Diatoms are major players in the global carbon cycle, and their metabolism is affected by ocean conditions. Understanding the impact of changing inorganic nutrients in the oceans on diatoms is crucial, given the changes in global carbon dioxide levels. Here, we present a genome-scale metabolic model (iMK1961) for Cylindrotheca closterium, an in silico resource to understand uncharacterized metabolic functions in this ubiquitous diatom. iMK1961 represents the largest diatom metabolic model to date, comprising 1961 open reading frames and 6718 reactions. With iMK1961, we identified the metabolic response signature to cope with drastic changes in growth conditions. Comparing model predictions with Tara Oceans transcriptomics data unraveled C. closterium's metabolism in situ. Unexpectedly, the diatom only grows photoautotrophically in 21% of the sunlit ocean samples, while the majority of the samples indicate a mixotrophic (71%) or, in some cases, even a heterotrophic (8%) lifestyle in the light. Our findings highlight C. closterium's metabolic flexibility and its potential role in global carbon cycling.

Bioinformatics and Systems Biology Graduate Program University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Center for Bioinformatics and Computational Biology University of Delaware 590 Avenue 1743 Newark DE 19713 USA

Center for Microbiome Innovation University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Department of Bioengineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Department of Computer and Information Sciences University of Delaware 18 Amstel Ave Newark DE 19716 USA

Department of Microbial and Environmental Genomics J Craig Venter Institute 4120 Capricorn Way La Jolla CA 92037 USA

Department of Parasitology Faculty of Science Charles University BIOCEV Vestec Czech Republic

Department of Pediatrics University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Program in Materials Science and Engineering University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

Scripps Institution of Oceanography University of California San Diego 9500 Gilman Drive La Jolla CA 92093 USA

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