title: Spatial distribution and abundance of ammonia-oxidizing microorganisms in deep-sea sediments of the Pacific Ocean.
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 × 10(5)-1.89 × 10(6) copies/g sediment (wet weight)] among different sites. Bacterial amoA gene abundances ranged from 5.28 × 10(3) to 2.29 × 10(6) 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.
authors.affiliation: Key Laboratory of Marine Biogenetic Resources, Third Institute of Oceanography, State Oceanic Administration, 178 Daxue Road, Xiamen, 361005, People's Republic of China, luozhuhua@tio.org.cn.
authors.forename: Zhu-Hua
authors.initials: ZH
authors.lastname: Luo
authors.forename: Wei
authors.initials: W
authors.lastname: Xu
authors.forename: Meng
authors.initials: M
authors.lastname: Li
authors.forename: Ji-Dong
authors.initials: JD
authors.lastname: Gu
authors.forename: Tian-Hua
authors.initials: TH
authors.lastname: Zhong
mesh_terms: D000332:Aerobiosis; D000641:Ammonia / Q000378:metabolism*; D001105:Archaea / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D001419:Bacteria / Q000145:classification* / Q000201:enzymology / Q000235:genetics*; D058448:Biota; D002244:Carbon / Q000032:analysis; D018628:Gene Dosage; D014644:Genetic Variation; D019015:Geologic Sediments / Q000382:microbiology*; D008969:Molecular Sequence Data; D058465:Nitrification; D009584:Nitrogen / Q000032:analysis; D010084:Oxidation-Reduction; D010088:Oxidoreductases / Q000235:genetics; D010140:Pacific Ocean; D012623:Seawater / Q000737:chemistry; D017422:Sequence Analysis, DNA
chemical_list: D002244:Carbon; D000641:Ammonia; D010088:Oxidoreductases; C045582:ammonia monooxygenase; D009584:Nitrogen