An atomic force microscopy investigation of cyanophage structure

Kuznetsov, Yurii G.; Chang, Sheng-Chieh; Credaroli, Arielle; Martiny, Jennifer B. H.; McPherson, Alexander

doi:10.1016/j.micron.2012.02.013

Cited by 11 publications

(6 citation statements)

References 22 publications

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“…Thus, both nontailed phage genera described here offer windows into a dominant marine phage type as they represent the first in culture infecting a Bacteroidetes bacterium, and join only four other marine nontailed phages in culture [two infecting Synechococcus (38,41), one infecting Pseudoalteromonas (only sequenced; ref. 42), and one infecting a host of unknown taxonomy (43)].…”

Section: Resultsmentioning

confidence: 99%

Twelve previously unknown phage genera are ubiquitous in global oceans

Holmfeldt

Solonenko

Shah

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

170

173

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Viruses are fundamental to ecosystems ranging from oceans to humans, yet our ability to study them is bottlenecked by the lack of ecologically relevant isolates, resulting in "unknowns" dominating culture-independent surveys. Here we present genomes from 31 phages infecting multiple strains of the aquatic bacterium Cellulophaga baltica (Bacteroidetes) to provide data for an underrepresented and environmentally abundant bacterial lineage. Comparative genomics delineated 12 phage groups that (i) each represent a new genus, and (ii) represent one novel and four wellknown viral families. This diversity contrasts the few well-studied marine phage systems, but parallels the diversity of phages infecting human-associated bacteria. Although all 12 Cellulophaga phages represent new genera, the podoviruses and icosahedral, nontailed ssDNA phages were exceptional, with genomes up to twice as large as those previously observed for each phage type. Structural novelty was also substantial, requiring experimental phage proteomics to identify 83% of the structural proteins. The presence of uncommon nucleotide metabolism genes in four genera likely underscores the importance of scavenging nutrient-rich molecules as previously seen for phages in marine environments. Metagenomic recruitment analyses suggest that these particular Cellulophaga phages are rare and may represent a first glimpse into the phage side of the rare biosphere. However, these analyses also revealed that these phage genera are widespread, occurring in 94% of 137 investigated metagenomes. Together, this diverse and novel collection of phages identifies a small but ubiquitous fraction of unknown marine viral diversity and provides numerous environmentally relevant phage-host systems for experimental hypothesis testing. model systems | phage genomics | phage taxonomy | queuosine biosynthesis | prophage

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Section: Resultsmentioning

confidence: 99%

Twelve previously unknown phage genera are ubiquitous in global oceans

Holmfeldt

Solonenko

Shah

et al. 2013

Proc. Natl. Acad. Sci. U.S.A.

170

173

View full text Add to dashboard Cite

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“…Comparatively, cultivation of phages allowing for the sequencing of clonal genomes: consequently, this improves the content of available databases. It also allows for the examination of physical features under high powered microscopy, such as transmission electron microscopy (TEM) and atomic force microscopy (AFM) [ 5 , 6 ].…”

Section: Resultsmentioning

confidence: 99%

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

Malki

Kula

Bruder

et al. 2015

Virol J

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BackgroundThe study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.FindingsFour phages were extracted from Lake Michigan on the same bacterial host, exhibiting similar morphological characteristics as shown under transmission electron microscopy. Growth characteristics of the phages were unique to each isolate. Each phage demonstrated a host-range spanning several phyla of bacteria – to date, such a broad host-range is yet to be reported. Genomic data reveals genomes of a similar size, and close similarities between the Lake Michigan phages and the Pseudomonas phage PB1, however, the majority of annotated genes present were ORFans and little insight was offered into mechanisms for host-range.ConclusionsThe phages isolated from Lake Michigan are capable of infecting several bacterial phyla, and demonstrate varied phenotypic characteristics despite similarities in host preference, and at the genomic level. We propose that such a broad host-range is likely related to the oligotrophic nature of Lake Michigan, and the competitive benefit that this characteristic may lend to phages in nature.

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“…Atomic force microscopy (AFM) is slowly emerging as an alternative to TEM for the determination of viral morphology, however to date it has only been used to image marine cyanophages [38]. AFM provides the potential to convert highly resolved digital images to quantitative data [39].…”

Section: Introductionmentioning

confidence: 99%

Characterisation of Host Growth after Infection with a Broad-Range Freshwater Cyanopodophage

et al. 2014

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Freshwater cyanophages are poorly characterised in comparison to their marine counterparts, however, the level of genetic diversity that exists in freshwater cyanophage communities is likely to exceed that found in marine environments, due to the habitat heterogeneity within freshwater systems. Many cyanophages are specialists, infecting a single host species or strain; however, some are less fastidious and infect a number of different host genotypes within the same species or even hosts from different genera. Few instances of host growth characterisation after infection by broad host-range phages have been described. Here we provide an initial characterisation of interactions between a cyanophage isolated from a freshwater fishing lake in the south of England and its hosts. Designated ΦMHI42, the phage is able to infect isolates from two genera of freshwater cyanobacteria, Planktothrix and Microcystis. Transmission Electron Microscopy and Atomic Force Microscopy indicate that ΦMHI42 is a member of the Podoviridae, albeit with a larger than expected capsid. The kinetics of host growth after infection with ΦMHI42 differed across host genera, species and strains in a way that was not related to the growth rate of the uninfected host. To our knowledge, this is the first characterisation of the growth of cyanobacteria in the presence of a broad host-range freshwater cyanophage.

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An atomic force microscopy investigation of cyanophage structure

Cited by 11 publications

References 22 publications

Twelve previously unknown phage genera are ubiquitous in global oceans

Twelve previously unknown phage genera are ubiquitous in global oceans

Bacteriophages isolated from Lake Michigan demonstrate broad host-range across several bacterial phyla

Characterisation of Host Growth after Infection with a Broad-Range Freshwater Cyanopodophage

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