Metagenome-guided bioprospection of Acidobacteriota isolates from Cerrado soils

• Grant number: 23/16173-3
• Support Opportunities: Regular Research Grants
• Start date: July 01, 2025
• End date: June 30, 2028
• Field of knowledge: Biological Sciences - Microbiology - Biology and Physiology of Microorganisms
• Principal Investigator: Filipe Pereira Matteoli
• Grantee: Filipe Pereira Matteoli
• Host Institution: Faculdade de Ciências (FC). Universidade Estadual Paulista (UNESP). Campus de Bauru. Bauru , SP, Brazil

Abstract

The Acidobacteriota phylum is one of the most diverse and abundant bacterial phyla on Earth, bearing high prevalence in Brazilian latosoils, which are characterized by having acidic pH. However, knowledge regarding its physiology, culture conditions, evolution, phylogeny, and ecology is still rudimentary due to the difficulty of isolating and growing acidobacterial strains by classical means because of its oligotrophic lifestyle and unknown energy acquisition pathways. Irrespective of these challenges, several metagenomes-assembled genomes have allowed to infer that the Acidobacteriota diversity may be comparable to the Pseudomonadota (formerly Proteobacteria) phylum, meaning that this phylum comprises a major fraction of soil prokaryotic diversity. Acidobacteria are frequently found in productive soils, such as those typical of Brazilian Cerrado under agronomic management, through culture-independent methods. Despite that, there is no availability of acidobacterial isolates nor whole genome data availability in public culture collections and databases derived from tropical strains, leading to poor taxonomic classification of sequences classified to this phylum. To tackle these issues, we propose: i. To perform a large ecological screening of Cerrado soil bacterial community, depicting acidobacterial community patterns associated with different Cerrado phytophysiognomies, locations, land use, and seasons. ii. Assembly state-of-the-art hybrid whole metagenomes from Cerrado soil samples bearing high abundance of acidobacterial sequences to extract carbohydrate-degradation pathways present in these prokaryotes. iii. Prepare custom culture media using the predicted carbohydrates to perform isolation and growth of acidobacterial pure colonies. iv. Characterize the isolates, sequence the acidobacterial pure colonies and describe new species if possible. These objectives encapsulate our laboratory's core values, which aim to integrate in silico analyses (i and ii) with microbiology wet lab procedures (iii and iv) as a strategy to solve complex questions. The results will uncover key knowledge associated with the Acidobacteriota biodiversity and ecophysiology while also contributing towards a smart framework for targeted isolation. (AU)