Isolation and characterization of phenol-degrading denitrifying bacteria

Phenol is a man-made as well as a naturally occurring aromatic compound and an important intermediate in the biodegradation of natural and industrial aromatic compounds. Whereas many microorganisms that are capable of aerobic phenol degradation have been isolated, only a few phenol-degrading anaerobic organisms have been described to date. In this study, three novel nitrate-reducing microorganisms that are capable of using phenol as a sole source of carbon were isolated and characterized. Phenol-degrading denitrifying pure cultures were obtained by enrichment culture from anaerobic sediments obtained from three different geographic locations, the East River in New York, N.Y., a Florida orange grove, and a rain forest in Costa Rica. The three strains were shown to be different from each other based on physiologic and metabolic properties. Even though analysis of membrane fatty acids did not result in identification of the organisms, the fatty acid profiles were found to be similar to those of Azoarcus species. Sequence analysis of 16S ribosomal DNA also indicated that the phenol-degrading isolates were closely related to members of the genus Azoarcus. The results of this study add three new members to the genus Azoarcus, which previously comprised only nitrogen-fixing species associated with plant roots and denitrifying toluene degraders.     

Microbial metabolism of pyridine, quinoline, acridine, and their derivatives under aerobic and anaerobic conditions

Our review of the metabolic pathways of pyridines and aza-arenes showed that biodegradation of heterocyclic aromatic compounds occurs under both aerobic and anaerobic conditions. Depending upon the environmental conditions, different types of bacteria, fungi, and enzymes are involved in the degradation process of these compounds. Our review indicated that different organisms are using different pathways to biotransform a substrate. Our review also showed that the transformation rate of the pyridine derivatives is dependent on the substituents. For example, pyridine carboxylic acids have the highest transformation rate followed by mono-hydroxypyridines, methylpyridines, aminopyridines, and halogenated pyridines. Through the isolation of metabolites, it was possible to demonstrate the mineralization pathway of various heterocyclic aromatic compounds. By using 14C-labeled substrates, it was possible to show that ring fission of a specific heterocyclic compound occurs at a specific position of the ring. Furthermore, many researchers have been able to isolate and characterize the microorganisms or even the enzymes involved in the transformation of these compounds or their derivatives. In studies involving 18O labeling as well as the use of cofactors and coenzymes, it was possible to prove that specific enzymes (e.g., mono- or dioxygenases) are involved in a particular degradation step. By using H2 18O, it could be shown that in certain transformation reactions, the oxygen was derived from water and that therefore these reactions might also occur under anaerobic conditions.     

Biocatalysis, biodegradation and bioinformatics

Biocatalysis, biodegradation and bioinformatics are prominent scientific fields in industrial microbiology and biotechnology. This paper describes developments in these fields with a focus on the role of David T Gibson as a researcher and mentor. He has pioneered studies on the mechanisms by which aerobic microorganisms transform aromatic hydrocarbons. In addition, his research has served as a model for further investigations into bacterial atrazine and dichloromethane catabolism described here. Microbial catabolism research requires information on organic chemistry, microorganisms, metabolic pathways, catabolic genes, and enzymes. These information needs are now being met more comprehensively by development of the University of Minnesota Biocatalysis/Biodegradation Database.     

The University of Minnesota Biocatalysis/Biodegradation Database: specialized metabolism for functional genomics

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://www.labmed.umn.edu/umbbd/i nde x.html) first became available on the web in 1995 to provide information on microbial biocatalytic reactions of, and biodegradation pathways for, organic chemical compounds, especially those produced by man. Its goal is to become a representative database of biodegradation, spanning the diversity of known microbial metabolic routes, organic functional groups, and environmental conditions under which biodegradation occurs. The database can be used to enhance understanding of basic biochemistry, biocatalysis leading to speciality chemical manufacture, and biodegradation of environmental pollutants. It is also a resource for functional genomics, since it contains information on enzymes and genes involved in specialized metabolism not found in intermediary metabolism databases, and thus can assist in assigning functions to genes homologous to such less common genes. With information on >400 reactions and compounds, it is poised to become a resource for prediction of microbial biodegradation pathways for compounds it does not contain, a process complementary to predicting the functions of new classes of microbial genes.     

Systematic Approach for Modeling Tetrachloroethene Biodegradation

The anaerobic biodegradation of tetrachloroethene (PCE) is a reasonably well understood process. Specific organisms capable of using PCE as an electron acceptor for growth require the addition of an electron donor to remove PCE from contaminated ground waters. However, competition from other anaerobic microorganisms for added electron donor will influence the rate and completeness of PCE degradation. The approach developed here allows for the explicit modeling of PCE and byproduct biodegradation as a function of electron donor and byproduct concentrations, and the microbiological ecology of the system. The approach is general and can be easily modified for ready use with in situ ground-water models or ex situ reactor models. Simulations conducted with models developed from this approach show the sensitivity of PCE biodegradation to input parameter values, in particular initial biomass concentrations. Additionally, the dechlorination rate will be strongly influenced by the microbial ecology of the system. Finally, comparison with experimental acclimation results indicates that existing kinetic constants may not be generally applicable. Better techniques for measuring the biomass of specific organism groups in mixed systems are required.     

Factors affecting the biodegradation of toluene in soil

The biodegradation of toluene in soil microcosms was examined in order to identify the physical, chemical, and biological factors which determine the fate and lifetime of organic chemicals in soils. Toluene degradation rates were proportional to the initial substrate concentration and these rates reached a maximum at a concentration of 200 micrograms/g. No degradation occurred above this concentration presumably due to the toxicity of the hydrocarbon to the soil microorganisms. Small differences were observed in the degradation rates in soils at different moisture content. However, the availability of water in soil appeared to limit toluene degradation only at a very low water content. The lifetime of toluene in soil was also related to the initial level and activity of the soil microorganisms. Toluene was metabolized rapidly in those soils which initially contained high levels of degrading microorganisms. Furthermore, exposure of the soil to toluene resulted in an increase in the number of degrading organisms. The lack of inorganic nutrients such as nitrogen prevented complete degradation of toluene in a clay soil which contained high levels of degrading microorganisms. The biodegradation of organic chemicals in soil is not an intrinsic property of the molecule and cannot be predicted without first delineating the environment in which it is found. The biodegradation of a compound is defined by the biological, physical, and chemical characteristics of the soil environment. The lifetime of a chemical in soil results from a combination of all three of these parameters.     

Modulation of antennal scanning in the honeybee by sucrose stimuli, serotonin, and octopamine: behavior and electrophysiology

The objective of this publication is to present a new dynamic aerobic biodegradation test method simulating a river. A laboratory cascade test system and standardized batch shake flask tests were used for biodegradation studies with the non-volatile and non-sorbing model compounds 2,4-dinitrophenol, naphthalene-1-sulphonic acid and sulphanilic acid. To be closer to the often very low concentrations of substances in the environment the concentrations of the compounds used were standard test concentrations and lower. 14C labelled compounds were measured at 50 micrograms/l, capillary electrophoresis at 5000 micrograms/l and the removal of dissolved organic carbon at 50000 micrograms/l. The test results obtained confirmed the known ultimate biodegradability of the test compounds and showed that biodegradation degrees, rates and degradation durations depended on the test systems, the concentrations of test compounds and the inocula. The river model is a suitable simulation test for natural dynamic surface waters which can be used to perform biodegradability studies at low test concentrations if adequate analytical tools, preferably radioactive-labelled substances, are available.     

Modeling Substrate Interactions during Aerobic Biodegradation of Mixtures of Vinyl Chloride and Ethene

Ethene (ETH) is often associated with vinyl chloride (VC) in contaminated groundwater, as it is formed along with vinyl chloride during reductive dechlorination of higher chloroethenes (e.g., perchloroethylene and trichloroethylene). In the present study the interaction between VC and ETH during their aerobic biodegradation by enrichment cultures was investigated. The cultures were able to use both compounds as growth substrates. In mixture experiments, the degradation rate of one substrate was affected by the presence of the other. A biokinetic model based on competitive inhibition described well the observed substrate interactions over a range of initial VC (0–144 μmol?L?1) and ETH (0–37.5 μmol?L?1) concentrations, using parameters estimated from single-substrate experiments. Notably, half-velocity coefficients could be used as competitive inhibition coefficients. This finding shows the importance of obtaining accurate measurements of half-velocity coefficients in order model competitive inhibition processes. Simulation results showed that when the initial ETH concentration was raised from 0 to 30 μmol?L?1, the apparent half-velocity coefficient for VC (KVCAPP) increased by nearly three times, from 12.9 to 35.4 μmol?L?1. This finding has strong environmental implications because a low half-velocity coefficient for VC is regarded as the major prerequisite for achieving efficient and complete VC degradation. Moreover, the effect of ETH on the efficiency of VC removal is strongly dependent on the KVC/KETH ratio, consequently determination of KETH for VC-degrading microbes is important when biodegradation (or bioaugmentation) is considered for clean up of VC-contaminated sites. Additional model simulations, using the ratio of KVC to KETH for previously characterized VC- and ETH-utilizing microorganisms (values ranged from 0.06 to 1.2) showed that their ability to degrade VC in the presence of ETH may differ significantly.     

Bacterial dehalogenation

Halogenated organic compounds are produced industrially in large quantities and represent an important class of environmental pollutants. However, an abundance of haloorganic compounds is also produced naturally. Bacteria have evolved several strategies for the enzyme-catalyzed dehalogenation and degradation of both haloaliphatic and haloaromatic compounds: (i) Oxidative dehalogenation is the result of mono- or dioxygenase-catalyzed, co-metabolic or metabolic reactions. (ii) In dehydrohalogenase-catalyzed dehalogenation, halide elimination leads to the formation of a double bond. (iii) Substitutive dehalogenation in most cases is a hydrolytic process, catalyzed by halidohydrolases, but there also is a "thiolytic" mechanism with glutathione as cosubstrate. Dehalogenation by halohydrin hydrogen-halide lyases is the result of an intramolecular substitution reaction. (iv) A distinct dechlorination mechanism involves methyl transfer from chloromethane onto tetrahydrofolate. (v) Reductive dehalogenations are co-metabolic processes, or they are specific reactions involved in substrate utilization (carbon metabolism), or reductive dehalogenation is coupled to energy conservation: some anaerobic bacteria use a specific haloorganic compound as electron acceptor of a respiratory process. This review discusses the mechanisms of enzyme-catalyzed dehalogenation reactions, describes some pathways of the bacterial degradation of haloorganic compounds, and indicates some trends in the biological treatment of organohalogen-polluted air, groundwater, soil, and sediments.     

Potential for 17β-Estradiol and Estrone Degradation in a Recharge Aquifer System

The potential for degradation of two important endocrine disrupting chemicals, 17β-estradiol (E2) and estrone (E1) in a wastewater effluent recharged aquifer system was assessed using lab scale microcosms. Biotransformation by microorganisms present in the aquifer material was found to be the major mode of removal for both organic contaminants in the microcosms. The addition of ultrafiltered secondary effluent, simulating recharge of aquifer, did not significantly alter the behavior of both E2 and E1 in the aquifer microcosms. A significant difference in E2 removal rates in microcosms that received E2 as a concentrated stock in methanol as opposed to direct dissolution of E2 into groundwater shows that the presence of methanol could alter the biodegradation kinetics of the organic pollutant of interest. The rapid utilization of methanol by indigenous methanol degraders, which was present as an alternative carbon substrate, caused rapid depletion of oxygen and, hence, development of anoxic conditions in the microcosms. Increased oxygen supply led to corresponding improved E2 biotransformation rates, indicating that E2 degradation under anoxic conditions was much slower than under aerobic conditions. On the other hand, in the presence of a high initial concentration of methanol, E1 was more persistent in the medium under aerobic conditions than under anoxic conditions. Apparently, the initial high concentration of methanol had an inhibitory effect on aerobic E1 degraders in the microcosms.     

Quantifying the biodegradation of phenanthrene by Pseudomonas stutzeri P16 in the presence of a nonionic surfactant

The low water solubility of polycyclic aromatic hydrocarbons is believed to limit their availability to microorganisms, which is a potential problem for bioremediation of polycyclic aromatic hydrocarbon-contaminated sites. Surfactants have been suggested to enhance the bioavailability of hydrophobic compounds, but both negative and positive effects of surfactants on biodegradation have been reported in the literature. Earlier, we presented mechanistic models of the effects of surfactants on phenanthrene dissolution and on the biodegradation kinetics of phenanthrene solubilized in surfactant micelles. In this study, we combined the biodegradation and dissolution models to quantify the influence of the surfactant Tergitol NP-10 on biodegradation of solid-phase phenanthrene by Pseudomonas stutzeri P16. Although micellized phenanthrene does not appear to be available directly to the bacterium, the ability of the surfactant to increase the phenanthrene dissolution rate resulted in an overall increase in bacterial growth rate in the presence of the surfactant. Experimental observations could be predicted well by the derived model with measured biokinetic and dissolution parameters. The proposed model therefore can serve as a base case for understanding the physical-chemical effects of surfactants on nonaqueous hydrocarbon bioavailability.     

Methanotrophs, Methylosinus trichosporium OB3b, sMMO, and their application to bioremediation

One of the most problematic groups of the USEPA and EU priority pollutants are the halogenated organic compounds. These substances have a wide range of industrial applications, such as solvents and cleaners. Inadequate disposal techniques and accidental spillages have led to their detection in soil, groundwater, and river sediments. Persistence of these compounds in the environment has resulted from low levels of biodegradation due to chemical structural features that preclude or retard biological attack. Research has indicated the idea that treatment systems based on methanotrophic co-metabolic transformation may be a cost-effective and efficient alternative to physical methods because of the potential for high transformation rates, the possibility of complete compound degradation without the formation of toxic metabolites, applicability to a broad spectrum of compounds, and the use of a widely available and inexpensive growth substrate. A substantial amount of work concerning methanotrophic cometabolic transformations has been carried out using the soluble form of methane monooxygenase (sMMO) from the obligate methanotroph Methylosinus trichosporium OB3b. This NADH-dependent monooxygenase is derepressed when cells are grown under copper stress. sMMO has a wider specificity than the particulate form. sMMO has been shown to degrade trichloroethylene (TCE) at a rate of at least one order of magnitude faster than obtained with other mixed and pure cultures, suggesting it has a wider application to bioremediation. Furthermore, sMMO catalyzes an unusually wide range of oxidation reactions, including the hydroxylation of alkanes, epoxidation of alkenes, ethers, halogenated methanes, cyclic and aromatic compounds including compounds, that are resistant to degradation in the environment. However, the practical application of methantrophs and Methylosinus trichosporium OB3b to the treatment of chlorinated organics has met with mixed success. Although oxidation rates are rapid, compound oxidation with M. trichosporium OB3b is difficult. This fastidious organism grows relatively slowly, which limits the speed with which sMMO expressing biomass can be generated. Furthermore, product toxicity toward the cell, affecting the stability of the enzyme when transforming certain compounds has been observed, for example, by the products of 1,2,3 trichlorobenzene hydroxylation (2,3,4- and 3,4,5-trichlorophenol) and of TCE degradation (chloral hydrate). Because of this toxicity and the inability of sMMO to further oxidize its own hydroxylation products, the ability of methane monoxygenase to carry out the monooxygenation of a wide variety of substituted aromatics and polyaromatics cannot be fully exploited in M. trichosporium OB3b. Many of these problems could be overcome by the use of either a mixed downstream heterotrophic population of organisms that could accommodate the products of hydroxylation or to express sMMO in an organism that could metabolize the products of hydroxylation. The latter of these two approaches would have several advantages. The main benefit would be the removal of the need for methane, which is required to induce sMMO in M. trichosporium OB3b, and supply carbon and energy to the cells that continuously oxidise the target compound, but also acts as a competitive inhibitor of sMMO. Instead, the recombinant could utilize the products of sMMO-mediated hydroxylation as a carbon source.     

Modeling of Biodegradation in an Old Unregulated European Landfill

In this note an example of modeling of biodegradation processes of an old abandoned municipal solid waste landfill for its simulation is illustrated using the landfill dynamic simulation tool MODUELO. In this program the waste biodegradation model is based on the quantification of organic matter, its chemical composition, biodegradability, accessibility to microorganisms, and the ratio nonbiodegradable leachable organic matter to gasifiable matter. Data from a characterization campaign, presented elsewhere, were used to determine these parameters. The experimental information was completed with safety factors (to compensate for sampling uncertainty) and literature values. The degradation rates were determined, after having calibrated the hydrological model, by fitting the temporal series of pollutants’ concentration measured in the leachate and the biogas composition. The achieved fit of the simulated series compared to the measured data is reported as the result of this work. Given the limited information available, the obtained simulation model is considered an acceptable tool to study the future evolution of the landfill in different circumstances.     

饮用水源中痕量有机物的生物膜降解

生物膜工艺是去除饮用水中痕量有机物的有效方法,共代谢是生物膜工艺中的重要方式。在微污染饮用水源中,自然有机物作为初级基质支持生物膜的生长,痕量有机物作为第二级基质被生物膜降解而被去除。     

New ecological aspects of extraorganism pathogenic microbial populations

The author summarizes the results of his own studies of pathogenic microorganisms and saprophytes, their intertransitional forms. The environmental pathogenic bacteria have been demonstrated to be autotropic, but in man and warm-blooded animals the organisms act as heterotrophic. This explains their wide range of metabolic plasticity and smooth distinction of saprophytes and parasites.     

Degradation of compounds containing carbon atoms by photooxidation in the presence of water

It was shown that all compounds containing carbon atoms, tested in this study, were degraded by the coincident influence of light, oxygen (air), and water. By this photooxidation, saturated as well as unsaturated aliphatic and aromatic compounds, monomeric, polymeric and high polymeric compounds were degraded and the carbon atoms of these compounds as well as carbon itself in form of amorphous carbon or diamond, were converted to carbon dioxide, if dispersed in water or together with water as very small solid, liquid, or gaseous particles. As such conditions occur extensively in nature, it was concluded that this degradation of organic substances is of great importance in nature, in addition to microbial and enzymatic degradation. This photooxidation further represents a possibility for pollution control to prevent damage to environment by degrading organic substances which are either slightly soluble or practically insoluble in water, as well as compounds which will not be destroyed by microbial and enzymatic degradation.     

Lipophilic compounds in biotechnology--interactions with cells and technological problems

Lipophilic compounds are of significant importance in modern biotechnology. Centerly of interest are the biodegradation as well as the biotransformation of such lipophilic and often water-immiscible substances. Both whole cells and/or enzymes are used for these processes. It is obvious that a wide range of problems arise in an application of such complex systems consisting of biocatalysts substrate(s), product(s), water, (in some cases water-immiscible organic solvents): (i) interactions between lipophilic compounds and the membranes resulting in the change of some physiological characteristics of the living system; (ii) problems in the transport of these compounds (substrates and/or products) within the complex structured reaction systems; (iii) the problem of increasing the solubility of the lipophilic and mostly water-immiscible compounds with a minimum of inhibition effects on the processes; (iv) the presence of lipophilic components may also cause changes of the transport processes within the system (e.g. immobilized cells) resulting in changed yield or activity of the biological system. These problems are critically discussed in this review in relation to the known modes of interaction of lipophilic compounds with membranes, the bioavailability of the substrates, and the cases of steroid biotransformations. An outlook of future aspects in research, development and application of such processes is given.     

Physiologo-biochemical characteristics if Gluconobacter oxydans and prospects for its use in biotechnology and biosensor systems (review)

Gluconobacter oxydans possesses a unique organization of metabolic systems, which are characterized by reduction of major dissimilation pathways, surface localization of main oxidative enzymes responsible for partial oxidation of carbon substrates, high performance of electron-transport chains, and accumulation of partially oxidized metabolites in the medium. These features allow us to use the cells of these microorganisms in biotechnology for production of several food products and medicines. The use of G. oxydans in biosensors for estimation of concentrations of sugars, aldoses and polyalcohols is promising. Physiological and biochemical features of these microorganisms enabling their use in biotechnology and receptor elements of biosensors are reviewed.     

Biogenesis of aroma constituents of fruits and vegetables

The aroma of fruits and vegetables may be considered to originate from the basic nutrients such as carbohydrates, proteins, and fats, as well as vitamins and minerals. These nutrients, in turn, are produced by photosynthetic and related metabolic activities occurring in the plant. Current interests in aroma of fruits and vegetables have been shifting from isolation and identification to elucidation of their formation pathways either of biogenetic or processing nature. This article is intended to provide a summary on the development and degradation of aroma of selected major fruits and vegetables, 20 in each category. It reveals that information concerning this matter is still meager at present and that much more exploratory research is needed.