Data from: Stage-specific biological nitrogen fixation depends on distinct carbon and nitrogen availability in long-term fertilized paddy fields
Data files
Jan 20, 2026 version files 22.22 KB
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Genus.csv
13.06 KB
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Phylum.csv
1.18 KB
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README.md
4.17 KB
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Soil_BNF_and_physicochemical_properties.csv
3.81 KB
Abstract
Industrial Haber-Bosch provides 32 Tg nitrogen (N) per year to global croplands. Such large amounts of N fertilization will reshape soil N cycles. One uncertainty is whether and how these long-term N inputs impact soil biological N2 fixation (BNF) associated with plant growth, a crucial microbial-driven process to decipher the balance between soil N and plant N in paddy fields. To fill this gap, we conducted a 10-year field experiment to systematically evaluate the impacts of three N fertilization rates (0, 75, and 150 kg N ha-1) on soil BNF activity, diazotrophic communities, and environmental dynamics at two typical rice growth stages (tillering and maturation) in paddy fields. Moderate N fertilization at a 75 kg N ha-1 rate significantly stimulated BNF activity and nifH gene abundance at the tillering stage, with increases of 20.9% and 49.7%, respectively. This enhancement was primarily due to the supply of available carbon (C) sources from organic acids, which promoted the BNF process to meet the N requirement from rice at the early stage. In contrast, BNF activity and nifH gene abundance decreased with increasing N levels at the maturation stages, reflecting the negative impact of N enrichment on diazotrophs. The accumulation of inorganic N and amino acids reduced the dependence on the BNF process. Stage-specific key diazotrophs, such as Rhizobium at tillering and Azoarcus at maturation, played pivotal roles in the soil BNF. Soil dissolved organic C and inorganic N were positively correlated with BNF at the tillering stage, but negatively at the maturation stage. Random Forest analysis further revealed that the BNF was primarily regulated by available nutrients at the tillering stage, while closely associated with the key diazotrophs at the maturation stage. This study highlights that the stage-specific BNF process depends on C availability and key diazotrophs with long-term N fertilization, providing a basis for optimized N management in paddy fields.
Dataset DOI: 10.5061/dryad.xwdbrv1t7
Description of the data and file structure
This dataset contains soil biological nitrogen fixation (BNF) activity, basic soil physicochemical properties, and diazotrophic community composition summarized at the phylum and genus levels. The data were generated from a long-term nitrogen fertilization field experiment in paddy fields and were used to examine stage-specific drivers of BNF across rice growth stages. All analyses presented in the associated article were based on the data provided in the three files described below.
Files and variables
File: Soil_BNF_and_physicochemical_properties.csv
Description: Soil biological nitrogen fixation (BNF) activity and basic soil physicochemical properties for all treatments and rice growth stages.
Variables
- Stage: Rice growth stages include the tillering and the maturation stage
- Treatment: Three treatments with different N fertilization rates: (i) N0 (control), without N fertilization; (ii) N75, moderate N fertilization at a rate of 75 kg N ha-1; and (iii) N150, high N fertilization at a rate of 150 kg N ha-1
- BNF (C2H4/g h): Soil biological nitrogen fixation activity
- nifH (copies/g): Soil nifH gene copies
- CO2 (μg C/g): Carbon dioxide emissions
- SOC (g/kg): Soil organic carbon
- TN (g/kg): Soil total nitrogen
- C/N ratio: The ratio of soil carbon to nitrogen
- DOC (mg/kg): Soil dissolved organic carbon
- NH4+-N (mg/kg): Soil ammonium nitrogen
- NO3--N (mg/kg): Soil nitrate nitrogen
- INN (mg/kg): Soil inorganic nitrogen
- DOC/INN: The ratio of soil dissolved organic carbon to inorganic nitrogen
- MBC (mg/kg): Soil microbial biomass carbon
- MBN (mg/kg): Soil microbial biomass nitrogen
- MBC/MBN: The ratio of soil microbial biomass carbon to microbial biomass nitrogen
- organic acid (μg/g): Soil organic acid
- citric acid (μg/g): Soil citric acid
- Total free amino acids (μg/g): Soil total free amino acids
- pH : soil pH
File: Genus.csv
Description: Relative abundance of diazotrophic communities at the genus level.
Variables
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Stage: Rice growth stages include the tillering and the maturation stage
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Treatment: Three treatments with different N fertilization rates: (i) N0 (control), without N fertilization; (ii) N75, moderate N fertilization at a rate of 75 kg N ha-1; and (iii) N150, high N fertilization at a rate of 150 kg N ha-1
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Explanation of taxonomic column names
Column names in the tabular data files represent microbial taxonomic assignments derived from sequence annotation.
Each column corresponds to a taxonomic unit, with taxonomy levels separated by semicolons in the following order:
k__: kingdom
p__: phylum
c__: class
o__: order
f__: family
g__: genus
For example: k__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Bradyrhizobiaceae;g__Bradyrhizobium represents sequences assigned to the genus Bradyrhizobium within the family Bradyrhizobiaceae.
File: Phylum.csv
Description: Relative abundance of diazotrophic communities at the phylum level.
Variables
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Stage: Rice growth stages include the tillering and the maturation stage
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Treatment: Three treatments with different N fertilization rates: (i) N0 (control), without N fertilization; (ii) N75, moderate N fertilization at a rate of 75 kg N ha-1; and (iii) N150, high N fertilization at a rate of 150 kg N ha-1
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Explanation of taxonomic column names
Column names in the tabular data files represent microbial taxonomic assignments derived from sequence annotation.
At the phylum level, column names such as Proteobacteria and Firmicutes indicate sequences that were successfully classified to a known phylum. Columns labeled as Unassigned;__ represent sequences that could not be confidently assigned to any recognized phylum based on the reference database.