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

• Published in: Antonie van Leeuwenhoek 2015-08, Vol.108 (2), p.329-342
• Main Authors: Luo, Zhu-Hua, Xu, Wei, Li, Meng, Gu, Ji-Dong, Zhong, Tian-Hua
• Format: Article
• Language: English
• Subjects: Aerobiosis; Ammonia; Ammonia - metabolism; ammonia monooxygenase; Archaea; Archaea - classification; Archaea - enzymology; Archaea - genetics; bacteria; Bacteria - classification; Bacteria - enzymology; Bacteria - genetics; Biomedical and Life Sciences; Biota; Carbon - analysis; carbon nitrogen ratio; Deep sea; Gene Dosage; genes; genetic markers; Genetic Variation; Geologic Sediments - microbiology; Life Sciences; Marine biology; Marine sediments; Medical Microbiology; Microbiology; Microorganisms; Molecular Sequence Data; Nitrification; nitrites; Nitrogen - analysis; Nitrosospira; nucleotide sequences; Oceans; Organic loading; Original Paper; oxidation; Oxidation-Reduction; Oxidoreductases - genetics; Pacific Ocean; Phylogenetics; phylogeny; Plant Sciences; quantitative polymerase chain reaction; Relative abundance; Seawater - chemistry; Sediments; Sequence Analysis, DNA; Soil Science & Conservation; Spatial distribution; Taxonomy
• ISSN: 0003-6072; 1572-9699
• DOI: 10.1007/s10482-015-0485-4

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.