Hyphomicrobium spp. thriving at lanthanide-enriched sites can complement biomining alternatives

Hyphomicrobium spp. thriving at lanthanide-enriched sites can complement biomining alternatives | 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 Article Hyphomicrobium spp. thriving at lanthanide-enriched sites can complement biomining alternatives James Valdés, Daniel Petrash, Kurt Konhauser This is a preprint; it has not been peer reviewed by a journal. https://doi.org/ 10.21203/rs.3.rs-2749876/v1 This work is licensed under a CC BY 4.0 License Status: Under Review Version 1 posted You are reading this latest preprint version Abstract Current biomining alternatives focus on exploiting metal-binding proteins with an exceptional affinity for lanthanides (Ln 3+ ). Herein, we developed an in-silico competition model for ionic binding indicating the α-proteobacterium, Hyphomicrobium methylovorum , possesses a protein that potentially binds Ln 3+ more efficiently than previous homologous protein studies demonstrate. Data regarding microbial receptors mediating acquisition of Ln 3+ for intracellular transport, however, remain scarce. We therefore determined the in-silico binding capacity of an H. methylovorum outer membrane receptor for a chelating siderophore of Ln 3+ . These in-silico results directed us to examine the microbiome of a former coal mine, now metal-polluted lake in Czechia, where we identified twelve distinct Hyphomicrobium spp. indigenous to the bottom ferruginous waters. As consortia members of Fe(II)-/Mn(II)-oxidizers within waters often enriched in Ln 3+ , our findings suggest that select Hyphomicrobium possess a sufficient molecular armament for scavenging Ln 3+ . Hyphomicrobium scavenging capacity of Ln 3+ can complement and diversify current alternatives implementing biotechnological mining methods. Biological sciences/Computational biology and bioinformatics/Protein function predictions Earth and environmental sciences/Ecology/Biogeochemistry/Element cycles Earth and environmental sciences/Ecology/Microbial ecology Biological sciences/Evolution/Phylogenetics Full Text Additional Declarations There is NO Competing Interest. Supplementary Files ValdesPetrashKonhauserSIAppendixTableS7.xlsx ValdesPetrashKonhauserSIAppendix.pdf Cite Share Download PDF Status: Under Review 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. 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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-2749876","acceptedTermsAndConditions":true,"allowDirectSubmit":false,"archivedVersions":[],"articleType":"Article","associatedPublications":[],"authors":[{"id":187605744,"identity":"bfd0254f-831d-443c-a654-f6720b7ce629","order_by":0,"name":"James Valdés","email":"data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAZAAAAAyAQMAAABI0h/eAAAABlBMVEX///8AAABVwtN+AAAACXBIWXMAAA7EAAAOxAGVKw4bAAAAzElEQVRIiWNgGAWjYFAC5gYJBgYbkrQwgrSkka7lMAkaDI4fbLzx4c/5PP7ZZwwYftTUMfD3HyCg5Uxis+XMttvFEudyDBh7jh1mkDhAQItkQ2KbNG/D7cSGMzwGzAxsBxgMGBsIaOl/2Cb958+5xPlgLf/qGIAkfsAvAbQFaHjiBpAWxjZmBgM2gloeNlv2tiUXG55hKzjY23eYR+IMAS1s/MkHb/z4Y5cnd4Z544Mf3+rkCIYYDCSACJBaHuLUw7SMglEwCkbBKMAKAPEGQUYDLGDDAAAAAElFTkSuQmCC","orcid":"https://orcid.org/0000-0002-0237-8061","institution":"Institute of Parasitology","correspondingAuthor":true,"submittingAuthor":false,"prefix":"","firstName":"James","middleName":"","lastName":"Valdés","suffix":""},{"id":187605745,"identity":"8499294d-ad06-4324-a8e1-121ed047c349","order_by":1,"name":"Daniel Petrash","email":"","orcid":"https://orcid.org/0000-0001-5039-0543","institution":"Czech Geological Survey","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Daniel","middleName":"","lastName":"Petrash","suffix":""},{"id":187605746,"identity":"76f7969b-5a58-47f4-b2b4-8be381d0ef76","order_by":2,"name":"Kurt Konhauser","email":"","orcid":"","institution":"University of Alberta","correspondingAuthor":false,"submittingAuthor":false,"prefix":"","firstName":"Kurt","middleName":"","lastName":"Konhauser","suffix":""}],"badges":[],"createdAt":"2023-03-29 05:21:15","currentVersionCode":1,"declarations":"","doi":"10.21203/rs.3.rs-2749876/v1","doiUrl":"https://doi.org/10.21203/rs.3.rs-2749876/v1","draftVersion":[],"editorialEvents":[],"editorialNote":"","failedWorkflow":false,"files":[{"id":50090496,"identity":"39d94f60-b0a9-4ed5-8ee5-9213ee283b16","added_by":"auto","created_at":"2024-01-24 11:24:59","extension":"pdf","order_by":1,"title":"","display":"","copyAsset":false,"role":"manuscript-pdf","size":3405879,"visible":true,"origin":"","legend":"","description":"","filename":"ValdesPetrashKonhauserScript.pdf","url":"https://assets-eu.researchsquare.com/files/rs-2749876/v1_covered_0a816608-8167-46d2-82f2-1ecf5634dd8f.pdf"},{"id":35012752,"identity":"4ca1c8e0-c9fc-41a3-83fb-1598c119583b","added_by":"auto","created_at":"2023-03-30 02:10:50","extension":"xlsx","order_by":2,"title":"","display":"","copyAsset":false,"role":"supplement","size":13255,"visible":true,"origin":"","legend":"","description":"","filename":"ValdesPetrashKonhauserSIAppendixTableS7.xlsx","url":"https://assets-eu.researchsquare.com/files/rs-2749876/v1/a110e35efb3807ace85b4312.xlsx"},{"id":35012753,"identity":"8b064cc5-5121-4e9c-83a6-46b9b9762822","added_by":"auto","created_at":"2023-03-30 02:10:51","extension":"pdf","order_by":3,"title":"","display":"","copyAsset":false,"role":"supplement","size":9532219,"visible":true,"origin":"","legend":"","description":"","filename":"ValdesPetrashKonhauserSIAppendix.pdf","url":"https://assets-eu.researchsquare.com/files/rs-2749876/v1/d759827df6b6064cede8b4d4.pdf"}],"financialInterests":"There is \u003cb\u003eNO\u003c/b\u003e Competing Interest.","formattedTitle":"\u003ci\u003eHyphomicrobium\u003c/i\u003e spp. thriving at lanthanide-enriched sites can complement biomining alternatives","fulltext":[],"fulltextSource":"","fullText":"","funders":[],"hasAdminPriorityOnWorkflow":false,"hasManuscriptDocX":false,"hasOptedInToPreprint":true,"hasPassedJournalQc":"","hasAnyPriority":true,"hideJournal":false,"highlight":"","institution":"","isAcceptedByJournal":true,"isAuthorSuppliedPdf":true,"isDeskRejected":"","isHiddenFromSearch":false,"isInQc":false,"isInWorkflow":false,"isPdf":true,"isPdfUpToDate":true,"isWithdrawnOrRetracted":false,"journal":{"display":true,"email":"[email protected]","identity":"nature-portfolio","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"","sideBox":"","snPcode":"","submissionUrl":"","title":"Nature Portfolio","twitterHandle":"","acdcEnabled":false,"dfaEnabled":false,"editorialSystem":"ejp","reportingPortfolio":"","inReviewEnabled":true,"inReviewRevisionsEnabled":false},"keywords":"","lastPublishedDoi":"10.21203/rs.3.rs-2749876/v1","lastPublishedDoiUrl":"https://doi.org/10.21203/rs.3.rs-2749876/v1","license":{"name":"CC BY 4.0","url":"https://creativecommons.org/licenses/by/4.0/"},"manuscriptAbstract":"Current biomining alternatives focus on exploiting metal-binding proteins with an exceptional affinity for lanthanides (Ln\u003csup\u003e3+\u003c/sup\u003e). Herein, we developed an \u003ci\u003ein-silico\u003c/i\u003e competition model for ionic binding indicating the α-proteobacterium, \u003ci\u003eHyphomicrobium methylovorum\u003c/i\u003e, possesses a protein that potentially binds Ln\u003csup\u003e3+\u003c/sup\u003e more efficiently than previous homologous protein studies demonstrate. Data regarding microbial receptors mediating acquisition of Ln\u003csup\u003e3+\u003c/sup\u003e for intracellular transport, however, remain scarce. We therefore determined the \u003ci\u003ein-silico\u003c/i\u003e binding capacity of an \u003ci\u003eH. methylovorum\u003c/i\u003e outer membrane receptor for a chelating siderophore of Ln\u003csup\u003e3+\u003c/sup\u003e. These \u003ci\u003ein-silico\u003c/i\u003e results directed us to examine the microbiome of a former coal mine, now metal-polluted lake in Czechia, where we identified twelve distinct \u003ci\u003eHyphomicrobium\u003c/i\u003e spp. indigenous to the bottom ferruginous waters. As consortia members of Fe(II)-/Mn(II)-oxidizers within waters often enriched in Ln\u003csup\u003e3+\u003c/sup\u003e, our findings suggest that select \u003ci\u003eHyphomicrobium\u003c/i\u003e possess a sufficient molecular armament for scavenging Ln\u003csup\u003e3+\u003c/sup\u003e. \u003ci\u003eHyphomicrobium\u003c/i\u003e scavenging capacity of Ln\u003csup\u003e3+\u003c/sup\u003e can complement and diversify current alternatives implementing biotechnological mining methods.","manuscriptTitle":"Hyphomicrobium spp. thriving at lanthanide-enriched sites can complement biomining alternatives","msid":"","msnumber":"","nonDraftVersions":[{"code":1,"date":"2023-03-30 02:10:46","doi":"10.21203/rs.3.rs-2749876/v1","editorialEvents":[],"status":"published","journal":{"display":true,"email":"[email protected]","identity":"communications-biology","isNatureJournal":true,"hasQc":false,"allowDirectSubmit":false,"externalIdentity":"commsbio","sideBox":"Learn more about [Communications Biology](http://www.nature.com/commsbio/)","snPcode":"","submissionUrl":"","title":"Communications Biology","twitterHandle":"","acdcEnabled":true,"dfaEnabled":true,"editorialSystem":"ejp","reportingPortfolio":"Communications Series","inReviewEnabled":true,"inReviewRevisionsEnabled":false}}],"origin":"","ownerIdentity":"146506ea-e4c4-4374-8f43-b70dcd99f774","owner":[],"postedDate":"March 30th, 2023","published":true,"recentEditorialEvents":[],"rejectedJournal":[],"revision":"","amendment":"","status":"under-review","subjectAreas":[{"id":20311188,"name":"Biological sciences/Computational biology and bioinformatics/Protein function predictions"},{"id":20311189,"name":"Earth and environmental sciences/Ecology/Biogeochemistry/Element cycles"},{"id":20311190,"name":"Earth and environmental sciences/Ecology/Microbial ecology"},{"id":20311191,"name":"Biological sciences/Evolution/Phylogenetics"}],"tags":[],"updatedAt":"2024-04-12T11:20:31+00:00","versionOfRecord":[],"versionCreatedAt":"2023-03-30 02:10:46","video":"","vorDoi":"","vorDoiUrl":"","workflowStages":[]},"version":"v1","identity":"rs-2749876","journalConfig":"researchsquare"},"__N_SSP":true},"page":"/article/[identity]/[[...version]]","query":{"redirect":"/article/rs-2749876","identity":"rs-2749876","version":["v1"]},"buildId":"7rjqhiLT3MXkJMwkYKINL","isFallback":false,"isExperimentalCompile":false,"dynamicIds":[84888],"gssp":true,"scriptLoader":[]}