Isolation and Characterization T4- and T7-Like Phages that Infect the Bacterial Plant Pathogen Agrobacterium tumefaciens

In the rhizosphere, bacteria–phage interactions are likely to have important impacts on the ecology of microbial communities and microbe–plant interactions. To better understand the dynamics of Agrobacteria–phage interactions, we have isolated diverse bacteriophages which infect the bacterial plant pathogen, Agrobacterium tumefaciens. Here, we complete the genomic characterization of Agrobacterium tumefaciens phages Atu_ph04 and Atu_ph08. Atu_ph04—a T4-like phage belonging to the Myoviridae family—was isolated from waste water and has a 143,349 bp genome that encodes 223 predicted open reading frames (ORFs). Based on phylogenetic analysis and whole-genome alignments, Atu_ph04 is a member of a newly described T4 superfamily that contains other Rhizobiales-infecting phages. Atu_ph08, a member of the Podoviridae T7-like family, was isolated from waste water, has a 59,034 bp genome, and encodes 75 ORFs. Based on phylogenetic analysis and whole-genome alignments, Atu_ph08 may form a new T7 superfamily which includes Sinorhizobium phage PCB5 and Ochrobactrum phage POI1126. Atu_ph08 is predicted to have lysogenic activity, as we found evidence of an integrase and several transcriptional repressors with similarity to proteins in transducing phage P22. Together, this data suggests that Agrobacterium phages are diverse in morphology, genomic content, and lifestyle.

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Isolation and characterization of a novel bacteriophage WO from Allonemobius socius crickets in Missouri

PLoS ONE ◽

10.1371/journal.pone.0250051 ◽

2021 ◽

Vol 16 (7) ◽

pp. e0250051

Author(s):

Jonah Kupritz ◽

John Martin ◽

Kerstin Fischer ◽

Kurt C. Curtis ◽

Joseph R. Fauver ◽

...

Keyword(s):

Phage Genome ◽

Surface Protein ◽

Fruit Fly ◽

Nematode Species ◽

Open Reading Frames ◽

Whole Genome Sequence ◽

Whole Genome ◽

Isolation And Characterization ◽

Allonemobius Socius

Wolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOAu of Drosophila simulans (94.46% identity) and WOCin2USA1 of the cherry fruit fly, Rhagoletis cingulata (99.33% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40–62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.

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Isolation and characterization of a novel Wolbachia bacteriophage from Allonemobius socius crickets in Missouri

10.1101/2021.03.31.437854 ◽

2021 ◽

Author(s):

Jonah Kupritz ◽

John Martin ◽

Kerstin Fischer ◽

Kurt C Curtis ◽

Joseph R Fauver ◽

...

Keyword(s):

Phage Genome ◽

Surface Protein ◽

Nematode Species ◽

Open Reading Frames ◽

Whole Genome Sequence ◽

Whole Genome ◽

Isolation And Characterization ◽

Long Tails ◽

Allonemobius Socius

AbstractWolbachia are endosymbionts of numerous arthropod and some nematode species, are important for their development and if present can cause distinct phenotypes of their hosts. Prophage DNA has been frequently detected in Wolbachia, but particles of Wolbachia bacteriophages (phage WO) have been only occasionally isolated. Here, we report the characterization and isolation of a phage WO of the southern ground cricket, Allonemobius socius, and provided the first whole-genome sequence of phage WO from this arthropod family outside of Asia. We screened A. socius abdomen DNA extracts from a cricket population in eastern Missouri by quantitative PCR for Wolbachia surface protein and phage WO capsid protein and found a prevalence of 55% and 50%, respectively, with many crickets positive for both. Immunohistochemistry using antibodies against Wolbachia surface protein showed many Wolbachia clusters in the reproductive system of female crickets. Whole-genome sequencing using Oxford Nanopore MinION and Illumina technology allowed for the assembly of a high-quality, 55 kb phage genome containing 63 open reading frames (ORF) encoding for phage WO structural proteins and host lysis and transcriptional manipulation. Taxonomically important regions of the assembled phage genome were validated by Sanger sequencing of PCR amplicons. Analysis of the nucleotides sequences of the ORFs encoding the large terminase subunit (ORF2) and minor capsid (ORF7) frequently used for phage WO phylogenetics showed highest homology to phage WOKue of the Mediterranean flour moth Ephestia kuehniella (94.18% identity) and WOLig of the coronet moth, Craniophora ligustri (96.86% identity), respectively. Transmission electron microscopy examination of cricket ovaries showed a high density of phage particles within Wolbachia cells. Isolation of phage WO revealed particles characterized by 40-62 nm diameter heads and up to 190 nm long tails. This study provides the first detailed description and genomic characterization of phage WO from North America that is easily accessible in a widely distributed cricket species.

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Larger Than Life: Isolation and Genomic Characterization of a Jumbo Phage That Infects the Bacterial Plant Pathogen, Agrobacterium tumefaciens

Frontiers in Microbiology ◽

10.3389/fmicb.2018.01861 ◽

2018 ◽

Vol 9 ◽

Cited By ~ 8

Author(s):

Hedieh Attai ◽

Maarten Boon ◽

Kenya Phillips ◽

Jean-Paul Noben ◽

Rob Lavigne ◽

...

Keyword(s):

Agrobacterium Tumefaciens ◽

Plant Pathogen ◽

Genomic Characterization ◽

Bacterial Plant Pathogen

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Atypical Adaptive and Cross-Protective Responses Against Peroxide Killing in a Bacterial Plant Pathogen, Agrobacterium tumefaciens

Current Microbiology ◽

10.1007/s00284-002-4011-3 ◽

2003 ◽

Vol 47 (4) ◽

pp. 323-326 ◽

Cited By ~ 13

Author(s):

Paiboon Vattanaviboon ◽

Warawan Eiamphungporn ◽

Skorn Mongkolsuk

Keyword(s):

Agrobacterium Tumefaciens ◽

Plant Pathogen ◽

Bacterial Plant Pathogen

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Phylogenetic Analysis of T-Box Genes Demonstrates the Importance of Amphioxus for Understanding Evolution of the Vertebrate Genome

Genetics ◽

10.1093/genetics/156.3.1249 ◽

2000 ◽

Vol 156 (3) ◽

pp. 1249-1257

Author(s):

Ilya Ruvinsky ◽

Lee M Silver ◽

Jeremy J Gibson-Brown

Keyword(s):

Phylogenetic Analysis ◽

Whole Genome Duplication ◽

Genome Duplication ◽

Gene Families ◽

Vertebrate Evolution ◽

Whole Genome ◽

Vertebrate Genome ◽

T Box ◽

Genetic Complexity ◽

History Of

Abstract The duplication of preexisting genes has played a major role in evolution. To understand the evolution of genetic complexity it is important to reconstruct the phylogenetic history of the genome. A widely held view suggests that the vertebrate genome evolved via two successive rounds of whole-genome duplication. To test this model we have isolated seven new T-box genes from the primitive chordate amphioxus. We find that each amphioxus gene generally corresponds to two or three vertebrate counterparts. A phylogenetic analysis of these genes supports the idea that a single whole-genome duplication took place early in vertebrate evolution, but cannot exclude the possibility that a second duplication later took place. The origin of additional paralogs evident in this and other gene families could be the result of subsequent, smaller-scale chromosomal duplications. Our findings highlight the importance of amphioxus as a key organism for understanding evolution of the vertebrate genome.

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Plant Pathogen Invasion Modifies the Eco-Evolutionary Host Plant Interactions of an Endangered Checkerspot Butterfly

Insects ◽

10.3390/insects12030246 ◽

2021 ◽

Vol 12 (3) ◽

pp. 246

Author(s):

Paul M. Severns ◽

Melinda Guzman-Martinez

Keyword(s):

Pacific Northwest ◽

Plant Pathogen ◽

Plantago Lanceolata ◽

Larval Feeding ◽

Plant Interactions ◽

Larval Food ◽

Disease Symptoms ◽

Pathogen Invasion ◽

The Pacific ◽

Germination Timing

New plant pathogen invasions typified by cryptic disease symptoms or those appearing sporadically in time and patchily in space, might go largely unnoticed and not taken seriously by ecologists. We present evidence that the recent invasion of Pyrenopeziza plantaginis (Dermateaceae) into the Pacific Northwest USA, which causes foliar necrosis in the fall and winter on Plantago lanceolata (plantain), the primary (non-native) foodplant for six of the eight extant Taylor’s checkerspot butterfly populations (Euphydryas editha taylori, endangered species), has altered eco-evolutionary foodplant interactions to a degree that threatens butterfly populations with extinction. Patterns of butterfly, larval food plant, and P. plantaginis disease development suggested the ancestral relationship was a two-foodplant system, with perennial Castilleja spp. supporting oviposition and pre-diapause larvae, and the annual Collinsia parviflora supporting post-diapause larvae. Plantain, in the absence of P. plantaginis disease, provided larval food resources throughout all butterfly life stages and may explain plantain’s initial adoption by Taylor’s checkerspot. However, in the presence of severe P. plantaginis disease, plantain-dependent butterfly populations experience a six-week period in the winter where post-diapause larvae lack essential plantain resources. Only C. parviflora, which is rare and competitively inferior under present habitat conditions, can fulfill the post-diapause larval feeding requirements in the presence of severe P. plantaginis disease. However, a germination timing experiment suggested C. parviflora to be suitably timed for only Washington Taylor’s checkerspot populations. The recent invasion by P. plantaginis appears to have rendered the ancestrally adaptive acquisition of plantain by Taylor’s checkerspot an unreliable, maladaptive foodplant interaction.

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Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽

10.3390/v13010027 ◽

2020 ◽

Vol 13 (1) ◽

pp. 27

Author(s):

Jun Kwon ◽

Sang Guen Kim ◽

Hyoun Joong Kim ◽

Sib Sankar Giri ◽

Sang Wha Kim ◽

...

Keyword(s):

Morphological Traits ◽

Open Reading Frames ◽

Genome Comparison ◽

The Novel ◽

Promising Alternative ◽

Isolation And Characterization ◽

Global Issue ◽

Reading Frames ◽

Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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