NifH detection/quantification (qPCR, RT-qPCR; nifH database)

What is being measured in 1 - 3 words
Approach: gene quantification
Context: Molecular
Spatial scale:
Temporal scale: Days, Seasons
Units: gene copies, transcripts
Community captured: diazotrophs (potential or active)
Co-measurements:

Method Overview

Quantification of nifH is typically performed using quantitative PCR (qPCR) to measure nifH gene copy numbers, providing an estimate of diazotroph abundance. Reverse transcription qPCR (RT-qPCR) targets nifH transcripts, enabling assessment of gene expression and thus potential nitrogenase activity

Output

nifH gene copy numbers (qPCR)
nifH transcript abundance (RT-qPCR)
Gene- or transcript-based estimates of nitrogen fixation potential

Scale of measurement

Molecular / gene-expression level
Quantitative
Community-integrated signal

Data generated

Ct (cycle threshold) values
Standard curves for absolute quantification
Gene or transcript copy number estimates
Metadata-linked abundance or expression tables

Units & currency

nifH gene copies L⁻¹ or g⁻¹
nifH transcripts L⁻¹ or g⁻¹
Relative expression (normalized units)
Fold change (RT-qPCR)

Sample size

Varies by study design
Includes biological replication and controls

Repositories & databases

Limitations

Gene copy number does not equal nitrogen fixation rate

Example Applications & Protocols

Classic examples

Recent applications

Protocols:

Standard nifH qPCR and RT-qPCR protocols
SYBR Green or probe-based detection methods
Custom laboratory SOPs optimized for primer sets and environmental matrices

Common calculations/conversions

Gene copies = Ct-based quantification using standard curves
Normalization to volume, mass, or biomass
Conversion of transcript abundance to relative expression levels

References