A review of ammonia-oxidizing bacteria and archaea in Chinese soils

Ju-Pei Shen,Hong J Di,Li-Mei Zhang,Ji-Zheng He

doi:10.3389/fmicb.2012.00296

Ju-Pei Shen, Hong J Di + Show 2 more

Open Access

https://doi.org/10.3389/fmicb.2012.00296

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Abstract

Ammonia (NH3) oxidation, the first and rate-limiting step of nitrification, is a key step in the global Nitrogen (N) cycle. Major advances have been made in recent years in our knowledge and understanding of the microbial communities involved in ammonia oxidation in a wide range of habitats, including Chinese agricultural soils. In this mini-review, we focus our attention on the distribution and community diversity of ammonia-oxidizing bacteria (AOB) and ammonia oxidizing archaea (AOA) in Chinese soils with variable soil properties and soil management practices. The niche differentiation of AOB and AOA in contrasting soils have been functionally demonstrated using DNA-SIP (stable isotope probing) methods, which have shown that AOA dominate nitrification processes in acidic soils, while AOB dominated in neutral, alkaline and N-rich soils. Finally, we discuss the composition and activity of ammonia oxidizers in paddy soils, as well as the mitigation of the greenhouse gas nitrous oxide (N2O) emissions and nitrate leaching via inhibition of nitrification by both AOB and AOA.

Highlights

Nitrification is a major process in the nitrogen (N) cycling, including a two-step process, the oxidation of ammonia to nitrite and subsequently nitrite to nitrate (Prosser, 1989)
These studies together confirm that the roles of ammonia-oxidizing bacteria (AOB) and ammonia-oxidizing archaea (AOA) in soil ammonia oxidation may vary dependent upon soil conditions, and can be hypothesized to occupy different ecological niches based on N availability and pH (He et al, 2012)
DCD is considered an effective inhibitor of nitrification by merit of its ability to inactivate the ammonia monooxygenase (AMO) enzyme produced by the actively nitrifying microbial community, regardless of whether the activity is dominated by AOA or AOB

Summary

INTRODUCTION

Nitrification is a major process in the nitrogen (N) cycling, including a two-step process, the oxidation of ammonia to nitrite and subsequently nitrite to nitrate (Prosser, 1989). The study on alkaline soils from the Fengqiu experiment station found that differences in fertilization regimes did not alter the abundance of AOA, but rather resulted in an increase in AOB abundance in soils receiving N fertilizer (Shen et al, 2008) This finding is consistent with the observation that N fertilizer amendment changed the abundance and composition of AOB, but had no significant effect on AOA community composition or abundance, in a semi-arid temperate grassland soil with neutral pH (Shen et al, 2011). Xia et al (2011) further demonstrated that AOB were the primary drivers of ammonia oxidation in an alkaline Chinese soil in a microcosm study which included weekly inorganic N additions These results support earlier findings in pH-neutral N-rich New Zealand grassland soils (Di et al, 2009), in which AOB were demonstrated to be more important than AOA for ammonia oxidation. These studies together confirm that the roles of AOB and AOA in soil ammonia oxidation may vary dependent upon soil conditions, and can be hypothesized to occupy different ecological niches based on N availability and pH (He et al, 2012)

FQ NPK

CONCLUSIONS AND PERSPECTIVES