Provided for non-commercial research and educational use. Not for reproduction, distribution or commercial use. This article was originally published in the Encyclopedia of Microbiology published by Elsevier, and the attached copy is provided by Elsevier for the author’s benefit and for the benefit of the author’s institution, for non-commercial research and educational use including without limitation use in instruction at your institution, sending it to specific colleagues who you know, and providing a copy to your institution’s administrator. All other uses, reproduction and distribution, including without limitation commercial reprints, selling or licensing copies or access, or posting on open internet sites, your personal or institution’s website or repository, are prohibited. For exceptions, permission may be sought for such use through Elsevier’s permissions site at: http://www.elsevier.com/locate/permissionusematerial E M Wellington. Actinobacteria. Encyclopedia of Microbiology. (Moselio Schaechter, Editor), pp. 26-[44] Oxford: Elsevier. Author's personal copy BACTERIA Contents Actinobacteria Bacillus Subtilis Caulobacter Chlamydia Clostridia Corynebacteria (including diphtheria) Cyanobacteria Escherichia Coli Gram-Negative Cocci, Pathogenic Gram-Negative Opportunistic Anaerobes: Friends and Foes Haemophilus Influenzae Helicobacter Pylori Legionella, Bartonella, Haemophilus Listeria Monocytogenes Lyme Disease Mycoplasma and Spiroplasma Myxococcus Pseudomonas Rhizobia Spirochetes Staphylococcus Streptococcus Pneumoniae Streptomyces Tuberculosis: Molecular Basis of Pathogenesis 25 Author's personal copy 26 Bacteria | Actinobacteria Actinobacteria A Ul-Hassan and E M Wellington, University of Warwick, Coventry, England, UK ª 2009 Elsevier Inc. All rights reserved. Defining Statement Genome Structure and Evolution Introduction Industrially Important Phenotypes of Actinobacteria Systematics of Actinobacteria Concluding Remarks Phylogeny of Actinobacteria Further Reading Glossary phylogeny Evolutionary history of a group of co-metabolism The metabolic transformation of a organisms. substance by one organism to a second substance, pseudogene A gene that has lost its protein-coding which serves as a primary source of carbon for another ability. organism. taxonomy Science of classification. mycelium The mass of hyphae that forms the vegetative and aerial parts of the streptomycete colony before sporulation. Abbreviations MLST multilocus sequence typing ARDRA Amplified ribosomal DNA Restriction PAHs polycyclic aromatic hydrocarbons analysis PCDOs Polychlorinated dibenzo-p-dioxins CGH comparative genomic hybridization PCR-RAPD PCR-randomly Amplified Polymorphic DF dibenzofuran DNA DR direct repeat PFGE pulse-field gel electrophoresis FAME fatty acid methyl ester analysis PyMS pyrolysis mass spectrometry GITs gastrointestinal tracts RFLP restriction fragment length HGT horizontal gene transfer polymorphism hsp heat shock protein rRNA ribosomal RNA IS insertion sequence TEs transposable elements ISP International Streptomyces Project VNTRs variable number tandem repeats LFRFA Low-frequency restriction fragment analysis Defining Statement and Actinomyces bovis in 1877 by Carl Otto Harz. Harz described A. bovis, causing a disease of cattle called The Actinobacteria form a distinct clade of Gram-positive ‘lumpy jaw’, as having thin filaments that ended in club- bacteria which contains a large number of genera. This shaped bodies that he considered to be ‘gonidia’ resem- diverse and important group encompasses key antibiotic- bling those of fungi, hence the name Actinomyces (Latin for producers, many soil bacteria critical for decomposition ray fungus). In hindsight, though, the ‘gonidia’ were and resilient species capable of growing in hostile, pol- almost certainly host cells and so the resemblance to luted environments. A few are medically important typical fungi was false. A number of other microorganisms pathogens including the causal agent of TB. were isolated, which had some of the same properties and were thought to belong to the same group as those men- tioned above, including the causative agents of leprosy Introduction and tuberculosis. This group of organisms was officially recognized as Actinomycetales in 1916 and it became appar- Some of the earliest descriptions of Actinobacteria were ent that they comprised a large heterogeneous group, those of Streptothrix foersteri in 1875 by Ferdinand Cohn which vary greatly in their physiological and biochemical Author's personal copy Bacteria | Actinobacteria 27 properties, though their phylogenetic position as true Systematics of Actinobacteria bacteria was not established until the 1960s. The Traditional Phenotypic Analysis Actinobacteria are now considered to be one of the largest phyla of the bacterial kingdom. The GC content of these The best-studied members of the Actinobacteria class organisms ranges from 54% in some corynebacteria to belong to the genus Streptomyces, which was proposed by more than 70% in streptomycetes. Tropheryma whipplei, Waksman and Henrici in 1943. Members of this genus the causative agent of Whipple’s disease, has a GC con- have high GC content DNA, being highly oxidative and tent of 46.3%, which is the lowest so far reported for forming extensive branching substrate and aerial hyphae. Actinobacteria. They also produce a variety of pigments responsible for The Actinobacteria are morphologically diverse and can the color of the substrate and aerial hyphae (Bergey’s range from coccoids (Micrococcus) and rods (Mycobacterium) Manual of Systematic Bacteriology). Streptomyces species are to branching mycelium (Streptomyces), many of which can prolific producers of antibiotics, and since the discovery also form spores. Actinobacterial species are ubiquitous in of actinomycin and streptomycin produced by S. antibio- the environment and can be isolated from both aquatic and ticus and S. griseus respectively during the early 1940s, the terrestrial habitats. New species of Actinobacteria have been interest in streptomycetes grew very rapidly. The discov- recovered from a diverse range of environments, including ery of Streptomyces species as rich sources of commercially medieval wall paintings, desert soil, butter, marine important antibiotics led to new techniques for the culti- sponges, and radon-containing hot springs. The ability of vation of these organisms. However, due to the lack of Actinobacteria to inhabit varied environments is due to their standards for the classification and identification of new ability to produce a variety of extracellular hydrolytic species, the new strains were described based on only enzymes, particularly in the soil, where they are responsi- small differences in morphological and pigmentation ble for the breakdown of dead plant, animal and fungal properties. This, along with the belief that one strain material, thus making them central organisms in carbon produced only one antibiotic, led to overspeciation of recycling. Some species can break down more complex, the genus, resulting in over 3000 species being described recalcitrant compounds, of which Rhodococcus species are a by the late 1970s. A number of methods were developed good example; they can degrade nitro-, di-nitrophenol, to overcome this problem, with the earliest being based pyridine, and nitroaromatic compounds. on only a few subjectively chosen characters focusing Actinobacteria are well-known for their ability to produce largely on morphological and pigmentation properties secondary metabolites, many of which have antibacterial that were rarely tested under standardized conditions. and antifungal properties. Of all the antibiotics produced Subsequently, biochemical, nutritional, and physiological by Actinobacteria, Streptomyces species are responsible for 80%, with smaller contributions by Micromonospora, characters were included, but as these were only Saccharopolyspora, Amycolatopsis, Actinoplanes,andNocardia.A applied to selected species they did not necessarily reflect number of species have developed complex symbiotic rela- the phylogeny of streptomycetes. The International tionships with plants and insects. A unique relationship has Streptomyces Project (ISP) was established in 1964 with an been reported between the European bee-wolf wasp, in aim to describe and classify extant type strains of which the female wasps carry Streptomyces species in Streptomyces using traditional tests under standardized their antennae and apply them to the brood cells. The conditions. This study resulted in more than 450 species bacteria are taken up by the larva and colonize the walls of being redescribed, but an attempt to delineate the genera the cocoon, where they protect it from fungal infestation. was futile. Streptomyces species also share beneficial relationships with The data collected by the ISP project were used by plants, with S. lydicus being found to enhance pea root several researchers to develop computer-assisted identifi- nodulation by Rhizobium species. The best-studied example cation systems. In 1962, Silvestri was the first to apply of a Streptomyces-eukaryotic relationship is between patho- numerical taxonomy to the genus Streptomyces, where genic strains such as Streptomyces scabies that cause scab in nearly 200 strains were tested for 100 unit characters. potatoes, carrots, beets, and other plants. Strains of Frankia This study highlighted the fact that many of the characters can fix nitrogen and are responsible for the nodulation of used to