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Among actinobacteria, <jats:italic>Nocardia<\/jats:italic> is one of the most important agricultural and industrial bacteria. Screening and isolation of <jats:italic>Nocardia<\/jats:italic> related bacteria from extreme habitats such as endolithic environments are beneficial for practical applications in agricultural and environmental biotechnology. In this work, bioinformatics analysis revealed that a novel strain <jats:italic>Nocardia mangyaensis<\/jats:italic> NH1 has the capacity to produce structurally varied bioactive compounds, which encoded by non-ribosomal peptide synthases (NRPS), polyketide synthase (PKS), and post-translationally modified peptides (RiPPs). Among NRPS, five gene clusters have a sequence homology with clusters encoding for siderophore synthesis. We also show that <jats:italic>N. mangyaensis<\/jats:italic> NH1 accumulates both catechol- and hydroxamate-type siderophores simultaneously under iron-deficient conditions. Untargeted LC\u2013MS\/MS analysis revealed a variety of metabolites, including siderophores, lipopeptides, cyclic peptides, and indole-3-acetic acid (IAA) in the culture medium of <jats:italic>N. mangyaensis<\/jats:italic> NH1 grown under iron deficiency. We demonstrate that four CAS (chrome azurol S)-positive fractions display variable affinity to metals, with a high Fe<jats:sup>3+<\/jats:sup> chelating capability. Additionally, three of these fractions exhibit antioxidant activity. A combination of iron scavenging metabolites produced by <jats:italic>N. mangyaensis<\/jats:italic> NH1 showed antifungal activity against several plant pathogenic fungi. We have shown that the pure culture of <jats:italic>N. mangyaensis<\/jats:italic> NH1 and its metabolites have no adverse impact on <jats:italic>Arabidopsis<\/jats:italic> seedlings. The ability of <jats:italic>N. mangyaensis<\/jats:italic> NH1 to produce siderophores with antifungal, metal-chelating, and antioxidant properties, when supplemented with phytohormones, has the potential to improve the release of macro- and micronutrients, increase soil fertility, promote plant growth and development, and enable the production of biofertilizers across diverse soil systems.<\/jats:p>","DOI":"10.1038\/s41598-024-54095-9","type":"journal-article","created":{"date-parts":[[2024,3,7]],"date-time":"2024-03-07T19:01:54Z","timestamp":1709838114000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":17,"title":["Genomic insights and anti-phytopathogenic potential of siderophore metabolome of endolithic Nocardia mangyaensis NH1"],"prefix":"10.1038","volume":"14","author":[{"given":"Irina V.","family":"Khilyas","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria I.","family":"Markelova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liia R.","family":"Valeeva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tatiana M.","family":"Ivoilova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elena","family":"Shagimardanova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alexander V.","family":"Laikov","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anna A.","family":"Elistratova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ekaterina S.","family":"Berkutova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Guenter","family":"Lochnit","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Margarita R.","family":"Sharipova","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2024,3,7]]},"reference":[{"key":"54095_CR1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2022.898979","author":"P Singh","year":"2022","unstructured":"Singh, P. et al. 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