GC-MS hydrocarbon degradation profile data of Pseudomonas frederiksbergensis SI8, a bacterium capable of degrading aromatics at low temperatures

The ability of the psychrotrophic bacterium Pseudomonas frederiksbergensis SI8 to grow and degrade aromatic hydrocarbons efficiently at low temperature is shown in this study. The robust growth of P. frederiksbergensis SI8 was demonstrated in jet fuel and an aromatic blend. The bacterium showed 2.5 to 3-fold faster growth in the aromatic blend than in jet fuel. The hydrocarbons degradation profile of P. frederiksbergensis SI8 at ambient temperature (i.e., 28 °C) and low temperature (i.e., 4 °C) was characterized by Gas Chromatography-Mass Spectrometry (GC–MS) analysis. GC–MS data demonstrated that P. frederiksbergensis SI8 is a novel psychrotrophic bacterium with the ability to degrade aromatic hydrocarbons at temperatures as low as 4 °C. Specifically, P. frederiksbergensis SI8 consumed toluene, ethylbenzene, n-propylbenzene and methyl ethyl benzene efficiently. The data presented here serves to characterize the hydrocarbon degradation profile of P. frederiksbergensis SI8 and corroborates the capacity of this bacterium to degrade aromatic hydrocarbons at low temperatures. The raw GC–MS data for the degradation of hydrocarbons by P. frederiksbergensis SI8 grown at 4 °C and 28 °C for 14 days have been deposited in Mendeley Data and can be retrieved from https://dx.doi.org/10.17632/z9292bvdmh.1 and https://dx.doi.org/10.17632/dp3sgwpj23.1. The datasets and raw data presented here were associated with the main research work “Metagenomic characterization reveals complex association of soil hydrocarbon-degrading bacteria” [1].

Toxicity and human health assessment of an alcohol-to-jet (ATJ) synthetic kerosene

A toxicological investigation was conducted for alcohol-to-jet (ATJ) fuels intended as a 50:50 blend with petroleum-derived fuel Jet Propulsion (JP)-8. The ATJ synthetic paraffinic kerosene (SPK) fuel was produced by Gevo (Englewood CO) and derived either from biomass (bio) or non-biomass sources. All toxicity tests were performed with one or both ATJ fuels following addition of a standard additive package required for JP-8. The primary fuel, Gevo (bio) ATJ SPK produced from biomass-derived iso-butanol, exhibited the same dermal irritation potential in rabbits as JP-8; the non-biomass-derived fuel was less irritating. The Gevo (bio) fuel was non-clastogenic in micronucleus testing with rats and neither version was mutagenic in the bacterial reverse mutation assay. A 90-day study was performed with Gevo (bio) ATJ SPK by exposing male and female Fischer 344 rats to target concentrations of 0, 200, 700 or 2000 mg/m³ of fuel, 6 hr per day, 5 days a week for 69 exposure days and included neurobehavioral assays and reproductive health evaluations in the study design. Results were negative or limited to irritant effects in the respiratory system due to exposure to a vapor and aerosol mixture in the 2000 mg/m³ exposure group. Occupational exposure limits for JP-8 were proposed for these ATJ fuels since these fuels display similar or somewhat lower toxicity than JP-8. As both versions of the Gevo ATJ jet fuel were similar, handling of either fuel alone or in a blend with petroleum-derived JP-8 appears unlikely to increase human health risks for workers.

Toxicity and occupational exposure assessment for hydroprocessed esters and fatty acids (HEFA) alternative jet fuels

The U.S. Air Force (USAF) has pursued development of alternative fuels to augment or replace petroleum-based jet fuels. Hydroprocessed esters and fatty acids (HEFA) renewable jet fuel is certified for use in commercial and USAF aircraft. HEFA feedstocks include camelina seed oil (Camelina sativa, HEFA-C); rendered animal fat (tallow, HEFA-T); and mixed fats and oils (HEFA-F). The aim of this study was to examine potential toxic effects associated with HEFA fuels exposures. All 3 HEFA fuels were less dermally irritating to rabbits than petroleum-derived JP-8 currently in use. Inhalation studies using male and female Fischer-344 rats included acute (1 day, with and without an 11-day recovery), 5-, 10- or 90-day durations. Rats were exposed to 0, 200, 700 or 2000 mg/m³ HEFA-F (6 hr/day, 5 days/week). Acute, 5 - and 10-day responses included minor urinalysis effects. Kidney weight increases might be attributed to male rat specific hyaline droplet formation. Nasal cavity changes included olfactory epithelial degeneration at 2000 mg/m³. Alveolar inflammation was observed at ≥700 mg/m³. For the 90-day study using HEFA-C, no significant neurobehavioral effects were detected. Minimal histopathological effects at 2000 mg/m³ included nasal epithelium goblet cell hyperplasia and olfactory epithelium degeneration. A concurrent micronucleus test was negative for evidence of genotoxicity. All HEFA fuels were negative for mutagenicity (Ames test). Sensory irritation (RD₅₀) values were determined to be 9578 mg/m³ for HEFA-C and greater than 10,000 mg/m³ for HEFA-T and HEFA-F in male Swiss-Webster mice. Overall, HEFA jet fuel was less toxic than JP-8. Occupational exposure levels of 200 mg/m³ for vapor and 5 mg/m³ for aerosol are recommended for HEFA-based jet fuels.

A comprehensive multi-omics approach uncovers adaptations for growth and survival of Pseudomonas aeruginosa on n-alkanes

Background

Examination of complex biological systems has long been achieved through methodical investigation of the system’s individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput “omic” technologies, however, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis). This strategy reduces the likelihood of improper conclusions, provides a framework for elucidation of genotype-phenotype relationships, and brings finer resolution to comparative genomic experiments. Here, we apply a multi-omic approach to analyze the gene expression profiles of two closely related Pseudomonas aeruginosa strains grown in n-alkanes or glycerol.

Results

The environmental P. aeruginosa isolate ATCC 33988 consumed medium-length (C₁₀–C₁₆) n-alkanes more rapidly than the laboratory strain PAO1, despite high genome sequence identity (average nucleotide identity >99%). Our data shows that ATCC 33988 induces a characteristic set of genes at the transcriptional, translational and post-translational levels during growth on alkanes, many of which differ from those expressed by PAO1. Of particular interest was the lack of expression from the rhl operon of the quorum sensing (QS) system, resulting in no measurable rhamnolipid production by ATCC 33988. Further examination showed that ATCC 33988 lacked the entire lasI/lasR arm of the QS response. Instead of promoting expression of QS genes, ATCC 33988 up-regulates a small subset of its genome, including operons responsible for specific alkaline proteases and sphingosine metabolism.

Conclusion

This work represents the first time results from RNA-seq, microarray, ribosome footprinting, proteomics, and small molecule LC-MS experiments have been integrated to compare gene expression in bacteria. Together, these data provide insights as to why strain ATCC 33988 is better adapted for growth and survival on n-alkanes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-017-3708-4) contains supplementary material, which is available to authorized users.

Investigation of waste incineration of fluorotelomer-based polymers as a potential source of PFOA in the environment

In light of the widespread presence of perfluorooctanoic acid (PFOA) in the environment, a comprehensive laboratory-scale study has developed data requested by the U.S. Environmental Protection Agency (EPA) to determine whether municipal and/or medical waste incineration of commercial fluorotelomer-based polymers (FTBPs) at end of life is a potential source of PFOA that may contribute to environmental and human exposures. The study was divided into two phases (I and II) and conducted in accordance with EPA Good Laboratory Practices (GLPs) as described in the quality assurance project plan (QAPP) for each phase. Phase I testing determined that the PFOA transport efficiency across the thermal reactor system to be used in Phase II was greater than 90%. Operating at 1000°C over 2s residence time with 3.2-6.6mgdscm(-1) hydrogen fluoride (HF), corrected to 7% oxygen (O2), and continuously monitored exhaust oxygen of 13%, Phase II testing of the FTBP composites in this thermal reactor system yielded results demonstrating that waste incineration of fluorotelomer-based polymers does not result in the formation of detectable levels of PFOA under conditions representative of typical municipal waste combustor (MWC) and medical waste incinerator (MWI) operations in the U.S. Therefore, waste incineration of these polymers is not expected to be a source of PFOA in the environment.

Transcriptional profiling suggests that multiple metabolic adaptations are required for effective proliferation of Pseudomonas aeruginosa in jet fuel

Fuel is a harsh environment for microbial growth. However, some bacteria can grow well due to their adaptive mechanisms. Our goal was to characterize the adaptations required for Pseudomonas aeruginosa proliferation in fuel. We have used DNA-microarrays and RT-PCR to characterize the transcriptional response of P. aeruginosa to fuel. Transcriptomics revealed that genes essential for medium- and long-chain n-alkane degradation including alkB1 and alkB2 were transcriptionally induced. Gas chromatography confirmed that P. aeruginosa possesses pathways to degrade different length n-alkanes, favoring the use of n-C11-18. Furthermore, a gamut of synergistic metabolic pathways, including porins, efflux pumps, biofilm formation, and iron transport, were transcriptionally regulated. Bioassays confirmed that efflux pumps and biofilm formation were required for growth in jet fuel. Furthermore, cell homeostasis appeared to be carefully maintained by the regulation of porins and efflux pumps. The Mex RND efflux pumps were required for fuel tolerance; blockage of these pumps precluded growth in fuel. This study provides a global understanding of the multiple metabolic adaptations required by bacteria for survival and proliferation in fuel-containing environments. This information can be applied to improve the fuel bioremediation properties of bacteria.

Rapid determination of total sulfur in fuels using gas chromatography with atomic emission detection

The purpose of this study is to determine whether gas chromatography (GC)-atomic emission detection (AED) can be used in a low-resolution mode for rapid, accurate determinations of total sulfur in fuels at trace levels to complement other popular methods of total sulfur analysis. A method for the rapid determination of total sulfur in fuels (called "fast GC-AED") is developed. The method is tested on gasoline, jet fuel, kerosene, and diesel fuel with sulfur concentrations ranging from 125 mg/L down to 2.5 mg/L. Fast GC-AED shows better performance than traditional GC-AED for total sulfur determinations, especially for complex mixtures containing many different sulfur-containing compounds at trace levels. This method also shows that GC-AED can be used for both rapid determinations of total sulfur and traditional determinations of speciated sulfur without requiring equipment changes. Fast GC-AED is competitive with other popular methods for sulfur analysis. The 5-min program that is developed for fast GC-AED is comparable with the time scale of other methods, such as wavelength dispersive X-ray fluorescence and UV-fluorescence (2 to 5 min). Fast GC-AED also compares favorably with UV-fluorescence for trace sulfur determinations, demonstrating accuracy down to 2.5-mg/L sulfur.

Trace-level measurement of complex combustion effluents and residues using multidimensional gas chromatography-mass spectrometry (MDGC-MS)

The identification and quantitation of non-method-specific target analytes have greater importance with respect to EPA's current combustion strategy. The risk associated with combustion process emissions must now be characterized. EPA has recently released draft guidance on procedures for the collection of emissions data to support and augment site-specific risk assessments (SSRAs) as part of the hazardous waste incineration permitting process. This guidance includes methodology for quantifying total organic (TO) emissions as a function of compound volatility. The ultimate intent is to compare the amount of organic material identified and quantified by target analyte-specific methodologies to organic emissions quantified by the TO methodology. The greater the amount accounted for by the target analyte-specific methodologies, the less uncertainty may be associated with the SSRAs. A limitation of this approach is that the target analyte-specific methodologies do not routinely quantify compounds of low toxicological interest; nor do they target products of incomplete combustion (PICs). Thus, the analysis can miss both toxic and non-toxic compounds. As a result, it is unknown whether the uncharacterized fraction of the TO emission possesses toxic properties. The hypothesis that we propose to test is that organic emissions and organics extracted from particulate matter (PM) are more complex than standard GC-MS-based instrumentation can currently measure. This complexity can affect quantitation for toxic compounds, thereby potentially affecting risk assessments. There is a pressing need to better characterize these organic emissions from hazardous waste incinerators and PM extracts from various other combustion sources. We will demonstrate that multidimensional gas chromatography-mass spectrometry (MDGC-MS) procedures significantly improve chromatographic separation for complex environmental samples. Sequential repetitive heart-cutting MDGC, with coupled mass spectrometry will be shown to be a complete analysis technique. The ability of this technique to disengage components from complex mixtures taken from hazardous and municipal waste incinerators will be shown.

Quantitation of a metal deactivator additive by derivatization and gas chromatography--mass spectrometry

The quantitative analysis of phenolic and amine-containing petroleum additives can be challenging. One such compound-N,N'-disalicylidene-1,2-propanediamine, a common metal deactivator additive (MDA)--is thought to inhibit fuel oxidation catalyzed by metals both in the fuel and on surfaces. The ability to measure the concentration of MDA in storage stability tests, thermal-stressing studies, and field samples is important. Quantitating low concentrations of MDA can be difficult because of surface adsorptivity due to the phenol and amine functional groups. This paper describes the shortcomings of direct-injection gas chromatography-mass spectrometry to quantitate MDA as well as a solution to the analytical problem using the common silylation agent BSA to derivatize the MDA. Results demonstrate that the silylation technique is suitable for the determination of MDA concentrations in aviation fuel samples and suggests that the MDA may be readily determined in other petroleum products with a lower detection limit for MDA of 0.5 mg/L. Measurements conducted in heated batch reactors indicate that MDA concentration is reduced as hydrocarbon fuels are stressed. In addition, only free or available MDA is measured by this technique, not MDA that is complexed with metals.

Neurotoxin formation from pilot-scale incineration of synthetic ester turbine lubricants with a triaryl phosphate additive

The high-temperature combustion of synthetic ester turbine engine lubricants has been performed by diluting the lubricant 5, 15, or 25% in diesel fuel and burning the mixture in a pilot-scale boiler facility. The effluent gas from this combustion system was carefully monitored for the formation of a potent neurotoxin, trimethylolpropane phosphate (TMPP). Although TMPP was not detected in the gaseous effluent, elevated levels of the neurotoxin were found in scrapings from the inside of the boiler system. Because of the extreme toxicity of this compound, significant dermal exposure could be a potential risk to incinerator operation and maintenance personnel.