Bioderivatization as a concept for renewable production of toxic or poorly soluble chemicals

Bio-based production has increasingly gained attention as an alternative technology to complement or even substitute petroleum-based production of valuable chemicals. This technology, however, relies on the use of microbial cell factories and at times faces several challenges, including toxicity of the target products to microbial hosts. Many plants and microorganisms are naturally capable of biosynthesizing toxic molecules, but they often convert them into derivatives with reduced toxicity or enhanced solubility before the molecules are stored or excreted. Inspired by this principle, a novel strategy, bioderivatization, was proposed. Bioderivatization is here defined as a purposeful biochemical derivatization of intended target molecules by altering the functional groups to overcome such challenges. Oacetylation and O-glucosylation were proposed and investigated as two bioderivatization strategies. As a proof-of-principle, the effect of bioderivatization on biosynthesis of a relatively toxic and poorly soluble chemical, 1-octanol, was evaluated. The existing 1-octanol pathway was first optimized to enable the production of 1-octanol at higher titer. Novel synthetic pathways to derivatize 1-octanol into octyl acetate and octyl glucoside were then implemented in Escherichia coli and cyanobacteria. The evaluation of bioderivatization on growth and productivity showed that the implementation of bioderivatization contributed to improved growth and/or productivity in most cases. To understand if the bioderivatization strategy can be implemented in a broader scope (i.e., to derivatize other toxic chemicals), this strategy was also applied to derivatize several other attractive chemicals from different chemical classes. The preliminary results successfully identified several potential chemical candidates, including 1-dodecanol, menthol, and eugenol that showed a higher degree of toxicity compared to their corresponding derivatives. Finally, this study was concluded by identification of several active key enzymes to derivatize these toxic compounds. Altogether, this study showed that bioderivatization could be considered a strategy to improve the bioproduction of toxic or poorly soluble chemicals.Open Acces

Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Abstract Background Efficient bioconversion of lignocellulosic biomass to bioethanol is one of key challenges in the situation of increasing bioethanol demand. The ethanologenic microbes for such conversion are required to possess abilities of utilization of various sugars including xylose and arabinose in lignocellulosic biomass. As required additional characteristics, there are a weak or no glucose repression that allows cells to simultaneously utilize various sugars together with glucose and thermotolerance for fermentation at high temperatures, which has several advantages including reduction of cooling cost. Spathaspora passalidarum ATCC MYA-4345, a type strains, isolated previously have mainly of these abilities or characteristics but its thermotolerance is not so strong and its glucose repression on xylose utilization is revealed. Results Newly isolated S. passalidarum CMUWF1–2 was found to have a high ability to produce ethanol from various sugars included in lignocellulosic biomass at high temperatures. The strain achieved ethanol yields of 0.43 g, 0.40 g and 0.20 g ethanol/g xylose at 30 °C, 37 °C and 40 °C, respectively. Interestingly, no significant glucose repression was observed in experiments with mixed sugars, being consistent with the strong resistance to 2-deoxyglucose, and antimycin A showed no effect on its growth in xylose medium. Moreover, the strain was tolerant to glucose and ethanol at concentrations up to 35.0% (w/v) and 8.0% (v/v), respectively. Conclusions S. passalidarum CMUWF1–2 was shown to achieve efficient production of ethanol from various sugars and a high ethanol yield from xylose with little accumulation of xylitol. The strain also exhibited stress-resistance including thermotolerance and no detectable glucose repression as beneficial characteristics. Therefore, S. passalidarum CMUWF1–2 has remarkable potential for conversion of lignocellulosic biomass to bioethanol

Additional file 5: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Figure S2. Effects of 2-DOG were examined on YPXyl plates containing various concentrations of 2-DOG. (PDF 411 kb

Additional file 6: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Figure S3. Effects of 2-DOG were examined on YPMan, YPGal, YPXyl, and YPAra plates with or without 0.01% 2-DOG. (PDF 367 kb

Additional file 7: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Figure S4. Glucose tolerance and ethanol tolerance of S. passalidarum CMUWF1–2. Glucose tolerance (a) and ethanol tolerance (b) of S. passalidarum CMUWF1–2 were compared with those of K. marxianus and S. stipitis. Data were reproduced by two independent experiments. (PDF 460 kb

Additional file 3: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Table S2. Parameters in YP medium containing a single sugar at various temperatures under a shaking condition (160 rpm). μx/s, Specific growth rate; γs, Specific sugar utilization rate; ±, S.D. from three independent experiments. (PDF 331 kb

Additional file 8: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Table S4. Comparison of xylose fermentation data in this study with those reported previously in S. passalidarum strains. acultivation times that required for reaching the maximum values or cultivation time of the end of the fermentation experiment.; bResults for the best fermentation (fourth fed batch); WV, working volume, n; data not available or not tested; ND, not detected. (PDF 471 kb

Additional file 1: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Table S1. Xylose-utilizing yeasts isolated from natural samples and its sources. (PDF 357 kb

Additional file 2: of Highly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1–2

Figure S1. A phylogenetic tree of CMUWF1–2 isolated in this study and other strains published in databases was constructed. Numbers indicate percentages of bootstrap sampling, derived from 1000 samples. The numbers in parentheses are GenBank accession numbers. Schizosaccharomyces pombe NRRL Y-12796 was an outgroup in the analysis. (PDF 389 kb

Bacterial Communities Associated with Crude Oil Bioremediation through Composting Approaches with Indigenous Bacterial Isolate

In this study, we aim to investigate the efficiency of crude oil bioremediation through composting and culture-assisted composting. First, forty-eight bacteria were isolated from a crude oil-contaminated soil, and the isolate with the highest crude oil degradation activity, identified as Pseudomonas aeruginosa, was selected. The bioremediation was then investigated and compared between crude oil-contaminated soil (S), the contaminated soil composted with fruit-based waste (SW), and the contaminated soil composted with the same waste with the addition of the selected bacterium (SWB). Both compost-based methods showed high efficiencies of crude oil bioremediation (78.1% and 83.84% for SW and SWB, respectively). However, only a slight difference between the treatments without and with the addition of P. aeruginosa was observed. To make a clear understanding of this point, bacterial communities throughout the 4-week bioremediation period were analyzed. It was found that the community dynamics between both composted treatments were similar, which corresponds with their similar bioremediation efficiencies. Interestingly, Pseudomonas disappeared from the system after one week, which suggests that this genus was not the key degrader or only involved in the early stage of the process. Altogether, our results elaborate that fruit-based composting is an effective approach for crude oil bioremediation