Grazer-induced transcriptomic and metabolomic response of the chain-forming diatom Skeletonema marinoi

Abstract

Diatoms and copepods are main actors in marine food webs. The prey-predator interactions between them affect bloom dynamics, shape marine ecosystems and impact the energy transfer to higher trophic levels. Recently it has been demonstrated that the presence of grazers may affect the diatom prey beyond the direct effect of grazing. Here, we investigated the response of the chain-forming centric diatom Skeletonema marinoi to grazer cues, including changes in morphology, gene expression and metabolic profile. S. marinoi cells were incubated with Calanus finmarchicus or with Centropages typicus and in both cases responded by reducing the chain length, whereas changes in gene expression indicated an activation of stress response, changes in the lipid and nitrogen metabolism, in cell cycle regulation and in frustule formation. Transcripts linked to G protein-coupled receptors and to nitric oxide synthesis were differentially expressed suggesting involvement of these signalling transduction pathways in the response. Downregulation of a lipoxygenase in the transcriptomic data and of its products in the metabolomic data also indicate an involvement of oxylipins. Our data contribute to a better understanding of the gene function in diatoms, providing information on the nature of genes implicated in the interaction with grazers, a crucial process in marine ecosystems.

Fig. 1

a The calanoid grazers Calanus finmarchicus and Centropages typicus were used in bottle incubations with Skeletonema marinoi, the chain-forming diatom depicted in the top right light micrograph. The inset electron micrograph details the connection between daughter cells, which is split up in response to copepod grazers. The white scale bar applies to the electron micrograph. b Chain length of Skeletonema marinoi after 65 and 89 h (T1 and T2) of exposure to Calanus finmarchicus or Centropages typicus. Grazer-free controls are shown in black, and grazer-exposed cultures in white. Both grazers induced a similar and significant shortening of chains. Bars show average values of three replicates, error bars denote standard error of mean

Fig. 2

a, b Plots showing the genes differentially expressed at T1 and T2, respectively. Fold changes in log scale are reported on the y axis, each dot represents a transcript, the dot size is proportional to the levels of expression measured as CPM (counts per million). Transcripts are arranged on the x axis according to their logCPM. c Venn diagram showing the number of shared and unique differentially expressed transcripts at the two time points. d Representation of GO terms significantly enriched among differentially expressed transcripts. The charts show the proportion of transcripts associated with the significant classes among differentially expressed transcripts at T1 (yellow) and T2 (green) and their respective proportion in the assembled reference transcriptome (red). On x axis, percentage is reported. On y axis, GO terms. The green shade indicates GO terms associated with cellular component, the purple to molecular function and the blue to biological processes

Fig. 3

a The Venn diagram shows the number of metabolites that are commonly regulated (up or down) at both occasions, as well as metabolites upregulated, or downregulated on a single occasion. No metabolites showed opposite regulation between T1 and T2. b, c Mirror plots showing the abundance of the individual compounds with copepod samples projected upwards in red and control samples mirrored downward in blue. The increased proportion of larger metabolites in copepod-treated cells is clear in b, but less so in c

Fig. 4

A schematic representation of a Skeletonema marinoi cell in the presence of copepods at T1 a and T2 b. Green arrows represent upregulation and red arrows downregulation. N nucleus, M mitochondrion, C chloroplast, GPCR G protein-coupled receptors, AC adenylate cyclase, TE transposable element, LOX lipoxygenase, NTR2 nitrate transporter, AMT ammonium transporter, NR nitrate reductase, NiR nitrite reductase, GSIII type-3 glutamine synthetase, HSPs heat shock proteins, NOS nitric oxide synthase, ACC acetyl-CoA carboxylase, FCPB fucoxanthin-chlorophyll a-c binding protein B