Award Abstract # 2201645
Drivers and effects of latent phage activation in marine SAR11

NSF Org: OCE
Division Of Ocean Sciences
Recipient: UNIVERSITY OF CALIFORNIA, LOS ANGELES
Initial Amendment Date: June 8, 2022
Latest Amendment Date: June 8, 2022
Award Number: 2201645
Award Instrument: Standard Grant
Program Manager: Jayne Gardiner
jgardine@nsf.gov
 (703)292-4828
OCE
 Division Of Ocean Sciences
GEO
 Directorate for Geosciences
Start Date: June 15, 2022
End Date: May 31, 2026 (Estimated)
Total Intended Award Amount: $440,316.00
Total Awarded Amount to Date: $440,316.00
Funds Obligated to Date: FY 2022 = $440,316.00
History of Investigator:
  • Ben Knowles (Principal Investigator)
    bwknowles@ucla.edu
Recipient Sponsored Research Office: University of California-Los Angeles
10889 WILSHIRE BLVD STE 700
LOS ANGELES
CA  US  90024-4200
(310)794-0102
Sponsor Congressional District: 36
Primary Place of Performance: University of California-Los Angeles
610 Charles E Young Dr. E
Los Angeles
CA  US  90095-7243
Primary Place of Performance
Congressional District:
36
Unique Entity Identifier (UEI): RN64EPNH8JC6
Parent UEI:
NSF Program(s): BIOLOGICAL OCEANOGRAPHY
Primary Program Source: 01002223DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 4444, 8811, 1174, 7656, 006Z, 9117
Program Element Code(s): 165000
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.050

ABSTRACT

Viruses are the most abundant biological entities in the ocean. When they infect plankton, they can alter food webs, induce shifts in nutrient cycles, and enhance genetic exchange. However, the mechanisms that control these important processes are largely unknown, which has limited our ability to predict infection outcomes in nature. The primary goal of this study is to identify key chemical, physical, and biological factors that influence host-virus interactions in cultured bacterioplankton and to use this information to build mathematical models that predict infection dynamics in diverse marine ecosystems. Most of the marine viruses available for detailed study kill bacteria following infection. This novel study focuses on SAR11, the most abundant marine bacteria, which harbor dormant viruses called prophages, to determine what causes prophage activation and host death. Specifically, the research team uses field surveys and laboratory experiments with SAR11-prophage pairs to generate data and mathematical models to predict the outcomes of viral infections in SAR11 and other marine microbes.
The conditions that trigger prophage activation and their corresponding contributions to ecosystem processes are largely hypothetical, due primarily to difficulties identifying and culturing host cells with prophages. It is becoming increasingly clear that the impact and importance of these infections are under-characterized and under-estimated. The proposed research revises estimates of prophage activation in globally-important SAR11 by quantifying infection occurrence, identifying prophage activation inducers, and testing the effects of maintaining virus DNA in the host genomes. The frequency of prophage infections is determined by analyzing bacterial metagenomes generated with long-read sequencing technology. Controlled growth experiments under a range of conditions that cause stress (physical, chemical, and biological) and evaluation of shifts in gene expression are employed to identify drivers of prophage activation. The outcomes of prophage infections in culture serve to parameterize key interactions in numerical models that can then predict outcomes in nature. This study fills critical gaps in knowledge about the mechanisms that maintain the large and genetically diverse populations of bacteria and viruses in the ocean and has the potential to change our understanding and capacity to predict host-virus interactions under changing environmental conditions.

This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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Knowles, B and Bonachela, J and Cieslik, N and DellaPenna, A and Diaz, B and Baetge, N and Behrenfeld, M and Naumovitz, K and Boss, E and Graff, J and Halsey, K and Haramaty, L and Karp-Boss, L and Bidle, K "Altered growth and death in dilution-based viral predation assays" PloS one , 2023 Citation Details

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