The biotechnological potential of natural populations of Burkholderiales bacteria for antibiotic production

Abstract

Summary Background. This study aimed to discover novel antibiotics produced by Burkholderia and Paraburkholderia bacteria as interesting sources of specialized metabolites. A novel collection of environmental Burkholderia and Paraburkholderia from the Bornean jungle, Sabah, Malaysia was assembled for the analysis. Methods. After evaluation of different growth media, a total of 98 environmental samples were screened for the presence of these bacteria by enrichment on Pseudomonas cepacia azelaic acid tryptamine (PCAT) medium. Molecular identification using the recA and 16S rRNA gene was performed and a total of 57 isolates were genome sequenced ahead of phylogenomic analyses. Antibiotic production by the jungle strains was evaluated using an antimicrobial antagonism overlay assay, genome mining, and high performance liquid chromatography (HPLC) analysis. Results. Over 50% of the 98 jungle samples were Burkholderia/Paraburkholderia recA PCRpositive. A total of 123 jungle isolates were purified and draft genome sequences were obtained for 57 of them. Genomic taxonomy identified that 45 isolates (85%) were within the newly described Paraburkholderia, and 13 isolates (15%) grouped within Burkholderia. Within the Paraburkholderia, 22 isolates were likely Paraburkholderia tropica, with a further 22 representing potentially novel taxa. All 12 Burkholderia isolates were members of the Burkholderia cepacia complex, including three that were likely a novel species group. The Burkholderia strains were all bioactive, but Paraburkholderia did not show antimicrobial activity under the conditions tested. Genome mining using antiSMASH showed that the capacity of Burkholderia to encode antibiotic biosynthesis gene clusters (BGCs) was greater than Paraburkholderia. Conclusions. The Bornean jungle in Sabah, Malaysia, is a rich source of Burkholderia and Paraburkholderia bacteria. Classification of these bacteria using genomic taxonomy approaches accurately identified known and novel species within the collection. The ii environmental Burkholderia cepacia complex (Bcc) jungle strains were promising antimicrobial producers, however, despite their taxonomic diversity, the Paraburkholderia did not show any antimicrobial activity