Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani

Naydja Moralles Maimone; Mario Cezar Pozza Junior; Lucianne Ferreira Paes de Oliveira; Dorian Rojas-Villalta; Simone Possedente de Lira; Leticia Barrientos; Kattia Núñez-Montero

doi:10.3389/fmicb.2023.1187321

Metabologenomics analysis of Pseudomonas sp. So3.2b, an Antarctic strain with bioactivity against Rhizoctonia solani

Front Microbiol. 2023 May 4:14:1187321. doi: 10.3389/fmicb.2023.1187321. eCollection 2023.

Authors

Naydja Moralles Maimone¹, Mario Cezar Pozza Junior¹, Lucianne Ferreira Paes de Oliveira¹, Dorian Rojas-Villalta², Simone Possedente de Lira¹, Leticia Barrientos³, Kattia Núñez-Montero⁴

Affiliations

¹ 'Luiz de Queiroz' Superior College of Agriculture, Department of Math, Chemistry, and Statistics, University of São Paulo, Piracicaba, São Paulo, Brazil.
² Biotechnology Research Center, Department of Biology, Instituto Tecnológico de Costa Rica, Cartago, Costa Rica.
³ Extreme Environments Biotechnology Lab, Center of Excellence in Translational Medicine, Universidad de La Frontera, Temuco, Chile.
⁴ Facultad Ciencias de la Salud, Instituto de Ciencias Biomédicas, Universidad Autónoma de Chile, Temuco, Chile.

Abstract

Introduction: Phytopathogenic fungi are a considerable concern for agriculture, as they can threaten the productivity of several crops worldwide. Meanwhile, natural microbial products are acknowledged to play an important role in modern agriculture as they comprehend a safer alternative to synthetic pesticides. Bacterial strains from underexplored environments are a promising source of bioactive metabolites.

Methods: We applied the OSMAC (One Strain, Many Compounds) cultivation approach, in vitro bioassays, and metabolo-genomics analyses to investigate the biochemical potential of Pseudomonas sp. So3.2b, a strain isolated from Antarctica. Crude extracts from OSMAC were analyzed through HPLC-QTOF-MS/MS, molecular networking, and annotation. The antifungal potential of the extracts was confirmed against Rhizoctonia solani strains. Moreover, the whole-genome sequence was studied for biosynthetic gene clusters (BGCs) identification and phylogenetic comparison.

Results and discussion: Molecular networking revealed that metabolite synthesis has growth media specificity, and it was reflected in bioassays results against R. solani. Bananamides, rhamnolipids, and butenolides-like molecules were annotated from the metabolome, and chemical novelty was also suggested by several unidentified compounds. Additionally, genome mining confirmed a wide variety of BGCs present in this strain, with low to no similarity with known molecules. An NRPS-encoding BGC was identified as responsible for producing the banamides-like molecules, while phylogenetic analysis demonstrated a close relationship with other rhizosphere bacteria. Therefore, by combining -omics approaches and in vitro bioassays, our study demonstrates that Pseudomonas sp. So3.2b has potential application to agriculture as a source of bioactive metabolites.

Keywords: OSMAC; bioactivity; bioprospecting; biosynthetic gene cluster; genomics; molecular networking; secondary metabolites.