Fig 1.
Experimental setup for metabolomics and transcriptomics analysis of co-culture of Skeletonema marinoi and Prymnesium parvum.
(A) The control groups were S. marinoi mono-culture and P. parvum mono-culture, while the treatment groups were S. marinoi in the presence of P. parvum and P. parvum in the presence of S. marinoi. (B) From the extracts of these groups, we acquired the endo- and exometabolome using LC-MS2, and C) RNA sequencing data.
Fig 2.
Metabolomics Workflow for the co-culture experiment.
The first section demonstrates the MS1 preprocessing workflow, which starts with the.mzML files. These files go through the parameter optimisation and subsequent steps, such as peak detection, grouping, retention time correction, and re-grouping of peaks. The preprocessed data is then converted to a feature list which are subjected to further statistical analysis and are used to link the MS1 features to their corresponding MS2 fragmentation spectra. Separately, the MS2 Fragmentation spectra undergo Metabolome Annotation Workflow (MAW), which annotates chemical structures to the metabolic features. The final candidate list is searched in the suspect list from each origin organism to find previously identified metabolites in the new experimental setup dataset.
Fig 3.
Chlorophyll a concentration measurement in the cells for eight days.
Both plots show the number of days on the x-axis and the chlorophyll a fluorescence measurement in relative fluorescence units (RFU) on the y-axis. All eight replicates for monocultures and all 4 replicates for co-culture were used to generate the fluorescence plot of the cultures over eight days (see S1 Table). The error bars represent the standard deviation among the mean of the replicates for the particular day. a) The plot for the chlorophyll a measurement of S. marinoi shows lower chlorophyll a fluorescence of the co-culture (purple) as compared to the mono-culture (green) as a general trend. b) The plot for the chlorophyll a measurement of P. parvum shows no distinction between the co-culture (purple) and the mono-culture (green) groups. However, there is an increase in the chlorophyll a concentration compared to the control after day 6 in the co-culture.
Table 1.
ANOVA and Welsch t-test.
Fig 4.
Abundant metabolites in experimental conditions.
The first section refers to the mono-culture of both microalgae in endo- and exometabolome. The metabolites are depicted in each section with a coloured outline and no colour filling. The second section refers to the experimental condition of co-culture for both microalgae in endo- and exometabolome, with coloured filling representation. With our dataset, we could only annotate the metabolite structures in co-culture conditions. The third section refers to the shared metabolites which were detected in the co-culture endometabolome of both microalgae. We do not consider the shared metabolites in extracellular space, which is represented by a dotted outline.
Table 2.
Experimental MS2 condition features, MSI level, and differentially produced features with MS2 spectra.
Table 3.
Chemical structure annotation of significant features with MAW.
Table 4.
Descriptive Statistics for S. marinoi and P. parvum transcriptome assembly.
Table 5.
Top 10 upregulated differentially expressed ORFs from S. marinoi and P. parvum.
Fig 5.
Volcano plots for the differentially repressed genes.
This scatter plot displays the relationship between the log fold change and the adjusted p-value of each gene (represented by the dots). The tentative names are also displayed for the top 30 differentially expressed ORFs. The horizontal line marks the adjusted p-value threshold, whereas the two vertical lines indicate possible log fold change thresholds (1 and −1).