The distribution of antibiotic resistance patterns within streptomycetes and their use in secondary metabolite screening

Selective isolation of bioactive soil actinomycetes belonging to the Streptomyces violaceusniger phenotypic cluster

AIMS

To devise and evaluate a strategy for isolating members of the Streptomyces violaceusniger phenotypic cluster, which are known to be a promising source of bioactive metabolites.

METHODS AND RESULTS

The treatment of four soil samples with 1.5% phenol (30 degrees C, 30 min) prior to inoculation on humic acid-vitamin (HV) agar eliminated most of the streptomycetes and other bacterial populations. The surviving streptomycetes on the HV isolation plates were subcultured, and species-group identification was made according to the probabilistic identification system of Williams et al. (1989). Of the 133 streptomycetes subcultured, 102 (77%), were assigned to the S. violaceusniger cluster. A test with an overlay technique revealed that all of these S. violaceusniger-cluster isolates had broad antimicrobial spectra, as they inhibited the growth of all test Gram-positive bacteria, yeasts and filamentous fungi. Antitumour activity against colon carcinoma cells was found among 68 or 67%, of these S. violaceusniger-cluster isolates, following growth in submerged culture.

CONCLUSIONS

Chemical pretreatment of soil samples with phenol reduces the growth of ubiquitous Streptomyces species, thereby facilitating the recovery of less-abundant S. violaceusniger-cluster strains that are characterized by high antimicrobial and antitumour activities.

SIGNIFICANCE AND IMPACT OF THE STUDY

The development and application of new methodologies with which to selectively isolate rare, bioactive streptomycete groups is important for discovering novel secondary metabolites with bioactive properties.

Genetic and phenotypic traits of streptomycetes used to characterize antibiotic activities of field-collected microbes

Although antibiotic production may contribute significantly to microbial fitness, there is limited information on the ecology of antibiotic-producing microbial populations in soil. Indeed, quantitative information on the variation in frequency and intensity of specific antibiotic inhibitory and resistance abilities within soil microbial communities is lacking. Among the streptomycetes, antibiotic production is highly variable and resistance to antibiotics is highly specific to individual microbial strains. The objective of this work was to genetically and phenotypically characterize a reference collection of streptomycetes for use in distinguishing inhibition and resistance phenotypes of field-collected microbes. Specifically, we examined inhibition and resistance abilities of all isolates in all possible pairwise combinations, genetic relatedness using BOX-PCR and 16S rDNA sequence analyses, nutrient utilization profiles, and antibiotic induction among all possible three-way combinations of isolates. Each streptomycete isolate possessed a unique set of phenotypic and genetic characteristics. However, there was little correspondence between phenotypic and genetic traits. This collection of reference isolates provides the potential for distinguishing 1024 inhibition and resistance phenotypes in field-collected microbes. Relationships between the genetic and phenotypic characteristics examined may provide preliminary insight into the distinct strategies that microbes use in optimizing their fitness in natural environments.Key words: antibiotic inhibition, resistance, nutrient utilization, BOX-PCR, 16S rDNA.

Spatial variation in frequency and intensity of antibiotic interactions among Streptomycetes from prairie soil

Antibiotic interactions are believed to be significant to microbial fitness in soil, yet little is known of the frequency, intensity, and diversity of antibiotic inhibition and resistance among indigenous microbes. To begin to address these issues, we studied the abilities of streptomycete isolates from prairie soil to inhibit growth and display resistance to antibiotics produced by a test collection of 10 streptomycete isolates. Wide variations in antibiotic inhibition and resistance for prairie isolates among three locations and four soil depths within a 1-m2 plot were revealed. Fewer than 10% of 153 prairie isolates inhibited all 10 test isolates, while more than 40% of the isolates did not inhibit any of the test isolates. No field isolate was resistant to all of the test isolates, nor was any isolate susceptible to all of the test isolates. No correlation between inhibition and resistance phenotypes was found, suggesting that inhibition and resistance are under independent selection. The significant spatial variation in the frequency and intensity of antibiotic inhibition implies that the fitness benefits of antibiotic production are not the same among locations in soil. In contrast, the consistency of resistance over space indicates that its significance to fitness across locations is stable or the costs of maintaining resistance in the absence of selection are small or nonexistent. The spatial clustering of antibiotic inhibitory activity suggests a variable matrix of selection pressures and microbial responses across the soil landscape.

The search for novel microbial fine chemicals, agrochemicals and biopharmaceuticals

An ever-increasing number of fine chemicals and enzymes is now produced based on microbial biotechnology. Microbial products generally display desired chirality, are biodegradable and are produced from renewable (agro)-substrates. Bioconversion reactions, based on the use of (immobilised) biocatalysts (cell or enzymes), yield interesting regio- and enantioselective molecules under mild reaction conditions, starting from racemic precursors. Furthermore these bioprocesses have a positive environmental impact. Ingenious screening procedures for novel microbial primary and secondary metabolites, bioactive peptides, proteins and enzymes reveal that only the tip of the iceberg has been explored. Examples of such novel microbial products pertain to enzymes, enzyme-inhibitors, biopolysaccharides, bio-plastics, bioactive peptides, bacteriocins, targeted toxins, alkaloids, steroids, immunomodulators, vaccines, antibiotics and lantibiotics, biopesticides, vitamins and related growth factors, amino acids and specialty sugars, polyols and organic acids, biomagnets, bioflavours and biopigments. Several trends are discussed which are now in vogue to detect novel useful compounds from microbes. Examples are given of those microbial metabolites and enzymes, which have attracted industrial interest.