Narrow-Host-Range Bacteriophages That Infect Rhizobium etli Associate with Distinct Genomic Types

Abstract

bIn this work, we isolated and characterized 14 bacteriophages that infect Rhizobium etli. They were obtained from rhizosphere soil of bean plants from agricultural lands in Mexico using an enrichment method. The host range of these phages was narrow but variable within a collection of 48 R. etli strains. We obtained the complete genome sequence of nine phages. Four phages were resistant to several restriction enzymes and in vivo cloning, probably due to nucleotide modifications. The genome size of the sequenced phages varied from 43 kb to 115 kb, with a median size of ϳ45 to 50 kb. A large proportion of open reading frames of these phage genomes (65 to 70%) consisted of hypothetical and orphan genes. The remainder encoded proteins needed for phage morphogenesis and DNA synthesis and processing, among other functions, and a minor percentage represented genes of bacterial origin. We classified these phages into four genomic types on the basis of their genomic similarity, gene content, and host range. Since there are no reports of similar sequences, we propose that these bacteriophages correspond to novel species. Bacteriophages have an enormous impact on the ecology and evolution of bacteria (1-3). It is well-known that bacteriophages are agents of gene mobilization across bacterial populations and that the majority of bacterial genomes harbor prophages as well as individual genes of phage origin (4-6). Conversely, temperate phages often carry bacterial genes as a result of prophage induction and recombination (7,8). Some reports indicate that phages exist for almost every known bacterial species (9). In the case of symbiotic nitrogen-fixing bacteria, such as Sinorhizobium meliloti (10, 11), Rhizobium leguminosarum (12-14), Mesorhizobium spp. (15), and Bradyrhizobium spp. (16), phages have been isolated and characterized, but no genome sequences have been reported. As a consequence, genomic comparisons have not been made. To date, only the complete genome sequence of phage 16-3 of S. meliloti has been determined (17).Lytic and temperate phages that infect rhizobial species have been isolated from soils and from lysogens induced after UV light treatment or mitomycin C exposure (11). The presence of phageresistant and -sensitive strains of Rhizobium suggests that phages play a substantial role in the selection or elimination of certain genotypes (11,(18)(19)(20). For instance, bacteriophages reduce the population density of susceptible strains of Rhizobium trifolii on the root surface, allowing resistant strains to form nodules (21,22). In field experiments, the persistence of genetically modified rhizobia has been explained in part by their resistance to phages (19).In the completely sequenced genomes of Rhizobium etli strains CFN42 and CIAT652 (23, 24), there are some open reading frames (ORFs) with relatively high degrees of identity to bacteriophage genes, such as DNA integrases, DNA transferases, lysozymes, and the small and large subunits of DNA terminase. In this work, we obtained a collection of 14 R. etli ...

Genomic and phenotypic characterization of Rhizobium gallicum phage vB_RglS_P106B

“…KF614509) and S. meliloti phage 16-3 (Semsey et al, 1999) are higher than that of P106B with a value of 59 %, whereas the average DNA G+C content of R. etli phage RHEph10 is 60.3 %. R. etli phages RHEph02, RHEph03, RHEph08 and RHEph09 all have genomes with a mean DNA G+C content of 49 % (Santamaría et al, 2014), which is a difference from the host genome similar to what we see with P106B.…”

“…To date, fifteen rhizobiophage genomes have been fully sequenced and are available in public databases: Sinorhizobium phage 16-3 (Deák et al, 2010;Ganyu et al, 2005;Semsey et al, 1999Semsey et al, , 2002, Sinorhizobium phage PBC5 (accession no. NC_003324.1), Rhizobium etli phages RHEph01-RHEph06 and RHEph08-RHEph10 (Santamaría et al, 2014), Rhizobium phages RR1-A and RR1-B (NC_021560.1 and NC_021557.1), Sinorhizobium meliloti phage wM12 (Brewer et al, 2014) and Rhizobium leguminosarum phage L338C (KF614509). To improve our understanding of rhizobiophage biology, we have undertaken the characterization of a novel Rhizobium gallicum phage.…”

Expression of a Peptidoglycan Hydrolase from Lytic Bacteriophages Atu_ph02 and Atu_ph03 Triggers Lysis of Agrobacterium tumefaciens

“…Bacteriophages capable of infecting A. tumefaciens strain C58 were isolated from wastewater samples using an enrichment protocol adapted from Santamaría et al (38) and described in detail in the supplemental material.…”

“…4A). Similar to Rhizobium etli phages RHEph02, RHEph03, RHEph08, and RHEph09 (38), phages Atu_ph02 and Atu_ph03 can be classified as members of the T7 supercluster on the bases of the similarity of their genome organizations and the presence of core T7 genes. There are 4 conserved core T7 genes, which are predicted to encode the T7-like RNA polymerase, large terminase, and structural proteins (Table S2).…”

Molecular Characterization of a Novel Temperate Sinorhizobium Bacteriophage, ФLM21, Encoding DNA Methyltransferase with CcrM-Like Specificity

“…2). We have performed an identical comparative analysis of 24 other known viruses of Alphaproteobacteria, including the recently found group of narrow-host-range bacteriophages that infect Rhizobium etli (83). It revealed only a low level of amino acid identity between a few (1 to 4) proteins of 9 phages, which suggests a lack of a significant phylogenetic relationship between ⌽LM21 and the other analyzed Alphaproteobacteria phages.…”