Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil’s Hole, Bermuda

Buchholz, Holger H; Michelsen, Michelle L.; Parsons, Rachel; Bates, Nicholas R.; Temperton, Ben

doi:10.1128/mra.01325-20

Cited by 9 publications

(21 citation statements)

References 30 publications

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“…General features of the four phages are summarised in Table 1. Shared gene network analysis (VConTACT2) using assembled contigs from Global Ocean Viromes (GOV2) and RefSeq (V88 with ICTV and NCBI taxonomy) viruses assigned Melnitz to the same cluster as the Pelagibacter myophages HTVC008M and Mosig (16,27), suggesting they belong to the same family (Figure 1). The four Melnitz genomes were shared across two clusters, the first contained an additional 15 viral contigs from nine different metagenomes.…”

Section: Resultsmentioning

confidence: 99%

“…A rpsU gene (encoding the bacterial 30S ribosomal subunit 21S) was found downstream adjacent to a tRNA-Arg (tct). Virally encoded S21 genes were previously identified in the Pelagibacter phages HTVC008M (16) and Mosig (27) as well as the OM43 phage Venkman (15). It is thought that the 21S subunit in phages might be required for initiating polypeptide synthesis and mediation of mRNA binding (45); the proximate tRNA sequence may support a translational and protein synthesis role of the viral ribosomal gene.…”

Section: Genomic Characterization Of Melnitz-like Methylophilales Phagesmentioning

confidence: 99%

“…To assess the breadth of host ranges, we challenged the SAR11 strains HTCC7211 and HTCC1062 and OM43 strains H5P1, D12P1 and C6P1 (15) with the phages Melnitz and Mosig (27), but found no evidence that either phage is able to replicate in cells beyond host class boundaries as observed via cell lysis (Supplementary Figure 10). Melnitz only infected D12P1 and H5P1, but not C6P1 or any SAR11, whereas Mosig only caused lysis in the Pelagibacter ubique HTCC1062.…”

Section: Melnitz-encoded Genes Suggest a Possible Host Transition Event From Sar11 To Om43mentioning

confidence: 99%

“…All contigs from the Global Ocean Virome (GOV2) dataset and a WEC virome (12,29), Methylophilales phage Venkman (15) and LD28 phage P19250A (109), all isolated Pelagibacter phages (15)(16)(17)(18)27) and Pelagibacter-like MAGs (28) were screened for contigs that share a viral population with the genomes of OM43 phages (95% ANI over 80% length) using ClusterGenomes.pl v5.1 (https://github.com/simroux/ClusterGenomes). Genes of all contigs were identified by Prodigal v2.6.3 (99) and imported into the Cyverse Discovery Environment 2.0 (available at https://de.cyverse.orge/), where vContact-Gene2Genome 1.1.0 was used to prepare protein sequences before protein clustering using VConTACT2 (v.0.9.8) with default settings (87) to assess relatedness via shared gene networks.…”

Section: Phylogeny and Network Analysismentioning

confidence: 99%

“…A phage-encoded riboswitch putatively controlling regulation of psbA was previously identified in a cyanophage (56). Of the 133 isolate phage genomes encoding tmRNAs only two phages other than Melnitz possessed a riboswitch (both glutamine): Pelagibacter phage Mosig (27) and Prochlorococcus phage AG-345-P14 (60). Additional riboswitches were identified in metagenomic assembled virome contigs.…”

Section: Marine Melnitz-like Phages May Use Glutamine Riboswitches To Regulate Genome Expressionmentioning

confidence: 99%

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Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage

Buchholz

Bolaños

Bell

et al. 2021

Preprint

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The methylotrophic OM43 clade are Gammaproteobacteria that comprise some of the smallest free-living cells known with highly streamlined genomes. OM43 represents an important microbial link between marine primary production and return of carbon back to the atmosphere. Bacteriophages shape microbial communities and are major drivers of mortality and global marine biogeochemistry. Recent cultivation efforts have brought the first viruses infecting members of the OM43 clade into culture. Here we characterize a novel myophage infecting OM43, called Melnitz. Melnitz was isolated independently on three separate occasions (with isolates sharing >99.95% average nucleotide identity) from water samples from a subtropical ocean gyre (Sargasso Sea) and temperate coastal (Western English Channel) systems. Metagenomic recruitment from global ocean viromes confirmed that Melnitz is globally ubiquitous, congruent with patterns of host abundance. Bacteria with streamlined genomes such as OM43 and the globally dominant SAR11 clade use riboswitches as an efficient method to regulate metabolism. Melnitz encodes a two-piece tmRNA (ssrA), controlled by a glutamine riboswitch, providing evidence that riboswitch use also occurs for regulation during phage infection of streamlined heterotrophs. Virally encoded tRNAs and ssrA found in Melnitz were phylogenetically more closely related to those found within the alphaproteobacterial SAR11 clade and their associated myophages than those within their gammaproteobacterial hosts. This suggests the possibility of an ancestral inter-class host transition event between SAR11 and OM43. Melnitz and a related myophage that infects SAR11 were unable to infect hosts of the SAR11 and OM43, respectively, suggesting host transition rather than a broadening of host range.

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Section: Resultsmentioning

confidence: 99%

Section: Genomic Characterization Of Melnitz-like Methylophilales Phagesmentioning

confidence: 99%

Section: Melnitz-encoded Genes Suggest a Possible Host Transition Event From Sar11 To Om43mentioning

confidence: 99%

Section: Phylogeny and Network Analysismentioning

confidence: 99%

Section: Marine Melnitz-like Phages May Use Glutamine Riboswitches To Regulate Genome Expressionmentioning

confidence: 99%

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Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage

Buchholz

Bolaños

Bell

et al. 2021

Preprint

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Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean

Locke

Bidle

Thamatrakoln

et al. 2022

Advances in Virus Research

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Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes

et al. 2023

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The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called “Polarivirus skadi”, which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.

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Draft Genome Sequences of Pelagimyophage Mosig EXVC030M and Pelagipodophage Lederberg EXVC029P, Isolated from Devil’s Hole, Bermuda

Cited by 9 publications

References 30 publications

Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage

Genomic evidence for inter-class host transition between abundant streamlined heterotrophs by a novel and ubiquitous marine Methylophage

Marine viruses and climate change: Virioplankton, the carbon cycle, and our future ocean

Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes

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