Gene expression dynamics of natural assemblages of heterotrophic flagellates during bacterivory

17 pages, 5 figures, 2 tables, supplementary information https://doi.org/10.1186/s40168-023-01571-5.-- Availability of data and materials: Raw data for “Jul17” incubation were already published at the NCBI BioSample database with accession number SAMN11783926 [38]. For the rest of the incubations, raw data are deposited at NCBI with accession number PRJNA973582. Assemblies, quantification, and functional annotation tables are available at FigShare (https://doi.org/10.6084/m9.figshare.22801697), and all code used for data processing and analyses is available at GitHub (https://github.com/aleixop/metaT_bacterivory)

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

Open Access funding provided thanks to the CRUE-CSIC agreement with Springer Nature. This research was supported by the Spanish Ministry of Science and Innovation projects ALLFLAGS (CTM2016-75083-R), DIVAS (PID2019-108457RB-I00) and the “Severo Ochoa Centre of Excellence” accreditation (CEX2019-000928-S), and the European Union projects SINGEK (H2020-MSCA-ITN-2015–675752) and GENEXLAB (EUR2022-134047, MICINN). AO was supported by a Spanish FPI grant. E.D.S. was supported by the MSCA-IF SMART (CZ.02.2.69/0.0/0.0/20_079/0017809)

Peer reviewed