In silico exploration of the genomic repertoire of Iranian aquatic bacteria: Prophage carriage, bioactive compound potential, CRISPR-Cas immunity, and integrated defensive-metabolic islands

TL;DR

This study explores the genomes of Iranian aquatic bacteria, revealing their potential for producing bioactive compounds and their complex defense systems.

Contribution

The study introduces the 'Fortress Hypothesis' to explain the co-localization of defense and biosynthesis systems in bacterial genomes.

Findings

23 multi-functional genomic islands were discovered, linking biosynthesis and defense systems.

Eight prophages were identified, encoding CAZymes and anti-CRISPR proteins.

CRISPR-Cas systems were found in 34 out of 38 strains, mostly Type I.

Abstract

The unique and underexplored aquatic ecosystems of Iran represent a significant reservoir of microbial diversity. This study presents the first comprehensive genomic survey of 38 native Iranian bacterial strains from hypersaline lakes and wetlands, integrating in silico analyses of their secondary metabolome, bacteriocin potential, resident prophages, and genomic architecture. Our genome mining revealed a prolific capacity for secondary metabolite production, identifying dozens of biosynthetic gene clusters (BGCs). Ectoine biosynthesis was ubiquitous, underscoring its role as a key osmoprotectant, while diverse BGCs for terpenes, polyketides, and hybrid metabolites were also prevalent. Concurrently, we identified a wide array of ribosomally synthesized and post-translationally modified peptides (RiPPs), including known bacteriocins. Furthermore, we characterized eight high-quality prophages integrated within these genomes, encoding auxiliary genes such as carbohydrate-active enzymes (CAZymes) and putative anti-CRISPR (ACR) proteins. The bacterial hosts themselves were equipped with robust defense systems, with CRISPR-Cas loci, predominantly Type I, detected in most strains. Crucially, we identified multi-functional genomic islands that physically link BGCs with defense systems (e.g., CRISPR-Cas, restriction-modification) and prophage regions. We propose the “Fortress Hypothesis” to explain this architecture, wherein the co-localization of metabolite production and defense machinery protects metabolic investment against phage predation and genetic loss. This integrative genomic arrangement highlights a sophisticated co-evolutionary strategy for survival in extreme environments. Our findings position these indigenous bacteria as a promising genetic repository for discovering novel bioactive compounds, enzymes, and biotechnological tools, with implications for antibiotic discovery, CRISPR modulation, and understanding adaptive microbial genomics in extreme niches.

•Discovery of 23 multi-functional genomic islands in bacterial genomes.•Proposed ‘Fortress Hypothesis' explains co-localized defense & biosynthesis.•Eight prophages encode auxiliary CAZymes and anti-CRISPR proteins.•CRISPR-Cas systems detected in 34 of 38 strains, predominantly Type I.•Diverse BGCs identified, including ubiquitous ectoine biosynthesis.

Discovery of 23 multi-functional genomic islands in bacterial genomes.

Proposed ‘Fortress Hypothesis' explains co-localized defense & biosynthesis.

Eight prophages encode auxiliary CAZymes and anti-CRISPR proteins.

CRISPR-Cas systems detected in 34 of 38 strains, predominantly Type I.

Diverse BGCs identified, including ubiquitous ectoine biosynthesis.

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