Advances in single-cell and spatial omics for studying symbiotic nitrogen fixation: comparative cellular and
Yan Shi1, Huiru Liu1, Weicai Yang2
1Yazhouwan National Laboratory, Sanya, Hainan, 572025, China.
Genome Biology
|March 12, 2026
Summary
Single-cell and spatial transcriptomics reveal cellular programs in legume root nodules for symbiotic nitrogen fixation. These advanced methods offer insights for engineering nitrogen fixation in crops.
Area of Science:
- Plant biology
- Molecular biology
- Genomics
Background:
- Symbiotic nitrogen fixation is crucial for sustainable agriculture.
- Root nodules in legumes host nitrogen-fixing bacteria.
- Understanding cellular and molecular mechanisms is key.
Purpose of the Study:
- To explore cellular heterogeneity and gene expression in symbiotic nitrogen fixation.
- To investigate epigenetic regulation of symbiotic genes.
- To compare nitrogen fixation across different plant species.
Main Methods:
- Single-cell transcriptomics
- Spatial transcriptomics
- Single-cell epigenomics (chromatin accessibility, 3D genome architecture)
- Comparative transcriptomic analyses
Main Results:
- Identified conserved and species-specific gene expression programs in root nodules.
- Revealed insights into immune recognition, nodule development, and metabolic regulation.
- Uncovered epigenetic mechanisms controlling symbiotic gene expression.
- Elucidated cellular-level regulatory networks and phenotypic diversity.
Conclusions:
- Single-cell and spatial transcriptomics provide powerful frameworks for studying symbiotic nitrogen fixation.
- Epigenomic data enhances understanding of gene regulation in symbiosis.
- Comparative analyses offer potential for engineering nitrogen fixation in non-legume crops.
Related Concept Videos
01:22Inorganic Nitrogen Assimilation
741
Nitrogen is an essential element in biological systems, forming a crucial component of proteins, nucleic acids, and other cellular constituents. Many bacteria and archaea acquire nitrogen in the form of nitrate (NO₃⁻) or ammonia (NH₃), which are then assimilated into biomolecules through specific enzymatic pathways.Assimilatory Nitrate ReductionWhen nitrate enters the cell, it undergoes a two-step reduction process known as assimilatory nitrate reduction. Initially, the enzyme...
741
02:11The Roles of Bacteria and Fungi in Plant Nutrition
47.7K
Plants have the impressive ability to create their own food through photosynthesis. However, plants often require assistance from organisms in the soil to acquire the nutrients they need to function correctly. Both bacteria and fungi have evolved symbiotic relationships with plants that help the species to thrive in a wide variety of environments.
47.7K
01:28Carbon-dioxide Fixation
817
Carbon dioxide fixation in prokaryotes enables the assimilation of inorganic carbon into organic molecules, supporting biosynthetic pathways, sustaining ecosystems, and contributing to the global carbon cycle. It also has industrial applications in carbon capture and bioproduct synthesis. Autotrophic organisms rely on this process to utilize CO₂ as a carbon source in diverse environments.The Calvin CycleThe Calvin cycle is the most widespread carbon fixation mechanism, primarily used by...
817
02:35Key Elements for Plant Nutrition
24.7K
Like all living organisms, plants require organic and inorganic nutrients to survive, reproduce, grow and maintain homeostasis. To identify nutrients that are essential for plant functioning, researchers have leveraged a technique called hydroponics. In hydroponic culture systems, plants are grown—without soil—in water-based solutions containing nutrients. At least 17 nutrients have been identified as essential elements required by plants. Plants acquire these elements from the...
24.7K
01:20Overview of Nitrogen Metabolism
12.4K
Nitrogen is a very important element for life because it is a major constituent of proteins and nucleic acids. It is a macronutrient, and in nature, it is recycled from organic compounds and stored in the form of ammonia, ammonium ions, nitrate, nitrite, or nitrogen gas by many metabolic processes. Many of these metabolic processes are carried out only by prokaryotes.
The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N2) from the air, but this...
The largest pool of nitrogen available in the terrestrial ecosystem is gaseous nitrogen (N2) from the air, but this...
12.4K