recA_lux that responds to genotoxins was employed to directly assess the adverse effects of the bioavailable fraction of mitomycin C (MMC), benzo[a]pyrene (BaP), chromium (VI) and lead (II) in amended soils and soil samples from two fragile areas in China without soil pre-treatment. The amended soils containing pollutants with the concentrations as low as 0.4 mg/kg MMC, 0.5 mg/kg BaP, 520 mg/kg Cr (VI) and 2072 mg/kg Pb (II) were found to be toxic. Soil particle-associated pollutants accounted for 86%, 100%, 29%, and 92% of the genotoxicity in the MMC, BaP, Cr (VI), and Pb (II) amended soil, respectively. The soils from contaminated sites were also valid to be genotoxic. The results suggest both free and soil particle-associated pollutants are bioavailable to soil organisms and a solid-phase contact bioreporter assay to soil contamination could provide a rapid screening tool for environmental risk assessment.

Assessment of planctomycetes cell viability after pollutants exposure

In this study, the growth of six different planctomycetes, a particular ubiquitous bacterial phylum, was assessed after exposure to pollutants. In addition and for comparative purposes, Pseudomonas putida, Escherichia coli and Vibrio anguillarum were tested. Each microorganism was exposed to several concentrations of 21 different pollutants. After exposure, bacteria were cultivated using the drop plate method. In general, the strains exhibited a great variation of sensitivity to pollutants in the order: V. anguillarum > planctomycetes > P. putida > E. coli. E. coli showed resistance to all pollutants tested, with the exception of phenol and sodium azide. Copper, Ridomil® (fungicide), hydrazine and phenol were the most toxic pollutants. Planctomycetes were resistant to extremely high concentrations of nitrate, nitrite and ammonium but they were the only bacteria sensitive to Previcur N® (fungicide). Sodium azide affected the growth on plates of E. coli, P. putida and V. anguillarum, but not of planctomycetes. However, this compound affected planctomycetes cell respiration but with less impact than in the aforementioned bacteria. Our results provide evidence for a diverse response of bacteria towards pollutants, which may influence the structuring of microbial communities in ecosystems under stress, and provide new insights on the ecophysiology of planctomycetes.