Unveiling plant-microbiota mutualistic interaction under the perspective of a bacterial genome isolated from sugarcane microbiome

Author(s)

Marcio Luiz Magrini

• Document type: Master's Dissertation
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2020-02-28

Examining board members

Paulo Arruda; Gabriela Felix Persinoti; Marcelo Mendes Brandão

• Advisor: Paulo Arruda

Abstract

This study's objectives were to assemble the genome, annotate the genes and identify metabolic functions of a bacteria isolated from the sugarcane microbiome. This bacteria, named Ensifer sp. B04, identified as a robust colonizer when inoculated in plants, stimulated plant growth, both isolated or in a synthetic community inoculum designed from the sugarcane microbiome. In this work, the Ensifer sp. B04 genome was sequenced in an Illumina HiSeq 2500 sequencer, through shotgun technology. Here, we identify the strategies used to assemble that genome and present a detailed analysis of its protein-coding genes. These genes were mapped and annotated from a functional genomics perspective, thus revealing operons, genomic cassettes and metabolic pathways potentially associated with colonization efficiency. The Ensifer sp. B04's genome has enriched genes regarding proteins and enzymes required for acquisition and metabolism of aminoacids, organic acids, carbohydrates and aromatic compounds exuded by plants' roots. A pangenomic analysis, comparing the B04 bacterium with 46 other bacteria of the same genera, revealed that non-nodulating bacteria have enriched genes related to ABC transporter proteins. Among these genes, the most enriched ones are related to transportation of sugar, nitrate, sulfonate, bicarbonate, branched chain amino acids, glycerol-3-phosphate, Fe3 + and proline/glycine betaine. This analysis also showed that the Ensifer B04 bacteria has a unique gene related to the proline/glycine betaine ABC transporter category. Our results show that the Ensifer sp. B04, although it does not show characteristics traditionally described as important for plant-bacterial interaction, such as nitrogen fixation and phytohormones production, it presents a broad spectrum of mechanisms related to the establishment of plants colonization. The analysis of genes, operons and cassettes related to these mechanisms, from a diversified perspective, reveals this bacterium's genomic potential regarding its ability to be a robust colonizer (AU)

• FAPESP's process: 17/05951-4 - Identification of plant growth promoting metabolic pathways in bacteria isolated from sugarcane microbiome
• Grantee: Marcio Luiz Magrini
• Support Opportunities: Scholarships in Brazil - Master