Active Soil Nitrifying Communities Revealed by In Situ Transcriptomics and Microcosm-Based Stable-Isotope Probing

Area of Science:

• Microbial Ecology
• Environmental Microbiology
• Soil Science

Background:

• Long-term nitrogen fertilization significantly impacts soil nitrifying communities, crucial for the global nitrogen cycle.
• The reliability of microcosm studies in reflecting dynamic changes of ammonia-oxidizing bacteria (AOB) and archaea (AOA) under field conditions is not well understood.

Purpose of the Study:

• To evaluate the transcriptional activities of nitrifying communities under in situ conditions.
• To compare in situ findings with 13C-labeled microcosm studies in soils with varied long-term nitrogen fertilization histories.
• To assess the influence of chronic nitrogen enrichment on the composition and activity of ammonia-oxidizing bacteria (AOB) and archaea (AOA).

Main Methods:

• Collected soil samples from 20 field plots with 5 different nitrogen fertilization treatments over 22 years.
• Employed in situ transcriptomics and microcosm-based DNA stable-isotope probing (SIP).
• Utilized high-throughput sequencing of 16S rRNA genes and transcripts, and real-time quantitative PCR.

Main Results:

• In situ and 13C-labeled microcosm studies showed largely similar transcriptional activities of nitrifying communities.
• Nitrogen fertilization significantly stimulated Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA in fresh and air-dried soils.
• DNA-based SIP revealed dominant labeling of Nitrosospira cluster 3-like AOB and Nitrososphaera viennensis-like AOA, with AOB showing an advantage over AOA in N-fertilized soils. Nitrobacter-like NOB dominated microcosms, while Nitrospira-like NOB were more prevalent in situ.

Conclusions:

• Long-term fertilization selects for physiologically versatile AOB and AOA adapted to varying ammonium concentrations.
• Microcosm studies provide reliable insights into the dynamics of active nitrifying communities under field conditions.
• The soil microbiome exhibits stability over time, and microcosms are valuable tools for studying environmental filtering effects on microbial guilds.