Actinobacteria are Gram-positive bacteria with high G+C DNA content that constitute one of the largest bacterial phyla, and they are ubiquitously distributed in both aquatic and terrestrial ecosystems. Many Actinobacteria have a mycelial lifestyle and undergo complex morphological differentiation. They also have an extensive secondary metabolism and produce about two-thirds of all naturally derived antibiotics in current clinical use, as well as many anticancer, anthelmintic, and antifungal compounds. Consequently, these bacteria are of major importance for biotechnology, medicine, and agriculture. Actinobacteria play diverse roles in their associations with various higher organisms, since their members have adopted different lifestyles, and the phylum includes pathogens (notably, species of Corynebacterium, Mycobacterium, Nocardia, Propionibacterium, and Tropheryma), soil inhabitants (e.g., Micromonospora and Streptomyces species), plant commensals (e.g., Frankia spp.), and gastrointestinal commensals (Bifidobacterium spp.). Actinobacteria also play an important role as symbionts and as pathogens in plant-associated microbial communities. This review presents an update on the biology of this important bacterial phylum.

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Taxonomy, Physiology, and Natural Products of Actinobacteria

Biodegradation potential of the genus Rhodococcus.

Biodegradation and Rhodococcus – masters of catabolic versatility

Biodesulfurization and the upgrading of petroleum distillates.

The degree of association of organic and inorganic pollutants is governed by the complex physico-chemical interactions at interfaces. This association involves sorption onto soil constituents, sequestration within the soil matrix (micropores) and partitioning in a nonaqueous phase liquid (NAPL) that will, ultimately, control the fate of the contaminants. NAPL represents organic substances that are relatively insoluble in water providing a long-term source of pollutant. They represent a continuous input into the water phase to replace degraded or dissipating concentrations. As a result the bioavailability of contaminants to biodegradation may be reduced (Ogram et al. 1985; Miller and Alexander 1991). The enhancement of natural biological degradation processes, in what is termed bioremediation, can be a preferred cost-effective method of removing contaminants from soil-contaminated and other contaminated environments. The role of microorganisms has been shown to be essential in the remediation of, at least, organic pollution, and the activity of microbial types naturally present can be enhanced by bioremediation techniques which include increased aeration of the polluted material and nutrient additions (Christofi et al. 1998; Ivshina et al. 1998). Supplementing the source of microorganisms capable of degrading particular pollutants (bioaugmentation) and the enhancement of the desorption of pollutants from particulates using surfactants can increase hydrocarbon degradation (Deschenes et al. 1995; Thibault et al. 1996; Christofi et al. 1998; Ivshina et al. 1998). It is only 10–15 years that the use of surfactants in increasing the availability of hydrophobic pollutants in soils and other environments has been considered (Vigon and Rubin 1989). Previous studies have revealed that surfactants can enhance pollutant desorption and availability (Oberbremer et al. 1990; Zang and Miller 1992; Volkering et al. 1995; Rahman et al. 2002). They have been applied in oil washing for secondary oil recovery and to clean oil pipes and oil reservoirs (Osipow 1962). In desorption, both synthetic and natural (biological) surfactants have been used. However, it is not always the case that increasing the bioavailability of nonpolar organic substances through the use of surfactants leads to increased degradation or removal. Synthetic surfactants have also been shown to decrease organic degradation (Bruheim et al. 1999) possibly through, for example, the toxic effects of the surfactant (Rouse et al. 1994). It can also be assumed that increasing bioavailability of a pollutant can lead to an increasing toxicity to degrading microorganisms. It has been shown that sorption of toxicants is one major factor controlling bioavailability and toxicity (Welp

https://sfamjournals.onlinelibrary.wiley.com/doi/pdf/10.1046/j.1365-2672.2002.01774.x

Microbial surfactants and their use in field studies of soil remediation.

The genus Rhodococcus

Bacteria of the genus Rhodococcus can degrade a wide range of organic pollutants and catalyse many useful biotransformations. There is a need for improved tests to identify Rhodococcus species. PCR-based methods for species identification offer advantages in terms of speed and accuracy over traditional methods and can allow direct detection of microbes in environmental samples., PCR tests, using primers targeted at species-specific sequences in the 16S rRNA gene, were successfully developed for R. globerulus, R. erythropolis, R. opacus and R. ruber. These tests gave positive results with all or most strains of target species but did not generally cross-react with other species. Cases of apparent cross-reaction were shown to be due to prior misclassification of strains of R. opacus as R. erythropolis and of strains of R. ruber as R. rhodochrous. A simple and rapid method for the extraction and purification of DNA from soil was developed and successfully applied to the PCR detection of indigenous R. erythropolis in an environmental sample. Cell lysis in the samples was achieved by lysozyme and sarkosyl treatment, aided by freeze-thaw cycles. Removal of humic compounds inhibitory to PCR was accomplished by CTAB treatment with solvent extraction and, if necessary, passage of extracts through Sepharose CL-6B in a spun-column format. Extracts prepared using a tris-EDTA buffer were much clearer than those prepared using a sodium phosphate buffer, indicating lower levels of humic compounds. A detection limit of 104 cfu g−1 of soil was achieved and the use of a secondary PCR allowed detection of 1 cfu g−1.

D. W. J. Aw

Papers

The genus Rhodococcus

Identification and environmental detection of Rhodococcus species by 16S rDNA‐targeted PCR

A REVIEWThe genus Rhodococcus