Encoding microbial metabolic logic: predicting biodegradation

Prediction of microbial metabolism is important for annotating genome sequences and for understanding the fate of chemicals in the environment. A metabolic pathway prediction system (PPS) has been developed that is freely available on the world wide web (), recognizes the organic functional groups found in a compound, and predicts transformations based on metabolic rules. These rules are designed largely by examining reactions catalogued in the University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD) and are generalized based on metabolic logic. The predictive accuracy of the PPS was tested: (1) using a 113-member set of compounds found in the database, (2) against a set of compounds whose metabolism was predicted by human experts, and (3) for consistency with experimental microbial growth studies. First, the system correctly predicted known metabolism for 111 of the 113 compounds containing C and H, O, N, S, P and/or halides that initiate existing pathways in the database, and also correctly predicted 410 of the 569 known pathway branches for these compounds. Second, computer predictions were compared to predictions by human experts for biodegradation of six compounds whose metabolism was not described in the literature. Third, the system predicted reactions liberating ammonia from three organonitrogen compounds, consistent with laboratory experiments showing that each compound served as the sole nitrogen source supporting microbial growth. The rule-based nature of the PPS makes it transparent, expandable, and adaptable.     

The University of Minnesota Biocatalysis/Biodegradation database: microorganisms, genomics and prediction

The University of Minnesota Biocatalysis/Biodegradation Database (http://www.labmed.umn.edu/umbbd/ ) begins its fifth year having met its initial goals. It contains approximately 100 pathways for microbial catabolic metabolism of primarily xenobiotic organic compounds, including information on approximately 650 reactions, 600 compounds and 400 enzymes, and containing approximately 250 microorganism entries. It includes information on most known microbial catabolic reaction types and the organic functional groups they transform. Having reached its first goals, it is ready to move beyond them. It is poised to grow in many different ways, including mirror sites; fold prediction for its sequenced enzymes; closer ties to genome and microbial strain databases; and the prediction of biodegradation pathways for compounds it does not contain.     

Yield prediction and stoichiometry of multi-step biodegradation reactions involving oxygenation

Microorganisms can initiate the degradation of organic compounds by oxygenation reactions that require the investment of energy and electrons. This diversion of energy and electrons away from synthesis reactions leads to decreased overall cell yields. A thermodynamic method was developed that improves the accuracy of cell yield prediction for compounds degraded through pathways involving oxygenation reactions. This method predicts yields and stoichiometry for each step in the biodegradation pathway, thus enabling modeling a multi-step biodegradation process in which oxygenations occur and intermediates may persist. EDTA and benzene biodegradation are presented as examples. The method compares favorably with other yield prediction methods while providing additional information of yields for intermediates produced in the degradation pathway.     

A stoichiometric organic matter decomposition model in a chemostat culture

Biodegradation, the disintegration of organic matter by microorganism, is essential for the cycling of environmental organic matter. Understanding and predicting the dynamics of this biodegradation have increasingly gained attention from the industries and government regulators. Since changes in environmental organic matter are strenuous to measure, mathematical models are essential in understanding and predicting the dynamics of organic matters. Empirical evidence suggests that grazers’ preying activity on microorganism helps to facilitate biodegradation. In this paper, we formulate and investigate a stoichiometry-based organic matter decomposition model in a chemostat culture that incorporates the dynamics of grazers. We determine the criteria for the uniform persistence and extinction of the species and chemicals. Our results show that (1) if at the unique internal steady state, the per capita growth rate of bacteria is greater than the sum of the bacteria’s death and dilution rates, then the bacteria will persist uniformly; (2) if in addition to this, (a) the grazers’ per capita growth rate is greater than the sum of the dilution rate and grazers’ death rate, and (b) the death rate of bacteria is less than some threshold, then the grazers will persist uniformly. These conditions can be achieved simultaneously if there are sufficient resources in the feed bottle. As opposed to the microcosm decomposition models’ results, in a chemostat culture, chemicals always persist. Besides the transcritical bifurcation observed in microcosm models, our chemostat model exhibits Hopf bifurcation and Rosenzweig’s paradox of enrichment phenomenon. Our sensitivity analysis suggests that the most effective way to facilitate degradation is to decrease the dilution rate.

     

The University of Minnesota Biocatalysis/Biodegradation Database: post-genomic data mining

The University of Minnesota Biocatalysis/Biodegradation Database (UM-BBD, http://umbbd.ahc.umn.edu/) provides curated information on microbial catabolism and related biotransformations, primarily for environmental pollutants. Currently, it contains information on over 130 metabolic pathways, 800 reactions, 750 compounds and 500 enzymes. In the past two years, it has increased its breath to include more examples of microbial metabolism of metals and metalloids; and expanded the types of information it includes to contain microbial biotransformations of, and binding interactions with many chemical elements. It has also increased the ways in which this data can be accessed (mined). Structure-based searching was added, for exact matches, similarity, or substructures. Analysis of UM-BBD reactions has lead to a prototype, guided, pathway prediction system. Guided prediction means that the user is shown all possible biotransformations at each step and guides the process to its conclusion. Mining the UM-BBD's data provides a unique view into how the microbial world recycles organic functional groups. UM-BBD users are encouraged to comment on all aspects of the database, including the information it contains and the tools by which it can be mined. The database and prediction system develop under the direction of the scientific community.     

Thermodynamic analysis of biodegradation pathways

Microorganisms provide a wealth of biodegradative potential in the reduction and elimination of xenobiotic compounds in the environment. One useful metric to evaluate potential biodegradation pathways is thermodynamic feasibility. However, experimental data for the thermodynamic properties of xenobiotics is scarce. The present work uses a group contribution method to study the thermodynamic properties of the University of Minnesota Biocatalysis/Biodegradation Database. The Gibbs free energies of formation and reaction are estimated for 914 compounds (81%) and 902 reactions (75%), respectively, in the database. The reactions are classified based on the minimum and maximum Gibbs free energy values, which accounts for uncertainty in the free energy estimates and a feasible concentration range relevant to biodegradation. Using the free energy estimates, the cumulative free energy change of 89 biodegradation pathways (51%) in the database could be estimated. A comparison of the likelihood of the biotransformation rules in the Pathway Prediction System and their thermodynamic feasibility was then carried out. This analysis revealed that when evaluating the feasibility of biodegradation pathways, it is important to consider the thermodynamic topology of the reactions in the context of the complete pathway. Group contribution is shown to be a viable tool for estimating, a priori, the thermodynamic feasibility and the relative likelihood of alternative biodegradation reactions. This work offers a useful tool to a broad range of researchers interested in estimating the feasibility of the reactions in existing or novel biodegradation pathways. Biotechnol. Bioeng. 2009;103: 532–541. © 2009 Wiley Periodicals, Inc.     

Computational framework for predictive biodegradation

As increasing amounts of anthropogenic chemicals are released into the environment, it is vital to human health and the preservation of ecosystems to evaluate the fate of these chemicals in the environment. It is useful to predict whether a particular compound is biodegradable and if alternate routes can be engineered for compounds already known to be biodegradable. In this work, we describe a computational framework (called BNICE) that can be used for the prediction of novel biodegradation pathways of xenobiotics. The framework was applied to 4‐chlorobiphenyl, phenanthrene, γ‐hexachlorocyclohexane, and 1,2,4‐trichlorobenzene, compounds representing various classes of xenobiotics with known biodegradation routes. BNICE reproduced the proposed biodegradation routes found experimentally, and in addition, it expanded the biodegradation reaction networks through the generation of novel compounds and reactions. The novel reactions involved in the biodegradation of 1,2,4‐trichlorobenzene were studied in depth, where pathway and thermodynamic analyses were performed. This work demonstrates that BNICE can be applied to generate novel pathways to degrade xenobiotic compounds that are thermodynamically feasible alternatives to known biodegradation routes and attractive targets for metabolic engineering. Biotechnol. Bioeng. 2009; 104: 1086–1097. © 2009 Wiley Periodicals, Inc.     

Estimation of Biodegradation Potential of Xenobiotic Organic Chemicals

A method is described to estimate the biodegradation potential of soluble, insoluble, and unknown organic chemicals. The method consists of two stages: (i) generation of a microbial inoculum in a bench scale semicontinuous activated sludge system during which microorganisms are acclimated to test material and the removal of dissolved organic carbon is monitored and (ii) biodegradability testing (CO₂ evolution) in a defined minimal medium containing the test material as the sole carbon and energy source and a dilute bacterial inoculum obtained from the supernatant of homogenized activated sludge generated in the semicontinuous activated sludge system. Removal and biodegradation are measured using nonspecific methods, at initial concentrations of 5 to 10 mg of dissolved organic carbon per liter. Biodegradability data are accurately described by a nonlinear computer model which allows the rate and extent of biodegradation for different compounds to be compared and statistically examined. The evaluation of data generated in the combined removability-biodegradability system allows the biodegradation potential of a variety of xenobiotic organic chemicals to be estimated.     

A computational framework for integration of lipidomics data into metabolic pathways

Lipids are important compounds for human physiology and as renewable resources for fuels and chemicals. In lipid research, there is a big gap between the currently available pathway-level representations of lipids and lipid structure databases in which the number of compounds is expanding rapidly with high-throughput mass spectrometry methods.In this work, we introduce a computational approach to bridge this gap by making associations between metabolic pathways and the lipid structures discovered increasingly thorough lipidomics studies. Our approach, called NICELips (Network Integrated Computational Explorer for Lipidomics), is based on the formulation of generalized enzymatic reaction rules for lipid metabolism, and it employs the generalized rules to postulate novel pathways of lipid metabolism. It further integrates all discovered lipids in biological networks of enzymatic reactions that consist their biosynthesis and biodegradation pathways.We illustrate the utility of our approach through a case study of bis(monoacylglycero)phosphate (BMP), a biologically important glycerophospholipid with immature synthesis and catabolic route(s). Using NICELips, we were able to propose various synthesis and degradation pathways for this compound and several other lipids with unknown metabolism like BMP, and in addition several alternative novel biosynthesis and biodegradation pathways for lipids with known metabolism. NICELips has potential applications in designing therapeutic interventions for lipid-associated disorders and in the metabolic engineering of model organisms for improving the biobased production of lipid-derived fuels and chemicals.     

多环芳烃厌氧生物降解研究进展

多环芳烃（PAHs）是环境中广泛分布的一类持久性有机污染物,对生态环境和公众健康具有极大危害。微生物降解是环境中去除多环芳烃污染的有效途径,近年来PAHs厌氧生物降解研究逐渐取代好氧降解成为人们关注的重点。本文从PAHs厌氧生物降解的研究背景出发,从不同厌氧还原反应体系、厌氧降解微生物、PAHs厌氧生物转化途径等方面阐述了PAHs厌氧生物降解的研究概况,归纳了对PAHs厌氧生物降解有积极作用的影响因素,提出了PAHs厌氧降解研究目前存在的问题,并对该领域未来研究方向作了简述和展望。希望为多环芳烃厌氧生物降解与环境修复研究与实践提供参考。     

Role of biomarkers in monitoring exposures to chemicals: present position,future prospects

Biomarkers are becoming increasingly important in toxicology and human health. Many research groups are carrying out studies to develop biomarkers of exposure to chemicals and apply these for human monitoring. There is considerable interest in the use and application of biomarkers to identify the nature and amounts of chemical exposures in occupational and environmental situations. Major research goals are to develop and validate biomarkers that reflect specific exposures and permit the prediction of the risk of disease in individuals and groups. One important objective is to prevent human cancer. This review presents a commentary and consensus views about the major developments on biomarkers for monitoring human exposure to chemicals. A particular emphasis is on monitoring exposures to carcinogens. Significant developments in the areas of new and existing biomarkers, analytical methodologies, validation studies and field trials together with auditing and quality assessment of data are discussed. New developments in the relatively young field of toxicogenomics possibly leading to the identification of individual susceptibility to both cancer and non-cancer endpoints are also considered. The construction and development of reliable databases that integrate information from genomic and proteomic research programmes should offer a promising future for the application of these technologies in the prediction of risks and prevention of diseases related to chemical exposures. Currently adducts of chemicals with macromolecules are important and useful biomarkers especially for certain individual chemicals where there are incidences of occupational exposure. For monitoring exposure to genotoxic compounds protein adducts, such as those formed with haemoglobin, are considered effective biomarkers for determining individual exposure doses of reactive chemicals. For other organic chemicals, the excreted urinary metabolites can also give a useful and complementary indication of exposure for acute exposures. These methods have revealed ‘backgrounds’ in people not knowingly exposed to chemicals and the sources and significance of these need to be determined, particularly in the context of their contribution to background health risks.     

Biodegradation of polyalcohol ethoxylate by a wastewater microbial consortium

Polyalcohol ethoxylate (PAE), an anionic surfactant, is the primary component in most laundry and dish wash detergents and is therefore highly loaded in domestic wastewater. Its biodegradation results in the formation of several metabolites and the fate of these metabolites through wastewater treatment plants, graywater recycling processes, and in the environment must be clearly understood. Biodegradation pathways for PAE were investigated in this project with a municipal wastewater microbial consortium. A microtiter-based oxygen sensor system was utilized to determine the preferential use of potential biodegradation products. Results show that while polyethylene glycols (PEGs) were readily degraded by PAE acclimated microorganisms, most of the carboxylic acids tested were not degraded. Biodegradation of PEGs suggests that hydrophobe–hydrophile scission was the dominant pathway for PAE biodegradation in this wastewater community. Ethylene glycol (EG) and diethylene glycol (DEG) were not utilized by microbial populations capable of degrading higher molecular weight EGs. It is possible that EG and DEG may accumulate. The microtiter-based oxygen sensor system was successfully utilized to elucidate information on PAE biodegradation pathways and could be applied to study biodegradation pathways for other important contaminants.     

Role of biomarkers in monitoring exposures to chemicals: present position, future prospects

Biomarkers are becoming increasingly important in toxicology and human health. Many research groups are carrying out studies to develop biomarkers of exposure to chemicals and apply these for human monitoring. There is considerable interest in the use and application of biomarkers to identify the nature and amounts of chemical exposures in occupational and environmental situations. Major research goals are to develop and validate biomarkers that reflect specific exposures and permit the prediction of the risk of disease in individuals and groups. One important objective is to prevent human cancer. This review presents a commentary and consensus views about the major developments on biomarkers for monitoring human exposure to chemicals. A particular emphasis is on monitoring exposures to carcinogens. Significant developments in the areas of new and existing biomarkers, analytical methodologies, validation studies and field trials together with auditing and quality assessment of data are discussed. New developments in the relatively young field of toxicogenomics possibly leading to the identification of individual susceptibility to both cancer and non-cancer endpoints are also considered. The construction and development of reliable databases that integrate information from genomic and proteomic research programmes should offer a promising future for the application of these technologies in the prediction of risks and prevention of diseases related to chemical exposures. Currently adducts of chemicals with macromolecules are important and useful biomarkers especially for certain individual chemicals where there are incidences of occupational exposure. For monitoring exposure to genotoxic compounds protein adducts, such as those formed with haemoglobin, are considered effective biomarkers for determining individual exposure doses of reactive chemicals. For other organic chemicals, the excreted urinary metabolites can also give a useful and complementary indication of exposure for acute exposures. These methods have revealed 'backgrounds' in people not knowingly exposed to chemicals and the sources and significance of these need to be determined, particularly in the context of their contribution to background health risks.     

Coupling pathway prediction and fluorescence spectroscopy to assess the impact of auxiliary substrates on micropollutant biodegradation

Some bacteria can degrade organic micropollutants (OMPs) as primary carbon sources. Due to typically low OMP concentrations, these bacteria may benefit from supplemental assimilation of natural substrates present in the pool of dissolved organic matter (DOM). The biodegradability of such auxiliary substrates and the impacts on OMP removal are tightly linked to biotransformation pathways. Here, we aimed to elucidate the biodegradability and effect of different DOM constituents for the carbofuran degrader Novosphingobium sp. KN65.2, using a novel approach that combines pathway prediction, laboratory experiments, and fluorescence spectroscopy. Pathway prediction suggested that ring hydroxylation reactions catalysed by Rieske-type dioxygenases and flavin-dependent monooxygenases determine the transformability of the 11 aromatic compounds used as model DOM constituents. Our approach further identified two groups with distinct transformation mechanisms amongst the four growth-supporting compounds selected for mixed substrate biodegradation experiments with the pesticide carbofuran (Group 1: 4-hydroxybenzoic acid, 4-hydroxybenzaldehyde; Group 2: p-coumaric acid, ferulic acid). Carbofuran biodegradation kinetics were stable in the presence of both Group 1 and Group 2 auxiliary substrates. However, Group 2 substrates would be preferable for bioremediation processes, as they showed constant biodegradation kinetics under different experimental conditions (pre-growing KN65.2 on carbofuran vs. DOM constituent). Furthermore, Group 2 substrates were utilisable by KN65.2 in the presence of a competitor (Pseudomonas fluorescens sp. P17). Our study thus presents a simple and cost-efficient approach that reveals mechanistic insights into OMP-DOM biodegradation.     

Biodegradation of the cyclic nitramine explosives RDX, HMX, and CL-20

Cyclic nitramine explosives are synthesized globally mainly as military munitions, and their use has resulted in environmental contamination. Several biodegradation pathways have been proposed, and these are based mainly on end-product characterization because many of the metabolic intermediates are hypothetical and unstable in water. Biodegradation mechanisms for cyclic nitramines include (a) formation of a nitramine free radical and loss of nitro functional groups, (b) reduction of nitro functional groups, (c) direct enzymatic cleavage, (d) α-hydroxylation, or (e) hydride ion transfer. Pathway intermediates spontaneously decompose in water producing nitrite, nitrous oxide, formaldehyde, or formic acid as common end-products. In vitro enzyme and functional gene expression studies have implicated a limited number of enzymes/genes involved in cyclic nitramine catabolism. Advances in molecular biology methods such as high-throughput DNA sequencing, microarray analysis, and nucleic acid sample preparation are providing access to biochemical and genetic information on cultivable and uncultivable microorganisms. This information can provide the knowledge base for rational engineering of bioremediation strategies, biosensor development, environmental monitoring, and green biosynthesis of explosives. This paper reviews recent developments on the biodegradation of cyclic nitramines and the potential of genomics to identify novel functional genes of explosive metabolism.     

Evidence for the occurrence of an oxygen limitation during soil bioremediation by solid-state fermentation

Bioremediation methods are a promising way of dealing with soil and subsoil contamination by organic substances. This biodegradation process is supported by micro-organisms which use the organic carbon from the pollutants as energy source and cells building blocks. The scope of this work is to study the main parameters of the process and the physical limiting steps. Several ground samples from an actual petroleum hydrocarbon contaminated site have been tested. Four fixed bed column reactors and one rotating fermentor are used, enabling the study of the influence of different operating variables on the biodegradation kinetics. The stoichiometric equation for bacteria growth and pollutant degradation has been established, allowing the determination of mass balances. Biodegradation monitoring is achieved by continuously measuring the emissions of carbon dioxide. Biodegradation rates and pollution load decrease in the two kinds of bioreactors are also compared.     

Organic compounds in re-circulated leachates of aerobic biological treated municipal solid waste

Biodegradation of organic matter is required to reduce the potential of municipal solid waste for producing gaseous emissions and leaching contaminants. Therefore, we studied leachates of an aerobic-treated waste from municipal solids and a sewage sludge mixture that were re-circulated to decrease the concentration of biodegradable organic matter in laboratory-scale reactors. After 12 months, the total organic C and biological and chemical oxygen demands were reduced, indicating the biodegradation of organic compounds in the leachates. Curie-point pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS) and pyrolysis-field ionization mass spectrometry (Py-FIMS) revealed that phenols, alkylaromatic compounds, N-containing compounds and carbohydrates were the predominate compounds in the leachates and solid waste. Leachate re-circulation led to a higher thermal stability of the residual organic matter as indicated by temperature-resolved Py-FIMS. Admixture of sewage sludge to solid waste was less effective in removing organic compounds from the leachates. It resulted in drastic higher and more bio-resistant loads of organic matter in the leachates and revealed increased proportions of alkylaromatic compounds. The biodegradation of organic matter in leachates, re-circulated through municipal solid waste, offers the potential for improved aerobic waste treatments and should be investigated on a larger scale.     

Aerobic biodegradation of the brominated flame retardants, dibromoneopentyl glycol and tribromoneopentyl alcohol

Halogenated organic compounds constitute one of the largest and most diverse groups of chemicals in the environment. Many of these compounds are toxic, persistent and, as a result of their often limited biodegradability, tend to bioaccumulate in the environment. Dibromoneopentyl glycol (DBNPG) and tribromoneopentyl alcohol (TBNPA) are brominated flame retardants commonly used as additives during the manufacture of plastic polymers and as chemical intermediates in the synthesis of other flame retardants. Both are classified as not readily biodegradable. In this paper, we demonstrate the biodegradation of both DBNPG and TBNPA by a common bacterial consortium under aerobic conditions in enrichment cultures containing yeast extract. DBNPG and TBNPA biodegradation is accompanied by a release of bromide into the medium, due to a biological debromination reaction. Molecular analysis of the clone library PCR amplified 16S rRNA gene was used to characterize the bacterial consortium involved in the biodegradation.     

Degradation of the main components of cellulose-paint thinner by the mould Scopulariopsis brevicaulis cultured on rice hulls

AIMS: Biodegradation of the main components of the cellulose-paint thinner (toluene, acetone, isopropanol and xylenes) by Scopulariopsis brevicaulis, isolated from a thinner biodegradation microbial consortium was investigated. METHODS AND RESULTS: Our results showed that 90% of S. brevicaulis conidia survived after 4 weeks in a cellulose-paint thinner saturated atmosphere. The mould was able to grow under these environmental conditions with a low development of conidia. The biodegradation potential of S. brevicaulis was established with and without support material (rice hulls). Biodegradation without support was very limited, <10% for all the components quantified. There was notable thinner biodegradation when the fungus was grown on rice hulls. CONCLUSIONS: Our results suggest the potential use of fungi in biofiltration systems employed in biodegradation of the main components of the cellulose-paint thinner. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first report of volatile organic compounds biodegradation by this fungal species.     

Biodegradation of endocrine‐disrupting compounds by ligninolytic fungi: mechanisms involved in the degradation

Without any doubt, endocrine‐disrupting compounds (EDCs) represent an environmental risk for wildlife and human beings. Endocrine‐disrupting effects were found for many chemicals in products for personal use, industrial compounds and even in classical persistent organic pollutants (POPs). In order to understand the fate of EDCs in the environment, it is highly important to identify and to clarify the biodegradation mechanisms that can lead to their decomposition. Ligninolytic fungi (LF) are interesting microorganisms that are capable of participating in a variety of versatile decomposition mechanisms. The microorganisms represent a useful model group and, moreover, LF or their enzymes can be actively used for decontamination. Potential optimization of the decontamination process provides another important reason why it is necessary for understanding the mechanisms of EDC transformation. This minireview summarizes current knowledge about the LF biodegradation mechanisms of the most important micropollutants (xenoestrogens), including nonylphenols, bisphenol A and 17α‐ethinylestradiol and polychlorinated biphenyls as POPs with endocrine‐disrupting potency. Generally, LF exhibit the ability to either polymerize the target pollutants or to substantially decompose the original structure using ligninolytic enzymes and cytochrome P‐450. Moreover, most of the transformation processes are accompanied by reduction of the endocrine‐disrupting activity or ecotoxicity.