PaGeD 2.0: um framework colaborativo para resolução taxonômica, descoberta de novas espécies e biogeografia microbiana em ecossistemas petrolíferos

• Processo: 25/24982-4
• Modalidade de apoio: Bolsas no Exterior - Estágio de Pesquisa - Pós-Doutorado
• Data de Início da vigência: 29 de abril de 2026
• Data de Término da vigência: 28 de novembro de 2026
• Área de conhecimento: Ciências Biológicas - Genética - Genética Molecular e de Microorganismos
• Pesquisador responsável: Valeria Maia Merzel
• Beneficiário: Kelly Johanna Hidalgo Martinez
• Supervisor: Luis Miguel Rodriguez Rojas
• Instituição Sede: Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA). Universidade Estadual de Campinas (UNICAMP). Paulínia , SP, Brasil
• Instituição Anfitriã: Aalborg University (AAU), Dinamarca
• Vinculado à bolsa: 24/15102-8 - Desenvolvimento de uma Plataforma Web para Análise e Exploração de Genomas Associados à Indústria de Petróleo e Gás: Expansão e Aplicações do Petroleum Associated Genome Database, BP.PD
• Assunto(s): Biologia computacional Ecologia microbiana Petróleo
• Palavra(s)-Chave do Pesquisador: bioinformática | Ecologia microbiana | Petróleo | Ecologia Microbiana

Resumo

Microorganisms thriving in petroleum-associated ecosystems (e.g., oilreservoirs, production waters) evolve under extreme physicochemical stressors-includinghydrocarbon toxicity, hypersalinity, and high pressure-driving the selection of uniqueadaptive traits. These environments represent an underexplored reservoir of microbialbiomarkers and bioindicators with biotechnological potential for applications such asbioremediation, corrosion mitigation, and bioenergy. Despite advances in microbialgenomics, critical gaps persist in resolving taxonomic ambiguities, classifying novel species,and mapping microbial biogeography across geochemical and operational gradients (e.g.,salinity, reservoir depth, hydrocarbon concentration). Under the current project (FAPESP2024/15102-8), we developed the Petroleum-associated Genome Database (PaGeD) (URL:https://paged.cpqba.unicamp.br/), a curated repository of 3,334 microbial genomes fromglobal Oil & Gas ecosystems (offshore platforms, refineries, injection waters), mappedthrough genome-resolved metagenomics. While PaGeD provides foundational insights intotaxonomic and functional diversity, challenges remain in democratizing taxonomicclassification, resolving phylogenomic relationships for uncultured lineages, and linkinggenomic data to geographic distribution patterns. To address these gaps, we propose acollaborative project between the Group of Microbial Ecology and Multi-omics (UNICAMP,Brazil) and the Microbial Ecology and Environmental Genomics Laboratory (University ofAalbor, Denmark), under the joint supervision of Prof. Dr. Valéria Maia Merzel and Prof. Dr.Luis Miguel Rodriguez-Rojas, leveraging his expertise in taxonomic tools (FastANI, MiGA -Microbial Genomes Atlas) and phylogenomic workflows. This initiative will enhance PaGeDthrough three interconnected advancements. First, a user-driven pipeline will enableresearchers to upload genomes and classify them taxonomically against PaGeD's databaseusing FastANI/MiGA, standardizing genome comparisons and improving species-levelresolution in industrial microbiomes. Second, phylogenomic reconstruction of conservedmarker genes will resolve evolutionary relationships among PaGeD genomes, identifyingnovel species and proposing provisional taxonomic assignments to guide future studies.Third, integration of metagenomic datasets will map the geographic distribution of PaGeDtaxa across oil-industrial regions, correlating their presence/absence with environmentalvariables like salinity and pH to identify microbial hotspots, such as corrosion-associatedtaxa in high-sulfide reservoirs. By bridging taxonomic precision, phylogenomic discovery,and spatial ecology, this collaboration will transform PaGeD into a dynamic platform forindustrial microbiome research. Outcomes include a user-friendly interface for taxonomicclassification, a framework for novel species description, and geographic heatmapshighlighting microbial distribution trends. Ultimately, these advancements will decodemicrobial "dark matter" into actionable solutions for energy and environmental challenges. (AU)