Building the phage-host-environment interaction data to scale from genes-to-ecosystems: Towards predictive modeling of wild microbial and viral community dynamics
EMSL Project ID
49003
Abstract
Ocean microbes and viruses are now at the forefront of Earth System studies. The enormous numbers of ocean viruses (typically >10^5 ml-1, usually ten for every microbial cell) are driving evolutionary forces of microbial processes through mortality, horizontal gene transfer, and the modulation of central host microbial metabolisms through metabolic reprogramming during infection. Microbial viruses (phages) directly and indirectly affect the global biogeochemical cycles mediated by their hosts (e.g., C through photosynthesis). A recently developed state-of-the-art multitrophic ecosystem model that now considers the role of viruses in interactions among nutrients, phytoplankton, heterotrophic bacteria, and zooplankton (NPHZ-V models) has successfully captured the innate feedback between lysis and nutrient pools and has generated compelling hypotheses. Progress in this theoretical realm highlights the critical need to collect omics-informed empirical data on virus-host-nutrient interactions to meaningfully integrate these processes and data types into the next generation of predictive, global Earth system models. We propose nutrient-based, hypothesis-driven experimental work to better understand the interplay between 'bottom-up' and 'top-down' processes during phage infection in a heterotrophic Pseudoalteromonas phage-host system. Host strain 13-15 will be infected with each a siphovirus, PSA-HS2, and a podovirus, PSA-HP1, under deplete and replete phosphate conditions to quantify the effect of host physiology on phage life history traits (replication rate, burst size, latent period), phage and host genic (transcriptome, proteome) interactions, and the resultant ecosystem impacts (e.g., altered cellular metabolite and biogeochemical profiles). Time points spanning the infection period will be sampled for genome-wide transcriptomic, proteomic, metabolomic, and lipidomic response of the uninfected control versus phage-infected host cells, as well as high-resolution organic matter characterization for a system-wide understanding of the fate of material under contrasting infection and nutrient regimes. This empirical data will inform NPHZ-V models by linking virus life history traits, gene regulation, and cellular products, all in the context of an experimentally controlled limiting resource. Given the importance of microbes and their viruses in the oceans, and likely any microbe-driven ecosystem, a grand challenge now is to advance from surveying diversity towards a predictive modeling capacity. It is generally thought that extrapolating from high-throughput genetic surveys to ecosystem functions will most valuably address this, and the only readily available phage-host model systems for such study are marine (though ours intimately interact with the "plants" of the sea to set up a plant-microbe-virus organismal triad). Our collaborative team partners expertise in virus-host model system development, viral 'omics, and ecological theory to optimally design experiments and generate requisite data to feed future theoretical development of 'genes to ecosystem' modeling.
Project Details
Project type
FICUS Research
Start Date
2015-10-01
End Date
2017-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members