Elicitation of Streptomyces lunalinharesii secondary metabolism through co-cultivation with Rhizoctonia solani

Mass Spectrometry-Based Molecular Networks Applied to Study the Molecular Interaction Between Two Endophytic Fungi Isolated From Tibouchina granulosa (Vell.) Cogn (Melastomataceae)

Establishing a microorganism as an endophyte involves complex molecular interactions with its host plant and a broader microbial community. Precise detection methods and comprehensive metabolite annotation are essential to study these interactions. This study focused on characterizing the chemical composition of metabolites produced by two endophytic fungi, Colletotrichum siamense and Xylaria berteroi, isolated from Tibouchina granulosa leaves in axenic conditions and coculture. We examined the fungal metabolites using ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HR-MS/MS) and analysis tools like Cytoscape and Global Natural Products Social Molecular Networking. Co-cultivation revealed unique compounds not produced in isolation, including N-acetyltryptamine. A total of 32 compounds were identified, many with biotechnological potential due to their bioactivities. The untargeted metabolomics approach demonstrated that interactions among these T. granulosa endophytes can activate inactive metabolic pathways under axenic conditions, potentially producing novel bioactive molecules. This study is the first study of the chemical profile and interaction between endophytes isolated from T. granulosa.

Enhancing Antifungal Drug Discovery Through Co-Culture with Antarctic Streptomyces albidoflavus Strain CBMAI 1855

Fungal infections pose a growing public health threat, creating an urgent clinical need for new antifungals. Natural products (NPs) from organisms in extreme environments are a promising source for novel drugs. Streptomyces albidoflavus CBMAI 1855 exhibited significant potential in this regard. This study aimed to (1) assess the antifungal spectrum of the CBMAI 1855 extract against key human pathogens, (2) elicit NP production through co-cultivation with fungi, correlating the metabolites with the biosynthetic gene clusters (BGCs), and (3) perform in silico toxicity predictions of the identified compounds to analyze their suitability for drug development. The crude extract of CBMAI 1855 exhibited broad-spectrum antifungal activity. The metabolomic analysis identified antifungal NPs such as antimycin A, fungimycin, surugamides, 9-(4-aminophenyl)-3,7-dihydroxy-2,4,6-trimethyl-9-oxo-nonoic acid, and ikarugamycin, with the latter two predicted to be the most suitable for drug development. Genome mining revealed three cryptic BGCs potentially encoding novel antifungals. These BGCs warrant a detailed investigation to elucidate their metabolic products and harness their potential. CBMAI 1855 is a prolific producer of multiple antifungal agents, offering a valuable source for drug discovery. This study highlights the importance of exploring microbial interactions to uncover therapeutics against fungal infections, with a detailed exploration of cryptic BGCs offering a pathway to novel antifungal compounds.

Bioactive Insecticides from Chemometric Diverse Ant-Associated Symbionts Streptomyces novaecaesareae and Streptomyces nojiriensis against the Fall Armyworm Larvae

The Streptomyces genus has long been recognized as a prolific and valuable source of diverse secondary metabolites. These metabolites contribute significantly to the intricate chemical diversity exhibited by Streptomyces, making them an indispensable reservoir for drug discovery, agricultural applications, and industrial processes. Exploiting the potential of these natural compounds holds the promise of ushering in a new era in insect pest management, reducing reliance on synthetic chemicals and fostering ecologically sustainable solutions. This study dives into the realm of chemo diversity within isolates of Streptomyces nojiriensis and Streptomyces novaecaesareae, with a specific focus on the production of insecticidal compounds. We explored chromatographic techniques for the identification and isolation of insecticidal compounds, and two bioactive compounds were identified in extracts of S. novaecaesareae. Valinomycin was identified from hexanic extracts of strain Asp59, while naphthomycin from ethyl acetate extracts of strain Asp58. These compounds showed insecticidal activity against first instars of Spodoptera frugiperda (Asp59: LC50 = 10.82 µg/µL, LC90 = 26.25 µg/µL; Asp58: LC50 = 15.05 µg/µL, LC90 = 38.84 µg/µL). Notably, this is the first report of naphthomycin as an insecticidal compound. The present study suggests that valinomycin and naphthomycin may be a novel biological source for the control of Spodoptera frugiperda in early stages.

Inhibition of Fusarium graminearum growth and spore germination by a Streptomyces amritsarensis strain capable of killing and growing on Microcystis scum

AIMS

Developing energy-saving and ecofriendly strategies for treating harvested Microcystis biomass.

METHODS AND RESULTS

Streptomyces amritsarensis HG-16 was first reported to effectively kill various morphotypes of natural Microcystis colonies at very high cell densities. Concurrently, HG-16 grown on lysed Microcystis maintained its antagonistic activity against plant pathogenic fungus Fusarium graminearum. It could completely inhibit spore germination and destroy mycelial structure of F. graminearum. Transcriptomic analysis revealed that HG-16 attacked F. graminearum in a comprehensive way: interfering with replication, transcription, and translation processes, inhibiting primary metabolisms, hindering energy production and simultaneously destroying stress-resistant systems of F. graminearum.

CONCLUSIONS

The findings of this study provide a sustainable and economical option for resource reclamation from Microcystis biomass: utilizing Microcystis slurry to propagate HG-16, which can subsequently be employed as a biocontrol agent for managing F. graminearum.

Transcriptomics integrated with metabolomics reveal the competitive relationship between co-cultured Trichoderma asperellum HG1 and Bacillus subtilis Tpb55

Microbial co-culture has proven to be an effective way to improve the ability of microorganisms to biocontrol. However, the interactive mechanisms of co-cultural microbes, especially between fungi and bacteria, have rarely been studied. By comparative analysis of morphology, transcriptomics and metabolomics, the interactive mechanisms of a sequential co-culture system of Trichoderma asperellum HG1 and Bacillus subtilis Tpb55 was explored in this study. The results revealed that co- culture has no significant effect on the growth and cell morphology of the two strains, but lead to mycelium wrinkling of HG1. RNA-seq analysis showed that co-culture significantly upregulated the HG1 genes concerning amino acid degradation and metabolism, proteolysis, resisting environmental stress, cell homeostasis, glycolysis, the glyoxylate cycle, and the citric acid (TCA) cycle, while Tpb55 genes related to cell homeostasis, spore formation and membrane fluidization were significantly upregulated, but genes associating to TCA, glycolytic cycles and fatty acid β-oxidation were significantly downregulated. Metabolomic results revealed that some amino acids related to energy metabolism were significantly altered in HG1, whereas palmitic acid, which is related to cell membrane functions, was upregulated in Tpb55. These results indicated that HG1 could interfere with carbon metabolism and cell membrane fluidity, but accelerate spore formation of Tpb55. Biophysical assays further convinced that co-culture could decrease ATP content and inhibit ATPase activity in HG1, and could promote spore formation and reduce the cell membrane fluidity of Tpb55. In addition, co-culture also accelerated the production of intracellular anti-oomycete compound octhilinone. The above results indicate that HG1 and Tpb55 are mainly in a competitive relationship in the co culture system. These findings provide new insights for understanding the interaction mechanism between co cultured microbes.

Computation-aided studies related to the induction of specialized metabolite biosynthesis in microbial co-cultures: An introductory overview

Co-cultivation is an effective method of inducing the production of specialized metabolites (SMs) in microbial strains. By mimicking the ecological interactions that take place in natural environment, this approach enables to trigger the biosynthesis of molecules which are not formed under monoculture conditions. Importantly, microbial co-cultivation may lead to the discovery of novel chemical entities of pharmaceutical interest. The experimental efforts aimed at the induction of SMs are greatly facilitated by computational techniques. The aim of this overview is to highlight the relevance of computational methods for the investigation of SM induction via microbial co-cultivation. The concepts related to the induction of SMs in microbial co-cultures are briefly introduced by addressing four areas associated with the SM induction workflows, namely the detection of SMs formed exclusively under co-culture conditions, the annotation of induced SMs, the identification of SM producer strains, and the optimization of fermentation conditions. The computational infrastructure associated with these areas, including the tools of multivariate data analysis, molecular networking, genome mining and mathematical optimization, is discussed in relation to the experimental results described in recent literature. The perspective on the future developments in the field, mainly in relation to the microbiome-related research, is also provided.

Optimization of the Production and Characterization of an Antifungal Protein by Bacillus velezensis Strain NT35 and Its Antifungal Activity against Ilyonectria robusta Causing Ginseng Rusty Root Rot

A biocontrol Bacillus velezensis strain, NT35, was isolated from the rhizosphere soil of ginseng, and its sterile filtrate was obtained through a 0.22 μm filter which had a significant inhibitory effect against Ilyonectria robusta, which causes rusty root rot in Panax ginseng. In order to obtain the best sterile filtrate, the medium fermentation conditions of the strain NT35 were optimized using response surface methodology (RSM), and the best composition was obtained. Therefore, the fermentation medium was composed of yeast extract powder 2.5%, cornmeal 1.5%, K2HPO4 1.5%, and (NH4)2SO4 2.5%. The optimal inoculum amount was 6%, at an initial pH value of 7.0 and culturing at 34 °C at 180 rpm. The antifungal protein 1-4-2F was obtained through precipitation via 30% (NH4)2SO4 precipitation, desalting by Sephadex G-25, ion-exchange chromatography, and gel filtration chromatography. Tricine-SDS-PAGE showed that the purified protein had a relative molecular weight of approximately 6.5 kDa. The protein 1-4-2F was relatively stable and had better antifungal activity at pH 4–10 and 20–100 °C under ultraviolet irradiation of 30 W. The amino acid sequence of protein 1-4-2F was obtained using mass spectrometry, and had 100% similarity to a hypothetical protein from B. velezensis YAU B9601-Y2 (Accession No: AFJ62117). Its molecular weight was 10.176 kDa, the isoelectric point was 9.08, and its sequence coverage reached 49%. The EC50 value of the protein 1-4-2F against I. robusta was 1.519 μg·mL−1. The mycelia morphology of I. robusta changed significantly after treatment with antifungal protein under microscopic observation; the branches of the mycelia increased, distorted, partially swelled into a spherical or elliptical shape, and even ruptured; and the cells became vacuoles.

Microbial Metabolites Annotation by Mass Spectrometry-Based Metabolomics

Since the discovery of penicillin, microbial metabolites have been extensively investigated for drug discovery purposes. In the last decades, microbial derived compounds have gained increasing attention in different fields from pharmacognosy to industry and agriculture. Microbial metabolites in microbiomes present specific functions and can be associated with the maintenance of the natural ecosystems. These metabolites may exhibit a broad range of biological activities of great interest to human purposes. Samples from either microbial isolated cultures or microbiomes consist of complex mixtures of metabolites and their analysis are not a simple process. Mass spectrometry-based metabolomics encompass a set of analytical methods that have brought several improvements to the microbial natural products field. This analytical tool allows the comprehensively detection of metabolites, and therefore, the access of the chemical profile from those biological samples. These analyses generate thousands of mass spectra which is challenging to analyse. In this context, bioinformatic metabolomics tools have been successfully employed to accelerate and facilitate the investigation of specialized microbial metabolites. Herein, we describe metabolomics tools used to provide chemical information for the metabolites, and furthermore, we discuss how they can improve investigation of microbial cultures and interactions.

Discovering New Natural Products Using Metabolomics-Based Approaches

The incessant search for new natural molecules with biological activities has forced researchers in the field of chemistry of natural products to seek different approaches for their prospection studies. In particular, researchers around the world are turning to approaches in metabolomics to avoid high rates of re-isolation of certain compounds, something recurrent in this branch of science. Thanks to the development of new technologies in the analytical instrumentation of spectroscopic and spectrometric techniques, as well as the advance in the computational processing modes of the results, metabolomics has been gaining more and more space in studies that involve the prospection of natural products. Thus, this chapter summarizes the precepts and good practices in the metabolomics of microbial natural products using mass spectrometry and nuclear magnetic resonance spectroscopy, and also summarizes several examples where this approach has been applied in the discovery of bioactive molecules.