Genome mining of alkaliphilic cyanobacterial consortia: Identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs

Background Alkaline soda lakes are extreme, high pH environments that nurture unique microbial communities, particularly cyanobacterial consortia. These alkaliphilic cyanobacterial consortia have potential for natural product discovery and sustainable biotechnology. This study aims to unlock the genetic and functional potential of such extremophilic consortia. We characterized three resilient Sodalinema (a filamentous cyanobacterium) dominated consortia enriched from Canadian soda lakes over 510 days. Utilizing a hybrid sequencing approach (Illumina and Nanopore) and metatranscriptomics at different pH, alkalinity and temperature, we generate high quality metagenome assembled genomes (MAGs) of cyanobacteria and their associated heterotrophs. Results Enrichment experiments showed that while the consortia originated from different conditions, all exhibited temperature optima at 21°C–30°C. Diversity declined over time as communities became dominated by Sodalinema . Phylogenetic analysis of Sodalinema MAGs revealed a distinct clade, dominated by Candidatus “Sodalinema alkaliphilum”. Metabolic pathway analysis showed that Sodalinema possessed complete pathways for vitamin B ₅ (pantathonate), vitamin B ₇ (biotin), and molybdenum cofactor. For key B vitamins (B ₁ , B ₉ , B ₁₂ ), Sodalinema exhibited incomplete biosynthetic pathways; however, identical deficiencies were identified in the autonomously growing Sodalinema yuhuli . This could suggest that Sodalinema utilizes alternative, currently uncharacterized biosynthetic routes or lacks a requirement for these cofactors. Metatranscriptomic analysis showed that Sodalinema grown at high-pH (10.2) exhibited higher expression of genes associated with phycocyanin and betacarotene pathways compared to those grown at pH 8.5. Genomic analysis identified diverse biosynthetic gene clusters (BGCs) across the consortia. Most of the consortium’s secondary metabolic potential was in the heterotrophic members. Roseinatronobacter encoded pathways for biosynthesis of N-acyl homoserine lactones, osmoprotectants, betalactone, and prodigiosin. Alkalimonas and Wenzhouxiangella contained gene clusters for lanthipeptide biosynthesis, and Kiloniellales possessed pathways for cyclodipeptides, hydrogen cyanide, and pyrroloquinoline quinone. These heterotroph-derived antimicrobials could facilitate niche defense, providing a mechanism to protect the cyanobacterial consortium from competing microbes or pathogens. Conclusions Through genomic and transcriptional profiling, we provided an insight into the metabolic landscape of alkaline algal consortia. We uncovered the functional roles of Sodalinema and its heterotrophic partners, positioning these extremophilic communities as promising platforms for the discovery of biotechnologically relevant compounds.