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Refining viral production estimation
Shaikh, H.M.; Van den Bremt, J.; Schellenberg, L.; Fernández Bejarano, S.J.; De Rijcke, M.; Brussaard, C.P.D. (2025). Refining viral production estimation. Environmental Microbiology Reports 17(6): e70258. https://dx.doi.org/10.1111/1758-2229.70258
In: Environmental Microbiology Reports. Wiley-Blackwell. ISSN 1758-2229
Peer reviewed article  
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Author keywords
    bacterial growth; lysogeny; lytic; marine viruses; mitomycin C; mortality; VIPCAL; viral production assay; viralprod
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  • Flemish contribution to LifeWatch.eu
Authors  Top 
  • Shaikh, H.M.
  • Van den Bremt, J.
  • Schellenberg, L.
  • Fernández Bejarano, S.J.
  • De Rijcke, M.
  • Brussaard, C.P.D.
Abstract
    Viral-mediated bacterial mortality and the prevalence of lysogeny are two key parameters for understanding the role of viral activity in aquatic ecosystems. The viral production assay is most commonly used to assess these parameters, with lytic and mitomycin C-induced viral production rates prevalently extracted using the linear regression or increment-based (VIPCAL) approach. A literature survey shows that 64% of the 89 viral production studies used the linear regression approach for lytic and 48% employed VIPCAL for lysogenic viral production rates. Our comparative evaluation highlights significant differences between these two approaches of estimating viral production rates. To refine estimations, we enhanced VIPCAL to VIPCAL-SE by incorporating standard error of the means to rigorously identify maxima–minima pairs, accounting for biological and ecological variabilities between replicates. We also included a bacterial net generation time endpoint to reduce estimation bias due to potential secondary infections, particularly relevant in more productive ecosystems. VIPCAL-SE is now available as a part of the viralprod R package and provides an opportunity for further standardisation in the field of aquatic viral ecology.
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