Vertical abundance variations of “incomplete ammonia oxidizers” and “comammox” in purple paddy soil in Chongqing

Abstract:

[Objective] Nitrification has been thought to be as a two-step process, where ammonia-oxidizing bacteria and archaea (AOB and AOA) first oxidize ammonia to nitrite, which nitrite-oxidizing bacteria (NOB) subsequently transfer to nitrate. Recently, the ability to oxidize ammonia has also been discovered in members of the genus Nitrospira, which were formerly supposed to only be capable of nitrite oxidation. The discovery of these bacteria that oxidize ammonia to nitrate (complete ammonia oxidizing bacteria, Comammox bacteria), refuted the dogma that the oxidation of ammonia and nitrite requires two distinct groups of microorganisms. The discovery of one-step nitrification and Comammox Nitrospira triggered many important scientific issues of the global nitrogen cycle, but relevant studies were still in the preliminary stage.[Methods] Using real-time quantitative PCR (Q-PCR), we characterized the distribution patterns of functional amoA gene abundances of Comammox (Clade A and Clade B), ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) at 5, 10, 20, and 40 cm soil depths (up-down error within 1 cm) of flooded paddy field (FPF) in Beibei, Chongqing in 2017.[Results] Quantitative PCR (Q-PCR) revealed that soil depth had a significant effect on different nitrifiers. Comammox Nitrospira were ecologically widespread and numerically abundant in all depths of the standard profile. The Comammox Clade A amoA gene copies were higher at deeper layers, while Comammox Clade B didn't show the same trends and its abundances varied between 1.85×10⁶ copies/g and 3.26×10⁶ copies/g in different depths of the standard profile. However, the abundance of Comammox Clade A was about to an order of magnitude more abundant than Comammox Clade B in paddy soils. On the contrary, the amoA gene abundances of AOA and AOB significantly decreased with increasing depth (P<0.05), both AOA and AOB amoA gene abundances were highest in the top layer (5 cm, 1.23×10⁷ copies/g and 1.83×10⁵ copies/g, respectively). The ratio of abundances of Comammox amoA genes to those of AOA and AOB increased significantly with the increase of soil depth, ranged from 10 to 2000.[Conclusion] The complete ammonia oxidizing bacteria (Comammox bacteria) are widely distributed in all soil depths of paddy soil and their abundances were significantly higher than "incomplete ammonia oxidizers (AOA, AOB)", which implicated that Comammox cannot be neglected in rice soil ecosystem.