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Biogeosciences An interactive open-access journal of the European Geosciences Union
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© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.
© Author(s) 2019. This work is distributed under
the Creative Commons Attribution 4.0 License.

Submitted as: research article 19 Dec 2019

Submitted as: research article | 19 Dec 2019

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This discussion paper is a preprint. It is a manuscript under review for the journal Biogeosciences (BG).

pH-based ecological coherence of active canonical methanotrophs in paddy soils

Jun Zhao, Yuanfeng Cai, and Zhongjun Jia Jun Zhao et al.
  • State Key Laboratory of Soil and Sustainable Agriculture, Institute of Soil Science, Chinese Academy of Sciences, Nanjing, 210008, Jiangsu Province, China

Abstract. Soil pH is considered one of the main determinants of the assembly of globally distributed microorganisms that catalyse the biogeochemical cycles of carbon and nitrogen. However, direct evidence for niche specialization of microorganisms in association with soil pH is still lacking. Using methane-oxidizing bacteria (methanotrophs) as a model system of carbon cycling, we show that pH is potentially the key driving force selecting for canonical gamma- (type I) and alpha- (type II) methanotrophs in rice paddy soils. DNA-based stable isotope probing (DNA-SIP) was combined with high-throughput sequencing to identify the taxonomic identities of active methanotrophs in physiochemically contrasting soils from 6 different paddy fields across China. Following microcosm amendment with 13CH4, methane was primarily consumed by Methylocystis-affiliated type II methanotrophs in soils with a relatively low pH (5.44–6.10), whereas Methylobacter/Methylosarcina-affiliated type I methanotrophs dominated methane consumption in soils with a high pH (7.02–8.02). Consumption of 13CH4 contributed 0.203 % to 1.25 % of soil organic carbon, but no significant difference was observed between high-pH and low-pH soils. The fertilization of ammonium nitrate resulted in no significant changes in the compositions of 13C-labelled methanotrophs in the soils, although significant inhibition of methane oxidation activity was consistently observed in low-pH soils. Mantel analysis further validated soil pH, rather than other parameters tested, had significant correlation to the variation of active methanotrophic compositions across different rice paddy soils. These results suggest that soil pH might have played pivotal roles in mediating the niche differentiation of ecologically important aerobic methanotrophs in terrestrial ecosystems and imply the importance of such niche specialization in regulating methane emissions in paddy field under increasingly intensified input of anthropogenic N fertilizers.

Jun Zhao et al.
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Status: open (until 30 Jan 2020)
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Jun Zhao et al.
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Short summary
We show that soil pH is a key factor selecting distinct phylotypes of methanotrophs in paddy soils. Type II methanotrophs dominated the methane oxidation in low-pH soils, while type I methanotrophs were more active in high-pH soils. This pH-based niche differentiation of active methanotrophs appeared to be independent of nitrogen fertilization, but the inhibition of type II methanotrophic rate in low-pH soils by the fertilization might aggravate the emission of methane from paddy soils.
We show that soil pH is a key factor selecting distinct phylotypes of methanotrophs in paddy...