MOLECULAR INSIGHTS INTO RESOURCE ALLOCATION STRATEGIES UNDER NUTRIENT STARVATION IN PELAGOMONAS CALCEOLATA

Abstract

Marine phytoplankton account for approximately 50% of global net primary production and play an essential role in global carbon and biogeochemical cycles. Among them, photosynthetic picoeukaryotes are small microbes that contribute significantly to primary producer biomass in warm, nutrient-poor oceanic regions. The geographic range of photosynthetic picoeukaryotes is expected to shift with climate change-induced warming and associated water column stratification, gyre expansion, and decreased surface ocean nutrient availability. Pelagomonas calceolata is a globally distributed and ecologically significant photosynthetic picoeukaryote, notably tolerant to nutrient-limited growth conditions. To elucidate P. calceolata’s strategies for growth in nutrient-poor environments we investigated how Pelagomonas reallocates its cellular resources under nitrogen and phosphorus starvation using proteomic analyses. Quadruplicate batch cultures of P. calceolata (CCMP1756) were grown under nutrient-replete conditions and subsequently transferred to nitrogen- or phosphorus-starved media and sampled during mid-exponential and stationary phases throughout the growth cycle. Growth rates, photosynthetic parameters and macromolecular quotas (protein, RNA, DNA, lipids, and carbohydrates) were measured to provide physiological context for mass spectrometry-based discovery proteomics. In total, 11,052 proteins corresponding to 62% of the genome-encoded proteome were identified – the highest proteome coverage obtained for Pelagomonas to date. Total cellular protein content declined sharply under nitrogen starvation (55% reduction) and more moderately under phosphorus starvation (37% reduction), indicating that nitrogen imposes a stronger constraint on proteome size. Under nutrient-replete conditions, the Pelagomonas proteome is dominated by photosynthetic machinery (20.7% of total proteome), alongside substantial allocation to ribosomal proteins (5.6%), transporters (5.6%) and histones (3.3%). Nitrogen starvation resulted in significant reductions in proteome allocation to ribosomal, photosynthetic, and ATP synthesis proteins alongside increased allocation to histones, transporters, and EGF-like domain-containing proteins. In contrast, phosphorus starvation resulted in increased proteome allocation toward the dark reactions (RuBisCO), and decreased protein allocation toward light reactions and transporters. Further comparison of manually curated coarse-grained protein groups with data-driven co-expression modules revealed that ribosomal protein allocation strongly predicts growth rate, supporting core assumptions of macromolecular and resource allocation theory, while WGCNA-derived modules better explained variation in carbon storage and particulate phosphorus quotas. These results reveal how Pelagomonas sustains productivity under nutrient stress and provide empirical grounding for defining proteome allocation in ecosystem and biogeochemical models of marine ecosystems.