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Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes

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Abstract

Nitrite-dependent anaerobic methane oxidation (n-damo) process is unique in linking the microbial carbon and nitrogen cycles, but the presence of n-damo bacteria in marine ecosystem and the associated environmental factors are still poorly understood. In the present study, detection of n-damo bacteria using 16S rRNA and pmoA gene-based PCR primers was successfully employed to reveal their diversity and distribution in the surface and subsurface sediments of the South China Sea (SCS). The widespread occurrence of n-damo bacteria in both the surface and subsurface sediments with high diversity has been confirmed in this study. The pmoA gene-amplified sequences clustered within three newly erected subclusters, namely SCS-1, SCS-2, and SCS-3, suggesting the unique niche specificity of n-damo bacteria in the marine ecosystem. Results indicated the presence of n-damo bacteria in the west Pacific Ocean with a wide distribution from the continental shelf (E201S) to the deep abyss (E407S and E407B). Community structures of n-damo bacteria in SCS are clearly different from those of nonmarine ones known. It is also found that NO x − and NH4 + affected the community structures and distribution of n-damo bacteria in the SCS sediments differently. Salinity is another important factor identified, shaping the n-damo communities in marine environments. The community based on pmoA gene-amplified sequences, and community richness and diversity based on 16S rRNA gene-amplified sequences correlated with temperature.

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Acknowledgments

This project was supported by the Hong Kong PhD Fellowship (JC), the University of Hong Kong Foundation PhD Fellowship (ZCZ), and RGC GRF grant no. 701913 (J-DG). Additional financial support for this research project was from the laboratory fund. We thank Dr. Li-Ying Wang and Miss Han Meng for the useful discussions and Ms Kelly Lau for the general laboratory assistance.

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  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

    Jing Chen, Zhi-Chao Zhou & Ji-Dong Gu

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  1. Jing Chen
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Correspondence to Ji-Dong Gu.

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Chen, J., Zhou, ZC. & Gu, JD. Occurrence and diversity of nitrite-dependent anaerobic methane oxidation bacteria in the sediments of the South China Sea revealed by amplification of both 16S rRNA and pmoA genes. Appl Microbiol Biotechnol 98, 5685–5696 (2014). https://doi.org/10.1007/s00253-014-5733-4

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