Presence Of Biphenyl Research Articles

Detection of gene clusters for biodegradation of alkanes and aromatic compounds in the Rhodococcus qingshengii VKM Ac-2784D genome.

Bacterial species of the genus Rhodococcus are known to be efficient degraders of hydrocarbons in contaminated soil. They are also employed for bioremediation of polluted environments. These bacteria are widely met in soil, water and living organisms. Previously, we have isolated the Rhodococcus qingshengii strain VKM Ac-2784D from the rhizosphere of couch grass growing on oil-contaminated soil. This strain can effectively degrade oil and some model compounds (naphthalene, anthracene and phenanthrene). The results of phylogenetic analysis show that this strain belongs to the species R. qingshengii. To understand the catabolic properties of this strain, we have studied its gene clusters possessing such properties. The alkane destruction genes are represented by two clusters and five separate alkB genes. The destruction of aromatic compounds involves two stages, namely central and peripheral. The R. qingshengii VKM Ac-2784D genome contains four out of eight known central metabolic pathways for the destruction of aromatic compounds. The structure of the gene clusters is similar to that of the known strains R. jostii RHA1 and R. ruber Chol-4. The peripheral pathways include the genes encoding proteins for benzoic acid destruction. The presence of biphenyl 2,3-dioxygeneses as well as gene clusters of benzoate and 2-hydroxypentandienoate pathways suggests that R. qingshengii VKM Ac-2784D could degrade polychlorinated biphenyls. The biodegradation ability can be enhanced by biosurfactants, which are known to be synthesized by Rhodococcus. The R. qingshengii VKM Ac-2784D genome contains the otsA, otsB, treY, treZ genes. The bioinformatics data are supported by the previous biochemical experiments that allow a mixture of species with a wide variation of metabolic pathways to be obtained.

Alkaline‐Earth Metal Mediated Benzene‐to‐Biphenyl Coupling

AbstractComplex [(DIPePBDI)Ca]2(C6H6), with a C6H62−dianion bridging two Ca2+ions, reacts with benzene to yield [(DIPePBDI)Ca]2(biphenyl) with a bridging biphenyl2−dianion (DIPePBDI=HC[C(Me)N‐DIPeP]2; DIPeP=2,6‐CH(Et)2‐phenyl). The biphenyl complex was also prepared by reacting [(DIPePBDI)Ca]2(C6H6) with biphenyl or by reduction of [(DIPePBDI)CaI]2with KC8in presence of biphenyl. Benzene‐benzene coupling was also observed when the deep purple product of ball‐milling [(DIPPBDI)CaI(THF)]2with K/KI was extracted with benzene (DIPP=2,6‐CH(Me)2‐phenyl) giving crystalline [(DIPPBDI)Ca(THF)]2(biphenyl) (52 % yield). Reduction of [(DIPePBDI)SrI]2with KC8gave highly labile [(DIPePBDI)Sr]2(C6H6) as a black powder (61 % yield) which reacts rapidly and selectively with benzene to [(DIPePBDI)Sr]2(biphenyl). DFT calculations show that the most likely route for biphenyl formation is a pathway in which the C6H62−dianion attacks neutral benzene. This is facilitated by metal‐benzene coordination.

Alkaline-Earth Metal Mediated Benzene-to-Biphenyl Coupling.

Complex [(DIPeP BDI)Ca]2 (C6 H6 ), with a C6 H6 2- dianion bridging two Ca2+ ions, reacts with benzene to yield [(DIPeP BDI)Ca]2 (biphenyl) with a bridging biphenyl2- dianion (DIPeP BDI=HC[C(Me)N-DIPeP]2 ; DIPeP=2,6-CH(Et)2 -phenyl). The biphenyl complex was also prepared by reacting [(DIPeP BDI)Ca]2 (C6 H6 ) with biphenyl or by reduction of [(DIPeP BDI)CaI]2 with KC8 in presence of biphenyl. Benzene-benzene coupling was also observed when the deep purple product of ball-milling [(DIPP BDI)CaI(THF)]2 with K/KI was extracted with benzene (DIPP=2,6-CH(Me)2 -phenyl) giving crystalline [(DIPP BDI)Ca(THF)]2 (biphenyl) (52 % yield). Reduction of [(DIPeP BDI)SrI]2 with KC8 gave highly labile [(DIPeP BDI)Sr]2 (C6 H6 ) as a black powder (61 % yield) which reacts rapidly and selectively with benzene to [(DIPeP BDI)Sr]2 (biphenyl). DFT calculations show that the most likely route for biphenyl formation is a pathway in which the C6 H6 2- dianion attacks neutral benzene. This is facilitated by metal-benzene coordination.

Idiomarina sp. Isolates from Cold and Temperate Environments as Biosurfactant Producers

Background: The cold-adapted Idiomarina sp. 185 from Antarctic shoreline sediment and the mesophilic Idiomarina sp. A19 from the brackish Lake Faro (Italy) were screened for their efficiency in biosurfactant production by a temperature-mediated approach, when grown in rich culture medium and mineral medium supplemented with biphenyl. Methods: oxidation of polychlorobiphenyls and standard screening tests were performed, i.e., E24 index detection, surface tension measurement, blood agar plate and C-TAB agar plate. Results: During incubation in rich medium, the strain Idiomarina sp. A19 produced an excellent stable emulsion, recording an E24 of 73.5%. During growth in mineral medium, isolates showed good efficiency in at least one performed condition by showing species-specific differences related to optimum temperature. In the presence of biphenyl, both Idiomarina isolates created stable emulsions (E24 ≈ 47.5 and 35%, respectively), as well as surface tension reductions of 30.05 and 35.5 mN/m, respectively. Further differences between isolates were observed by phenotypic characterization. The genome mining approach on available deposited genome sequences for closest relatives offered further insights about the presence of genes for biphenyl degradation, especially for microorganisms derived from different extreme environments. Conclusions: Our results allowed for an interesting comparison which underlined differences in metabolic patterns and in the kinetics of BS production, probably due to the different origins of the strains.

Genetic mapping of highly versatile and solvent‐tolerant Pseudomonas putida B6‐2 (ATCC BAA‐2545) as a ‘superstar’ for mineralization of PAHs and dioxin‐like compounds

Polycyclic aromatic hydrocarbons (PAHs) and dioxin-like compounds, including sulfur, nitrogen and oxygen heterocycles, are widespread and toxic environmental pollutants. A wide variety of microorganisms capable of growing with aromatic polycyclic compounds are essential for bioremediation of the contaminated sites and the Earth's carbon cycle. Here, cells of Pseudomonas putida B6-2 (ATCC BAA-2545) grown in the presence of biphenyl (BP) are able to simultaneously degrade PAHs and their derivatives, even when they are present as mixtures, and tolerate high concentrations of extremely toxic solvents. Genetic analysis of the 6.37 Mb genome of strain B6-2 reveals coexistence of gene clusters responsible for central catabolic systems of aromatic compounds and for solvent tolerance. We used functional transcriptomics and proteomics to identify the candidate genes associated with catabolism of BP and a mixture of BP, dibenzofuran, dibenzothiophene and carbazole. Moreover, we observed dynamic changes in transcriptional levels with BP, including in metabolic pathways of aromatic compounds, chemotaxis, efflux pumps and transporters potentially involved in adaptation to PAHs. This study on the highly versatile activities of strain B6-2 suggests it to be a potentially useful model for bioremediation of polluted sites and for investigation of biochemical, genetic and evolutionary aspects of Pseudomonas.

Organic Based Additives Impact on Thermal Behavior of Ammonium Perchlorate: Superior 4, 4′‐Bipyridine Versus Inferior Biphenyl

AbstractFor the first time, the thermal decomposition behavior of heterogeneous mixtures of ammonium perchlorate (AP) with two organic additives – 4, 4’‐Bipyridine, and biphenyl – were investigated. The heterogeneous mixtures of the additives and ammonium perchlorate were prepared by dissolving 1, 2, 3, 4, and 5 mg of the organic additives and 100 mg ammonium perchlorate in 2 ml of methanol as solvent. After that, the thermal decomposition behavior of prepared solid heterogeneous mixtures was monitored by thermogravimetry analysis, differential scanning calorimetry, and mass spectrometry analysis. The effect of the 4, 4’‐Bipyridine on thermal decomposition of AP enhanced the released heat from 479 to 1842 J g−1 and produced a decrease of decomposition temperature from 433 °C to 308 °C while the thermal decomposition of AP in the presence of biphenyl did not change as dramatically as it did with 4, 4’‐Bipyridine. With biphenyl, the decomposition temperature was found to be similar to that of pure AP and the evolved heat was about 718 J g−1. The gaseous products of decomposition of 4, 4’‐Bipyridine /ammonium perchlorate were monitored by mass spectrometric analysis. The main evolved decomposition gases of pure AP are N2O, O2, Cl2, ClO, ClO2, ClO3, HClO4, and HCl, while the major gaseous products of the 5:100 (w/w) mixture of 4, 4’‐Bipyridine with AP were detected as N2, NO, N2O, O2, Cl2, ClO, ClO2, ClO3, HClO4, HCl and 4, 4’‐Bipyridine. The change in the composition of volatile products indicates a change in the mechanism of AP decomposition from proton transfer to electron transfer in the presence of 4, 4’‐Bipyridine.

Sediment Organic Matter in Areas of Intense Methane Release in the Laptev Sea: Characteristics of Molecular Composition

Abstract —We present results of study of the molecular composition of organic matter (OM) in the bottom sediments of the Laptev Sea by gas chromatography–mass spectrometry, isotope gas chromatography–mass spectrometry, and Rock-Eval pyrolytic analysis. The OM of all collected sediment samples shows a significant terrigenous contribution. Compounds that are biomarkers of methanotrophic microorganisms are also found. A positive correlation between the contents of the studied biomarkers and the contents of pelite and total organic carbon is observed at the sites with documented intense methane bubbling. For example, the average content of C30 hopenes at the “methane” stations is twice higher than that at the “background” ones. The average content of C32 αβ-hopanes in sediment samples from the methane seepage area is 1.5 times higher than that at the background stations. We suggest that the increased C30 αβ-hopane content (~1.5 times higher within the methane seepage area) and the decreased moretane index relative to the C31 hopane index are due to the inflow of OM of petroleum origin. The presence of biphenyl in sediments indicates its petroleum origin, which supports our assumption of the migratory nature of petroleum hydrocarbons in the methane seepage area. Triterpenoids found in the sediment OM indicate diagenetic bacterial transformation of OM in the methane seepage areas, which shows that methane has been released for a long time. We assume the intense activity of the consortium of methanotrophs and sulfate reducers in the methane seepage areas.

Synthesis of a 30-Membered Macrocycle Incorporating Two Ruthenium Sandwich Complexes

The first macrocycle incorporating two ruthenium sandwich complexes has been synthesised. Key step is a cyclodimerisation by double etherification of a p-chlorophenylalanine-derived [RuCp*]+ complex. Silica-based cation exchange chromatography allowed the separation of dicationic diastereomers. Assignment of the relative configurations was possible by X-ray structure determination. Partial demetalation in acetonitrile proceeded in high yield by irradiation in the presence of biphenyl

Bacterial cell membrane adaptation responses on stress caused with the environmental pollutants

Abstract The effect of polychlorinated biphenyls on biomass production, lipid accumulation, and on the fatty acid profile of the major membrane lipids of Alcaligenes xylosoxidans isolated from a soil long-term contaminated with polychlorinated biphenyls was examined. The lowest bacterial growth was observed in the presence of biphenyl and polychlorinated biphenyls. On the other hand, the highest growth stimulation was observed in the presence polychlorinated biphenyls. Higher growth ability was observed when polychlorinated biphenyls or 3-chlorobenzoic acid were added after three days of cultivation. Higher lipid accumulation corresponded with lower growth ability. The importance of time when bacterial strain meets polychlorinated biphenyls or 3-chlorobenzoic acid should be emphasized. The addition of toxic organic compound later in stationary growth phase led to better survival and evoked lower membrane adaptation. However, polychlorinated biphenyls or 3-chlorobenzoic acid amendment at the beginning of cultivation stimulated adaptation responses as membrane saturation, cis to trans isomerisation, and branched fatty acids alteration and decreased growth ability. Palmitic acid and 17-cyclopropyl fatty acid were observed as prevalent in the bacterial membrane as well as in the total lipids.

Isolation of Biphenyl and Polychlorinated Biphenyl-Degrading Bacteria and Their Degradation Pathway

Four strains of biphenyl-degrading bacteria were isolated from a sewage and identified from the Rhodococcus genus (SK-1, SK-3, and SK-4) and Aquamicrobium genus (SK-2) by 16S rRNA sequence. Among these strains, strain SK-2 was most suitable for biphenyl degradation. When 0.65, 1.3, 2.6, or 3.9mM of biphenyl was used, the biphenyl was completely degraded within 24 and 96h of culture, respectively. However, in the case of 6.5 and 9.75mM of biphenyl, the biphenyl degradation yields were about 80% and 46.7% after 120h of culture, respectively. The isolated strains could degrade a broad spectrum of aromatic compounds including high-chlorinated polychlorinated biphenyl (PCB) congeners in the presence of biphenyl. In addition, strain SK-2 could utilize PCB congeners containing one to six chlorine substituents such as 2,2',4,4',5,5'-hexachlorobiphenyl. The PCB utilization rate by the strain SK-2 was increased compared to that of other PCB congener-utilizing bacteria. The four isolates metabolized 4-chlorobiphenyl to 4-chlorobenzoic acid and 2-hydroxy-6-oxo-6-(4'-chlorophenyl)-hexa-2,4-dienoic acid. These results suggest the isolated strains might be good candidates for the bioremediation of PCB-contaminated soil, especially high-saline soils.

Preliminary analysis of glutathione S-transferase homolog fromLactobacillus casei Zhang

Glutathione S-transfera ses (GSTs) constitute a large protein family. Some of them are proved to be associated with biphenyl metabolism. In this study, we described a homolog of GST gene inLactobacillus casei Zhang that revealed by genome analysis. The GST gene itself as well as the adjacent gene context was highly conserved among differentL. casei isolates. Phylogenetic investigation suggested that the GST gene was acquired via horizontal gene transfer event, possibly from gamma subdivision. Additional survival experiment indicated that it may not benefit theL. casei host for growing in the presence of biphenyl. It was for the first time discovered that GST was encoded byLactobacillaceae species.

Assessment of bioaccumulation of biphenyls in the trophic chain of a coastal area of Parana, Brazil

The presence of biphenyl was investigated in sediments and water in Paranagua Bay. Chemicals compounds like biphenyl can cause several effects on the ecosystems such as bioaccumulation. Biphenyl and similar compounds are subject to bioaccumulation, which in turn may harm the local ecosystem. The bioaccumulation in the local trophic chain was evaluated using a mathematical model based on toxicokinetic properties of the compound in the organisms. The results showed that even in water, the concentration of biphenyl was high, 0.82 ng/L. Also, in the fishes, the concentrations calculated by the model were higher than the maximum than the maximum allowed for human consumption.

Polycyclic Aromatic Compounds-mediated Electrochemical Reduction of Alkyl Mesylates

Abstract Electrochemical reduction of alkyl mesylates was successfully carried out by using an undivided cell equipped with a Pt cathode and an Mg anode in the presence of biphenyl and t-BuOH. The reaction could proceed efficiently under mild conditions to give the corresponding alkanes in moderate to good yields. This procedure could also be applicable to chemoselective reduction of mesylates having functional groups such as epoxide, olefin, acetal, hydroxy, or cyano groups.

Method for Assessment of Viability and Morphological Changes of Bacteria in the Early Stage of Colony Formation on a Simulated Natural Environment

A quantitative analysis of changes in the physiological status of bacterial cells is a fundamental type of study in microbiological research. We devised a method for measuring the viability of bacteria in the early stage of colony formation on a simulated natural environment. In this method, a solid medium containing soil extract was used, and the formation of bacterial microcolonies on a membrane filter was determined by use of a laser scanning cytometer combined with live-dead fluorescent dyes. A polychlorinated biphenyl degrader, Comamonas testosteroni TK102, was used in this study. Surprisingly, approximately 20% of the microcolonies had their growth stopped and eventually died. In the presence of biphenyl, the growth arrest was increased to 50%, and filamentous cells were observed in the colonies. Predicted intermediate metabolites of biphenyl were added to the medium to determine the relationship between the change of viability and the production of metabolites, and the addition of 2,3-dihydroxybiphenyl showed low viability. The arrest was not observed to occur on nutrient-rich medium, suggesting that the change in viability might occur in a nutrient-poor natural condition. The results of this study demonstrated that toxic metabolites of xenobiotics might change cell viability in the natural environment.

Detection of polychlorinated biphenyls employing chemical dechlorination followed by biphenyl whole cell sensing system

Polychlorinated biphenyls (PCBs) are a mixture of 209 individual chlorinated compounds commonly known as PCB congeners. These compounds are hydrophobic and are persistent in the environment. Their use was banned in the US a few decades ago because of harmful health effects. Therefore, detection of PCBs in environmental samples is increasingly important. To that end, we have developed a two-step simple and sensitive method for the detection of total PCBs. Specifically, our method involves dechlorination of PCBs to biphenyl followed by detection of biphenyl using a whole cell sensing system as the detection system. The whole cell sensing system consists of cells of the strain Pseudomonas pseudoalcaligenes KF707 harboring plasmid pSD7000. Plasmid pSD7000 contains the gene of lacZ, a reporter protein under the control of the bph operon. The detection is achieved through the emission of light afforded by the expression of reporter protein triggered by the presence of biphenyl. Due to the fact that this operon is activated only by few PCB congeners, a chemical dechlorination method was employed to convert all PCBs to biphenyl, and thus all the PCBs present in a given sample are able to be detected. The results showed that PCB congeners were rapidly (30 min) and efficiently (>98.5%) dechlorinated to biphenyl using a Mg/K2PdCl6 catalyst, and the biphenyl could be subsequently quantified using the whole cell sensing system. This hybrid analytical method that combines classical dechlorination with novel biosensing methods may find applications in the on-site monitoring of PCBs contamination levels.

Growth of polychlorinated-biphenyl-degrading bacteria in the presence of biphenyl and chlorobiphenyls generates oxidative stress and massive accumulation of inorganic polyphosphate.

Inorganic polyphosphate (polyP) plays a significant role in increasing bacterial cell resistance to unfavorable environmental conditions and in regulating different biochemical processes. Using transmission electron microscopy of the polychlorinated biphenyl (PCB)-degrading bacterium Pseudomonas sp. strain B4 grown in defined medium with biphenyl as the sole carbon source, we observed large and abundant electron-dense granules at all stages of growth and following a shift from glucose to biphenyl or chlorobiphenyls. Using energy dispersive X-ray analysis and electron energy loss spectroscopy with an integrated energy-filtered transmission electron microscope, we demonstrated that these granules were mainly composed of phosphate. Using sensitive enzymatic methods to quantify cellular polyP, we confirmed that this polymer accumulates in PCB-degrading bacteria when they grow in the presence of biphenyl and chlorobiphenyls. Concomitant increases in the levels of the general stress protein GroEl and reactive oxygen species were also observed in chlorobiphenyl-grown cells, indicating that these bacteria adjust their physiology with a stress response when they are confronted with compounds that serve as carbon and energy sources and at the same time are chemical stressors.

Study of the biodegradation process of polychlorinated biphenyls in liquid medium and soil by a new isolated aerobic bacterium ( Janibacter sp.)

We have isolated and characterised a novel aerobic bacterial strain, designated MS3-02, belonging to the genus Janibacter sp. The capability of this new strain to degrade polychlorinated biphenyls (PCBs) in a commercial mixture (Aroclor 1242) in liquid medium and in soil (sterile and non sterile soil), under laboratory scale, has been evaluated. MS3-02 was isolated from the soil around of an incinerator, located in the east of Madrid (Spain). Gas-chromatographic analysis showed that MS3-02 was able to reduce most peaks observed in the chromatogram between 70% and 100% after seven days of incubation in a culture mineral medium containing yeast extract, but without the addition of biphenyl. The presence of biphenyl in the culture medium decreased the rate of PCB degradation by this bacterium. Comparing the performance of the MS3-02 in liquid culture medium and in soil, degradation was less efficient in sterile soil and still less efficient in non sterile soil. Under the best conditions (sterile soil and 20 weeks of incubation) MS3-02 was able to reduce, between 50% and 100%, nine of the main gas-chromatographic peaks in Aroclor 1242.

Molecular Modeling of Bulk Impurity Segregation and Impurity-Mediated Crystal Habit Modification of Naphthalene and Phenanthrene in the Presence of Heteroimpurity Species

The ability to predict particle morphology (shape) in the presence of habit-modifying impurities is of great use in allowing the optimization of growth conditions to produce a required crystal habit. Previous morphological modeling techniques developed by the authors1,2 utilized the attachment energy method, which assumes knowledge of the solid-state structure, to simulate the shape of organic particulate solids while keeping the position of the impurity in the lattice fixed. These techniques are improved upon here by allowing the orientation of the adsorbing impurity molecule to be relaxed with respect to the intermolecular forces of the crystal bulk using a restricted molecular mechanics approach. This results in far more accurate attachment energiesand hence morphological simulationsthan could be achieved before. The calculations also allow improved binding energies for additives in different crystal faces to be ascertained; these can be used as a measure of the equilibrium impurity segregation coefficient for liquid/solid solidification. The method is illustrated by considering the morphological impact of a variety of host/additive systems, including naphthalene doped by biphenyl and phenanthrene crystallizing in the presence of biphenyl or anthracene. A forward look to the development of this approach for more complex systems is also provided.

Enhancement of aerobic microbial degradation of polychlorinated biphenyl in soil microcosms

This article reports the results of various biodegradation experiments on polychlorinated biphenyl (PCB)-contaminated sandy soil employing a mixed culture of acclimatized bacteria. Following the optimization of different variables without chemical pretreatment, the elimination rate achieved of Aroclor 1242 in slurry-phase reactors was 61% after four months of treatment, with the presence of biphenyl as cosubstrate being the most important factor affecting PCB biodegradation. The biodegradation occurred as a first-order process, and it proved most effective in respect to dichlorinated biphenyls (100% removal), followed by trichlorinated (92%) and tetrachlorinated biphenyls (24%). The results also showed that the degradability of PCBs in soil may be enhanced by an advanced oxidation pretreatment (Fenton reaction), producing almost 100% elimination of PCBs at the end of the integrated chemical-biological process and 72% mineralization of the intermediates generated during the chemical pretreatment.

Microbial Degradation and Chemical Oxidation of Sandy Sediment Contaminated with Polychlorinated Biphenyl

This paper reports the results of various biodegradation experiments on polychlorinated biphenyl (PCB)-contaminated sandy sediment employing a mixed culture of acclimatized bacteria. Following the optimization of different variables, the elimination rate achieved of Aroclor 1242 in slurry phase reactors was 61% after 4 months of treatment. The presence of biphenyl as a cosubstrate was the most important factor affecting PCB biodegradation. The biodegradation occurred as a first-order process, and proved most effective with respect to dichlorinated (100% removal), followed by trichlorinated (92%) and tetrachlorinated biphenyls (24%). The results of the treatment of polychlorinated biphenyl (PCB) contaminated sandy sediment with the Fenton advanced oxidation process (AOP) confirm that the oxidation process occurs on the PCBs adsorbed to particles, producing 98% elimination of the original PCB structure after 72 h. The degree of elimination was found to be dependent on the level of congener chlorination, and the process follows pseudo first-order kinetics. In addition, the Fenton chemical oxidation process may be complemented by subsequent aerobic biologic degradation which, after 15 days, produces 70% mineralization of the products generated during the chemical oxidation process.