Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

Abstract

Background Marine heterotrophic flagellates (HF) are dominant bacterivores in the ocean, where they represent the trophic link between bacteria and higher trophic levels and participate in the recycling of inorganic nutrients for regenerated primary production. Studying their activity and function in the ecosystem is challenging since most of the HFs in the ocean are still uncultured. In the present work, we investigated gene expression of natural HF communities during bacterivory in four unamended seawater incubations. Results The most abundant species growing in our incubations belonged to the taxonomic groups MAST-4, MAST-7, Chrysophyceae, and Telonemia. Gene expression dynamics were similar between incubations and could be divided into three states based on microbial counts, each state displaying distinct expression patterns. The analysis of samples where HF growth was highest revealed some highly expressed genes that could be related to bacterivory. Using available genomic and transcriptomic references, we identified 25 species growing in our incubations and used those to compare the expression levels of these specific genes. Conclusions Our results indicate that several peptidases, together with some glycoside hydrolases and glycosyltransferases, are more expressed in phagotrophic than in phototrophic species, and thus could be used to infer the process of bacterivory in natural assemblages.

Protistan community composition and metabolism in the North Pacific Subtropical Gyre: Influences of mesoscale eddies and depth

“…We show in this study that transcript relative abundance data provide a promising avenue to identify shifts in the nutritional physiology of protists. However, changes in the relative abundances of phototrophy-and heterotrophy-associated transcripts across samples must be evaluated in the context of known nutritional strategy information for specific taxonomic groups, as many of the enzymes that are involved in phototrophic and heterotrophic nutritional processes are also involved in other pathways (Labarre et al, 2020;Obiol et al, 2023;Rogers & Keeling, 2004;Yutin et al, 2009). For example, endocytosis and V-type ATPases are thought to be involved in the uptake of food contents and the acidification of phagosomes in heterotrophic protists (Hu et al, 2018;Labarre et al, 2020); however, transcripts associated with these processes can also be involved in other pathways that are not related to heterotrophy.…”

“…Phototrophic metabolism, for example, is recognizable in protistan transcriptomic data because photosynthetic pathways are well-studied and highly conserved across taxonomic groups (Becker et al, 2021;Worden et al, 2015). Pathways involved in protistan heterotrophic metabolism are less welldescribed, but some recent studies have begun to characterize heterotrophic metabolism using transcriptomic and proteomic approaches (Burns et al, 2018;Koppelle et al, 2022;Labarre et al, 2020;Lambert et al, 2022;McKie-Krisberg et al, 2018;Obiol et al, 2023;Rubin et al, 2019;Yutin et al, 2009). Culture-based transcriptomic studies have aided our ability to identify specific proteins and pathways that may be associated with grazing processes in protists.…”