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Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean

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Abstract

Nitrification, the aerobic oxidation of ammonia to nitrate via nitrite, is performed by nitrifying microbes including ammonia-oxidizing bacteria (AOB) and archaea (AOA). In the current study, the phylogenetic diversity and abundance of AOB and AOA in deep-sea sediments of the Pacific Ocean were investigated using ammonia monooxygenase subunit A (amoA) coding genes as molecular markers. The study uncovered 3 AOB unique operational taxonomic units (OTUs, defined at sequence groups that differ by ≤5 %), which indicates lower diversity than AOA (13 OTUs obtained). All AOB amoA gene sequences were phylogenetically related to amoA sequences similar to those found in marine Nitrosospira species, and all AOA amoA gene sequences were affiliated with the marine sediment clade. Quantitative PCR revealed similar archaeal amoA gene abundances [1.68 × 105–1.89 × 106 copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 103 to 2.29 × 106 copies/g sediment (wet weight). The AOA/AOB amoA gene abundance ratios ranged from 0.012 to 162 and were negatively correlated with total C and C/N ratio. These results suggest that organic loading may be a key factor regulating the relative abundance of AOA and AOB in deep-sea environments of the Pacific Ocean.

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Acknowledgments

The work was financially supported by the China Ocean Mineral Resources R&D Association (COMRA) Program (DY125-15-R-01) and the National Key Basic Research Program of China (“973”-Program, 2015CB755903).

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    Authors and Affiliations

    1. Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen, 361005, People’s Republic of China

      Zhu-Hua Luo, Wei Xu & Tian-Hua Zhong

    2. Fujian Collaborative Innovation Center for Exploitation and Utilization of Marine Biological Resources, 178 Daxue Road, Xiamen, 361005, People’s Republic of China

      Zhu-Hua Luo, Wei Xu & Tian-Hua Zhong

    3. Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People’s Republic of China

      Meng Li

    4. School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, People’s Republic of China

      Ji-Dong Gu

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    1. Zhu-Hua Luo
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    Zhu-Hua Luo and Wei Xu have contributed equally to the work.

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    Luo, ZH., Xu, W., Li, M. et al. Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean. Antonie van Leeuwenhoek 108, 329–342 (2015). https://doi.org/10.1007/s10482-015-0485-4

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