Producing microbial oils for food and industrial uses requires not only high lipid yield, but also the desired fatty-acid profile at the harvest timepoint. To link cultivation conditions to lipid outcomes, we grew the oleaginous fungus Mortierella alpina with nitrate, ammonium, or urea as the nitrogen source, sampling cultures at days 3, 6, and 9 for quantitative proteomics and lipidomics.
Across the dataset, the strongest protein-level patterns separated samples by nitrogen source and by cultivation time. These protein abundance changes grouped into four main functional themes that explained most of this structure: (1) precursor supply (NADPH and acetyl-CoA generation), (2) glycerol backbone provision (glycerol-3-phosphate and phosphatidic acid), (3) triacylglycerol (TAG) assembly and lipid-droplet machinery (including DGAT/LPAT-associated signals), and (4) nitrogen transport and assimilation.
Over time in nitrate- and ammonium-grown cultures, proteins linked to precursor supply and lipid storage increased toward later timepoints, while proteins involved in nitrogen uptake/assimilation decreased—consistent with a shift from nitrogen acquisition during growth toward lipid storage as cultivation progresses. Several TAG-assembly–related proteins peaked around day 6 and then levelled off.
Under urea, these time-dependent trends were weaker or delayed, and pathway summaries indicated lower activity in central carbon and amino-acid metabolism during the early to mid cultivation period.
Lipid measurements changed in parallel with these protein patterns. Storage lipids increased with time in all conditions, while fatty-acid composition depended on both nitrogen source and time: palmitate (16:0) and oleate (18:1) were lower under urea, α-linolenate (18:3) showed a mid-course dip, and PUFA-rich TG species became more prominent late in cultivation. At the lipid-class level, DG, TG, PC, PE, and PS increased with time, whereas PA, PG, and PI were relatively favoured under ammonium.
Overall, nitrogen source and harvest timing emerge as practical process levers associated with coordinated shifts in protein expression and lipid composition, supporting design-to-profile lipid production in M. alpina.