Three novel Pseudomonas phages isolated from composting provide insights into the evolution and diversity of tailed phages

BMC Genomics

Research Article

Chris Upton¹  Layla Farage Martins²  Luciana Principal Antunes²  Karen Cristina Lombardi²  Gianlucca Gonçalves Nicastro²  Ronaldo Bento Quaggio²  Aline Maria da Silva²  Ana Paula Silva de Souza²  João Carlos Setubal³  Deyvid Amgarten⁴  Elliott Watanabe Kitajima⁵ 

[1] Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada;Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil;Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil;Biocomplexity Institute of Virginia Tech, Blacksburg, VA, USA;Departamento de Bioquímica, Instituto de Química, Universidade de São Paulo, São Paulo, Brazil;Programa de Pós-Graduação Interunidades em Bioinformática, Universidade de São Paulo, São Paulo, Brazil;Departamento de Fitopatologia e Nematologia, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, Brazil;

关键词: Bacteriophages;    Composting;    Homing endonucleases;    tRNA genes;    Genomics;    Metagenomics;    Pseudomonas aeruginosa;    Siphoviridae;    Podoviridae;   

DOI  :  10.1186/s12864-017-3729-z

 received in 2016-11-10, accepted in 2017-04-26,  发布年份 2017

来源: Springer

【 摘 要 】

BackgroundAmong viruses, bacteriophages are a group of special interest due to their capacity of infecting bacteria that are important for biotechnology and human health. Composting is a microbial-driven process in which complex organic matter is converted into humus-like substances. In thermophilic composting, the degradation activity is carried out primarily by bacteria and little is known about the presence and role of bacteriophages in this process.ResultsUsing Pseudomonas aeruginosa as host, we isolated three new phages from a composting operation at the Sao Paulo Zoo Park (Brazil). One of the isolated phages is similar to Pseudomonas phage Ab18 and belongs to the Siphoviridae YuA-like viral genus. The other two isolated phages are similar to each other and present genomes sharing low similarity with phage genomes in public databases; we therefore hypothesize that they belong to a new genus in the Podoviridae family. Detailed genomic descriptions and comparisons of the three phages are presented, as well as two new clusters of phage genomes in the Viral Orthologous Clusters database of large DNA viruses. We found sequences encoding homing endonucleases that disrupt a putative ribonucleotide reductase gene and an RNA polymerase subunit 2 gene in two of the phages. These findings provide insights about the evolution of two-subunits RNA polymerases and the possible role of homing endonucleases in this process. Infection tests on 30 different strains of bacteria reveal a narrow host range for the three phages, restricted to P. aeruginosa PA14 and three other P. aeruginosa clinical isolates. Biofilm dissolution assays suggest that these phages could be promising antimicrobial agents against P. aeruginosa PA14 infections. Analyses on composting metagenomic and metatranscriptomic data indicate association between abundance variations in both phage and host populations in the environment.ConclusionThe results about the newly discovered and described phages contribute to the understanding of tailed bacteriophage diversity, evolution, and role in the complex composting environment.

【 授权许可】

CC BY   
© The Author(s). 2017