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Peer-reviewedCC BY 4.0Frontiers in Microbiology

Ecological structuring of biosynthetic potential across terrestrial soil-associated Streptomyces genomes

  • Hajar Mhammedi1,2
  • Sajida Mhammedi3
  • Said Bouda1
  • Youssef El Hilali Alaoui1,2
  • Adil Essarioui2
  1. 1Laboratory of Agro-Industrial and Medical Biotechnology, Faculty of Sciences and Techniques, Sultan Moulay Slimane University
  2. 2Oasis System Research Unit, National Institute of Agricultural Research, Regional Center of Agricultural Research of Errachidia
  3. 3Laboratory of Engineering and Research in Artificial Intelligence (LIRIA), National School of Artificial Intelligence and Digitalization (ENIAD), Mohammed First University
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Abstract

Streptomyces populations represent one of the richest reservoirs of microbial specialized metabolites, although the ecological organization of their biosynthetic diversity remains insufficiently resolved at large genomic scales. In the present study, 14,597 publicly available genome assemblies were initially screened. Environmental metadata associated with each genome were subsequently retrieved from the corresponding NCBI BioSample records and systematically curated to retain genomes originating from terrestrial soil-associated environments while excluding marine, freshwater, clinical, laboratory, industrial, and other non-terrestrial sources. Standardized climatic and edaphic variables were examined using principal component analysis (PCA), K-means clustering, and Kruskal–Wallis tests to evaluate ecological differentiation across terrestrial soil-associated Streptomyces populations, with false discovery rate (FDR) adjustment applied to inter-cluster comparisons. PCA revealed pronounced environmental structuring, with Principal Component 1 (PC1) explaining 44.3% of the total variance and Principal Component 2 (PC2) contributing 31.1%, together accounting for 75.4%. K-means clustering resolved three environmentally coherent groups with distinct soil and climatic profiles. Significant differentiation was detected for soil pH, rainfall, temperature, soil organic carbon, and clay content, with adjusted p -values below 0.001. Genome mining using GECCO (GEne Cluster prediction with COnditional Random Fields) revealed extensive biosynthetic diversity dominated by polyketide- and non-ribosomal peptide-associated gene clusters. Total biosynthetic richness also differed significantly among ecological groups (Kruskal–Wallis statistic = 7.28, p < 0.05). This study provides a large-scale ecological-genomic framework linking environmental differentiation with biosynthetic organization across terrestrial soil-associated Streptomyces populations, advancing understanding of soil microbial and metabolic diversity.

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Cite

BibTeXRIS
BibTeX
@article{mhammedi2026ecological,
  title = {{Ecological structuring of biosynthetic potential across terrestrial soil-associated Streptomyces genomes}},
  author = {Hajar Mhammedi and Sajida Mhammedi and Said Bouda and Youssef El Hilali Alaoui and Adil Essarioui},
  journal = {Frontiers in Microbiology},
  year = {2026},
  month = oct,
  doi = {10.3389/fmicb.2026.1884766},
  url = {https://www.frontiersin.org/articles/10.3389/fmicb.2026.1884766/full},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - Ecological structuring of biosynthetic potential across terrestrial soil-associated Streptomyces genomes
AU  - Hajar Mhammedi
AU  - Sajida Mhammedi
AU  - Said Bouda
AU  - Youssef El Hilali Alaoui
AU  - Adil Essarioui
PY  - 2026
DA  - 2026/10/21
JO  - Frontiers in Microbiology
DO  - 10.3389/fmicb.2026.1884766
UR  - https://www.frontiersin.org/articles/10.3389/fmicb.2026.1884766/full
AB  - Streptomyces populations represent one of the richest reservoirs of microbial specialized metabolites, although the ecological organization of their biosynthetic diversity remains insufficiently resolved at large genomic scales. In the present study, 14,597 publicly available genome assemblies were initially screened. Environmental metadata associated with each genome were subsequently retrieved from the corresponding NCBI BioSample records and systematically curated to retain genomes originating from terrestrial soil-associated environments while excluding marine, freshwater, clinical, laboratory, industrial, and other non-terrestrial sources. Standardized climatic and edaphic variables were examined using principal component analysis (PCA), K-means clustering, and Kruskal–Wallis tests to evaluate ecological differentiation across terrestrial soil-associated Streptomyces populations, with false discovery rate (FDR) adjustment applied to inter-cluster comparisons. PCA revealed pronounced environmental structuring, with Principal Component 1 (PC1) explaining 44.3% of the total variance and Principal Component 2 (PC2) contributing 31.1%, together accounting for 75.4%. K-means clustering resolved three environmentally coherent groups with distinct soil and climatic profiles. Significant differentiation was detected for soil pH, rainfall, temperature, soil organic carbon, and clay content, with adjusted p -values below 0.001. Genome mining using GECCO (GEne Cluster prediction with COnditional Random Fields) revealed extensive biosynthetic diversity dominated by polyketide- and non-ribosomal peptide-associated gene clusters. Total biosynthetic richness also differed significantly among ecological groups (Kruskal–Wallis statistic = 7.28, p < 0.05). This study provides a large-scale ecological-genomic framework linking environmental differentiation with biosynthetic organization across terrestrial soil-associated Streptomyces populations, advancing understanding of soil microbial and metabolic diversity.
SN  - 1664-302X
ER  -