The microbial community of a biofilm lining the wall of a pristine cave in Western New Guinea

• Published in: Microbiological research 2020-12, Vol.241, p.126584, Article 126584
• Main Authors: Turrini, Paolo, Tescari, Marco, Visaggio, Daniela, Pirolo, Mattia, Lugli, Gabriele Andrea, Ventura, Marco, Frangipani, Emanuela, Visca, Paolo
• Format: Article
• Language: English
• Subjects: 16S rRNA; Antibiotics; Culturomics; Karst caves; MLSA; Shotgun sequencing
• ISSN: 0944-5013; 1618-0623
• DOI: 10.1016/j.micres.2020.126584

•A biofilm-like microbial community from a pristine cave in New Guinea was studied.•Metagenomic analyses revealed the predominance of Proteobacteria and Actinobacteria.•Chemoorganotrophy was the main metabolism of microbial community members.•Antibiotic resistance was predicted by metagenome analysis and confirmed in vitro.•Several unassignable taxonomic entities were isolated from the community. Caves are extreme environments inhabited by microbial communities adapted to thrive oligotrophic conditions. Cave microbes are organised in complex ecological networks and have developed survival strategies involving the production and release of a large variety of secondary metabolites, including antibiotic-like compounds. In this study, the structure and the metabolic features of a biofilm-like microbial community lining the walls of a pristine karst cavity (the Yumugi river cave) located in a remote region of the Western New Guinea were investigated. 16S rRNA and shotgun sequence analyses highlighted the prevalence of chemoorganotrophic phyla (Proteobacteria, Actinobacteria, Firmicutes and Acidobacteria), consistent with metabolic predictions inferred from the cave metagenome analysis. Few clinically relevant antimicrobial resistance genes were detected. A culture-based approach allowed the isolation of some heterotrophic members of the bacterial community, and antimicrobial susceptibility testing revealed an overall high level of resistance to different antimicrobials classes. Isolates presumptively representing new uncharacterized members of genus Pseudomonas displayed interesting antibiotic properties against Gram-positive indicator strains. Our work supports the hypothesis that caves represent a reservoir for new bacterial species and drug discovery research.