Single cell uptake (SIP-SIMS/nanoSIMS; CHIP-SIMS; CARD-FISH paired with nanoSIMS)

• Page authors: Christian Furbo Reeder, PRIMO
• Responsible curator: Christian Furbo Reeder

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What is being measured in 1 - 3 words
Approach: single-cell isotope analysis
Context: incubation
Spatial scale: µm
Temporal scale: hours–days
Units: isotope enrichment, uptake rates
Community captured: active single cells
Co-measurements: incubation time, tracer enrichment, temperature, nutrients

Method Overview

Single-cell uptake methods combine stable isotope probing (SIP) with secondary ion mass spectrometry (SIMS) to quantify nutrient assimilation at the level of individual cells. In nitrogen fixation studies, samples are incubated with ¹⁵N₂, followed by analysis using nanoSIMS or related platforms. Taxonomic or functional identity can be resolved using complementary labeling techniques such as CARD-FISH or CHIP-SIMS, enabling direct linkage between nitrogen uptake and specific microbial taxa or functional groups. These approaches provide quantitative, cell-specific measurements of nitrogen assimilation and metabolic activity.

Output

• Single-cell isotope enrichment values
• Cell-specific nutrient uptake rates
• Taxon-resolved nitrogen assimilation
• Spatial patterns of isotope incorporation

Scale of measurement

• Single-cell
• Quantitative
• Taxon-specific activity

Data generated

• NanoSIMS ion images
• Isotopic ratio measurements (e.g., ¹⁵N/¹⁴N)
• Cell-specific uptake rate calculations
• Linked microscopy and hybridization images

Units & currency

• Atom percent ¹⁵N
• Excess isotope enrichment
• fmol N cell⁻¹ h⁻¹
• Relative enrichment above natural abundance

Sample size

• Typically:
  • 10–100 analyzed cells per sample
  • 3–10 samples per treatment
• Limited throughput relative to bulk methods

Limitations

• Low throughput and high analytical cost
• Requires specialized instrumentation and expertise
• Incubation conditions may alter in situ activity
• Taxonomic identification depends on probe specificity and labeling efficiency

Example Applications & Protocols

Recent applications

Protocols:

• ¹⁵N₂ tracer incubation protocols
• CARD-FISH combined with nanoSIMS workflows
• CHIP-SIMS and SIP-SIMS sample preparation protocols
• Custom laboratory SOPs for fixation, hybridization, and nanoSIMS analysis

Common calculations/conversions

• Atom percent excess = measured atom % − natural abundance
• Single-cell uptake rate = (isotope enrichment × cellular N content) / incubation time
• Correction for tracer enrichment and dilution
• Scaling single-cell rates to community-level estimates (with caution)