Salinity Regulation of the Interaction of Halovirus SNJ1 with Its Host and Alteration of the Halovirus Replication Strategy to Adapt to the Variable Ecosystem

Mei, Yadong; He, Congcong; Huang, Yongchi; Liu, Ying; Zhang, Ziqian; Chen, Xiangdong; Shen, Ping

doi:10.1371/journal.pone.0123874

Cited by 15 publications

(13 citation statements)

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“…J7-2, viral adsorption rates and lytic/lysogenic rates were measured at varying salt concentrations. Adsorption and lytic rate were found to increase with salt concentration, whereas the lysogenic rate decreased (Mei et al, 2015). In a system of tropical coastal lagoons, salinity was found to be one of the main factors positively affecting viral abundance (Junger et al, 2018).…”

Section: Resultsmentioning

confidence: 99%

Iroki: automatic customization and visualization of phylogenetic trees

Harrison

McAllister

et al. 2017

Preprint

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Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki’s utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal (http://virome.dbi.udel.edu). Iroki’s source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.

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Section: Resultsmentioning

confidence: 99%

Iroki: automatic customization and visualization of phylogenetic trees

Harrison

McAllister

et al. 2017

Preprint

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“…Samples for thin-section electron microscopy (HITACHI-HT 7700, Hitachi High-Tech, Tokyo, Japan) were prepared according to a previously described method [ 27 ]. Samples for scanning electron microscopy (HITACHI S-3000N, Hitachi High-Tech, Tokyo, Japan) were done according to the previous protocol with modification [ 28 ], instead of 2.5% glutaraldehyde in 0.2 mol/L phosphate buffer using 2.5% glutaraldehyde in NaCl solution with the NaCl concentration identical to that of the corresponding media during the process of immobilization.…”

Section: Methodsmentioning

confidence: 99%

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2

et al. 2017

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The halophilic archaea (haloarchaea) live in hyersaline environments such as salt lakes, salt ponds and marine salterns. To cope with the salt stress conditions, haloarchaea have developed two fundamentally different strategies: the "salt-in" strategy and the "compatible-solute" strategy. Although investigation of the molecular mechanisms underlying the tolerance to high salt concentrations has made outstanding achievements, experimental study from the aspect of transcription is rare. In the present study, we monitored cellular physiology of Natrinema sp. J7-2 cells incubated in different salinity media (15%, 25% and 30% NaCl) from several aspects, such as cellular morphology, growth, global transcriptome and the content of intracellular free amino acids. The results showed that the cells were polymorphic and fragile at a low salt concentration (15% NaCl) but had a long, slender rod shape at high salt concentrations (25% and 30% NaCl). The cells grew best in 25% NaCl, mediocre in 30% NaCl and struggled in 15% NaCl. An RNA-seq analysis revealed differentially expressed genes (DEGs) in various salinity media. A total of 1,148 genes were differentially expressed, consisting of 719 DEGs (348 up-regulated and 371 down-regulated genes) between cells in 15% vs 25% NaCl, and 733 DEGs (521 up-regulated and 212 down-regulated genes) between cells in 25% vs 30% NaCl. Moreover, 304 genes were commonly differentially expressed in both 15% vs 25% and 25% vs30% NaCl. The DEGs were enriched in different KEGG metabolic pathways, such as amino acids, glycerolipid, ribosome, nitrogen, protoporphyrin, porphyrin and porhiniods. The intracellular predominant free amino acids consisted of the glutamate family (Glu, Arg and Pro), aspartate family (Asp) and aromatic amino acids (Phe and Trp), especially Glu and Asp.

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“…J7‐1 is growing optimally at 18% NaCl concentration. At this salinity, SNJ1 favours lysogenic life style, but exhibits mostly lytic behaviour at salinities well above 18% NaCl (Mei et al ., ). Similar observations have been recorded for haloarchaeal siphoviruses HHTV‐1 and HCTV‐1, pleolipovirus HHPV‐1, and halobacterial myovirus SCTP‐2 for which maximal adsorption rates were measured at NaCl concentrations between 3 and 4 M NaCl (Kukkaro and Bamford, ).…”

Section: Halovirus Morphotypes and Life Stylesmentioning

confidence: 97%

Virus‐host interplay in high salt environments

Atanasova

Bamford

Oksanen

2016

Environ Microbiol Rep

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Interaction of viruses and cells has tremendous impact on cellular and viral evolution, nutrient cycling and decay of organic matter. Thus, viruses can indirectly affect complex processes such as climate change and microbial pathogenicity. During recent decades, studies on extreme environments have introduced us to archaeal viruses and viruses infecting extremophilic bacteria or eukaryotes. Hypersaline environments are known to contain strikingly high numbers of viruses (∼10(9) particles per ml). Halophilic archaea, bacteria and eukaryotes inhabiting hypersaline environments have only a few cellular predators, indicating that the role of viruses is highly important in these ecosystems. Viruses thriving in high salt are called haloviruses and to date more than 100 such viruses have been described. Virulent, temperate, and persistent halovirus life cycles have been observed among the known isolates including the recently described SNJ1-SNJ2 temperate virus pair which is the first example of an interplay between two haloviruses in one host cell. In addition to direct virus and cell isolations, metagenomics have provided a wealth of information about virus-host dynamics in hypersaline environments suggesting that halovirus populations and halophilic microorganisms are dynamic over time and spatially distributed around the highly saline environments on the Earth.

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Salinity Regulation of the Interaction of Halovirus SNJ1 with Its Host and Alteration of the Halovirus Replication Strategy to Adapt to the Variable Ecosystem

Cited by 15 publications

References 50 publications

Iroki: automatic customization and visualization of phylogenetic trees

Iroki: automatic customization and visualization of phylogenetic trees

Effects of salinity on the cellular physiological responses of Natrinema sp. J7-2

Virus‐host interplay in high salt environments

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