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

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

Naydja Moralles Maimone  1 , Mario Cezar Pozza Junior  1 , Lucianne Ferreira Paes de Oliveira  1 , Dorian Rojas-Villalta  2 , Simone Possedente de Lira  1 , Leticia Barrientos  3 , Kattia Núñez-Montero  4
Affiliations

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

Naydja Moralles Maimone et al. Front Microbiol. .

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.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
Bray-Curtis-based PCoA highlighting the chemical dissimilarity between extracts of Pseudomonas sp. cultivated on different culture media (A). Venn diagram with the total number of features detected on the extracts (B).
Figure 2
Figure 2
Molecular families generated by GNPS molecular networking with level 3 annotations (MSI) obtained in the NAP analysis.
Figure 3
Figure 3
Syntenic comparison by alignment and identification of local collinearity blocks (LCBs) between the biosynthetic gene clusters from bananamide DF of Pseudomonas sp. COW3 (accession MN480426.1) and homologous regions of Non-Ribosomal Peptide Synthases (NRPS) cluster in the region 7 of the Antarctic Pseudomonas sp. So3.2b. Gene graphics represent each cluster with homologous LCBs color matching. Similar plots for LBCs are shown on the top of genes graphics. Homologous genes are labeled with its annotation description, additional biosynthetic genes are pointed by arrows and other genes are presented as white boxes.
See this image and copyright information in PMC

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