Microbiology of Hydrocarbon-Degrading Pseudomonas
The genus Pseudomonas is summarily described with respect to the phenotypic and genomic properties of its member species, which have been considered in the development of the current taxonomic treatment. The chapter emphasizes the biochemical versatility
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. Timmis (ed.), Handbook of Hydrocarbon and Lipid Microbiology, DOI 10.1007/978-3-540-77587-4_129, # Springer-Verlag Berlin Heidelberg, 2010
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Microbiology of Hydrocarbon-Degrading Pseudomonas
Abstract: The genus Pseudomonas is summarily described with respect to the phenotypic and genomic properties of its member species, which have been considered in the development of the current taxonomic treatment. The chapter emphasizes the biochemical versatility of the species of the genus, which is manifested in the capacity of many strains to degrade a number of aliphatic, aromatic, poly-aromatic hydrocarbons and various derivatives, among a vast variety of miscellaneous organic compounds. The observed degradation capabilities of Pseudomonas are considered with respect to the metabolic potential encoded in the genomes of strains for which the genome sequences have been determined. Strains of Pseudomonas species are able to grow in simple media and the nutritional versatility of a number of them includes the ability to utilize many compounds as substrates that may be toxic to most other prokaryotes and to higher organisms, as observed in environmental analyses of Pseudomonas. These properties point to Pseudomonas as particularly important agents in the design of bioremediation applications.
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Taxonomy of Pseudomonas
The evolution of Pseudomonas modern taxonomy comprises three stages. During the first stage, the most comprehensive phenotypic analysis of many strains of the known species of the genus Pseudomonas resulted in an extensive compilation of the morphology and physiology (Stanier et al., 1966). The nutritional properties of the strains were at the center of the physiological properties. In the second stage, nucleic acid similarity studies confirmed the differentiation of species based on phenotypic characters although, unexpectedly, DNA/DNA hybridization experiments revealed that many species did not share any detectable homology. This awkward situation, which pointed to marked genomic differences between some species, led to a third stage, during which ribosomal RNA (rRNA) and total DNA were chosen as partners of nucleic acid hybridizations. Strikingly, these experiments showed that, far from representing a single concise genus, Pseudomonas (sensu lato) was actually comprised of a community of at least five distinct groups which could represent different genera and even members of different bacterial families (Palleroni et al., 1973). From historical and phylogenetic standpoints, the third stage could be considered to be the most significant. Shortly after the results on Pseudomonas were published, similar experiments, focusing on strains of Clostridium, gave comparable results to those observed for Pseudomonas, and the authors emphasized the advantages of this new approach as a guide to bacterial systematics into areas that appeared, until then, beyond the reach of experimental taxonomy (Johnson and Francis, 1975). Soon thereafter, rRNA homologies, using total RNA or the small (16S) component, were be
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