Establishing Host-Virus Link Through Host Metabolism: Viral DNA SIP Validation Using T4 Bacteriophage and E. coli.
Journal
Current microbiology
ISSN: 1432-0991
Titre abrégé: Curr Microbiol
Pays: United States
ID NLM: 7808448
Informations de publication
Date de publication:
14 Jul 2024
14 Jul 2024
Historique:
received:
02
05
2024
accepted:
14
06
2024
medline:
14
7
2024
pubmed:
14
7
2024
entrez:
14
7
2024
Statut:
epublish
Résumé
DNA Stable Isotope Probing is emerging as a potent methodology for investigating host-virus interactions, based on the essential reliance of viruses on host organisms for the production of virions. Despite the anticipated link between host isotopic compositions and the generated virions, the application of stable isotope probing to viral DNA has never been evaluated on simple biological models. In this study, we assessed the efficacy of this method on the bacteriophage T4 and its host, Escherichia coli. Through the cultivation of E. coli cells on a
Identifiants
pubmed: 39003664
doi: 10.1007/s00284-024-03774-x
pii: 10.1007/s00284-024-03774-x
doi:
Substances chimiques
DNA, Viral
0
Glucose
IY9XDZ35W2
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
266Subventions
Organisme : Agence Nationale de la Recherche
ID : ANR-17-CE05-0011
Informations de copyright
© 2024. The Author(s).
Références
Radajewski S, Ineson P, Parekh NR, Murrell JC (2000) Stable-isotope probing as a tool in microbial ecology. Nature 403:646–649. https://doi.org/10.1038/35001054
doi: 10.1038/35001054
pubmed: 10688198
Lee CG, Watanabe T, Fujita Y et al (2012) Heterotrophic growth of cyanobacteria and phage-mediated microbial loop in soil: examination by stable isotope probing (SIP) method. Soil Sci Plant Nutr 58:161–168. https://doi.org/10.1080/00380768.2012.658739
doi: 10.1080/00380768.2012.658739
Lee S, Sieradzki ET, Nicol GW, Hazard C (2023) Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification. ISME J 17:309–314. https://doi.org/10.1038/s41396-022-01341-5
doi: 10.1038/s41396-022-01341-5
pubmed: 36414709
Lee S, Sieradzki ET, Nicolas AM et al (2021) Methane-derived carbon flows into host–virus networks at different trophic levels in soil. Proc Natl Acad Sci USA 118:e2105124118. https://doi.org/10.1073/pnas.2105124118
doi: 10.1073/pnas.2105124118
pubmed: 34349022
pmcid: 8364182
Li Y, Watanabe T, Murase J et al (2013) Identification of the major capsid gene (g23) of T4-type bacteriophages that assimilate substrates from root cap cells under aerobic and anaerobic soil conditions using a DNA–SIP approach. Soil Biol Biochem 63:97–105. https://doi.org/10.1016/j.soilbio.2013.03.026
doi: 10.1016/j.soilbio.2013.03.026
Ngo VQH, Enault F, Midoux C et al (2022) Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics. Environ Microbiol 24:4853–4868. https://doi.org/10.1111/1462-2920.16120
doi: 10.1111/1462-2920.16120
pubmed: 35848130
pmcid: 9796341
Pasulka AL, Thamatrakoln K, Kopf SH et al (2018) Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environ Microbiol 20:671–692. https://doi.org/10.1111/1462-2920.13996
doi: 10.1111/1462-2920.13996
pubmed: 29159966
Greenlon A, Sieradzki E, Zablocki O et al (2022) Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems. mSystems 7:e00417. https://doi.org/10.1128/msystems.00417-22
doi: 10.1128/msystems.00417-22
pubmed: 36300946
pmcid: 9765451
Chapleur O, Wu T-D, Guerquin-Kern J-L et al (2013) SIMSISH technique does not alter the apparent isotopic composition of bacterial cells. PLoS ONE 8:e77522. https://doi.org/10.1371/journal.pone.0077522
doi: 10.1371/journal.pone.0077522
pubmed: 24204855
pmcid: 3812282
Chapleur O, Bize A, Serain T et al (2014) Co-inoculating ruminal content neither provides active hydrolytic microbes nor improves methanization of
doi: 10.1111/1574-6941.12249
pubmed: 24219327
Birnie GD, Rickwood D (2014) Centrifugal separations in molecular and cell biology. Butterworth-Heinemann
Labrie SJ, Samson JE, Moineau S (2010) Bacteriophage resistance mechanisms. Nat Rev Microbiol 8:317–327. https://doi.org/10.1038/nrmicro2315
doi: 10.1038/nrmicro2315
pubmed: 20348932
Schildkraut CL, Marmur J, Doty P (1962) Determination of the base composition of deoxyribonucleic acid from its buoyant density in CsCl. J Mol Biol 4:430–443. https://doi.org/10.1016/S0022-2836(62)80100-4
doi: 10.1016/S0022-2836(62)80100-4
pubmed: 14498379
Morella NM, Yang SC, Hernandez CA, Koskella B (2018) Rapid quantification of bacteriophages and their bacterial hosts in vitro and in vivo using droplet digital PCR. J Virol Methods 259:18–24. https://doi.org/10.1016/j.jviromet.2018.05.007
doi: 10.1016/j.jviromet.2018.05.007
pubmed: 29859196
Marbouty M, Baudry L, Cournac A, Koszul R (2017) Scaffolding bacterial genomes and probing host–virus interactions in gut microbiome by proximity ligation (chromosome capture) assay. Sci Adv 3:e1602105. https://doi.org/10.1126/sciadv.1602105
doi: 10.1126/sciadv.1602105
pubmed: 28232956
pmcid: 5315449
Sakowski EG, Arora-Williams K, Tian F et al (2021) Interaction dynamics and virus–host range for estuarine actinophages captured by epicPCR. Nat Microbiol 6:630–642. https://doi.org/10.1038/s41564-021-00873-4
doi: 10.1038/s41564-021-00873-4
pubmed: 33633401
Deng L, Ignacio-Espinoza JC, Gregory AC et al (2014) Viral tagging reveals discrete populations in Synechococcus viral genome sequence space. Nature 513:242–245. https://doi.org/10.1038/nature13459
doi: 10.1038/nature13459
pubmed: 25043051