Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87

Zrelovs, Nikita; Cernooka, E.; Dislers, Andris; Kazāks, Andris

doi:10.1007/s00705-019-04516-2

Cited by 10 publications

(4 citation statements)

References 28 publications

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“…Over 100 haloviruses have been isolated to date, most of which infect extreme halophilic archaea. Among these 100 haloviruses, only ~30 phages infect halophilic bacteria [ 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 ]. Currently, the research on culturable bacterial haloviruses mainly focuses on their morphological, physiological, and biochemical characteristics; research on the viral genome is still relatively scarce.…”

Section: Introductionmentioning

confidence: 99%

“…Currently, the research on culturable bacterial haloviruses mainly focuses on their morphological, physiological, and biochemical characteristics; research on the viral genome is still relatively scarce. Due to the small number of isolates, the genomes of only 16 bacterial haloviruses have been analyzed in detail [ 17 , 21 , 22 , 24 , 25 , 26 , 27 ], hindering our understanding of virus–host interactions. Four Marseille viruses and one Mimivirus isolated from a hypersaline environment in Tunisia using the halophilic amoeba as the host are the only known eukaryotic haloviruses [ 28 ].…”

Section: Introductionmentioning

confidence: 99%

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Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

Diao

Sun

et al. 2023

Viruses

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Salt mines are a special type of hypersaline environment. Current research mainly focuses on prokaryotes, and the understanding of viruses in salt mines remains limited. Understanding viruses in hypersaline environments is of great significance for revealing the formation and maintenance of microbial communities, energy flow and element cycling, and host ecological functions. A phage infecting Halomonas titanicae was isolated from Yipinglang Salt Mine in China, designated Halomonas titanicae phage vB_HtiS_YPHTV-1 (YPHTV-1). Transmission electron microscopy revealed that YPHTV-1 had an icosahedral head with a diameter of 49.12 ± 0.15 nm (n = 5) and a long noncontractile tail with a length of 141.7 ± 0.58 nm (n = 5), indicating that it was a siphovirus. The one-step growth curve showed that the burst size of YPHTV-1 was 69 plaque forming units (PFUs) cell−1. The genome of YPHTV-1 was 37,980 bp with a GC content of 36.2%. The phylogenetic analysis of the six conserved proteins indicated that YPHTV-1 formed a cluster with Bacillus phages and was separated from phages infecting Halomonas. The average nucleotide identity (ANI), phylogenetic, and network analyses indicated that the phage YPHTV-1 represented a new genus under Caudoviricetes. In total, 57 open reading frames (ORFs) were predicted in the YPHTV-1 genome, 30 of which could be annotated in the database. Notably, several auxiliary metabolic genes were encoded by YPHTV-1, such as ImmA/IrrE family metalloendopeptidase, mannose-binding lectin (MBL) folding metallohydrolase, M15 family of metal peptidases, MazG-like family protein, O antigen ligase, and acyltransferase. These genes potentially enabled the host bacterium to resist ionizing radiation, ultraviolet light (UV), mitomycin C, β-lactam antibiotic, high osmotic pressure, and nutritional deficiencies. These findings highlight the role of haloviruses in the life cycle of halobacteria.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

Diao

Sun

et al. 2023

Viruses

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“…The majority of haloviruses isolated to date are haloarchaeal viruses, with a few halobacterial viruses. Since the isolation of the first halobacterial virus F9-11 in a hypersaline soil in 1988 ( Calvo et al, 1988 ), a total of 29 halobacterial viruses have been reported ( Calvo et al, 1988 , 1991 ; Kauri et al, 1991 ; Calvo et al, 1994 ; Goel et al, 1996 ; Seaman and Day, 2007 ; Mobberley et al, 2008 ; Kukkaro and Bamford, 2009 ; Aalto et al, 2012 ; Atanasova et al, 2012 ; Shen et al, 2012 ; Yu et al, 2015 ; Atanasova et al, 2015b ; Fu et al, 2016 ; Villamor et al, 2017 ; Wang and Li, 2018 ; Rodela et al, 2019 ; Zrelovs et al, 2020 ; Olonade et al, 2021 ; Wang et al, 2022 ), with hosts including Halomonas , Salicola , Pseudomonas , Salinivibrio , Salisaeta , Salinibacter , Chromohalobacter , and Virgibacillus . Most studies have focused on virus morphology as well as physiological and biochemical characteristics, while only 15 halobacterial virus genomes have been published in GenBank.…”

Section: Introductionmentioning

confidence: 99%

Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii

Diao

et al. 2022

Front. Microbiol.

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Bacteriophages function as a regulator of host communities and metabolism. Many phages have been isolated and sequenced in environments such as the ocean, but very little is known about hypersaline environments. Phages infecting members of the genus Chromohalobacter remain poorly understood, and no Chromohalobacter phage genome has been reported. In this study, a halovirus infecting Chromohalobacter sp. F3, YPCBV-1, was isolated from Yipinglang salt mine. YPCBV-1 could only infect host strain F3 with burst size of 6.3 PFU/cell. It could produce progeny in 5%–20% (w/v) NaCl with an optimal concentration of 10% (w/v), but the optimal adsorption NaCl concentration was 5%–8% (w/v). YPCBV-1 is sensitive to pure water and depends on NaCl or KCl solutions to survive. YPCBV-1 stability increased with increasing salinity but decreased in NaCl saturated solutions, and it has a broader salinity adaptation than the host. YPCBV-1 has a double-stranded DNA of 36,002 bp with a G + C content of 67.09% and contains a total of 55 predicted ORFs and no tRNA genes. Phylogenetic analysis and genomic network analysis suggested that YPCBV-1 is a novel Mu-like phage under the class Caudoviricetes. Auxiliary metabolic gene, SUMF1/EgtB/PvdO family non-heme iron enzyme, with possible roles in antioxidant was found in YPCBV-1. Moreover, DGR-associated genes were predicted in YPCBV-1 genome, which potentially produce hypervariable phage tail fiber. These findings shed light on the halovirus-host interaction in hypersaline environments.

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“…Excitingly, many novel viruses have recently been isolated and sequenced and phage metagenomes have provided enormous amounts of novel genomic data. [6][7][8][9][10][11][12][13][14][15][16] However, the uncharacterized functions encoded by so much novel phage diversity limit our ability to go beyond a genome/imagebased classification. Therefore, phage sequence data cannot be translated directly into tangible knowledge of the impacts of phages on microbial ecology.…”

Section: Introductionmentioning

confidence: 99%

Rethinking Phage Ecology by Rooting it Within an Established Plant Framework

Clokie

Blasdel

Demars

et al. 2020

PHAGE

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Despite the abundance and significance of bacteriophages to microbial ecosystems, no broad ecological frameworks exist within which to determine ''bacteriophage types'' that reflect their ecological strategies and ways in which they interact with bacterial cells. To address this, we repurposed the well-established Grime's triangular CSR framework, which classifies plants according to three axes: competitiveness (C), ability to tolerate stress (S), and capacity to cope with disturbance (R). This framework is distinguished from other accepted schemes, as it seeks to identify individual characteristics of plants to understand their biological strategies and roles within an ecosystem. Our repurposing of the CSR triangle is based on phage transcription and the observation that typically phages have three major distinguishable transcription phases: early, middle, and late. We hypothesize that the proportion of genes expressed in these phases reflects key information about the phage ''ecological strategy,'' namely the C, S, and R strategies, allowing us to examine phages in a similar way to how plants are projected onto the triangle. In the ''phage version'' of this scheme, we suggest: (1) that some phages prioritize the early phase of transcription that shuts off host defense mechanisms, which reflects competitiveness; (2) other phages prioritize tuning resource management mechanisms in the cell such as nucleotide metabolism during their ''mid'' expression profile to tolerate stress; and (3) a further subset of phages (termed Ruderals) survive disturbance by investing significant resources into regeneration so they express a higher proportion of their genes during late infection. We examined 42 published phage transcriptomes and show that they fall into discrete CSR categories according to their expression profiles. We discuss these positions in the context of their biology, which is largely consistent with our predictions of specific phage characteristics. In this opinion article, we suggest a starting point to ascribe phages into different functional types and thus understand them in an ecological framework. We suggest that this may have farreaching implications for the application of phages in therapy and their exploitation to manipulate bacterial communities. We invite further use of this framework via our online tool; www.PhageCSR.ml.

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Isolation and characterization of the novel Virgibacillus-infecting bacteriophage Mimir87

Cited by 10 publications

References 28 publications

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

Genomic Characterization of a Halovirus Representing a Novel Siphoviral Cluster

Characterization and genomic analysis of a novel halovirus infecting Chromohalobacter beijerinckii

Rethinking Phage Ecology by Rooting it Within an Established Plant Framework

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