Construction of a bioreporter by heterogeneously expressing a Vibrio natriegens recA::luxCDABE fusion in Escherichia coli, and genotoxicity assessments of petrochemical-contaminated groundwater in northern China

Redesign of ultrasensitive and robust RecA gene circuit to sense DNA damage

SOS box of the recA promoter, PVRecA from Vibrio natriegens was characterized, cloned and expressed in a probiotic strain E. coli Nissle 1917. This promoter was then rationally engineered according to predicted interactions between LexA repressor and PVRecA . The redesigned PVRecA-AT promoter showed a sensitive and robust response to DNA damage induced by UV and genotoxic compounds. Rational design of PVRecA coupled to an amplification gene circuit increased circuit output amplitude 4.3-fold in response to a DNA damaging compound mitomycin C. A TetR-based negative feedback loop was added to the PVRecA-AT amplifier to achieve a robust SOS system, resistant to environmental fluctuations in parameters including pH, temperature, oxygen and nutrient conditions. We found that E. coli Nissle 1917 with optimized PVRecA-AT adapted to UV exposure and increased SOS response 128-fold over 40 h cultivation in turbidostat mini-reactor. We also showed the potential of this PVRecA-AT system as an optogenetic actuator, which can be controlled spatially through UV radiation. We demonstrated that the optimized SOS responding gene circuits were able to detect carcinogenic biomarker molecules with clinically relevant concentrations. The ultrasensitive SOS gene circuits in probiotic E. coli Nissle 1917 would be potentially useful for bacterial diagnosis.

Microbial degradation of organophosphorus pesticides: novel degraders, kinetics, functional genes, and genotoxicity assessment

Farmland soil sprayed with organophosphorus pesticides (OPs) annually was investigated for the identification and characterization of OP-degrading microorganisms. Six bacterial strains were identified, including Brevundimonas faecalis MA-B12 and Alcaligenes faecalis subsp. parafaecalis MA-B13 for methamidophos degradation, Citrobacter freundii TF-B21 and Ochrobactrum intermedium TF-B23 for trichlorfon degradation, Ochrobactrum intermedium DV-B31 for dichlorvos degradation, and Bacillus cereus for dimethoate degradation. The optimal biodegradation conditions for OPs were obtained at pH 7.0 and incubation temperature ranging from 28 to 37 °C. In an 8-day batch test, biodegradation of the four OPs all followed first-order kinetics, with biodegradation rates ranging from 58.08 to 96.42%. Functional genes responsible for OPs degradation were obtained, including ophB, ampA, opdE, opd, opdA, and mpd. As these strains were indigenous strains isolated from farmland soils, they can be potentially used as bacterial consortium for the bioremediation of mixed OP-contaminated soils. A time-course genotoxicity assessment of the degradation products was done by a bacterial whole-cell bioreporter, revealing that biodegradation of trichlorfon, dichlorvos, and dimethoate resulted a decreased genotoxicity within 5 days, which, however, significantly increased on day 8. The result demonstrated that more toxic products may be produced during the biodegradation processes of OPs, and more attention should be put not only on the pesticides themselves, but also on the toxic effects of their degradation products. To the best of our knowledge, this is for the first time that the genotoxicity of OP degradation products was evaluated by the bioreporter assay, broadening our understanding on the genotoxic risks of OPs during biodegradation process. Graphical Abstract.

Advances of magnetic nanoparticles in environmental application: environmental remediation and (bio)sensors as case studies

Nanotechnology is an emerging technique drawing increasing attentions in biomedical, electronic, environmental, and industrial application. Nanoparticles (NPs) possess unique optical, electrical, catalytic, and thermal properties, among which magnetic NPs (MNPs) are one of the most important groups with excellent superparamagnetism property, large surface area, and biocompatibility. In this review, methods for synthesizing and functionalizing MNPs are summarized and linked to their applications in environmental science as either adsorbents or catalysts for removing contaminants from environmental matrices, illustrating stronger reactivity, higher removal capacity, and fast kinetics. Additionally, we also comprehensively discuss the application of MNPs as (bio)sensors to selectively and sensitively detect the presence of environmental contaminants or pathogenic bacteria. This work summarizes the recent progresses of using MNPs as powerful tools in environmental science and engineering, raising their state-of-art application from environmental perspectives and benefiting researchers interested in NPs and environmental studies.

A whole-cell bioreporter assay for quantitative genotoxicity evaluation of environmental samples

Whole-cell bioreporters have emerged as promising tools for genotoxicity evaluation, due to their rapidity, cost-effectiveness, sensitivity and selectivity. In this study, a method for detecting genotoxicity in environmental samples was developed using the bioluminescent whole-cell bioreporter Escherichia coli recA::luxCDABE. To further test its performance in a real world scenario, the E. coli bioreporter was applied in two cases: i) soil samples collected from chromium(VI) contaminated sites; ii) crude oil contaminated seawater collected after the Jiaozhou Bay oil spill which occurred in 2013. The chromium(VI) contaminated soils were pretreated by water extraction, and directly exposed to the bioreporter in two phases: aqueous soil extraction (water phase) and soil supernatant (solid phase). The results indicated that both extractable and soil particle fixed chromium(VI) were bioavailable to the bioreporter, and the solid-phase contact bioreporter assay provided a more precise evaluation of soil genotoxicity. For crude oil contaminated seawater, the response of the bioreporter clearly illustrated the spatial and time change in genotoxicity surrounding the spill site, suggesting that the crude oil degradation process decreased the genotoxic risk to ecosystem. In addition, the performance of the bioreporter was simulated by a modified cross-regulation gene expression model, which quantitatively described the DNA damage response of the E. coli bioreporter. Accordingly, the bioluminescent response of the bioreporter was calculated as the mitomycin C equivalent, enabling quantitative comparison of genotoxicities between different environmental samples. This bioreporter assay provides a rapid and sensitive screening tool for direct genotoxicity assessment of environmental samples.