Effect of light and prey availability on gene expression of the mixotrophic chrysophyte, Ochromonas sp.

Abstract

Background Ochromonas is a genus of mixotrophic chrysophytes that is found ubiquitously in many aquatic environments. Species in this genus can be important consumers of bacteria but vary in their ability to perform photosynthesis. We studied the effect of light and bacteria on growth and gene expression of a predominantly phagotrophic Ochromonas species. Axenic cultures of Ochromonas sp. were fed with heat-killed bacteria (HKB) and grown in constant light or darkness. RNA was extracted from cultures in the light or in the dark with HKB present (Light + HKB; Dark + HKB), and in the light after HKB were depleted (Light + depleted HKB).ResultsThere were no significant differences in the growth or bacterial ingestion rates between algae grown in light or dark conditions. The availability of light led to a differential expression of only 8% of genes in the transcriptome. A number of genes associated with photosynthesis, phagotrophy, and tetrapyrrole synthesis was upregulated in the Light + HKB treatment compared to Dark + HKB. Conversely, the comparison between the Light + HKB and Light + depleted HKB treatments revealed that the presence of HKB led to differential expression of 59% of genes, including the majority of genes involved in major carbon and nitrogen metabolic pathways. Genes coding for unidirectional enzymes for the utilization of glucose were upregulated in the presence of HKB, implying increased glycolytic activities during phagotrophy. Algae without HKB upregulated their expression of genes coding for ammonium transporters, implying uptake of inorganic nitrogen from the culture medium when prey were unavailable.ConclusionsTranscriptomic results agreed with previous observations that light had minimal effect on the population growth of Ochromonas sp. However, light led to the upregulation of a number of phototrophy- and phagotrophy-related genes, while the availability of bacterial prey led to prominent changes in major carbon and nitrogen metabolic pathways. Our study demonstrated the potential of transcriptomic approaches to improve our understanding of the trophic physiologies of complex mixotrophs, and revealed responses in Ochromonas sp. not apparent from traditional culture studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3549-1) contains supplementary material, which is available to authorized users.

Comparative Transcriptomics Reveals Distinct Gene Expressions of a Model Ciliated Protozoan Feeding on Bacteria-Free Medium, Digestible, and Digestion-Resistant Bacteria

“…Relative to the SPP, Tetrahymena fed with E. coli exhibited downregulation of carbon metabolism-related genes involved in glycolysis, TCA and glyoxylate cycle (MS gene), suggesting weaker glycolytic activity and less energy production during metabolizing protein-rich bacterial carbon sources in digestible bacteria treatment. This observation in the heterotrophic protist is different from previous findings for a mixotrophic alga Ochromonas, which had upregulated expression of the genes encoding for unidirectional enzymes GCK and PFK, implying a higher glycolytic activity when feeding on a bacteria prey [15]. A mixotrophic haptophyte Prymnesium parvum feeding on bacteria and ciliates also exhibited upregulation of the genes involved in TCA and the glyoxylate cycle [16].…”

“…These contradictory results for the heterotrophic Tetrahymena and the mixotrophs might be related to their different trophic lifestyles. The bacterial prey might have provided an extra organic carbon source in the form of fatty acids to Prymnesium parvum, resulting in the higher expression of glycolysis for producing energy [16], and the increased expression of carbon metabolism in Ochromonas might be due to extra phosphoenolpyruvate converted from bacterial amino acids by the enzyme phosphoenolpyruvate carboxykinase (PEPCK) [15]. However, neither fatty acid pathways nor PEPCK were found to be overexpressed in Tetrahymena feeding on E. coli compared to the SPP treatment; perhaps it was because the SPP medium contains more sugars than the SPP mixed with digestible bacterial cells, which might also be different from the sugar-depleted mediums used to culture those mixotrophic protists [15,16].…”

“…We also identified that GH genes affiliated with N-acetylglucosaminidases (GH3, GH18/class II chitinases, and GH20), lysozymes (GH25, and GH18/class I chitinases), lytic transglycosylases GH35, GH13 (for α-starch), GH5 (for glucan), and GH38 (for α-mannan) in Tetrahymena were significantly downregulated (or non-differential) in the ECO but upregulated in the BAC treatment compared with the SPP (Figure 5). Lower or non-differential expression of glycosidases and lysozymes was also observed in the microarray study for a heterotrophic protist Dictyostelium feeding on E. coli (vs. axenic medium) [18] and in transcriptomic studies for the mixotrophic chrysophyte Ochromonas feeding on heat-killed bacteria [15,17]. Protein is usually richer than carbohydrates in a bacterial cell [69,70].…”

“…Transcriptomic analysis has increasingly been exploited as a high throughput approach to understand the physiological and molecular responses of microbial eukaryotes to environmental factors and to identify the genes that are associated with specific nutritional strategies [13]. Using a transcriptomic approach, some phototrophic or mixotrophic algae (e.g., diatoms and dinoflagellates) have been studied, demonstrating specific genes involving biochemical synthesis, fatty acid oxidation, TCA cycle, nitrogen and/or iron uptakes were up-and downregulated in response to the presence of bacterial preys [14][15][16][17]. Knowledge of the metabolic processes involved in heterotrophic nutrition has been gleaned mostly from a few transcriptomic studies focused on identifying the genes involved in phagocytosis, e.g., in prey recognition, transcription regulation, and phagosomal membrane formation, as revealed in the slime mold Dictyostelium discoideum [18].…”

A shifting balance: responses of mixotrophic marine algae to cooling and warming under UVR

“…However, Lie et al . () found no significant differences in the ingestion rates of Ochromonas sp. populations grown under light and dark conditions, whereas genes associated with photosynthesis were overexpressed during the light phase.…”