Biochemistry of microbial degradation

Life on the planet depends on microbial activity. The recycling of carbon, nitrogen, sulphur, oxygen, phosphate and all the other elements that constitute living matter are continuously in flux: microorganisms participate in key steps in these processes and without them life would cease within a few short years. The comparatively recent advent of man-made chemicals has now challenged the environment: where degradation does not occur, accumulation must perforce take place. Surprisingly though, even the most recalcitrant of molecules are gradually broken down and very few materials are truly impervious to microbial attack. Microorganisms, by their rapid growth rates, have the most rapid turn-over of their DNA of all living cells. Consequently they can evolve altered genes and therefore produce novel enzymes for handling "foreign" compounds - the xenobiotics - in a manner not seen with such effect in other organisms. Evolution, with the production of micro-organisms able to degrade molecules hitherto intractable to breakdown, is therefore a continuing event. Now, through the agency of genetic manipulation, it is possible to accelerate this process of natural evolution in a very directed manner. The time-scale before a new microorganism emerges that can utilize a recalcitrant molecule has now been considerably shortened by the application of well-understood genetic principles into microbiology. However, before these principles can be successfully used, it is essential that we understand the mechanism by which molecules are degraded, otherwise we shall not know where best to direct these efforts.

Table of Contents:
1. Biodegradation of components of petroleum.- I. Introduction.- II. Uptake of hydrocarbons by microorganisms.- III. Degradation of aliphatic hydrocarbons.- IV. Degradation of cycloaliphatic compounds.- V. Degradation of nitrogen-, sulphur- and oxygen-containing components (NSO) of petroleum.- VI. Genetics of biodegradation.- VII. Relevance of petroleum component biodegradation.- VIII. Conclusions.- 2. Microbial metabolism and transformation of selected monoterpenes.- I. Introduction.- II. Current studies.- III. Cytochrome P450 oxygenases and monoterpene metabolism.- IV. 1,8-Cineole and 1,4-cineole.- V. ?-Pinene and car-3-ene.- VI. Metabolism of monoterpenes by fungi.- 3. Formation and function of biosurfactants for degradation of water-insoluble substrates.- I. Introduction.- II. Structures of extracellular amphiphiles.- III. Biosynthetic routes to biosurfactants.- IV. Microbial growth and kinetics of biosurfactant formation.- V. Biosurfactants in natural habitats.- 4. Biodegradation of oils, fats and fatty acids.- I. Introduction.- II. Microbial utilization of oils and fats.- III. Lipases and phospholipases.- IV. Uptake and oxidation of fatty acids.- 5. Biodegradation of anionic surfactants and related molecules.- I. Introduction.- II. An overview of surfactant biodegradation.- III. Biodegradation pathways, enzymes and mechanisms.- IV. Postscript.- 6. Biochemistry and physiology of the degradation of nitrilotriacetic acid and other metal complexing agents.- I. Introduction.- II. Nitrilotriacetic acid.- III. Other chelating agents.- 7. Enzymes and mechanisms involved in microbial cellulolysis.- I. Introduction.- II. Fungal cellulases.- III. Structure/functional relationships in fungal and bacterial cellulases.- IV. Stereochemical course of hydrolysis by cellulases.-V. Conclusions.- 8. Biodegradation of lignin and hemicelluloses.- I. Introduction.- II. Hemicellulose.- III. Lignin.- IV. Lignin-carbohydrate complexes.- V. Enzymatic treatments of pulps.- VI. Conclusions.- 9. Physiology of microbial degradation of chitin and chitosan.- I. Introduction: chitin and chitosan.- II. Pathways of chitin degradation.- III. Identification and assay of chitinolytic activities.- IV. Autolytic and morphogenetic chitinolysis.- V. Nutritional chitinolysis.- VI. Chitinolysis in pathogenesis and symbiosis.- VII. Degradation of chitosan.- VIII. Biotechnology of chitinases and chitosanases.- IX. Specific inhibitors of chitinases.- X. Sequence homologies of chitinases.- XI. Conclusions.- 10. Biodegradation of starch and ?-glycan polymers.- I. Introduction.- II. Microbial amylosaccharidase synthesis, regulation, and localization.- III. Biochemistry of amylosaccharidases.- IV. Molecular biology of amylosaccharidases.- V. Biotechnology of amylosaccharidases.- VI. Future directions.- 11. The physiology of aromatic hydrocarbon degrading bacteria.- I. Introduction.- II. Benzene.- III. Arenes.- IV. Biphenyl.- V. Tetralin.- VI. Fused-ring aromatic compounds.- VII. Mixed substrates.- VIII. Conclusions.- 12. Microbial dehalogenation of haloaliphatic compounds.- I. Introduction.- II. Dehalogenation of Haloalkanoic Acids (HAAs).- III. Dehalogenation of haloalkanes under aerobic conditions 399.- IV. Dehalogenation of haloalkanes under anaerobic conditions.- V. Dehalogenation of haloalcohols.- VI. Plasmids encoding genes for haloaliphatic dehalogenase.- VII. Conclusions.- 13. Biodegradation of halogenated aromatic compounds.- I. Introduction.- II. Dehalogenation of aromatic compounds.- III. Biodegradation of halogenated benzoic acids.- IV. Biodegradation ofhalogenated benzenes.- V. Biodegradation of halogenated phenols.- VI. Biodegradation of halogenated anilines.- VII. Biodegradation of halogenated phenoxyacetic acids.- VIII. Biodegradation of halogenated biphenyls.- IX. Biodegradation of halogenated dibenzo-p-dioxins and dibenzofurans.- 14. Bacterial degradation of N-heterocyclic compounds.- I. Introduction.- II. Degradation of pyridine and derivatives.- III. Degradation of quinoline and derivatives.- IV. Isoquinoline.- V. The degradation of indole and derivatives.- VI. Concluding remarks.- 15. Biodegradation of inorganic nitrogen compounds.- I. Introduction.- II. Degradation of organic nitrogen compounds by animals.- III. Nitrification in soil and water.- IV. Denitrification.- V. Cyanide production and metabolism.- VI. Summary and conclusions.- 16. Biochemistry of anaerobic biodegradation of aromatic compounds.- I. Introduction.- II. Principles.- III. Anaerobic microorganisms.- IV. Channelling reactions.- V. Ring reduction and hydration.- VI. From alicyclic compounds to central metabolites.- VII. Chimeric pathways.- VIII. Comparison of aerobic and anaerobic pathways.- 17. Biocorrosion: the action of sulphate-reducing bacteria.- I. Introduction.- II. Biofilms.- III. Sulphate-reducing bacteria.- IV. Microbially influenced corrosion.- V. Concluding remarks.- Index of compounds.- Index of organisms.