Phylum Actinobacteria (high G+C Gram-positive Bacteria)

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  • phylum Actinobacteria
    • class Actinobacteria
      • order Acidimicrobiales
        • family Acidimicrobiaceae (Acidimicrobium)
      • order Rubrobacterales
        • family Rubrobacteraceae (e.g.Rubrobacter, Thermoleophilum)
        • family Patulibacteraceae (Patulibacter)
      • order Coriobacteriales
        • family Coriobacteriaceae (e.g. Atopobium, Slakia)
      • order Sphaerobacterales
        • family Sphaerobacteraceae (Sphaerobacter)
      • order Actinomycetales
        • family Actinomycetaceae(e.g. Actinomyces, Arcanobacterium)
        • family Micrococcaceae (e.g. Micrococcus, Arthrobacter)
        • family Bogoriellaceae (Bogoriella)
        • family Rarobacteraceae (Rarobacter)
        • family Sanguibacteraceae (Sanguibacter)
        • family Brevibacteriaceae (Brevibacterium)
        • family Cellulomonadaceae (e.g. Cellulomonas, Oerskovia)
        • family Dermabacteraceae (Dermabacter, Brachybacterium)
        • family Dermatophilaceae (Dermatophilus, Kineosphaera)
        • family Dermacoccaceae(Dermococcus,Demetria,Kytococus)
        • family Intrasporangiaceae (e.g. Janibacter, Tetrasphaera)
        • family Jonesiaceae (Jonesia)
        • family Microbacteriaceae (e.g. Microbacterium, Agromyces)
        • family Beutenbergiaceae (Beutenbergia, Georgenia, Salana)
        • family Promicromonosporaceae (e.g. Promicromonospora)
        • family Catenulisporaceae (Actinospica, Catenulispora)
        • family Corynebacteriaceae (e.g. Corynebacterium)
        • family Dietziaceae (Dietzia)
        • family Gordoniaceae (Gordonia, Skermania, Millisia)
        • family Mycobacteriaceae (Mycobacterium)
        • family Nocardiaceae (e.g. Nocardia, Rhodococcus)
        • family Tsukamurellaceae (Tsukamurella)
        • family Williamsiaceae (Williamsia)
        • family Segniliparaceae (Segniliparus)
        • family Micromonosporaceae (e.g. Micromonospora)
        • family Propionibacteriaceae (e.g. Propionibacterium)
        • family Nocardioidaceae (e.g. Nocardoides, Aeromicrobium)
        • family Pseudonocardiaceae (e.g. Pseudonocardia)
        • family Actinosynnemataceae (e.g. Lentzea, Saccharothrix)
        • family Streptomycetaceae (e.g. Streptomyces, Kitasatospora)
        • family Streptosporangiaceae (e.g. Streptosporangium)
        • family Nocardiopsaceae (e.g. Nocardopsis, Thermobifida)
        • family Thermomonosporaceae (e.g. Thermomonospora)
        • family Frankiaceae (Frankia)
        • family Geodermatophilaceae (e.g. Blastococcus)
        • family Microsphaeraceae (Microsphaera)
        • family Sporichthyaceae (Sporichthya)
        • family Acidothermaceae (Acidothermus)
        • family Kineosporiaceae (e.g.Kineosporia,Cryptosporangium)
        • family Nakamurellaceae (Quadrasphaera, Nakamurella)
        • family Glycomycetaceae (Glycomyces, Stackebrandtia)
      • order Bifidobacteriales
        • family Bifidobacteriaceae (e.g. Bifidobacterium)

About this phylum

Diversity

Familiar actinobacteria, such as Mycobacterium, Corynebacterium, Micrococcus and Streptomyces, are members of a single Order, the Actinobacteriales, which span a relatively small phylogenetic range, but a large number of Families, genera and species. The outlying branch containing of Sphaerobacter, Thermoleophilum, Acidimicrobium, and relatives is generally considered part of the actinobacteria (as shown here), but there are contrary data suggesting instead that these organisms might instead be members of the Thermomicrobium branch of the Chloroflexi.

Metabolism

The actinobacteria are generally aerobic respirers. A few exceptions, such as Propionobacterium and Bifidobacterium, are anaerobic or aerotolerant. A few are moderately thermophilic (up to ca. 60°C), but most are mesophilic. Chemoorganotrophic, but growth substrates vary widely. Members of this group (most notably Streptomyces and Actinomyces) are well known for their ability to produce antibiotics; these and Bacillus are probably the most common bacterial sources of antibiotics.

Morphology

These organisms are typically nonmotile rods, filaments, or sometimes cocci. Rod-shaped cells are usually uneven, irregular, or club-shaped (coryneform). Endospores are not produced, but filamentous species often form spores (sometimes called “arthrospores” to distinguish them from endospores) that are not particularly resistant but rather are reproductive and important in dispersal.

Many Actinobacteria, including the mycobacteria, corynebacteria, nocardia, and rhodococci, have a mycolic acid outer membrane. This is not the typical outer membrane seen in Gram-negative Bacteria; typical membrane lipids and lipopolysaccharides are not present. Instead, the typically thick Gram-positive-type cell wall is covered in an arabinogalactan polysaccharide layer, which in turn is covered by a mycolic acid bilayer. This is a true lipid outer membrane, not a “waxy coating”, as it is often described. As in Gram-negative Bacteria, this outer membrane incorporates a variety of proteins, including porins. The mycolic acid outer membrane is a potent permeability barrier, even more so that the outer phospholipid membrane of Gram-negative Bacteria. It is not known whether this mycolic acid outer membrane represents a highly-altered descendent of an ancestral Gram-negative outer membrane or an independently-derived addition to an ancestral Gram-positive envelop.

Habitat

Most actinobacteria are soil organisms; one genus, Streptomyces, forms a white growth commonly seen in decaying wood (easily mistaken for fungus) and gives good soil its rich earthy odor. A few are symbionts or pathogens of plants and animals, including some notorious examples; Mycobacterium tuberculosis and M. leprae, Corynebacterium diphtheria. More common than pathogens are the commensals, such as Bifidobacterium, which is common in the gut and beneficial, and is often used in probiotics.

Coryneform actinobacteria

These organisms are typified by their club-like or irregular rod-shaped cells. Pairs of cells after division are angled or V-shaped; this is referred to as either “snapping” or “Chinese letter” division. This is caused by asymmetric fracturing of an outer layer of the cell wall after cytokinesis. These organisms are common symbionts of the skin and mucous membranes of animals, and the surfaces of plants, as well as being abundant in the soil. The most well-known genera in this group are Corynebacterium and Arthrobacter. Arthrobacteria are very common soil and root surface inhabitants that are typically pleomorphic; small cocci in stationary phase, and irregular rods with jointed or V-shaped pairs during rapid growth. Corynebacteria are common symbionts of animals; a few species are pathogens, including of course C. diphtheriae, the causative agent of Whooping cough. Members of this genus are typically club-shaped, and also often pleomorphic.

Example : Arthrobacter globiformis

Arthrobacter
Arthrobacter globiformis : Photo by:T. Tamura, T. Nishii & K. Hatano

A. globiformis is one of the most numerically abundant easily cultivated inhabitants of neutral pH or alkaline soils, and is also abundant on the aerial surfaces of plants. This genus is easily recognized morphologically, but distinguishing species requires analysis of the cell wall sugars and amino acids, or rRNA sequence analysis. Stationary phase cells are small cocci; upon transfer to typical rich media, these cocci swell, then produce outgrowths to generate irregular rods-shaped cells, which divide by “snapping” division, producing V-shaped pairs of cells or sometime longer pseudo-hyphae. As cells enter stationary phase, divisions continue as growth slows, resulting in the formation of cocci. Colonies on plates will contain both coyneform/rod-shaped cells and cocci, and when examined microscopically so are often mistakenly thought to be impure or contaminated. These organisms can use a remarkably wide range of organic substrates for growth and energy, including nicotine, the antibiotic puromycin, and a range of herbicides. Most are also nitrogen fixers.

Filamentous actinobacteria

Streptomyces and related genera form branched filamentous hyphae, and although usually much thinner, otherwise resemble the filamentous fungi. This is no coincidence, but it represents an evolutionary convergence because of their common habitat and lifestyle rather than any specific evolutionary relationship.

The filamentous actinobacteria have a complex life cycle that includes programmed cell death and cellular differentiation; these are truly multicellular Bacteria. Initial growth from spores on solid media is in the form of branching vegetative hyphae. These hyphae are mostly non-septated; DNA replication produces new nucleoids, but no cytokinesis occurs, and so the filaments share a common syncytial cytoplasm. Filament growth occurs only at the tips; branching is required to allow logarithmic growth because, of course, individual hyphal tips have a limit to their growth rate. Vegetative hyphae give rise to waxy aerial hyphae that grow upward away from the growth substrate. This growth is at the expense of the underlying vegetative hyphae, which undergo programmed cells death (although their cell walls remain largely intact and serve as a supporting structure for the aerial hyphae). The growth tips of the aerial hyphae then undergo cytokinesis to create a series of individual cells, which develop into dormant spores. Again, this growth and development of spores is at the expense of the aerial hyphae.

It is important to remember that the “arthrospores” of these actinobacteria are distinct from the endospores of the firmicutes. Both are metabolically inactive resting stages of the life cycle, but arthrospores are produced in great numbers from each aerial hyphum (they are reproductive), are readily dispersed by the air or water, but are not particular resistant to harsh treatment. Endospores, on the other hand, are extremely resistant to heat and chemical assault, but are not reproductive (a mother cell produces a single spore) and are not readily dispersable.

Species of filamentous actinobacteria are distinguished morphologically, mostly on the basis of the structure and morphology of their spore-bearing hyphae. These organisms are metabolically diverse; most can use a very wide range of growth substrates. They produce a wide range of antibiotics, including aminoglycosides (e.g. streptomycin), macrolides (e.g. erythromycin), tetracycine and chloramphenicol, just to name a few. Interestingly, the filamentous actinobacteria have linear rather than circular chromosomes, with unique telomeres.

Example : Streptomyces antibioticus

Streptomyces
Streptomyces antibioticus, stained to reveal living (green) and dead (red) cells in both septate and asyptate hyphae
photo by Nora Ausmees, University of Uppsala

S. antibioticus is a typical member of the genus Streptomyces, and has long been used in the industrial production of the important antibiotic actinomycin. More recently, S. antibioticus is being used as a model system for more detailed examination of the life cycle of filamentous actinobacteria. Although still poorly understood, this life cycle is turning out to be far more complex than previously imagined, particularly in terms of the horizontal (as opposed to vertical) spatial organization, and waves of growth in specific spatial arrangements. For example, the initial germination hyphae is cellular rather than syncytial, and upon reaching a specified density, alternating cells in these filaments die. Vegetative, syncytial hyphae are the outgrowths of the surviving cells from these initial filaments.

Acid-fast Bacteria

The mycolic acids of the outer membrane of the genus Mycobacterium and relatives are much longer than those of other actinobacteria than contain mycolic acids. As a result, these species can be specifically stained using the “acid fast” stain first developed by Robert Koch during his work to identify the cause of tuberculosis. In culture, the mycobacteria typically grow as branched or unbranched filaments, but these filaments are chains of individual cells rather than syncytial hyphae. Most of the mycobacteria are soil inhabitants, and some are important in the bioremediation of pollutants that are otherwise recalcitrant. A few are human and animal pathogens, most notably Mycobacterium tuberculosis and M. leprae.

Example : Mycobacterium ulcerans

Mycobacterium
Mycobacterium ulcerans (red) in a tissue sample from a Buruli patient : Porteals, et al PLoS 2:e178, Fig 7

M. ulcerans is the causative agent of Buruli (or Barnsdale) ulcer, a necrotic disease of the skin and surrounding soft tissue and bone. Lesions are most common on the arms and legs, primarily in children, and although not generally fatal typically results in permanent disfiguration. Although not as well known (or understood) as leprosy or tuberculosis, which are caused by related species of Mycobacterium, Buruli ulcer has surpassed these diseases in frequency in some parts of impoverished central and western Africa. Unlike M. leprae or M. tuberculosis, M. ulcerans is an environmental pathogen, probably from transmitted to humans from aquatic insects.

Deeply-branching questionable members

There are some organisms that, although currently classified as actinobacteria, are on such deep branches that their placement amongst the actinobacteria are uncertain. One of these, Sphaerobacter, is almost certainly really a deep branch of the chloroflexi rather than the actinobacteria. The opposite may be the case for the genus Thermoleophilum; originally classified a member of the green non-sulfur Bacteria (chloroflexi), there is some evidence that it may instead be an actinobacterium, where it is currently classified as a relative of Rubrobacter. Alternatively, it may represent an independent phylum of Bacteria.

Example : Thermoleophilum album

Thermoleophilum
Thermoleophilum album : The Prokaryotes pp3782 - JJ Perry

T. album is one of only two species of the genus Thermoleophilum (the other is T. minutum). These organisms are very small (ca. 0.5 x 1μm), obligately aerobic Gram-negative (in terms of staining) rods. All isolates of these species are thermophilic, growing optimally at about 60°C, and have been isolated from hot spring sediments and dark muds exposed to solar heating from a wide range of sites scattered around the United States. The unique feature of these organisms is that they can grow only on long-chain n-alkanes, i.e. wax. No other substrates can be used for either carbon or energy, not even the alcohol derivatives of growth substrates.