Single-Cell Analyses in Microbial Ecology

Microbial communities underpin processes from nutrient cycling to human health, yet their functional and genetic diversity is often obscured by bulk‐population approaches. Single‐cell analyses overcome this limitation by isolating and characterising individual cells, thereby revealing heterogeneity in genome content, metabolic activity and ecological roles. Key advances include high‐resolution imaging techniques that link taxonomic identity to in situ activity, novel amplification chemistries that enhance genome recovery from uncultured cells, and quantitative assays that measure viability and abundance at unprecedented scales. By integrating fluorescence‐based sorting, click‐chemistry tagging, stable‐isotope probing and low‐bias whole‐genome amplification, researchers can now reconstruct genomes, detect metabolic traits and track dynamic responses of single microbes within complex environmental matrices. These capabilities are transforming our understanding of microbial ecology, informing biotechnological applications such as bioremediation, crop‐growth promotion and precision microbiome engineering.

Research from Nature Portfolio

Recent developments have streamlined single‐cell workflows and expanded their ecological reach. A geometric viability assay now quantifies viable cells across orders of magnitude in minutes, replacing traditional colony‐forming unit tests and enabling high‐throughput assessment of bacterial, fungal and biofilm samples with minimal reagent use. In soils, bioorthogonal non-canonical amino acid tagging combined with fluorescence-activated cell sorting has delineated the active fraction of microbial assemblages, uncovering distinct phylogenetic compositions among translationally active cells at different depths. A thermostable‐enzyme based whole‐genome amplification method further boosts recovery of high G+C content genomes from individual bacteria, archaea and viral particles, while simultaneously capturing cell‐size data. Together, these innovations offer a scalable platform for linking single‐cell genotype, morphology and activity directly in environmental contexts.

Single-Cell Analyses in Microbial Ecology publication trend

The graph below shows the total number of articles in single-cell analyses in microbial ecology across all publications each year (not limited to Nature Index journals).

Technical terms

Single‐cell genomics: Techniques enabling isolation and sequencing of the genome from an individual microbial cell.

BONCAT: Bioorthogonal non‐canonical amino acid tagging, a method that incorporates synthetic amino acid analogues into newly synthesised proteins for fluorescence labelling.

FACS: Fluorescence-activated cell sorting, a flow cytometry technique that separates individual cells based on fluorescence signals.

NanoSIMS: Nanoscale secondary ion mass spectrometry, an imaging method that maps elemental and isotopic composition at subcellular resolution.

Multiple displacement amplification (MDA): A whole‐genome amplification protocol using phi29 DNA polymerase to generate large amounts of DNA from single cells.

Geometric viability assay (GVA): A high‐throughput assay that estimates viable cell counts by analysing the spatial distribution of microcolonies in a confined geometry.

Fluorescence in situ hybridisation (FISH): A molecular technique using fluorescent probes to detect specific nucleic acid sequences within intact cells.

References

1. A high-throughput and low-waste viability assay for microbes. Nature Microbiology (2023).
2. Probing the active fraction of soil microbiomes using BONCAT-FACS. Nature Communications (2019).
3. Improved genome recovery and integrated cell-size analyses of individual uncultured microbial cells and viral particles. Nature Communications (2017).
4. Gold‐FISH enables targeted NanoSIMS analysis of plant‐associated bacteria. New Phytologist (2023).
5. The quest for environmental analytical microbiology: absolute quantitative microbiome using cellular internal standards. Microbiome (2025).
6. In situ visualization of newly synthesized proteins in environmental microbes using amino acid tagging and click chemistry. Environmental Microbiology (2014).