Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment

In the vast expanse of aquatic ecosystems, a hidden world thrives—one inhabited by giant viruses, the enigmatic giants of the microbial world. Despite their global distribution and fundamental roles in shaping ecosystems, much about these giant viruses remains shrouded in mystery. However, a recent study has provided unprecedented insights into their ecology and interactions with their native hosts, shedding light on their ecological importance and impact.

Researchers from the Weizmann Institute of Science applied a single-cell RNA sequencing (scRNA-seq) approach to samples collected during an induced algal bloom—an event teeming with microbial activity. This innovative approach allowed them to identify and pair active giant viruses with their elusive protist hosts, unlocking a trove of hidden interactions within the microbial realm.

A pipeline for detecting host–virus pairs in the natural environment

Fig. 1

a,b, Samples collected from the natural environment (a) and fixed in methanol (b). c, Resuspended cells partitioned by a 10x Chromium microfluidic device. Partitioned cells were combined with beads containing cell-specific barcodes and sample barcodes. d, Cells lysed within each droplet and RNA reverse transcribed. Each transcript was assigned a UMI. e, The cDNA pooled from all cells and sequenced using Illumina. f, Cells computationally demultiplexed by their cell-specific barcodes using Cell Ranger. g, Reads from all cells aligned to a reference of giant virus marker genes using 10x Cell Ranger to identify cells expressing viral transcripts. h, A subset of cells with high expression of viral transcripts selected for subsequent analysis. i, Single-cell transcripts recruited from each selected cell. j, Trimmed single-cell reads (60 bp) assembled to generate longer single-cell transcripts (110–2,050 bp). k, Prediction of the host encoding for the transcripts determined using assembled sequence homology analysis to 18S rRNA. The virus was identified using the homology of raw reads mapped to core NCLDV genes. l, Cells containing 18S rRNA from multiple sources removed. m, Taxonomy was assigned to the host and virus using transcripts and reads from each cell and phylogenetic analysis of 18S rRNA genes (host) and NCLDV marker genes (virus). Black arrows indicate the direction of the pipeline. Grey arrows point to the intermediate output of each step. 

What they discovered was nothing short of astonishing. Within the intricate tapestry of microbial life, they detected hundreds of single cells from various host lineages, each harboring a diverse array of giant viruses. Among these hosts were members of the algal groups Chrysophycae and Prymnesiophycae, as well as heterotrophic flagellates belonging to the class Katablepharidaceae—a group rarely studied in the context of viral infections.

Of particular interest was the discovery of a rare giant virus lineage known as Imitervirales-07, which had taken residence within the Katablepharid population. This giant virus exhibited a remarkable arsenal of cell-fate regulation genes, hinting at its potential role in orchestrating the fate of its host cells. Through meticulous analysis of temporal dynamics, the researchers uncovered the pivotal role played by the Imitervirales-07 in regulating the population size of its host Katablepharids—a revelation with profound implications for microbial ecology.

This study represents a significant leap forward in our understanding of giant viruses and their intricate dance with their microbial hosts. By harnessing the power of scRNA-seq, these researchers have unveiled previously unknown host-virus interactions, providing crucial insights into the ecological dynamics of aquatic ecosystems. Furthermore, these findings underscore the importance of studying microbial communities at the single-cell level, offering a glimpse into the hidden world of microbial interactions and their broader ecological significance.

Fromm A, Hevroni G, Vincent F et al. (2024) Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment. Nat Microbiol [Epub ahead of print]. [abstract]

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