Bacterial chemotaxis to naphthalene desorbing from a nonaqueous liquid

Bacterial chemotaxis has the potential to increase the rate of degradation of chemoattractants, but its influence on degradation of hydrophobic attractants initially dissolved in a non-aqueous-phase liquid (NAPL) has not been examined. We studied the effect of chemotaxis by Pseudomonas putida G7 on naphthalene mass transfer and degradation in a system in which the naphthalene was dissolved in a model NAPL. Chemotaxis by wild-type P. putida G7 increased the rates of naphthalene desorption and degradation relative to rates observed with nonchemotactic and nonmotile mutant strains. While biodegradation alone influenced the rate of substrate desorption by increasing the concentration gradient against which desorption occurred, chemotaxis created an even steeper gradient as the cells accumulated near the NAPL source. The extent to which chemotaxis affected naphthalene desorption and degradation depended on the initial bacterial and naphthalene concentrations, reflecting the influences of these variables on concentration gradients and on the relative rates of mass transfer and biodegradation. The results of this study suggest that chemotaxis can substantially increase the rates of mass transfer and degradation of NAPL-associated hydrophobic pollutants.     

Bacterial Chemotaxis to Naphthalene Desorbing from a Nonaqueous Liquid

Bacterial chemotaxis has the potential to increase the rate of degradation of chemoattractants, but its influence on degradation of hydrophobic attractants initially dissolved in a non-aqueous-phase liquid (NAPL) has not been examined. We studied the effect of chemotaxis by Pseudomonas putida G7 on naphthalene mass transfer and degradation in a system in which the naphthalene was dissolved in a model NAPL. Chemotaxis by wild-type P. putida G7 increased the rates of naphthalene desorption and degradation relative to rates observed with nonchemotactic and nonmotile mutant strains. While biodegradation alone influenced the rate of substrate desorption by increasing the concentration gradient against which desorption occurred, chemotaxis created an even steeper gradient as the cells accumulated near the NAPL source. The extent to which chemotaxis affected naphthalene desorption and degradation depended on the initial bacterial and naphthalene concentrations, reflecting the influences of these variables on concentration gradients and on the relative rates of mass transfer and biodegradation. The results of this study suggest that chemotaxis can substantially increase the rates of mass transfer and degradation of NAPL-associated hydrophobic pollutants.     

Quantitative analysis of experiments on bacterial chemotaxis to naphthalene

A mathematical model was developed to quantify chemotaxis to naphthalene by Pseudomonas putida G7 (PpG7) and its influence on naphthalene degradation. The model was first used to estimate the three transport parameters (coefficients for naphthalene diffusion, random motility, and chemotactic sensitivity) by fitting it to experimental data on naphthalene removal from a discrete source in an aqueous system. The best-fit value of naphthalene diffusivity was close to the value estimated from molecular properties with the Wilke-Chang equation. Simulations applied to a non-chemotactic mutant strain only fit the experimental data well if random motility was negligible, suggesting that motility may be lost rapidly in the absence of substrate or that gravity may influence net random motion in a vertically oriented experimental system. For the chemotactic wild-type strain, random motility and gravity were predicted to have a negligible impact on naphthalene removal relative to the impact of chemotaxis. Based on simulations using the best-fit value of the chemotactic sensitivity coefficient, initial cell concentrations for a non-chemotactic strain would have to be several orders of magnitude higher than for a chemotactic strain to achieve similar rates of naphthalene removal under the experimental conditions we evaluated. The model was also applied to an experimental system representing an adaptation of the conventional capillary assay to evaluate chemotaxis in porous media. Our analysis suggests that it may be possible to quantify chemotaxis in porous media systems by simply adjusting the model's transport parameters to account for tortuosity, as has been suggested by others.     

NahY, a Catabolic Plasmid-Encoded Receptor Required for Chemotaxis of Pseudomonas putida to the Aromatic Hydrocarbon Naphthalene

Pseudomonas putida G7 exhibits chemotaxis to naphthalene, but the molecular basis for this was not known. A new gene, nahY, was found to be cotranscribed with meta cleavage pathway genes on the NAH7 catabolic plasmid for naphthalene degradation. The nahY gene encodes a 538-amino-acid protein with a membrane topology and a C-terminal region that resemble those of chemotaxis transducer proteins. A P. putida G7 nahY mutant grew on naphthalene but was not chemotactic to this aromatic hydrocarbon. The protein NahY thus appears to function as a chemoreceptor for naphthalene or a related compound. The presence of nahY on a catabolic plasmid implies that chemotaxis may facilitate biodegradation.     

Growth kinetics of Pseudomonas putida G7 on naphthalene and occurrence of naphthalene toxicity during nutrient deprivation

The objectives of this work were (1) to demonstrate how the chemostat approach could be modified to allow determination of kinetic parameters for a sparingly soluble, volatile substrate such as naphthalene and (2) to examine the influence of the interactions of various nutrients on possible growth-inhibitory effects of naphthalene. Pseudomonas putida G7 was used as a model naphthalene-degrading microorganism. Naphthalene was found to be toxic to P. putida G7 in the absence of a nitrogen source or oxygen. The death rate of cells grown on minimal medium plus naphthalene and then exposed to naphthalene under anoxic conditions was higher than that observed under oxic conditions in the absence of a nitrogen source. The presence of necessary nutrients for the biodegradation of PAH compounds is indicated to be important for the survival of microorganisms that are capable of PAH degradation. The amounts of ammonia and oxygen necessary for naphthalene biodegradation and for suppression of naphthalene toxicity were calculated from growth yield coefficients. A chemostat culture of P. putida G7 using naphthalene as a carbon and energy source was accomplished by using a feed augmented with a methanol solution of naphthalene so as to provide sufficient growth to allow accurate evaluation of kinetic parameters. When naphthalene was the growth-limiting substrate, the degradation of naphthalene followed Monod kinetics. Maximum specific growth rate (micrometer) and Monod constant (Ks) were 0.627 +/- 0.007 h-1 and 0.234 +/- 0.0185 mg/L, respectively. The evaluation of biodegradation parameters will allow a mathematical model to be applied to predict the long-term behavior of PAH compounds in soil when combined with PAH transport parameters.     

Anaerobic degradation of naphthalene by a pure culture of a novel type of marine sulphate-reducing bacterium

Incubation of marine sediment in anoxic, sulphate-rich medium in the presence of naphthalene resulted in the enrichment of sulphate-reducing bacteria. Pure cultures with short, oval cells (1.3 by 1.3–1.9 μm) were isolated that grew with naphthalene as the only organic carbon source and electron donor for sulphate reduction to sulphide. One strain, NaphS2, was characterized. It affiliated with completely oxidizing sulphate-reducing bacteria of the δ-subclass of the Proteobacteria, as revealed by 16S rRNA sequence analysis. 2-Naphthoate, benzoate, pyruvate and acetate were used in addition to naphthalene. Quantification of substrate consumption, sulphide formation and formed cell mass revealed that naphthalene was completely oxidized with sulphate as the electron acceptor.     

Initial reactions in the oxidation of naphthalene by Pseudomonas putida.

A strain of Pseudomonas putida that can utilize naphthalene as its sole source of carbon and energy was isolated from soil. A mutant strain of this organism, P. putida 119, when grown on glucose in the presence of naphthalene, accumulates optically pure (+)-cis-1(R),2(S)-dihydroxy-1,2-dihydronaphthalene in the culture medium. The cis relative stereochemistry in this molecule was established by nuclear magnetic resonance spectrometry. Radiochemical trapping experiments established that this cis dihydrodiol is an intermediate in the metabolism of naphthalene by P. Fluorescens (formerly ATCC, 17483), P. putida (ATCC, 17484), and a Pseudomonas species (NCIB 9816), as well as the parent strain of P. putida described in this report. Formation of the cis dihydrodiol is catalyzed by a dioxygenase which requires either NADH or NADPH as an electron donor. A double label procedure is described for determining the origin of oxygen in the cis dihydrodiol under conditions where this metabolite would not normally accumulate. Several aromatic hydrocarbons are oxidized by cell extracts prepared from naphthalene-grown cells of P. putida. The cis dihydrodiol is converted to 1,2-dihydroxynaphthalene by an NAD+-dependent dehydrogenase. This enzyme is specific for the (+) isomer of the dihydrodiol and shows a primary isotope effect when the dihydrodiol is substituted at C-2 with deuterium.     

Oxaloacetate inhibition of succinate oxidation in tightly coupled liver mitochondria with ferricyanide as an electron acceptor

When ferricyanide is used as an artificial electron acceptor, succinate oxidation by tightly coupled liver mitochondria becomes inhibited after 1–3 min. No inhibition occurs in the presence of rotenone or glutamate establishing that oxaloacetate causes the inhibtion. Oxygen consumption by mitochondria oxidizing succinate does not become inhibited in the absence of rotenone suggesting that oxaloacetate accumulates to a greater extent when ferricyanide is added than when oxygen is the terminal acceptor. Higher levels of oxaloacetate in the ferricyanide reaction are apparently due to an increased rate of synthesis rather than a decreased rate of removal. Thus it appears that when succinate is the substrate and oxygen the terminal acceptor a control mechanism exists which blocks oxidation of malate. When ferricyanide is added as an artificial electron acceptor this control is lost and oxaloacetate accumulates to inhibit succinate oxidation.     

Bacterial chemotaxis to naphthalene

The chemotaxis of two pseudomonads, P. putida AZ (Naph+) and P. putida AZ (Naph-), differing in the ability to metabolize naphthalene was studied by the known capillary method of Adler and the densitometric method devised in our laboratory. The migration of P. putida AZ (Naph+) cells toward increasing levels of naphthalene was accompanied by the formation of a migrating front of converted naphthalene. P. putida AZ (Naph-) cells, too, exhibited positive chemotaxis to naphthalene, but they did not form the front of converted naphthalene. The analysis of experimental data in terms of a kinetic model of bacterial chemotaxis showed that the densitometric method is a potential tool for studying bacterial chemotaxis to hydrophobic organic substances.     

Residence time calculation for chemotactic bacteria within porous media

Local chemical gradients can have a significant impact on bacterial population distributions within subsurface environments by evoking chemotactic responses. These local gradients may be created by consumption of a slowly diffusing nutrient, generation of a local food source from cell lysis, or dissolution of nonaqueous phase liquids trapped within the interstices of a soil matrix. We used a random walk simulation algorithm to study the effect of a local microscopic gradient on the swimming behavior of bacteria in a porous medium. The model porous medium was constructed using molecular dynamics simulations applied to a fluid of equal-sized spheres. The chemoattractant gradient was approximated with spherical symmetry, and the parameters for the swimming behavior of soil bacterium Pseudomonas putida were based on literature values. Two different mechanisms for bacterial chemotaxis, one in which the bacteria responded to both positive and negative gradients, and the other in which they responded only to positive gradients, were compared. The results of the computer simulations showed that chemotaxis can increase migration through a porous medium in response to microscopic-scale gradients. The simulation results also suggested that a more significant role of chemotaxis may be to increase the residence time of the bacteria in the vicinity of an attractant source.     

Chemotaxis of Pseudomonas spp. to the polyaromatic hydrocarbon naphthalene.

Two naphthalene-degrading bacteria, Pseudomonas putida G7 and Pseudomonas sp. strain NCIB 9816-4, were chemotactically attracted to naphthalene in drop assays and modified capillary assays. Growth on naphthalene or salicylate induced the chemotactic response. P. putida G7 was also chemotactic to biphenyl; other polyaromatic hydrocarbons that were tested did not appear to be chemoattractants for either Pseudomonas strain. Strains that were cured of the naphthalene degradation plasmid were not attracted to naphthalene.     

An electron transfer dependent membrane potential in chromaffin-vesicle ghosts

Adrenal medullary chromaffin-vesicle membranes contain a transmembrane electron carrier that may provide reducing equivalents for intravesicular dopamine beta-hydroxylase in vivo. This electron transfer system can generate a membrane potential (inside positive) across resealed chromaffin-vesicle membranes (ghosts) by passing electrons from an internal electron donor to an external electron acceptor. Both ascorbic acid and isoascorbic acid are suitable electron donors. As an electron acceptor, ferricyanide elicits a transient increase in membrane potential at physiological temperatures. A stable membrane potential can be produced by coupling the chromaffin-vesicle electron-transfer system to cytochrome oxidase by using cytochrome c. The membrane potential is generated by transferring electrons from the internal electron donor to cytochrome c. Cytochrome c is then reoxidized by cytochrome oxidase. In this coupled system, the rate of electron transfer can be measured as the rate of oxygen consumption. The chromaffin-vesicle electron-transfer system reduces cytochrome c relatively slowly, but the rate is greatly accelerated by low concentrations of ferrocyanide. Accordingly, stable electron transfer dependent membrane potentials require cytochrome c, oxygen, and ferrocyanide. They are abolished by the cytochrome oxidase inhibitor cyanide. This membrane potential drives reserpine-sensitive norepinephrine transport, confirming the location of the electron-transfer system in the chromaffin-vesicle membrane. This also demonstrates the potential usefulness of the electron transfer driven membrane potential for studying energy-linked processes in this membrane.     

Inhibition of Cyclooxygenase Activity of Prostaglandin-H-Synthase by Excess Substrate (Molecular Oxygen)

For the cyclooxygenase reaction of prostaglandin-H-synthase isolated from ram vesicular glands, dependences of the initial reaction rate, the maximal yield of the product, and the rate constant of enzyme inactivation in the course of reac- tion on oxygen concentration were studied in the absence and in the presence of electron donor in the reaction medium. It is shown that in the absence of electron donor the cyclooxygenase reaction is strictly governed by Michaelis-Menten kinet- ics over a wide range of oxygen concentrations (5–800 μM). In the presence of electron donor in the reaction medium it was found that cyclooxygenase reaction is inhibited by an excess of dissolved oxygen: the maximal values of the initial reaction rate and yield of the product are attained at oxygen concentration 50 μM, and its increase to 500 μM causes twofold decrease in the initial rate and maximal yield. The rate constant of enzyme inactivation in the course of reaction increases on increase in oxygen concentration both in the presence and in the absence of electron donor.     

Experimental and modeling study of diauxic lag of Pseudomonas denitrificans switching from oxic to anoxic conditions

We have shown that Pseudomonas denitrificans undergo a diauxie when switching from dissolved oxygen to nitrate as terminal electron acceptor. The length of time under aeration significantly affected the length of the diauxic lag, whereas the presence or absence of nitrate in the culture under aeration had a marginal effect. Nitrate consumption was very low during the lag period and then increased rapidly, coinciding with exponentially increasing biomass concentrations. Biochemical rate expressions that account for enzyme synthesis and activity in response to culture conditions and enzyme specific levels were developed. The new model successfully predicts the different lengths of diauxic lags observed in the experiments as well as the growth pattern and nitrate uptake.     

Resolution of the 4-hydroxy-3-methylbenzoate hydroxylase of Pseudomonas putida into two protein components

Abstract 4-Hydroxy-3-methylbenzoate hydroxylase of Pseudomonas putida was found to be inducible, rather than constitutive, extremely unstable and requires an electron donor (NADH or NADPH) and molecular oxygen for activity, suggesting a mono-oxygenase type of enzyme. It was resolved into two protein components by ion-exchange chromatography. The first protein component was identified as an NADH: acceptor (DCIP) oxido-reductase, with the second catalysing the hydroxylation reaction. A mechanism illustrating the role of each reaction of this mono-oxygenase in the hydroxylation reaction is proposed.     

利用硝酸盐和亚硝酸盐同步富集厌氧甲烷氧化微生物的比较实验

【背景】反硝化厌氧甲烷氧化(Denitrifying anaerobic methane oxidation,DAMO)是以硝酸盐或亚硝酸盐为电子受体以甲烷为电子供体的厌氧氧化过程,对认识全球碳氮循环、削减温室气体排放和开发废水脱氮新技术等方面具有重要意义。【目的】认识以硝酸盐和亚硝酸盐为电子受体的DAMO微生物富集过程和结果的差异性。【方法】在序批式反应器(Sequencing batch reaetor,SBR)内接种混合物,分别以硝酸盐和亚硝酸盐为电子受体连续培养800 d,定期检测反应器基质浓度变化、计算转化速率;利用16S rRNA基因系统发育分析研究功能微生物的多样性,利用实时荧光定量PCR技术定量测定功能微生物。【结果】以亚硝酸盐为电子受体的1、3号反应器富集到了DAMO细菌,未检测到DAMO古菌;以硝酸盐为电子受体的2号反应器富集到了DAMO细菌和古菌的混合物;3个反应器的脱氮速率经过初始低速期、快速提升期,最终达到稳定,但2号快速提升期开始时间比1、3号晚了80 d左右,达到稳定的时间更长,稳定最大速率为1、3号的44.7%、40.3%。【结论】硝酸盐和亚硝酸盐对富集产物有决定性影响;以硝酸盐为电子受体富集得到的DAMO古菌和细菌协同体系可以长期稳定共存,DAMO古菌可能是协同体系中脱氮速率的限制性因素。     

A material-balance approach for modeling bacterial chemotaxis to a consumable substrate in the capillary assay

A mathematical model was developed to simulate the movement of chemotactic bacteria into and within a capillary tube containing a metabolizable chemoattractant. The model was based on a material balance that accounts for the transport of bacteria and chemoattractant as well as consumption of the substrate throughout the capillary assay system. By solving the model with a numerical method, it was possible to predict the concentration of substrate and bacteria at points within the capillary and throughout the chamber. The model was tested for its ability to simulate the results of capillary assay experiments performed with Pseudomonas putida G7 and one of its chemoattractants, naphthalene, under conditions wherein naphthalene consumption was expected to affect the flux of bacteria into the capillary. While variations in the chemotactic responses were evident among different experiments, the model could simulate the accumulation of cells in the capillary using previously determined parameters, including the chemotactic sensitivity and random motility coefficients, chi(0) and mu. In particular, model predictions were consistent with the experimental observation that the chemotactic response in the capillary is diminished under conditions wherein consumption would be expected to be significant.     

Transformation of carbon tetrachloride under sulfate reducing conditions

The removal of carbon tetrachloride under sulfate reducing conditions was studied in an an aerobic packed-bed reactor. Carbon tetrachloride, up to a concentration of 30 μM, was completely converted. Chloroform and dichloromethane were the main transformation products, but part of the carbon tetrachloride was also completely dechlorinated to unknown products. Gram-positive sulfate-reducing bacteria were involved in the reductive dechlorination of carbon tetrachloride to chloroform and dichloromethane since both molybdate, an inhibitor of sulfate reduction, and vancomycin, an inhibitor of gram-positive bacteria completely inhibited carbon tetrachloride transformation. Carbon tetrachloride transformation by these bacteria was a cometabolic process and depended on the input of an electron donor and electron acceptor (sulfate). The rate of carbon tetrachloride transformation by sulfate reducing bacteria depended on the type of electron donor present. A transformation rate of 5.1 nmol·ml^-1·h^-1 was found with ethanol as electron donor. At carbon tetrachloride concentrations higher than18 μM, sulfate reduction and reductive dechlorination of carbon tetrachloride decreased and complete inhibition was observed at a carbon tetrachloride concentration of 56.6 μM. It is not clear what type of microorganisms were involved in the observed partial complete dechlorination of carbon tetrachloride. Sulfate reducing bacteria probably did not play a role since inhibition of these bacteria with molybdate had no effect on the complete dechlorination of carbon tetrachloride. This revised version was published online in August 2006 with corrections to the Cover Date.     

Influence of electron donor/acceptor concentrations on hydrous ferric oxide (HFO) bioreduction

Dissimilatory metal-reducing bacteria (DMRB) facilitate the reduction of Feand Mn oxides in anoxic soils and sediments and play an important role inthe cycling of these metals and other elements such as carbon in aqueousenvironments. Previous studies investigating the reduction of Fe(III) oxidesby DMRB focused on reactions under constant initial electron donor (lactate)and electron acceptor (Fe oxide) concentrations. Because the concentrationsof these reactants can vary greatly in the environment and would be expectedto influence the rate and extent of oxide reduction, the influence of variableelectron acceptor and donor concentrations on hydrous ferric oxide (HFO)bioreduction was investigated. Batch experiments were conducted in pH 7 HCO₃– buffered media using Shewanella putrefaciens strain CN32. In general, the rate of Fe(III) reduction decreased with increasing HFO:lactateratios, resulting in a relatively greater proportion of crystalline Fe(III) oxidesof relatively low availability for DMRB. HFO was transformed to a variety ofcrystalline minerals including goethite, lepidocrocite, and siderite but was almostcompletely dissolved at high lactate to HFO ratios. These results indicate thatelectron donor and acceptor concentrations can greatly impact the bioreductionof HFO and the suite of Fe minerals formed as a result of reduction. The respirationdriven rate of Fe(II) formation from HFO is believed to be a primary factor governingthe array of ferrous and ferric iron phases formed during reduction.