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Marine microbial interactions – physiology, genomics and ecological modeling

Final Report Summary - MICROBES-2-MODEL (Marine microbial interactions – physiology, genomics and ecological modeling.)


“Microbes-2-Model”, Daniel Sher (University of Haifa)


Interactions between marine microorganisms such as symbiosis, competition, and allelopathy determine the structure and function of microbial communities, yet are relatively unstudied. We must understand these interactions at multiple levels in order to predict how marine microbial communities will evolve in a changing world. During the period of the Marie Curie Career Integration Grant, we characterize the physiological processes and gene expression patterns occurring during co-culture between two strains of Prochlorococcus, the most abundant photosynthetic organism in the oceans, and heterotrophic marine bacteria from the genus Alteromonas, using the resulting data to generate, parameterize and test mathematical models of microbial interactions.

We showed that one Alteromonas strain, HOT1A3, enhances Prochlorococcus MIT9313 growth, yet above a certain threshold inhibits it. In contrast, no such inhibition was observed between this Alteromonas strains and a different Prochlorococcus strain, MED4, or between Alteromonas strain HOT2G3 and either of the Prochlorococcus strains studied. The transcriptomes of the two Prochlorococcus strains differed markedly in response to co-culture with HOT1A3, as did the transcriptome of MIT9313 when cultured with high (inhibitory) and low (sub-inhibitory) doses of the Alteromonas. Many of the differences in gene expression could potentially be related to different stress levels and their effect on photosynthesis and protein production. Most interestingly, MIT9313 responds to co-culture by expressing a suit of novel, short genes, some of which may encode novel signaling peptides. A simple mathematical model of Prochlorococcus growth, based on the classical Droop “internal stores” formulation, represented well the growth phase of laboratory batch cultures but failed to accurately reproduce the stationary and decline phases, unless excretion was explicitly represented. We propose that excretion, mortality and nutrient remineralization, processes, as well as direct chemical communication, should be incorporated into models of marine phytoplankton, and studying these processes will benefit from better cross-talk between experimentalists and modelers.

These results provide an important stepping stone towards explicitly representing microbial interactions in global biogeochemical models. The results of the Microbes-2-Model project have been published in three peer-reviewed papers, with another under review and several more being prepared for publication. These results were produced through the hard work of the research group I have established, currently comprising eight people (lab manager, postdocs, PhD and MSc students). We have established fruitful collaborations with research groups in Israel, the US, Germany and Italy, and have obtained funding from several research agencies to support additional aspects of this project, most recently from the prestigious Human Frontiers Science Program.