Isolation and Characterization of Natural, Antibiotic-Producing Bacteria in Pure- and Co-Culture

Catherine Ann Darcey


Rapid emergence of bacterial antibiotic resistance has diminished the effectiveness of nearly all clinical antibiotics;  thus, the search for novel compounds must continue in order to replenish the antibiotic drug pipeline. Natural products are a logical starting point for discovery of new molecules with antibiotic activity, and natural rhizosphere environments remain a practical source of new antibiotic producers. Increased success of culturing natural soil bacteria, combined with the knowledge that for every teaspoon of productive soil there are approximately 100 million to 1 billion bacteria, highlights the need to explore natural rhizosphere communities for undiscovered bioactive compounds. Furthermore, metabolite induction via microorganism co-culture, has been reported to activate cryptic biosynthetic gene clusters and enhance chemical diversity for novel drug discovery. Here, bacterial strains were isolated from various plant-, rhizosphere-, and aquatic- environments throughout Western North Carolina and screened for antibiotic production, both in pure culture and in pairwise co-cultures, using a high-throughput antagonism assay against a range of Gram-positive and Gram-negative bacterial targets including Staphylococcus aureus and Escherichia coli. Pure cultured-based screening reports 25 antibiotic-producing bacteria that were isolated from soil- and plant-associated environments. Each bacterium was phylogenetically identified via 16S rDNA amplification and sequencing. Antagonistic organisms include members of several common genera, including Pseudomonas, Serratia and Streptomyces, as well as less characterized groups including Janthinobacteria and Rahnella species. Antifungal activity against the pathogenic fungus Fusarium was also assessed, with 16% of the antibacterial isolates also exhibiting antifungal activity. Co-culture based screening of over 6,651 pairwise combinations of bacteria reports no activation of antibiotic production, despite recently published research results which suggest such interaction-induced production is common. Ongoing work seeks to characterize the bacterial producers and the natural products being produced, with the long-term goal being the discovery of novel compounds with clinical and agricultural applications.


Antibacterial; Antifungal; Pure- and Co- Culture

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