Showing papers on "Microbial biodegradation published in 2008"

Microbial biodegradation of polyaromatic hydrocarbons.

Abstract: Polycyclic aromatic hydrocarbons (PAHs) are widespread in various ecosystems and are pollutants of great concern due to their potential toxicity, mutagenicity and carcinogenicity. Because of their hydrophobic nature, most PAHs bind to particulates in soil and sediments, rendering them less available for biological uptake. Microbial degradation represents the major mechanism responsible for the ecological recovery of PAH-contaminated sites. The goal of this review is to provide an outline of the current knowledge of microbial PAH catabolism. In the past decade, the genetic regulation of the pathway involved in naphthalene degradation by different gram-negative and gram-positive bacteria was studied in great detail. Based on both genomic and proteomic data, a deeper understanding of some high-molecular-weight PAH degradation pathways in bacteria was provided. The ability of nonligninolytic and ligninolytic fungi to transform or metabolize PAH pollutants has received considerable attention, and the biochemical principles underlying the degradation of PAHs were examined. In addition, this review summarizes the information known about the biochemical processes that determine the fate of the individual components of PAH mixtures in polluted ecosystems. A deeper understanding of the microorganism-mediated mechanisms of catalysis of PAHs will facilitate the development of new methods to enhance the bioremediation of PAH-contaminated sites.

Anaerobic biodegradation of aromatic hydrocarbons: pathways and prospects.

Abstract: Aromatic hydrocarbons contaminate many environments worldwide, and their removal often relies on microbial bioremediation. Whereas aerobic biodegradation has been well studied for decades, anaerobic hydrocarbon biodegradation is a nascent field undergoing rapid shifts in concept and scope. This review presents known metabolic pathways used by microbes to degrade aromatic hydrocarbons using various terminal electron acceptors; an outline of the few catabolic genes and enzymes currently characterized; and speculation about current and potential applications for anaerobic degradation of aromatic hydrocarbons.

Influence of molecular structure on the biodegradability of naphthenic acids.

Abstract: Large volumes of toxic aqueous tailings containing a complex mixture of naphthenic acids (NAs; CnH2n+ZO2) are produced in northern Alberta by the oil sands industry. Because of their persistence and contribution to toxicity, there is an urgent need to understand the fate of NAs under a variety of remediation scenarios. In a previous study, we developed a highly specific HPLC−high resolution mass spectrometry method for the analysis of NAs. Here we apply this method to determine quantitative structure−persistence relationships and kinetics for commercial NAs and NAs in oil sands process water (OSPW) during aerobic microbial biodegradation. Biodegradation of commercial NAs revealed that the mixture contained a substantial labile fraction, which was rapidly biodegraded, and a recalcitrant fraction composed of highly branched compounds. Conversely, NAs in OSPW were predominantly recalcitrant, and degraded slowly by first-order kinetics. Carbon number (n) had little effect on the rate of biodegradation, wherea...

Methane-Producing Microbial Community in a Coal Bed of the

Abstract: A series of molecular and geochemical studies were performed to study microbial, coal bed methane formation in the eastern Illinois Basin. Results suggest that organic matter is biodegraded to simple molecules, such as H2 and CO2, which fuel methanogenesis and the generation of large coal bed methane reserves. Small-subunit rRNA analysis of both the in situ microbial community and highly purified, methanogenic enrichments indicated that Methanocorpusculum is the dominant genus. Additionally, we characterized this methanogenic microorganism using scanning electron microscopy and distribution of intact polar cell membrane lipids. Phylogenetic studies of coal water samples helped us develop a model of methanogenic biodegradation of macromolecular coal and coal-derived oil by a complex microbial community. Based on enrichments, phylogenetic analyses, and calculated free energies at in situ subsurface conditions for relevant metabolisms (H2-utilizing methanogenesis, acetoclastic methanogenesis, and homoacetogenesis), H2-utilizing methanogenesis appears to be the dominant terminal process of biodegradation of coal organic matter at this location. Isotopic signatures of methane accumulations in coals (56), shales (31), biodegraded oils (2, 34), and ocean floor sediments (35) demonstrate that much subsurface methane production results from microbial activity. Coal is extremely rich in complex organic matter (OM) and therefore could be considered a very attractive carbon source for microbial biodegradation. However, coal is a solid rock, often dominated by recalcitrant, partially aromatic, and largely lignin-derived macromolecules which tend to be relatively resistant to degradation. The ratelimiting step of coal biodegradation is the initial fragmentation of the macromolecular, polycyclic, lignin-derived aromatic network of coal. Lignin degradation can be achieved by extracellular enzymes used by fungi and some microbes (11, 14), and it has also been shown that up to 40% of the weight of some coals can be dissolved using extracted microbial enzymes (47). Furthermore, numerous microbiological studies have developed

Microbial degradation of chlorinated phenols

Abstract: Chlorophenols have been introduced into the environment through their use as biocides and as by-products of chlorine bleaching in the pulp and paper industry. Chlorophenols are subject to both anaerobic and aerobic metabolism. Under anaerobic conditions, chlorinated phenols can undergo reductive dechlorination when suitable electron-donating substrates are available. Halorespiring bacteria are known which can use both low and highly chlorinated congeners of chlorophenol as electron acceptors to support growth. Many strains of halorespiring bacteria have the capacity to eliminate ortho-chlorines; however only bacteria from the species Desulfitobacteriumhafniense (formerly frappieri) can eliminate para- and meta-chlorines in addition to ortho-chlorines. Once dechlorinated, the phenolic carbon skeletons are completely converted to methane and carbon dioxide by other anaerobic microorganisms in the environment. Under aerobic conditions, both lower and higher chlorinated phenols can serve as sole electron and carbon sources supporting growth. The best studied strains utilizing pentachlorophenol belong to the genera Mycobacterium and Sphingomonas. Two main strategies are used by aerobic bacteria for the degradation of chlorophenols. Lower chlorinated phenols for the most part are initially attacked by monooxygenases yielding chlorocatechols as the first intermediates. On the other hand, polychlorinated phenols are converted to chlorohydroquinones as the initial intermediates. Fungi and some bacteria are additionally known that cometabolize chlorinated phenols.

Microbial degradation of chlorinated benzenes.

Abstract: Chlorinated benzenes are important industrial intermediates and solvents. Their widespread use has resulted in broad distribution of these compounds in the environment. Chlorobenzenes (CBs) are subject to both aerobic and anaerobic metabolism. Under aerobic conditions, CBs with four or less chlorine groups are susceptible to oxidation by aerobic bacteria, including bacteria (Burkholderia, Pseudomonas, etc.) that grow on such compounds as the sole source of carbon and energy. Sound evidence for the mineralization of CBs has been provided based on stoichiometric release of chloride or mineralization of 14C-labeled CBs to 14CO2. The degradative attack of CBs by these strains is initiated with dioxygenases eventually yielding chlorocatechols as intermediates in a pathway leading to CO2 and chloride. Higher CBs are readily reductively dehalogenated to lower chlorinated benzenes in anaerobic environments. Halorespiring bacteria from the genus Dehalococcoides are implicated in this conversion. Lower chlorinated benzenes are less readily converted, and mono-chlorinated benzene is recalcitrant to biotransformation under anaerobic conditions.

Microbial degradation of phenols: a review

Abstract: The microbial degradation of phenols has been reviewed including the phenol-degrading microbes, factors affecting degradability, and the use of biotechnology with emphasis on degradation mechanisms and their kinetics. The mechanism of microbial degradation depends on aerobic and anaerobic conditions. Under aerobic conditions, degradation of phenol was shown to be initiated by oxygenation into catechols as intermediates followed by a ring cleavage at either the ortho or meta position, depending on the type of strain. Anaerobic biodegradation of phenol occurs by carboxylation followed by dehydroxylation (reducing reaction) and dearomatisation. It was also clear that the parameters used in the Haldane model are not constants but vary, hence it may never be possible to describe the kinetic properties of a microbial cell with a single set of constants.

Biodegradation kinetics of select polycyclic aromatic hydrocarbon (PAH) mixtures by Sphingomonas paucimobilis EPA505

Abstract: Many contaminated sites commonly have complex mixtures of polycyclic aromatic hydrocarbons (PAHs) whose individual microbial biodegradation may be altered in mixtures. Biodegradation kinetics for fluorene, naphthalene, 1,5-dimethylnaphthalene and 1-methylfluorene were evaluated in sole substrate, binary and ternary systems using Sphingomonas paucimobilis EPA505. The first order rate constants for fluorene, naphthalene, 1,5-dimethylnaphthalene, and 1-methylfluorene were comparable; yet Monod parameters were significantly different for the tested PAHs. S. paucimobilis completely degraded all the components in binary and ternary mixtures; however, the initial degradation rates of individual components decreased in the presence of competitive PAHs. Results from the mixture experiments indicate competitive interactions, demonstrated mathematically. The generated model appropriately predicted the biodegradation kinetics in mixtures using parameter estimates from the sole substrate experiments, validating the hypothesis of a common rate-determining step. Biodegradation kinetics in mixtures were affected by the affinity coefficients of the co-occurring PAHs and mixture composition. Experiments with equal concentrations of substrates demonstrated the effect of concentration on competitive inhibition. Ternary experiments with naphthalene, 1,5-dimethylnaphthalene and 1-methylfluorene revealed delayed degradation, where depletion of naphthalene and 1,5-dimethylnapthalene occurred rapidly only after the complete removal of 1-methylfluorene. The substrate interactions observed in mixtures require a multisubstrate model to account for simultaneous degradation of substrates. PAH contaminated sites are far more complex than even ternary mixtures; however these studies clearly demonstrate the effect that interactions can have on individual chemical kinetics. Consequently, predicting natural or enhanced degradation of PAHs cannot be based on single compound kinetics as this assumption would likely overestimate the rate of disappearance.

Quantifying microbial utilization of petroleum hydrocarbons in salt marsh sediments by using the 13C content of bacterial rRNA.

Abstract: Natural remediation of oil spills is catalyzed by complex microbial consortia. Here we took a wholecommunity approach to investigate bacterial incorporation of petroleum hydrocarbons from a simulated oil spill. We utilized the natural difference in carbon isotopic abundance between a salt marsh ecosystem supported by the 13 C-enriched C4 grass Spartina alterniflora and 13 C-depleted petroleum to monitor changes in the 13 C content of biomass. Magnetic bead capture methods for selective recovery of bacterial RNA were used to monitor the 13 C content of bacterial biomass during a 2-week experiment. The data show that by the end of the experiment, up to 26% of bacterial biomass was derived from consumption of the freshly spilled oil. The results contrast with the inertness of a nearby relict spill, which occurred in 1969 in West Falmouth, MA. Sequences of 16S rRNA genes from our experimental samples also were consistent with previous reports suggesting the importance of Gamma- and Deltaproteobacteria and Firmicutes in the remineralization of hydrocarbons. The magnetic bead capture approach makes it possible to quantify uptake of petroleum hydrocarbons by microbes in situ. Although employed here at the domain level, RNA capture procedures can be highly specific. The same strategy could be used with genus-level specificity, something which is not currently possible using the 13 C content of biomarker lipids. Coastal environments are threatened by petroleum spills ranging from low-level discharges to catastrophic accidents. Large spills commonly are followed by clean-up efforts, but complete containment is rare. In all cases, remediation ultimately depends on microbial degradation. The rate of this natural bioremediation varies with physical and biological factors (temperature, wind and wave action, macroecology, and microbial community diversity), all of which have been extensively studied and reviewed (3, 4, 23, 27, 42, 69).

Microbial degradation of organophosphonates by soil bacteria

Abstract: Bacteria that can utilize glyphosate (GP) or methylphosphonic acid (MPA) as a sole phosphorus source have been isolated from soil samples polluted with organophosphonates (OP). No matter which of these compounds was predominant in the native habitat of the strains, all of them utilized methylphosphonate. Some of the strains isolated from GP-polluted soil could utilize both phosphorus sources. Strains growing on glyphosate only were not isolated. The isolates retained high destructive activity after long-term storage of cells in lyophilized state, freezing to −20°C, and maintenance on various media under mineral oil. When phosphorusstarved cells (with 2% phosphorus) were used as inoculum, the efficiency of OP biodegradation significantly increased (1.5-fold).

Development of engineered natural organic sorbents for environmental applications. 4. Effects on biodegradation and distribution of pyrene in soils.

Abstract: The effects of engineered natural organic amendments on the biodegradation and distribution of pyrene in soils were assessed. Pyrene was aged for 105 days in soils amended with either raw or superheated water (SHW)-processed Ml peat or soybean stalks, and then subjected to biodegradation with specifically selected microorganisms for 130 days. Initial rates of pyrene mineralization in the soils were increased by addition of raw Ml peat, but markedly decreased by additions of SHW-processed Ml peat and both processed and raw soybean stalks. Pyrene sorbed by the processed organic sorbents was, however, slowly but steadily degraded by microorganisms over a greater than 4-month test period. Pyrene distributions in the soils were examined by sequential extractions of samples before and after biodegradation. Fractions of pyrene extracted readily with water orwater/methanol mixtures were decreased substantially in both soils by the addition of processed amendments, while the nonextractable fractions associated with humic and fulvic acids and humin were increased markedly. The results demonstrate that SHW-processed amendments effectively reduce the ecological and human availability and aqueous phase extractability of organic contaminants while facilitating their steady microbial degradation and eventually complete remediation.

Degradation rates of aged petroleum hydrocarbons are likely to be mass transfer dependent in the field.

Abstract: Evidence for on site biodegradation may be difficult to provide at heterogeneous sites without additional experiments in controlled laboratory conditions. In this study, microbial activities measured as CO2 and CH4 production were compared in situ, in intact soil cores and in bottle microcosms containing sieved soils. In addition, biodegradation rates were determined by measuring the decrease in petroleum hydrocarbon concentrations at 7°C in aerobic and anaerobic conditions. Elevated concentrations of CO2 and CH4 in the soil gas phase indicated that both the aerobic and anaerobic microbial activity potentials were high at the contaminated site. Aerobic and anaerobic microbial degradation rates in laboratory experiments of petroleum hydrocarbons were highest in soils from the most contaminated point and degradation in the aerobic and anaerobic microcosms was linear throughout the incubation, indicating mass-transfer-dependent degradation. Different results for microbial activity measurements were obtained in laboratory studies depending on pretreatment and size of the sample, even when the environmental conditions were mimicked. These differences may be related to differences in the gas exchange rates as well as in changes in the bioavailability of the contaminant in different analyses. When predicting by modeling the behavior of an aged contaminant it is relevant to adapt the models in use to correspond to conditions relevant at the contaminated sites. The variables used in the models should be based on data from the site and on experiments performed using the original aged contaminant without any additions.

Bioremediation of Petroleum Hydrocarbons in Cold Regions: Temperature effects on biodegradation of petroleum contaminants in cold soils

Abstract: Introduction Bioremediation in cold climates is frequently regarded with skepticism. Owners of polluted sites and regulatory agencies may doubt the effectiveness of biological degradation at near freezing temperatures. While it is true that biodegradation rates decrease with decreasing temperatures, this does not mean that bioremediation is inappropriate for cold regions. Microbial degradation of hydrocarbons occurs even around 0 °C (Chapter 4). In remote alpine, Arctic, and Antarctic locations, excavation and shipping of contaminated soil may be prohibitively expensive. Bioremediation may be the most cost-effective alternative. This chapter discusses microbial adaptation to cold temperatures as well as results of laboratory and field studies of bioremediation at low temperatures. Microorganisms can grow at temperatures ranging from subzero to more than 100 °C. Microbes are divided into four groups based on the range of temperature at which they can grow. The psychrophiles grows at temperatures below 20 °C, the mesophiles between 20 °C and 44 °C, the thermophiles between 45 °C and 70 °C, and the hyperthermophiles require growth temperatures above 70 °C to over 110 °C. The term “cold-adapted microorganisms” (CAMs) is frequently used for describing bacteria growing at or close to zero degrees Celsius. Depending on the cardinal temperatures (the minimal, the optimal, and the maximum growth temperature), CAMs can be classified as psychrophiles or psychrotrophs . Morita's (1975) definition, which holds that psychrophiles have a maximum growth temperature of less than 20 °C and an optimal growth temperature of less than 15 °C, while psychrotrophs have a maximum temperature of 40 °C and an optimal growth temperature higher than 15 °C, is widely accepted.

Degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria

Abstract: Accidental spills, industrial discharges and gasoline leakage from underground storage tanks have resulted in serious pollution of the environment with monoaromatic hydrocarbons, such as benzene, toluene, ethylbenzene and xylene (so-called BTEX) High concentrations of BTEX have been detected in soils, sediments and groundwater The mobility and toxicity of the BTEX compounds are of major concern In situ bioremediation of BTEX by using naturally occurring microorganisms or introduced microorganisms is a very attractive option BTEX compounds are known to be transformed (or degraded) by microorganisms under aerobic and anaerobic conditions As BTEX compounds are often present in the anaerobic zones of the environment, anaerobic bioremediation is an attractive remediation technique The bottleneck in the application of anaerobic techniques is the lack of knowledge about the anaerobic biodegradation of benzene In particular, little is known about the bacteria involved in anaerobic benzene degradation and the anaerobic benzene degradation pathway has still not been elucidated The aim of the research presented in this thesis was to gain more insight in the degradation of benzene and other aromatic hydrocarbons by anaerobic bacteria In particular, the physiology and phylogeny of the bacteria responsible for the degradation were studied and the results have been presented in this thesis Anaerobic benzene and toluene degradation was studied with different electron acceptors in batch experiments inoculated with material from an aquifer polluted by BTEX-containing landfill leachate (Banisveld landfill near Boxtel, The Netherlands) Benzene was not degraded during one year of incubation Toluene degradation, on the other hand, was observed with nitrate, MnO2 and Fe(III)NTA as electron acceptors After further enrichment and several isolation attempts, a novel betaproteobacterial bacterium, strain G5G6, was obtained in pure culture Strain G5G6 is able to grow with toluene as the sole electron donor and carbon source, and amorphous and soluble Fe(III)-species, nitrate and MnO2 as electron acceptors Strain G5G6 has several other interesting physiological and phylogenetic characteristics, which will be subject of future research Strain G5G6 represents a novel species in a novel genus for which we propose the name Georgfuchsia toluolica In general, aerobic degradation of BTEX is a faster process than anaerobic BTEX degradation However, for a number of reasons application of oxygen-dependent processes in the subsurface are technically and financially often not appealing Therefore, an alternative bioremediation strategy would be to introduce oxygen in an alternative way, eg by in situ production Chlorate reduction is a way to produce molecular oxygen in situ under anaerobic conditions The formation of oxygen during chlorate reduction may result in rapid oxidation of compounds which are slowly degraded under anaerobic conditions; an example of such a compound is benzene Therefore, benzene degradation coupled to the reduction of chlorate (ClO3-) was studied in this thesis With mixed material from a wastewater treatment plant and soil samples obtained from a location contaminated with benzene, a benzene-degrading chlorate-reducing stable enrichment culture was obtained This stable enrichment consisted of about five different bacterial species Cross feeding involving interspecies oxygen transfer is a likely mechanism in this enrichment One of these species, strain BC, was obtained in pure culture Phylogenetic analysis showed that strain BC is a Alicycliphilus denitrificans strain Strain BC is able to degrade benzene in conjunction with chlorate reduction Oxygenase genes putatively encoding the enzymes performing the initial steps in aerobic degradation of benzene, were detected in strain BC This demonstrates the existence of aerobic benzene bacterial biodegradation pathways under essentially anaerobic conditions Thus, aerobic pathways can be employed under conditions where no external oxygen is supplied The new insights into toluene degradation under anaerobic conditions and benzene degradation coupled to chlorate reduction, as described in this thesis, can be applied for the improvement or development of in situ bioremediation strategies for BTEX contamination

Effect of rhizosphere on soil microbial community and in-situ pyrene biodegradation

Abstract: To access the influence of a vegetation on soil microorganisms toward organic pollutant biogegration, this study examined the rhizospheric effects of four plant species (sudan grass, white clover, alfalfa, and fescue) on the soil microbial community and in-situ pyrene (PYR) biodegradation The results indicated that the spiked PYR levels in soils decreased substantially compared to the control soil without planting With equal planted densities, the efficiencies of PYR degradation in rhizosphere with sudan grass, white clover, alfalfa and fescue were 340%, 284%, 277%, and 99%, respectively However, on the basis of equal root biomass the efficiencies were in order of white clover >> alfalfa > sudan > fescue The increased PYR biodegradation was attributed to the enhanced bacterial population and activity induced by plant roots in the rhizosphere Soil microbial species and biomasses were elucidated in terms of microbial phospholipid ester-linked fatty acid (PLFA) biomarkers The principal component analysis (PCA) revealed significant changes in PLFA pattern in planted and non-planted soils spiked with PYR Total PLFAs in planted soils were all higher than those in non-planted soils PLFA assemblages indicated that bacteria were the primary PYR degrading microorganisms, and that Gram-positive bacteria exhibited higher tolerance to PYR than Gram-negative bacteria did

Simulating test of microbial degradation of natural gas

Abstract: In order to study changes of gas component and carbon isotopic composition after microbial degradation of natural gas,microbes that degrade crude oil and live in near wellbore soils are cultured and enriched,then are used to perform simulating test of gas biodegradation.Oilfield microbes can degrade hydrocarbon components of natural gas.After biodegradation,iC4/nC4,C3/nC4,C2/C3 and C2/nC4 values increase,indicating that normal butane is easier to be biodegraded than isobutene,propane and ethane,and that propane is easier to be degraded than ethane.The variations of 13C values of heavy hydrocarbons are all lower than 1‰,except for that of CO2 which significantly get lighter,with enriched 12C in the range of 7.4‰ to 11.9‰,possibly due to the short time of biodegradation.Both gas component and carbon isotopic composition features show that biodegradation of propane has no priority over normal butane.The microbes inoculated in some samples may contain methane-oxidizing bacteria,resulting in larger 13C value of methane ranging from 1.8‰ to 1.9‰.

Microbial Adaptation to Boreal Saturated Subsurface: Implications in Bioremediation of Polychlorophenols

Abstract: Saturated subsurface environments pose challenges to the intrinsic microbiology. Prevailing environmental conditions (temperature, pH, bioavailability of substrates and nutrients) affect microbial biodegradation activity, which is often favored by certain redox conditions. Microbial adaptation in each redox environment proceeds by selection and enrichment of indigenous bacteria, evolution of novel catabolic pathways and horizontal gene transfer (Wilson et al. 1985; van der Meer et al. 1998; Tiirola et al. 2002b). Formation of biofilms enables microbial retainment, co-operation among microorganisms and enhanced gene transfer among organisms (Singh et al. 2006). Chlorophenols are toxic and persistent pollutants mainly originating from anthropogenic sources. Polychlorophenols, i.e. tri-, tetra-, and/or pentachlorophenol