Divergent transcriptional responses of conserved cellular machinery to warming and phosphorus limitation in freshwater phytoplankton

Lakes are simultaneously warming and becoming phosphorus limited, but whether phytoplankton taxa of the same phylum respond through similar molecular mechanisms remains unclear, challenging a common assumption underlying predictions of ecological responses to environmental change. We cultured four freshwater phytoplankton species, including two diatoms ( Fragilaria crotonensis and Nitzschia palea ) and two cyanobacteria ( Microcystis aeruginosa and Synechococcus sp.), across factorial gradients of temperature (20, 24 and 28 °C) and phosphorus (P) limitation, and characterized gene expression using RNA-seq, differential expression analysis and signed gene set enrichment. We generated predictions for expected responses for categories of gene functions derived from the growth rate (GRH) and temperature-dependent physiology hypotheses (TDPH). Warming and P limitation engaged largely the predicted functional categories in all species, however the direction of the response was not conserved, even within phyla—the two cyanobacteria regulated photosynthesis, ribosomal and chaperone genes in opposite directions. Ribosome- and translation-related genes gave the strongest warming response and, in N. palea , reversed direction within the species, increasing between 20 and 24 °C and decreasing between 24 and 28 °C, below the strain′s thermal optimum estimated under moderate P limitation. Ribosomal allocation thus supported each hypothesis in different species and temperature ranges and was not predicted by thermal position alone. Where the interaction effects could be tested, P limitation rarely recruited novel pathways but modified existing warming responses, suppressing them in F. crotonensis and amplifying and redirecting them in M. aeruginosa . Molecular responses to combined drivers therefore diverge among related taxa, cautioning against aggregating species into functional groups when forecasting phytoplankton responses to global change.