Comparative genomics reveals new functional insights in uncultured MAST species

Abstract

Heterotrophic lineages of stramenopiles exhibit enormous diversity in morphology, lifestyle, and habitat. Among them, the marine stramenopiles (MASTs) represent numerous independent lineages that are only known from environmental sequences retrieved from marine samples. The core energy metabolism characterizing these unicellular eukaryotes is poorly understood. Here, we used single-cell genomics to retrieve, annotate, and compare the genomes of 15 MAST species, obtained by coassembling sequences from 140 individual cells sampled from the marine surface plankton. Functional annotations from their gene repertoires are compatible with all of them being phagocytotic. The unique presence of rhodopsin genes in MAST species, together with their widespread expression in oceanic waters, supports the idea that MASTs may be capable of using sunlight to thrive in the photic ocean. Additional subsets of genes used in phagocytosis, such as proton pumps for vacuole acidification and peptidases for prey digestion, did not reveal particular trends in MAST genomes as compared with nonphagocytotic stramenopiles, except a larger presence and diversity of V-PPase genes. Our analysis reflects the complexity of phagocytosis machinery in microbial eukaryotes, which contrasts with the well-defined set of genes for photosynthesis. These new genomic data provide the essential framework to study ecophysiology of uncultured species and to gain better understanding of the function of rhodopsins and related carotenoids in stramenopiles.

Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

“…The first MerMAIDs reported were seven homologous ACRs identified in metagenomic samples ( 22 ). Recently, close homologs were found in unclassified stramenopile species ( 5 , 26 ), which suggests that the original MerMAIDs also originate from stramenopiles. We have identified 20 additional MerMAID homologs, nine haptophyte ACR homologs, and two Labyrinthulea ACR homologs ( Data Set S1 ) in metagenomic databases ( Data Set S4 ).…”

Oceanic heterotrophic flagellates are dominated by a few widespread taxa

“…Having identified the putatively most relevant HFs in the ocean, a renewed effort to culture them should be made, as these could be developed into new model organisms to be used to gain a better understanding of the role of HFs in the ecosystem. Single cell genomics is also a promising alternative to capture the genomes of these dominant species (Labarre et al 2021), which can then be used in comparative genomics or to interpret complex metagenomic and metatranscriptomic data sets. Overall, our work paves the road for future studies on marine HFs, highlighting key species that may be playing crucial roles in the plankton.…”

Cation and anion channelrhodopsins: Sequence motifs and taxonomic distribution

“…The first MerMAIDs reported were seven homologous ACRs identified in metagenomic samples (22). Recently, close homologs were found in unclassified stramenopile species (5, 25), which suggests that the original MerMAIDs also originate from stramenopiles. We have identified 20 additional MerMAID homologs, nine haptophyte ACR homologs and two Labyrinthulea ACR homologs (Data Set S1) in metagenomic databases (Data Set S4).…”