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A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils

  • Soil Microbiology
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Abstract

Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4.5). Our results support the numerical and functional dominance of AOA over AOB in acidic soils as bacterial amoA gene and transcript were both under detection limits and archaeal amoA, in contrast, were abundant and responded to the fluctuations of environmental factors. Organic matter from tree residues was proposed as the main source of microbial available nitrogen, and the potential co-precipitation of dissolved organic matter (DOM) with soluble Al3+ species in acidic soil matrix may further restrict the amount of nitrogen sources required by AOB besides NH3/NH4 + equilibrium. Although AOA were better adapted to oligotrophic environments, they were susceptible to the toxicity of exchangeable Al3+. Phylotypes affiliated to Nitrososphaera, Nitrososphaera sister group, and Nitrosotalea were detected by amoA gene and transcript. Nitrosotalea devantaerra and Nitrososphaera sister group were the major AOA. Compared to the genomic DNA data, higher relative abundances of Nitrososphaera and Nitrososphaera sister group were recognized in amoA transcript inferred AOA communities, where Nitrosotalea relative abundance was found lower, implying the functional activities of Nitrososphaera sister group and Nitrososphaera were easily underestimated and Nitrosotalea did not attribute proportionally to nitrification in extremely acidic soils. Further comparison of the different AOA community compositions and relative abundance of each phylotypes revealed by amoA genes and transcripts make it possible to identify the functional AOA species and assess their ecological role in extremely acidic soils.

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Acknowledgements

This research was financially supported by a PhD studentship from the University of Hong Kong (RW), a research grant from the National Natural Science Foundation of China [31470562] (Y-FW), and a Shenzhen Scientific Grant (JCYJ20140722112616608 to WSL) from the Shenzhen Science and Technology Innovation Committee of P.R. China.

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Authors and Affiliations

  1. Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, Faculty of Science, The University of Hong Kong, Pokfulam Road, Hong Kong, SAR, People’s Republic of China

    Ruo-Nan Wu, Han Meng & Ji-Dong Gu

  2. Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization, Guangdong Academy of Forestry, Guangzhou, People’s Republic of China

    Yong-Feng Wang

  3. Laboratory of Microbial Ecology and Toxicology, Guangdong Academy of Forestry, Guangzhou, People’s Republic of China

    Yong-Feng Wang

  4. Shenzhen R&D Key Laboratory of Alien Pest Detection Technology, Shenzhen Entry-Exit Inspection and Quarantine Bureau, Shenzhen, People’s Republic of China

    Wensheng Lan

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  1. Ruo-Nan Wu
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  2. Han Meng
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Correspondence to Ji-Dong Gu.

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This study was funded by the National Natural Science Foundation of China (Grant No. 31470562 to YFW), a Shenzhen Scientific Grant (JCYJ20140722112616608 to WSL) from the Shenzhen Science and Technology Innovation Committee, and a Hong Kong PhD Fellowship (RW).

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Wu, RN., Meng, H., Wang, YF. et al. A More Comprehensive Community of Ammonia-Oxidizing Archaea (AOA) Revealed by Genomic DNA and RNA Analyses of amoA Gene in Subtropical Acidic Forest Soils. Microb Ecol 74, 910–922 (2017). https://doi.org/10.1007/s00248-017-1045-4

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