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

Genome mining of alkaliphilic cyanobacterial consortia: Identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs | Research Square window.SnipcartSettings = { analytics: { enabled: false } }; (function() { var accessVector = localStorage.getItem('access_vector') || ''; window.dataLayer = window.dataLayer || []; if (accessVector) { window.dataLayer.push({ user: { profile: { profileInfo: { snid: accessVector } } } }); } })(); (function(w,d,s,l,i){w[l]=w[l]||[];w[l].push({'gtm.start':new Date().getTime(),event:'gtm.js'});var f=d.getElementsByTagName(s)[0],j=d.createElement(s),dl=l!='dataLayer'?'&l='+l:'';j.async=true;j.src='https://www.googletagmanager.com/gtm.js?id='+i+dl;f.parentNode.insertBefore(j,f);})(window,document,'script','dataLayer','GTM-K279D39R'); Browse Preprints In Review Journals COVID-19 Preprints AJE Video Bytes Research Tools Research Promotion AJE Professional Editing AJE Rubriq About Preprint Platform In Review Editorial Policies Our Team Advisory Board Help Center Sign In Submit a Preprint Cite Share Download PDF Research Article Genome mining of alkaliphilic cyanobacterial consortia: Identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs Ruchita Solanki, Everet Wiszniak, Lianchun Yi, Gamaliel Cabria, and 2 more This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-8928116/v1 This work is licensed under a CC BY 4.0 License Status: Posted Version 1 posted You are reading this latest preprint version Abstract 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. Cyanobacterial consortia Sodalinema Biosynthetic gene clusters Metagenome assembled genomes Metatranscriptomics Full Text Additional Declarations No competing interests reported. Supplementary Files Supplementarytables.xlsx Supportingfigures.docx Cite Share Download PDF Status: Posted Version 1 posted You are reading this latest preprint version Research Square lets you share your work early, gain feedback from the community, and start making changes to your manuscript prior to peer review in a journal. As a division of Research Square Company, we’re committed to making research communication faster, fairer, and more useful. We do this by developing innovative software and high quality services for the global research community. Our growing team is made up of researchers and industry professionals working together to solve the most critical problems facing scientific publishing. Also discoverable on Platform About Our Team In Review Editorial Policies Advisory Board Help Center Resources Author Services Accessibility API Access RSS feed Manage Cookie Preferences © Research Square 2026 | ISSN 2693-5015 (online) Privacy Policy Terms of Service Do Not Sell My Personal Information {"props":{"pageProps":{"initialData":{"identity":"rs-8928116","acceptedTermsAndConditions":true,"allowDirectSubmit":true,"archivedVersions":[],"articleType":"Research Article","associatedPublications":[],"authors":[{"id":599648282,"identity":"bdda79c3-5e67-4a31-a893-aaa86612265f","order_by":0,"name":"Ruchita 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heterotrophs","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":false,"hideJournal":true,"highlight":"","institution":"","isAcceptedByJournal":false,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true},"keywords":"Cyanobacterial consortia, Sodalinema, Biosynthetic gene clusters, Metagenome assembled genomes, Metatranscriptomics","lastPublishedDoi":"10.21203/rs.3.rs-8928116/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-8928116/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"\u003cp\u003e\u003cstrong\u003eBackground\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eAlkaline 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 \u003cem\u003eSodalinema\u003c/em\u003e (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.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eResults\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eEnrichment 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 \u003cem\u003eSodalinema\u003c/em\u003e. Phylogenetic analysis of \u003cem\u003eSodalinema\u003c/em\u003e MAGs revealed a distinct clade, dominated by \u003cem\u003eCandidatus\u003c/em\u003e “Sodalinema alkaliphilum”. Metabolic pathway analysis showed that \u003cem\u003eSodalinema\u003c/em\u003e possessed complete pathways for vitamin B\u003csub\u003e5\u003c/sub\u003e (pantathonate), vitamin B\u003csub\u003e7\u003c/sub\u003e (biotin), and molybdenum cofactor. For key B vitamins (B\u003csub\u003e1\u003c/sub\u003e, B\u003csub\u003e9\u003c/sub\u003e, B\u003csub\u003e12\u003c/sub\u003e), \u003cem\u003eSodalinema\u003c/em\u003e exhibited incomplete biosynthetic pathways; however, identical deficiencies were identified in the autonomously growing \u003cem\u003eSodalinema yuhuli\u003c/em\u003e. This could suggest that \u003cem\u003eSodalinema\u003c/em\u003e utilizes alternative, currently uncharacterized biosynthetic routes or lacks a requirement for these cofactors. Metatranscriptomic analysis showed that \u003cem\u003eSodalinema\u003c/em\u003e 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.\u003c/p\u003e\n\u003cp\u003eMost of the consortium’s secondary metabolic potential was in the heterotrophic members. \u003cem\u003eRoseinatronobacter\u003c/em\u003e encoded pathways for biosynthesis of N-acyl homoserine lactones, osmoprotectants, betalactone, and prodigiosin. \u003cem\u003eAlkalimonas\u003c/em\u003e and \u003cem\u003eWenzhouxiangella\u003c/em\u003e contained gene clusters for lanthipeptide biosynthesis, and \u003cem\u003eKiloniellales\u003c/em\u003e 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.\u003c/p\u003e\n\u003cp\u003e\u003cstrong\u003eConclusions\u003c/strong\u003e\u003c/p\u003e\n\u003cp\u003eThrough genomic and transcriptional profiling, we provided an insight into the metabolic landscape of alkaline algal consortia. We uncovered the functional roles of \u003cem\u003eSodalinema\u003c/em\u003e and its heterotrophic partners, positioning these extremophilic communities as promising platforms for the discovery of biotechnologically relevant compounds.\u003c/p\u003e","manuscriptTitle":"Genome mining of alkaliphilic cyanobacterial consortia: Identification of biosynthetic gene clusters in Sodalinema and associated heterotrophs","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2026-03-05 17:44:42","doi":"10.21203/rs.3.rs-8928116/v1","editorialEvents":[{"type":"communityComments","content":0}],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"researchsquare","isNatureJournal":false,"hasQc":true,"allowDirectSubmit":true,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"/submission","title":"Research Square","twitterHandle":"researchsquare","acdcEnabled":true,"dfaEnabled":false,"editorialSystem":"","reportingPortfolio":"","inReviewEnabled":false,"inReviewRevisionsEnabled":true}}],"origin":"","ownerIdentity":"23f3589d-6da2-4b52-aa99-20870839a7e0","owner":[],"postedDate":"March 5th, 2026","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"posted","subjectAreas":[],"tags":[],"updatedAt":"2026-04-08T21:24:14+00:00","versionOfRecord":[],"versionCreatedAt":"2026-03-05 17:44:42","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-8928116","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-8928116","identity":"rs-8928116","version":["v1"]},"buildId":"XKTyCvWXoU3ODBz1xrDgd","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}