Development of a Web Platform for Analysis and Exploration of Genomes Associated with the Oil and Gas Industry: Expansion and Applications of Petroleum Associated Genome Database

• Grant number: 24/15102-8
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: January 01, 2025
• End date: December 31, 2026
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Valeria Maia Merzel
• Grantee: Kelly Johanna Hidalgo Martinez
• Host Institution: Centro Pluridisciplinar de Pesquisas Químicas, Biológicas e Agrícolas (CPQBA). Universidade Estadual de Campinas (UNICAMP). Paulínia , SP, Brazil

Abstract

The microbiomes associated with the oil and gas industry play a significant role in the processes involved in the oil production chain due to their active participation in biogeochemical cycles and, therefore, in the transformation of petroleum compounds and their derivatives. The actions of microorganisms in these processes can cause harmful damage to the industry, such as oil biodegradation in reservoirs, souring of petroleum, microbially influenced corrosion (MIC) of metallic surfaces, biofouling, among others. However, at the same time, the microbiomes associated with these environments can be beneficial, for example, in the bioremediation of oil spills, biodessulfurization, and/or the production of biosurfactants to improve secondary recovery in oil wells. Despite their relevance, knowledge about microorganisms with these capabilities in environments associated with the oil production chain is still scarce. Genome-focused analyses can help fill this gap. In a previous study, our research group compiled genomes from over 150 studies, which were retrieved from major databases (i.e., NCBI, JGI/IMG, GROS), aiming to structure a repository of genes and genomes associated with the oil and gas industry (PaGeD - Petroleum Associated Genome Database; Hidalgo et al., in preparation). The PaGeD comprises 3,334 genomes (3,014 MAGs, 319 isolates, and 1 SAG - Single-amplified genome), organized into 2,522 species-level clusters, obtained from various samples, such as oil-polluted environments, biocorrosion samples, oil reservoirs, production water, injection water, and formation water, among others. The initial analyses revealed limited geographical distribution and specific niche, meaning specific microbial communities in each sample type. More than 50% of the clusters, grouped at the species level, potentially correspond to new taxa, showing the low representativeness of cultivated microorganisms from oil and gas industry samples. PaGeD expands the current understanding of oil-associated microbiomes and provides a large catalog of genomes for future analyses to decipher beneficial and harmful microorganisms and their impact on the industry. This project aims to expand and consolidate this repository and use the information contained therein in two main research lines: i) to develop a publicly accessible web platform, promoting free access to genomic, physiological, and metabolic information of these microorganisms with a view to the bioprospecting of various molecules or studies in microbial taxonomy and ecology, facilitating data analysis by the scientific community; and ii) to define bioindicators (taxonomic groups) and/or biomarkers (functional genes) for different types of samples related to the oil production chain.