Evaluation of Mixotrophy-Associated Gene Expression in Two Species of Polar Marine Algae

Abstract

Mixotrophic flagellates can comprise significant proportions of plankton biomass in marine ecosystems. Despite the growing recognition of the importance of this ecological strategy, and the identification of major environmental factors controlling phagotrophic behavior (light and nutrients), the physiological and molecular mechanisms underlying mixotrophic behavior are still unclear. In this study, we performed RNA-Seq transcriptomic analysis for two mixotrophic prasinophytes, Micromonas polaris and Pyramimonas tychotreta, under dissolved nutrient regimes that altered their ingestion of bacteria prey. Though the strains examined were polar isolates, both belong to genera with widespread distribution. Our aim was to characterize the transcriptomes of these two non-model phytoflagellates, identify transcripts consistent with phagotrophic activity and assess their differential expression in response to nutrient stress. De novo assembly of the transcriptomes yielded large numbers of novel coding transcripts with no known match within public databases. A summary of the transcripts by Gene Ontology terms showed many expected expression patterns, including genes involved in photosynthetic pathways and enzymes implicated in nutrient uptake pathways. Searches of KEGG databases identified several genes associated with intra-cellular digestive pathways actively transcribed in both prasinophytes. Differential expression analysis showed a larger response in P. tychotreta, where 23,373 genes were up-regulated and 1,752 were down-regulated in the low nutrient treatment when phagotrophy was enhanced. In contrast, in M. polaris, low nutrient treatments resulted in up-regulation of 314 transcripts while down-regulating 371. With respect to phagotrophic-related expression, 37 genes were co-expressed in both P. tychotreta and M. polaris, and although the response was less pronounced in M. polaris, it is consistent with differences in observed ingestion behavior. This study presents the first genomic data for Pyramimonas tychotreta, and also contributes to the limited available data for Micromonas polaris. Furthermore, it provides insight into the presence of genes associated with phagocytosis within the Prasinophyceae and contributes to the understanding of potential target genes required for the construction of a complete model of gene regulation of phagocytic behavior in algae.

Top-Down and Bottom-Up Controls on Microeukaryotic Diversity (i.e., Amplicon Analyses of SAR Lineages) and Function (i.e., Metatranscriptome Analyses) Assessed in Microcosm Experiments

“…We evaluate the possibility of lineage-specific changes in predation among nanosized community members by looking at genes involved in phagocytosis. While we observed an upregulation of actin for the nanosized ciliates in bloom condition (Supplementary Figure S6), we did not see an increase in expression for phagotrophic genes such as the ARP complex and RAC GF identified by Yutin et al (2009) and a longer list of genes identified in two other studies (Burns et al, 2018;McKie-Krisberg et al, 2018; Supplementary Figure S7). These analyses are consistent with an indirect response of nanosized ciliates rather than an increase in grazing in response to added phytoplankton.…”

Influence of Irradiance and Temperature on the Virus MpoV-45T Infecting the Arctic Picophytoplankter Micromonas polaris

“…Finally, the autumn to winter transition will be mainly dominated by lowered temperature and light availability (condition A), as in early spring, reducing viral impact again in response to the low light. Under dark conditions, infection of other Micromonas species is reported to halt [29,43,59,60], yet, M. polaris may potentially survive the winter as a mixotroph [61,62]. If so, it might be that it has enough energy to produce viruses upon infection, presenting an alternative explanation for the low abundances of Micromonas and high abundances of its viruses in Arctic winter metagenomes [63].…”

The dynamic trophic architecture of open-ocean protist communities revealed through machine-guided metatranscriptomics

“…Both models accurately predicted phototrophy in the high nutrient condition. However, both models also predicted phototrophy in the low-nutrient condition, which could reflect either the limited bacterial grazing documented in the experiment (48) or the absence of representative mixotrophic Pyramimonas sp. transcriptomes in the training set.…”

“…Pyramimonas tychotetra (Fig. S6) was cultured under high- or low-nutrient conditions, with the low nutrient condition intended to induce phagotrophy though only low levels of bacterivory were observed (48). Both models accurately predicted phototrophy in the high nutrient condition.…”

“…We next challenged the models with transcriptomes not present in the MMETSP dataset ( Pyramimonas tychotetra were chosen as they are known mixotrophs, and in each instance, experiments were carried out that modulated the availability of light, prey, or nutrients in an effort to drive organisms into distinct nutritional modes (Table S6) (22,47,48). Particle ingestion by M. polaris was detected in both the high-and low-nutrient conditions employed (48) and both models accordingly classified M. polaris from both conditions as mixotrophic. Pyramimonas tychotetra (Fig.…”