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Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods

Pasulka, Alexis L. and Thamatrakoln, Kimberlee and Kopf, Sebastian H. and Guan, Yunbin and Poulos, Bonnie and Moradian, Annie and Sweredoski, Michael J. and Hess, Sonja and Sullivan, Mathew B. and Bidle, Kay D. and Orphan, Victoria J. (2018) Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environmental Microbiology, 20 (2). pp. 671-692. ISSN 1462-2912. https://resolver.caltech.edu/CaltechAUTHORS:20171127-134624207

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Abstract

While the collective impact of marine viruses has become more apparent over the last decade, a deeper understanding of virus-host dynamics and the role of viruses in nutrient cycling would benefit from direct observations at the single-virus level. We describe two new complementary approaches - stable isotope probing coupled with nanoscale secondary ion mass spectrometry (nanoSIMS) and fluorescence-based biorthogonal non-canonical amino acid tagging (BONCAT) - for studying the activity and biogeochemical influence of marine viruses. These tools were developed and tested using several ecologically relevant model systems (Emiliania huxleyi/EhV207, Synechococcus sp. WH8101/Syn1, and Escherichia coli/T7). By resolving carbon and nitrogen enrichment in viral particles, we demonstrate the power of nanoSIMS tracer experiments in obtaining quantitative estimates for the total number of viruses produced directly from a particular production pathway (by isotopically labeling host substrates). Additionally, we show through laboratory experiments and a pilot field study that BONCAT can be used to directly quantify viral production (via epifluorescence microscopy) with minor sample manipulation and no dependency on conversion factors. This technique can also be used to detect newly synthesized viral proteins. Together these tools will help fill critical gaps in our understanding of the biogeochemical impact of viruses in the ocean.


Item Type:Article
Related URLs:
URLURL TypeDescription
https://doi.org/10.1111/1462-2920.13996DOIArticle
http://onlinelibrary.wiley.com/doi/10.1111/1462-2920.13996/abstractPublisherArticle
ORCID:
AuthorORCID
Kopf, Sebastian H.0000-0002-2044-0201
Guan, Yunbin0000-0002-7636-3735
Moradian, Annie0000-0002-0407-2031
Sweredoski, Michael J.0000-0003-0878-3831
Hess, Sonja0000-0002-5904-9816
Orphan, Victoria J.0000-0002-5374-6178
Additional Information:© 2017 Wiley. Issue online: 14 February 2018; Version of record online: 14 December 2017; Accepted manuscript online: 21 November 2017; Manuscript Accepted: 12 November 2017; Manuscript Revised: 10 November 2017; Manuscript Received: 8 August 2017. We thank K. Dawson and G. Chadwick for many insightful conversations regarding data interpretation and analysis and R. Hatzenpichler and B. Babin for useful discussions regarding BONCAT and click chemistry. We also thank J. Nissomov, F. Natale and J. Latham for their technical assistance with the E. huxleyi-EhV experiments as well as Jennifer Brum and Sarah Schwenck for help exploring the use of TEM microscopy for mapping Syn1 viral particles. This work was funded by the Gordon and Betty Moore Foundation through Grant GBMF3780 to VJO, GBMF3789 to KDB and GBMF3305 and GBMF3790 to MBS as well as NSF Biological Oceanography awards to KT, KDB (OCE-1559179) and MBS (OCE-1536989). ALP was supported by an NSF OCE Postdoctoral Research Fellowship. The Caltech Proteome Exploration Laboratory is supported by the Gordon and Betty Moore Foundation through grant GBMF775, the Beckman Institute, and NIH (S10OD020013).
Funders:
Funding AgencyGrant Number
Gordon and Betty Moore FoundationGBMF3780
Gordon and Betty Moore FoundationGBMF3789
Gordon and Betty Moore FoundationGBMF3305
Gordon and Betty Moore FoundationGBMF3790
NSFOCE-1559179
NSFOCE-1536989
NSF Postdoctoral FellowshipUNSPECIFIED
Gordon and Betty Moore FoundationGBMF775
Caltech Beckman InstituteUNSPECIFIED
NIHS10OD020013
Subject Keywords:viral ecology; nanoSIMS; proteomics; click chemistry; cyanophage; trophic transfer; stable isotope probing
Issue or Number:2
Record Number:CaltechAUTHORS:20171127-134624207
Persistent URL:https://resolver.caltech.edu/CaltechAUTHORS:20171127-134624207
Official Citation:Pasulka, A. L., Thamatrakoln, K., Kopf, S. H., Guan, Y., Poulos, B., Moradian, A., Sweredoski, M. J., Hess, S., Sullivan, M. B., Bidle, K. D. and Orphan, V. J. (2018), Interrogating marine virus-host interactions and elemental transfer with BONCAT and nanoSIMS-based methods. Environ Microbiol, 20: 671–692. doi:10.1111/1462-2920.13996
Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:83447
Collection:CaltechAUTHORS
Deposited By: Tony Diaz
Deposited On:27 Nov 2017 22:04
Last Modified:27 Nov 2019 00:08

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