Abundance and diversity of denitrifying bacterial communities associated with N₂O emission under long-term organic farming

Hui Han^a, Chen Chen^a, Mohan Bai^a, Ting Xu^a,b, Hefa Yang^c, Aiming Shi^c, Guo-chun Ding^a,b, Ji Li^a,b

College of Resources and Environmental Science, Beijing Key Laboratory of Biodiversity and Organic Farming, China Agricultural University, Yuanmingyuan West Road No. 2, 100193, Beijing, China.

Abstract

Nitrous oxide (N₂O), a powerful greenhouse gas, is produced and consumed through denitrifying bacteria. However, the abundance, diversity and succession of denitrifying bacteria and their association with farming systems are largely unknown. Therefore, the objectives of the present study were: (1) to unravel the influence of long-term organic farming on diversity of nirK-, nirS- and nosZ-type denitrifying microorganisms; and (2) to analyze the association of diversity and abundance of these denitrifying microorganism with the emission of N₂O from soil. The abundance and diversity of denitrifying bacteria with nirK, nirS and nosZ were compared among organic (ORG), integrated (INT), and conventional (CON) vegetable greenhouses located in northern China over four growing seasons using quantitative PCR and high-throughput DNA sequencing of PCR-amplified products. As compared to CON, the abundance of nosZ gene was significantly higher in the ORG, in which the N₂O emission was 35% lower. In general, both abundance and diversity of nitrite reducing populations (nirK- and nirS-type) was influenced by growing seasons rather than farming systems. Additionally, dominant denitrifying populations displayed irregular, periodical, or persistent succession patterns. Co-occurrence network revealed that nirK-, nirS- and nosZ-type denitrifying bacteria formed microbial hubs associated with soil temperature, NO₃−-N content, or pH. In summary, long-term organic farming enriched N₂O reducing bacterial populations, while having little effect on nitrite reducing populations which mainly succeeded seasonally.

Keywords: Organic farming, Denitrifying bacteria, Abundance, Diversity, High-throughput sequencing.