Unraveling the Role of Phages on the Evolution of Plant Beneficial and Pathogenic Rhizobacteria

• Grant number: 18/19247-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: January 01, 2019
• End date: February 23, 2020
• Field of knowledge: Biological Sciences - Microbiology - Applied Microbiology
• Principal Investigator: João Carlos Setubal
• Grantee: Lucas Palma Perez Braga
• Host Institution: Instituto de Química (IQ). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated scholarship(s): 19/24097-0 - Screening for ecogenomic signatures of phage-bacteria interactions in natural microbiomes exposed to environmental disturbances, BE.EP.PD

Abstract

Many beneficial and pathogenic rhizobacteria are both well described and characterized in literature. We know who they are and what they do. However, we don't know why and how they evolve pathogenic or beneficial traits. Viruses infecting bacteria (phages) modulate host niche adaptation. Genomic evidences demonstrate that prophages contribute to the evolution of virulence. Most of the toxins are produced by prophage-related regions, and genes involved in secretion systems seem to be phage-like elements. Plant beneficial traits can also be related with prophages. Therefore, the present proposal aims to combine advanced tools in molecular and computational microbiology, including experiments with robust design and the use of statistical learning tools, for analyzing metagenome-assembled genomes (MAGs) and public available genomes, to identify phage-derived patterns that are influenced by ecological processes in rhizobacteria genomes. This work will contribute to improve our knowledge about how the use of microbial resources can be better optimized in agricultural systems, specially considering prevention of pathogenic traits and stimulation of beneficial traits in rhizosphere microbiome.

Scientific publications

(7)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

BRAGA, LUCAS P. P.; COUTINHO, FELIPE H.; AMGARTEN, DEYVID E.; KOT, WITOLD; HANSEN, LARS; SETUBAL, JOAO C.; PHILIPPOT, LAURENT. Novel virocell metabolic potential revealed in agricultural soils by virus-enriched soil metagenome analysis. ENVIRONMENTAL MICROBIOLOGY REPORTS, v. 13, n. 3, p. 348-354, JUN 2021. (18/19247-0, 19/24097-0)

BRAGA, LUCAS P. P.; SPOR, AYME; KOT, WITOLD; BREUIL, MARIE-CHRISTINE; HANSEN, LARS H.; SETUBAL, JOAO C.; PHILIPPOT, LAURENT. Impact of phages on soil bacterial communities and nitrogen availability under different assembly scenarios. MICROBIOME, v. 8, n. 1, APR 6 2020. (18/19247-0)

PEREZ BRAGA, LUCAS PALMA; PEREIRA, ROBERTA VERCIANO; MARTINS, LAYLA FARAGE; SILVA MOURA, LIVIA MARIA; SANCHEZ, FABIO BELTRAME; LEISTER PATANE, JOSE SALVATORE; DA SILVA, ALINE MARIA; SETUBAL, JOAO CARLOS. Genome-resolved metagenome and metatranscriptome analyses of thermophilic composting reveal key bacterial players and their metabolic interactions. BMC Genomics, v. 22, n. 1, SEP 10 2021. (11/50870-6, 18/19247-0)

BRAGA, LUCAS P. P.; TANENTZAP, ANDREW J.; LEE, BENJAMIN; TSAI, SIU MUI; RAAIJMAKERS, JOS M.; MENDES, RODRIGO; MENDES, LUCAS W.. Diversity of viruses and viroids in the rhizosphere of common bean cultivars differing in resistance to the fungal root pathogen Fusarium oxysporum. APPLIED SOIL ECOLOGY, v. 190, p. 7-pg., 2023-06-22. (19/16043-7, 18/19247-0, 14/03217-3, 15/00251-9)

THOMPSON, LAUREN M.; KUHN, MCKENZIE A.; WINDER, JOHANNA C.; BRAGA, LUCAS P. P.; HUTCHINS, RYAN H. S.; TANENTZAP, ANDREW J.; ST. LOUIS, VINCENT L.; OLEFELDT, DAVID. Controls on methylmercury concentrations in lakes and streams of peatland-rich catchments along a 1700 km permafrost gradient. Limnology and Oceanography, v. N/A, p. 15-pg., 2023-01-18. (19/24097-0, 18/19247-0)

BRAGA, LUCAS P. P.; ORLAND, CHLOE; EMILSON, ERIK J. S.; FITCH, AMELIA A.; OSTERHOLZ, HELENA; DITTMAR, THORSTEN; BASILIKO, NATHAN; MYKYTCZUK, NADIA C. S.; TANENTZAP, ANDREW J.. Viruses direct carbon cycling in lake sediments under global change. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, v. 119, n. 41, p. 12-pg., 2022-10-11. (19/24097-0, 18/19247-0)

BRAGA, LUCAS P. P.; SCHUMACHER, ROBERT I.. Awaking the dormant virome in the rhizosphere. Molecular Ecology, v. 32, n. 11, p. 15-pg., 2023-06-01. (18/19247-0)