Single-cell RNA-sequencing (community)

• Page authors: PRIMO
• Responsible curator: Hagen Buck-Wiese

---

Viral infection across the plankton community (scRNA-seq)
Approach: community-level single-cell RNA sequencing; viral transcripts detected in individually barcoded cells
Context: in situ
Spatial scale: single cell
Temporal scale: hours to days
Units: % of cells with viral transcripts; molecule cell-1
Community captured: individual cells across the full plankton community
Co-measurements: host cell abundance

Method Overview

Community-level single-cell RNA sequencing (scRNA-seq) captures the transcriptomes of individual cells across the entire planktonic community without prior cell type selection. Seawater is collected, cells are fixed or kept live, dissociated (if necessary), and encapsulated in microdroplets or nanowells with barcoded oligonucleotides (e.g., 10x Genomics Chromium, Drop-seq). Each cell's RNA is reverse-transcribed using the barcode, creating a library where each read is associated with a unique cell. After sequencing, reads are demultiplexed by barcode and assembled into per-cell transcriptomes. Viral transcripts detected in individual cell libraries, combined with host taxonomic assignment from eukaryotic or prokaryotic marker genes, reveal which community members are infected and the frequency of infection.

Scale of measurement

Single-cell resolution across taxonomically diverse community members. Thousands of cells can be profiled simultaneously, enabling statistically robust estimates of infection frequency.

Data generated

Per-cell transcriptomes enabling: (1) taxonomic classification of each cell; (2) detection of viral transcripts indicating active infection; (3) identification of which host taxa are infected by which viruses. The proportion of infected cells per taxon is a measure of virus–host specificity.

Units & currency

Units are % of cells with viral transcripts per taxon; molecule cell^-1. The currency is transcript molecules.

Sample size

Typical samples are < 1 L in volume; thousands of individual cells are profiled per experiment.

Repositories & databases

Sequencing data deposited at NCBI SRA; viral and host reference databases.

Limitations

Only ~5% of cellular transcripts are captured per cell in most droplet-based scRNA-seq protocols, limiting detection of low-abundance viral transcripts. Taxonomic assignment of viral and host transcripts depends on database completeness. Cell encapsulation can cause doublets (two cells captured together), complicating per-cell analyses.

Example Applications & Protocols

Classic examples

• Fromm et al. (2024) Single-cell RNA-seq of the rare virosphere reveals the native hosts of giant viruses in the marine environment

Common calculations/conversions

• Infection frequency per taxon = (cells of taxon X with viral reads / total cells assigned to taxon X) × 100.