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

Abstract

IntroductionThe antibiotic crisis is a major human health problem. Bioprospecting screenings suggest that proteobacteria and other extremophile microorganisms have biosynthetic potential for the production novel antimicrobial compounds. An Antarctic Sphingomonas strain (So64.6b) previously showed interesting antibiotic activity and elicitation response, then a relationship between environmental adaptations and its biosynthetic potential was hypothesized. We aimed to determine the genomic characteristics in So64.6b strain related to evolutive traits for the adaptation to the Antarctic environment that could lead to its diversity of potentially novel antibiotic metabolites.MethodsThe complete genome sequence of the Antarctic strain was obtained and mined for Biosynthetic Gene Clusters (BGCs) and other unique genes related to adaptation to extreme environments. Comparative genome analysis based on multi-locus phylogenomics, BGC phylogeny, and pangenomics were conducted within the closest genus, aiming to determine the taxonomic affiliation and differential characteristics of the Antarctic strain.Results and discussionThe Antarctic strain So64.6b showed a closest identity with Sphingomonas alpina, however containing a significant genomic difference of ortholog cluster related to degradation multiple pollutants. Strain So64.6b had a total of six BGC, which were predicted with low to no similarity with other reported clusters; three were associated with potential novel antibiotic compounds using ARTS tool. Phylogenetic and synteny analysis of a common BGC showed great diversity between Sphingomonas genus but grouping in clades according to similar isolation environments, suggesting an evolution of BGCs that could be linked to the specific ecosystems. Comparative genomic analysis also showed that Sphingomonas species isolated from extreme environments had the greatest number of predicted BGCs and a higher percentage of genetic content devoted to BGCs than the isolates from mesophilic environments. In addition, some extreme-exclusive clusters were found related to oxidative and thermal stress adaptations, while pangenome analysis showed unique resistance genes on the Antarctic strain included in genetic islands. Altogether, our results showed the unique genetic content on Antarctic strain Sphingomonas sp. So64.6, −a probable new species of this genetically divergent genus–, which could have potentially novel antibiotic compounds acquired to cope with Antarctic poly-extreme conditions.

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

“…A similar approach to the one we used in this work was applied by Wang et al (2020) to detect antifungal compounds produced by P. aeruginosa , where they compared metabolomics and genomics data of a bioactive (isolated from housefly gut) and an inactive strain (isolated from a wastewater treatment plant). Other similar approaches have been proposed to other Antarctic microorganisms of the proteobacteria phylum for natural product discovery ( Núñez-Montero et al, 2020 , 2022 ), and for several other bacteria from diverse environments ( Maansson et al, 2016 ; Paulus et al, 2017 ; Tareen et al, 2022 ). Metabologenomics have been applied to fungi at a lower scale as the presence of introns in their genome makes gene prediction even more complex, but successful examples are available in literature ( Gonçalves et al, 2022 ; Hebra et al, 2022 ), and some tools are being developed to facilitate metabologenomics analysis of data from fungi strains ( Caesar et al, 2023 ).…”

Benchmarking AI-based plasmid annotation tools for antibiotic resistance genes mining from metagenome of the Virilla River, Costa Rica

“…As mentioned, traces of these pharmaceutical compounds such as ofloxacin and cephalexin have been found in the Virilla River [5], representing a sanitary risk for microbial communities, ecological relations, and major organism aquatic organisms [40]- [42]. ARGs are commonly mobilized between bacteria through MGEs, such as plasmids, in processes of HGT (e.g., conjugation and transformation), pathways related to environmental conditions [7], [43]. The presence of pollutants and human contaminants in aquatic environments is another factor involved in the aggravation of ARGs' dissemination [7], [44].…”

Insights into Co-Cultivation of Photosynthetic Microorganisms for Novel Molecule Discovery and Enhanced Production of Specialized Metabolites

“…Although extremophiles have been less studied than popular biosynthetic strains, the metabolic adaptation of extremophilic photosynthetic microorganisms increases the chances of finding biotechnological applications [82,83]. In addition, these extremophiles are known to be a promising source of new antimicrobial molecules [84], which is relevant to the bioprospecting effort to fight against the global antibiotic resistance crisis [12]. Therefore, we consider that extremophiles must be a focus of research for the scientific community to find natural products and biotechnological potential, employing the cocultivation approach.…”

“…As stated, the plasticity of extreme photosynthetic microorganisms, their evolution history, and the selective pressure they face to adapt to a wide range of environments make them a hot spot for discovering microorganisms with relevant biotechnological applications [84]. For example, extremophilic cyanobacteria Aliinostoc alkaliphilum are considered promising for new antimicrobial discovery, as they have been shown to be active against the pathogens Staphylococcus aureus, Bacillus cereus, Aspergillus flavus, and Mucor sp.…”