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

• Published in: Applied microbiology and biotechnology Vol. 98; no. 12; pp. 5685 - 5696
• Main Authors: Chen, Jing, Zhou, Zhi-Chao, Gu, Ji-Dong
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer-Verlag 01.06.2014; Springer Berlin Heidelberg; Springer; Springer Nature B.V
• Subjects: ammonium compounds; Anaerobiosis; Aquatic ecology; Bacteria; Bacteria - classification; Bacteria - enzymology; Bacteria - genetics; Biodegradation; Biodiversity; Biomedical and Life Sciences; Biotechnology; carbon; Carbon cycle; China; Cluster Analysis; community structure; continental shelf; DNA primers; DNA, Bacterial - chemistry; DNA, Bacterial - genetics; DNA, Ribosomal - chemistry; DNA, Ribosomal - genetics; ecosystems; Environmental aspects; environmental factors; Genes; Geologic Sediments; Investigations; Life Sciences; marine environment; Methane; Methane - metabolism; Methane biosynthesis; Methods and Protocols; Microbial Genetics and Genomics; Microbiology; Microorganisms; Molecular Sequence Data; nitrates; nitrites; Nitrites - metabolism; nitrogen; Oxidation; Oxidation-Reduction; Oxidation-reduction reaction; Pacific Ocean; Phylogeny; Physiological aspects; polymerase chain reaction; ribosomal RNA; RNA, Ribosomal, 16S - genetics; Salinity; Sediments; Sequence Analysis, DNA; Studies; temperature; China; Pacific Ocean; South China Sea; n-damo; South China Sea; Marine; gene; Diversity; Distribution; Anaerobic methane oxidation
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-014-5733-4

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.