Ammonium-Generating Microbial Consortia in Paddy Soil Revealed by DNA-Stable Isotope Probing and Metatranscriptomics

Area of Science:

• Agricultural Microbiology
• Soil Science
• Environmental Microbiology

Background:

• Rice paddy soils are vital agricultural systems, relying on microbial communities for nitrogen fertility.
• Key nitrogen transformations, including dissimilatory nitrate reduction to ammonium (DNRA), nitrogen fixation, and denitrification, are interconnected in these environments.
• The specific microorganisms driving ammonium generation and their roles in these linked processes remain incompletely understood.

Purpose of the Study:

• To identify and characterize the microbial consortia responsible for ammonium generation in rice paddy soils.
• To elucidate the roles of specific bacterial taxa in multiple reductive nitrogen transformations under varying substrate conditions.

Main Methods:

• Stable isotope probing using ¹⁵NO₃^-, ¹⁵N₂O, and ¹⁵N₂.
• High-throughput sequencing of 16S rRNA genes.
• Metatranscriptomic analysis to identify active microbial players.

Main Results:

• Several bacterial families, including *Geobacteraceae*, *Bacillaceae*, *Rhodocyclaceae*, *Anaeromyxobacteraceae*, and *Clostridiaceae*, were identified as active ammonium generators.
• These bacterial groups demonstrated involvement under different nitrogen substrate conditions (e.g., nitrate, N₂O, N₂).
• Many identified bacteria also participate in other critical paddy soil processes, such as iron/sulfate reduction and straw decomposition.

Conclusions:

• This study reveals the key bacterial drivers of ammonium generation in rice paddy soils.
• Identified microbial consortia are involved in multiple reductive nitrogen transformations, highlighting their functional diversity.
• These findings enhance our understanding of nitrogen cycling and overall soil metabolism in sustainable agricultural systems.