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RESEARCH ARTICLE

Ecological niche differentiation of ammonia-oxidising archaea and bacteria in acidic soils due to land use change

Shenyan Dai A , Qian Liu A , Jun Zhao A E and Jinbo Zhang B C D E
+ Author Affiliations
- Author Affiliations

A School of Geography Sciences, Nanjing Normal University, Nanjing 210023, China.

B Key Laboratory of Virtual Geographical Environment (Nanjing Normal University), Ministry of Education, Nanjing, 210023, China.

C State Key Laboratory Cultivation Base of Geographical Environment Evolution (Jiangsu Province), Nanjing, 210023, China.

D Jiangsu Center for Collaborative Innovation in Geographical Information Resource Development and Application, Nanjing, 210023, China.

E Corresponding author. Email: junzhao37@126.com; zhangjinbo@njnu.edu.cn

Soil Research - https://doi.org/10.1071/SR16356
Submitted: 14 December 2016  Accepted: 7 July 2017   Published online: 4 September 2017

Abstract

Nitrification can be driven by either ammonia-oxidising bacteria (AOB) or ammonia-oxidising archaea (AOA) and is a central process in the nitrogen cycle. However, to date, it is not clear how the ecological niche differentiation of AOB and AOA are affected by land use and management changes in strongly acidic soils in subtropical China. In this study, three different land-use acidic soils – forest, upland, and paddy soils – were collected and a DNA Stable-Isotope Probing experiment performed to determine the relative contributions of AOA and AOB to ammonia oxidation in these soils. The results showed that AOA, but not AOB, amoA genes were detected in 13C-labelled DNA in the forest and paddy soils; however, only AOB amoA genes were detected in 13C-labelled DNA in the upland agricultural soils. The growth and activity of AOA and AOB in the different land-use soils provided direct evidence for the shift in roles for AOA and AOB in ammonia oxidation. AOA played the predominant role in ammonia oxidation in acidic forest and paddy soils. However, AOB, not AOA, mainly regulated the ammonia oxidation in acidic upland agricultural soils. Phylogenetic analysis indicated that AOA members within the marine Group1.1a-associated lineage dominated nitrification in the forest and paddy soils. Ammonia oxidation in the upland soil was catalysed by Nitrosospira cluster 3-like AOB. The moisture condition was likely the main reason inducing the ecological niche differentiation between upland and paddy soils; and AOA was more suitable for growth in the flooded, low oxygen conditions.

Additional keywords: ammonia oxidation, DNA Stable-Isotope Probing experiment, forest soil, paddy soil, upland soil.


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