Evaluation of Apple Root-Associated Endophytic Streptomyces pulveraceus Strain ES16 by an OSMAC-Assisted Metabolomics Approach

Abstract

The One Strain Many Compounds approach (OSMAC) is a powerful and comprehensive method that enables the chemo-diversity evaluation of microorganisms. This is achieved by variations of physicochemical cultivation parameters and by providing biotic and abiotic triggers to mimic microorganisms' natural environment in the lab. This approach can reactivate the silent biosynthetic routes of specific metabolites typically not biosynthesized under standard laboratory conditions. In the present study, we combined the OSMAC approach with static headspace solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS), high-performance liquid chromatography-high-resolution tandem mass spectrometry (HPLC-HRMSn), and matrix-assisted laser desorption/ionization high-resolution mass spectrometry imaging (MALDI-HRMSI) to evaluate the chemoecological significance of an apple root-associated endophytic Streptomyces pulveraceus strain ES16. We employed the OSMAC approach by cultivating the endophyte in six different media conditions and performed temporal studies over 14 days. Analysis of the volatilome revealed that only under stressful conditions associated with sporulation, endophytic S. pulveraceus ES16 produces geosmin, a volatile semiochemical known to attract the soil arthropods Collembola (springtails) specifically. Subsequently, targeted metabolic profiling revealed polycyclic tetramate macrolactams (PTMs) production by the endophyte under stress, which are bioactive against various pathogens. Additionally, the endophyte produced the iron-chelating siderophore, mirubactin, under the same conditions. The structures of the compounds were evaluated using HRMSn and by comparison with literature data. Finally, MALDI-HRMSI revealed the produced compounds' spatial-temporal distribution over 14 days. The compounds were profusely secreted into the medium after production. Our results indicate that endophytic S. pulveraceus ES16 can release the signal molecule geosmin, chemical defense compounds such as the PTMs, as well as the siderophore mirubactin into the host plant apoplast or the soil for ecologically meaningful purposes, which are discussed.

Isolation, Identification, and Antibacterial Mechanisms of Bacillus amyloliquefaciens QSB-6 and Its Effect on Plant Roots

“…The above results indicated that strain QSB-6 is a good biological control agent against Fusarium . However, Many biocontrol bacterial strains are sensitive to external conditions (i.e., light, high temperature, soil pH extremes), resulting in poor control efficacy in the field ( Alabouvette et al, 2009 ; Armin et al, 2021 ). We therefore investigated the physical and chemical properties of extracellular metabolites from strain QSB-6.…”

“…The antibacterial substances produced by specific strains also differ. Antibacterial substances that inhibit pathogens tend not to act alone, but instead two or more antibacterial substances act synergistically to produce antibacterial effects ( Hyakumachi et al, 2014 ; Carrión et al, 2019 ; Joo et al, 2020 ; Newman and Cragg, 2020 ; Armin et al, 2021 ). 2,4-Diacetylphloroglucinol (DAPG) and phenazines (PHZ) produced by Pseudomonas species have been used as antibiotics to control disease suppressive soils and Fusarium wilt ( Weller et al, 2002 ; Haas and Defago, 2005 ; Mazurier et al, 2009 ; Raaijmakers and Mazzola, 2012 ).…”

Metabolomic Insights Into Endophyte-Derived Bioactive Compounds

“…The application of the One Strain Many Compounds (OSMAC) approach enables the researchers to explore the chemodiversity of microorganisms ( Figure 2 ). In one such study involving an OSMAC-assisted metabolomics approach, Armin et al (2021a) investigated the metabolic potential of Streptomyces pulveraceus strain ES16 (an apple-associated root endophytic bacteria) by growing it in six different media (ranging from nutrient-rich to minimal media) for a period of 3, 7, and 14 days. Using various state-of-art techniques such as SPME-GC-MS (for expressed volatilome), HPLC-HRMS n (to target the expressed metabolome), and MALDI-HRMSI (for spatial-temporal visualization of metabolites), the authors demonstrated the production of geosmin (a volatile chemical that attracts soil arthropods), mirubactin (iron-chelating siderophore) and polycyclic tetramate macrolactams (biocontrol activity against various pathogens) under stress conditions ( Armin et al, 2021a ).…”

“…In one such study involving an OSMAC-assisted metabolomics approach, Armin et al (2021a) investigated the metabolic potential of Streptomyces pulveraceus strain ES16 (an apple-associated root endophytic bacteria) by growing it in six different media (ranging from nutrient-rich to minimal media) for a period of 3, 7, and 14 days. Using various state-of-art techniques such as SPME-GC-MS (for expressed volatilome), HPLC-HRMS n (to target the expressed metabolome), and MALDI-HRMSI (for spatial-temporal visualization of metabolites), the authors demonstrated the production of geosmin (a volatile chemical that attracts soil arthropods), mirubactin (iron-chelating siderophore) and polycyclic tetramate macrolactams (biocontrol activity against various pathogens) under stress conditions ( Armin et al, 2021a ). In addition to chemical OSMAC (by alteration/optimization of chemical media), biological OSMAC involving interaction with other microbial species (endophytic or pathogenic) can be used to increase the diversity of endophyte-derived bioactive compounds ( Armin et al, 2021b ).…”

Production of Siderophores by an Apple Root-Associated Streptomyces ciscaucasicus Strain GS2 Using Chemical and Biological OSMAC Approaches

“…These included modified 523 medium, Glucose Yeast Malt medium (GYM), Lysogeny medium (LB), nutrient medium (agar, NA; broth, NB), potato dextrose medium (agar, PDA; broth, PDB), and streptomyces medium (SM). The OSMAC conditions, physio-chemical triggers, and selection pressures presented by each of these six media were recently published [68]. The components of the media are detailed in Table S1.…”