Ammonia- and Methane-Oxidizing Bacteria: The Abundance, Niches and Compositional Differences for Diverse Soil Layers in Three Flooded Paddy Fields

Jian Zhang,Yao Meng,Jiabao Li,Xianjun Jiang,Si Shen,Dalu Guo,Hongyan Luo,Jianjun Li,Olusanya A Olatunji,Kaiwen Pan

doi:10.3390/su12030953

Abstract

Ammonia oxidizing bacteria (AOB), Ammonia oxidizing archaea (AOA) and methane oxidizing bacteria (MOB) play cogent roles in oxidation and nitrification processes, and hence have important ecological functions in several ecosystems. However, their distribution and compositional differences in different long-term flooded paddy fields (FPFs) management at different soil depths remains under-investigated. Using qPCR and phylogenetic analysis, this study investigated the abundance, niches, and compositional differences of AOA, AOB, and MOB along with their potential nitrification and oxidation rate in three soil layers from three FPFs (ShaPingBa (SPB), HeChuan (HC), and JiDi (JD)) in Chongqing, China. In all the FPFs, CH4 oxidation occurred mainly in the surface (0–3 cm) and subsurface layers (3–5 cm). A significant difference in potential methane oxidation and nitrification rates was observed among the three FPFs, in which SPB had the highest. The higher amoA genes are the marker for abundance of AOA compared to AOB while pmoA genes, which is the marker for MOB abundance and diversity, indicated their significant role in the nitrification process across the three FPFs. The phylogenetic analysis revealed that AOA were mainly composed of Nitrososphaera, Nitrosospumilus, and Nitrosotalea, while the genus Nitrosomonas accounted for the greatest proportion of AOB in the three soil layers. MOB were mainly composed of Methylocaldum and Methylocystis genera. Overall, this finding pointed to niche differences as well as suitability of the surface and subsurface soil environments for the co-occurrence of ammonia oxidation and methane oxidation in FPFs.

Highlights

Nitrification, through which ammonia (NH3) is converted into nitrite (NO2-) or nitrate (NO3-), is a key process in global nitrogen (N) cycling and is strongly linked with the release of greenhouse gases to the atmosphere, NO2- leaching into ground water and N availability for plant use [1]
Compared to the surface soil layer (0–3 cm), the potential nitrification rate in HC soil was significantly lower in the bottom layer (5–20 cm), it was higher in SPB and JD soil (Figure 1)
Some studies have suggested that the oxidation of NH3 is mainly attributed to Ammonia oxidizing Archaea (AOA) [31,32], the presence of both AOA and Ammonia oxidizing Bacteria (AOB) in all the three flooded paddy fields (FPFs) in the present study indicated that the two groups could jointly play a role in the transformation of NH3 to NO3

Summary

Introduction

Nitrification, through which ammonia (NH3) is converted into nitrite (NO2-) or nitrate (NO3-), is a key process in global nitrogen (N) cycling and is strongly linked with the release of greenhouse gases to the atmosphere, NO2- leaching into ground water and N availability for plant use [1]. The oxidation of the second most abundant greenhouse gas, methane (CH4), is conducted by methane-oxidizing bacteria (MOB) [3]. MOB minimize the amounts of CH4 emitted into the atmosphere [4]. MOB are Gram-negative bacteria that utilize CH4 as the exclusive carbon and energy source. They oxidize CH4 in the aerobic environments such as the rhizosphere and the soil-water interface before it is transported into the atmosphere [5]. Elucidating on MOB abundance and activity in the aerobic region, in paddy fields, is critical for enhancement of the understanding of CH4 oxidation and the reduction of greenhouse gases from rice fields

Methods

Results

Discussion

Conclusion