Genomic and Metabolomic Analysis of Antarctic Bacteria Revealed Culture and Elicitation Conditions for the Production of Antimicrobial Compounds

Abstract

Concern about finding new antibiotics against drug-resistant pathogens is increasing every year. Antarctic bacteria have been proposed as an unexplored source of bioactive metabolites; however, most biosynthetic gene clusters (BGCs) producing secondary metabolites remain silent under common culture conditions. Our work aimed to characterize elicitation conditions for the production of antibacterial secondary metabolites from 34 Antarctic bacterial strains based on MS/MS metabolomics and genome mining approaches. Bacterial strains were cultivated under different nutrient and elicitation conditions, including the addition of lipopolysaccharide (LPS), sodium nitroprusside (SNP), and coculture. Metabolomes were obtained by HPLC-QTOF-MS/MS and analyzed through molecular networking. Antibacterial activity was determined, and seven strains were selected for genome sequencing and analysis. Biosynthesis pathways were activated by all the elicitation treatments, which varies among strains and dependents of culture media. Increased antibacterial activity was observed for a few strains and addition of LPS was related with inhibition of Gram-negative pathogens. Antibiotic BGCs were found for all selected strains and the expressions of putative actinomycin, carotenoids, and bacillibactin were characterized by comparison of genomic and metabolomic data. This work established the use of promising new elicitors for bioprospection of Antarctic bacteria and highlights the importance of new “-omics” comparative approaches for drug discovery.

Stenotrophomonas maltophilia from Nepal Producing Two Novel Antibiotic Inactivating Enzymes, a Class A β-Lactamase KBL-1 and an Aminoglycoside 6′- N -Acetyltransferase AAC(6′)-Iap

“…CP002986 ) identical to a strain of S. maltophilia JV3 obtained from the rhizosphere in Brazil and 90.17% (nt 3279480 to 3286016; GenBank accession no. CP050452 ) identical to a strain of S. maltophilia SoD9b obtained in the Collins Glacier beach area in Antarctica ( 12 ). The upstream ( hemE-orfF - aroB - aroK-orfG-orfH - pdxH ) and downstream ( prpR - prpB - prpC - acnD ) regions of not aac(6′)-Iap were identical to those in S. maltophilia K279a harboring aac(6′)-Iam ( 9 ), IOMTU250 harboring aac(6′)-Iak ( 10 ).…”

Antarctic Sphingomonas sp. So64.6b showed evolutive divergence within its genus, including new biosynthetic gene clusters

“…In previous work, we reported an Antarctic Sphingomonas strain So64.6b with antibiotic activity in response to elicitation treatments (Núñez-Montero et al, 2020). Moreover, during elicitation treatments, it exceeded the number of metabolites capable of producing under regular conditions (Núñez-Montero et al, 2020).…”

Mucilaginibacter sp. Strain Metal(loid) and Antibiotic Resistance Isolated from Estuarine Soil Contaminated Mine Tailing from the Fundão Dam

“…The mechanism as cross-resistance is responsible for bacteria co-selection, which could maintain and promote antibiotic resistance in indigenous bacterial populations even in the absence of antibiotics [69,70]. This topic is a public health concern since soil bacteria could transfer ARG to pathogenic bacteria of clinic relevance [71,72].…”