Project: Microbial ecosystems in silico, in the lab and in the field: understanding interactions between abundant marine bacterial taxa

Every drop of seawater contains around one million microorganisms (bacteria, small algae and other organisms such as ciliates and diatoms). These marine microbes feed the entire marine ecosystem, modulate global cycles of carbon and other elements, and impact climate. With the advances in genome-sequencing technology, we can now identify the microbes and assess their genetic and metabolic capacities, yet we still cannot deduce from the genomes of these organisms how they will grow - and interact - in nature. The proposed project will tackle this challenge through a tightly integrated combination of mathematical modeling, laboratory experiments and field work in the Eastern Mediterranean, to identify genes and pathways dictating how environmentally-relevant microbes grow and interact in the sea. We will produce genome-scale mathematical models of the metabolism of Prochlorococus, the numerically-dominant photosynthetic bacteria in large swaths of the ocean, and of Alteromonas, abundant marine bacteria which make their living by consuming and respiring organic molecules produced by Prochlorococcus and other photosynthetic microbes. We will test these models using laboratory cultures of these organisms grown alone and together, and determine to what extent the models and laboratory cultures represent the growth and death of these organisms in the Eastern Mediterranean. This study will be useful for scientists of many disciplines, including not only marine biology, oceanography and ecology but also genetics, medicine and agriculture. Our results will shed light on the dynamics of some of the most common organisms in the world, responsible for the production of up to 20% of the oxygen we breathe. Our collaborative study will foster the development and training of the next generation of marine scientists, and will be used in outreach activities designed to share with high-school students and the general public the excitement of marine research and the need to responsibly utilize and sustain the oceans for the sake of future generations.

The proposed project will tackle the challenge of understanding microbial interactions from the underlying genetic data through a tightly integrated combination of genome scale modeling, laboratory experiments and field work in the Eastern Mediterranean. We aim to identify genomic traits dictating how environmentally-relevant primary producers and heterotrophic bacteria interact. Genome-scale (dynamic flux balance analysis, dFBA) models of Prochlorococus MED4 and of Alteromonas HOT1A3 will be produced and calibrated using high-throughput measurements of growth and physiological parameters in laboratory batch cultures, combined with detailed analysis of specific metabolites; The dFBA models will be combined in-silico and the results compared to laboratory co-cultures. Model-data discrepancies will provide opportunities to revisit the models, suggesting the mediation of alternative processes such as allelopathy or other types of chemical signaling. Finally, time-series data on the community composition and function during the summer/fall Prochlorococcus bloom in the hyper-oligotrophic Eastern Mediterranean, combined with field experiments (microcosms), will provide a test of hypotheses generated in the lab. This study will provide the first detailed "roadmap" linking genomic traits (genes and metabolic pathways) and rate measurements with species interactions in environmentally-relevant marine microbes. Genome-scale models will likely be embedded in a not-so-distant future in global-scale models of the Earth System, and the proposed study will provide a critical stepping-stone towards predicting how marine microbial systems will evolve in a changing world. The strong human impact on marine ecosystems, and the need for quantitative and predictive understanding of how they will respond to a changing environment, calls for interdisciplinary research and training for the next generation of scientists and decision makers. Models and data generated by our work will be integrated into a novel educational exploration-focused, web- and field-based educational module. This module will introduce key concepts in microbiology, environmental sciences and oceanography to intermediate- and high-school students.

(Note: acronym HADFBA = Heterotroph-Autotroph Dynamic Flux Balance Analysis)