Diversity and quantity of ammonia-oxidizing Archaea and Bacteria in sediment of the Pearl River Estuary, China

• Published in: Applied microbiology and biotechnology Vol. 90; no. 3; pp. 1137 - 1145
• Main Authors: Jin, Tao, Zhang, Tong, Ye, Lin, Lee, On On, Wong, Yue Him, Qian, Pei Yuan
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-05-2011; Springer; Springer Nature B.V
• Subjects: Ammonia; Ammonia - metabolism; Analysis; Archaea; Archaea - classification; Archaea - genetics; Archaea - isolation & purification; Archaea - metabolism; Bacteria; Bacteria - classification; Bacteria - genetics; Bacteria - isolation & purification; Bacteria - metabolism; Biodiversity; Biological and medical sciences; Biotechnology; China; Cloning; Community composition; Environmental Biotechnology; Estuaries; Fundamental and applied biological sciences. Psychology; Genes; Geologic Sediments - microbiology; Laboratories; Life Sciences; Microbial Genetics and Genomics; Microbiology; Microorganisms; Molecular Sequence Data; Nitrates; Nitrogen; Oxidation; Phylogeny; Plastics; Polymorphism; Relative abundance; Rivers; Rivers - microbiology; RNA; Salinity; Sediment samplers; Sediments; Sediments (Geology); Studies; China; South China Sea; China, People's Rep., Zhu R; China, People's Rep; A) gene; qPCR; Ammonia-oxidizing bacteria (AOB); Ammonia monooxygenase α-subunit; Ammonia-oxidizing archaea (AOA); T-RFLP; Ammonia monooxygenase α-subunit (amoA) gene; Archaeobacteria; Diversity; Estuaries; Rivers; Subunit; Sediments; Ammonia; Restriction fragment length polymorphism; Gene; ammonia oxidizing bacteria; Bacteria; Oxidation
• ISSN: 0175-7598; 1432-0614
• DOI: 10.1007/s00253-011-3107-8

The diversity and abundance of ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) in the sediment of the Pearl River Estuary were investigated by cloning and quantitative real-time polymerase chain reaction (qPCR). From one sediment sample S16, 36 AOA OTUs (3% cutoff) were obtained from three clone libraries constructed using three primer sets for
amo
A gene. Among the 36 OTUs, six were shared by all three clone libraries, two appeared in two clone libraries, and the other 28 were only recovered in one of the libraries. For AOB, only seven OTUs (based on 16S rRNA gene) and eight OTUs (based on
amo
A gene) were obtained, showing lower diversity than AOA. The qPCR results revealed that AOA
amo
A gene copy numbers ranged from 9.6 × 10
6
to 5.1 × 10
7
copies per gram of sediment and AOB
amo
A gene ranged from 9.5 × 10
4
to 6.2 × 10
5
copies per gram of sediment, indicating that the dominant ammonia-oxidizing microorganisms in the sediment of the Pearl River Estuary were AOA. The terminal restriction fragment length polymorphism results showed that the relative abundance of AOB species in the sediment samples of different salinity were significantly different, indicating that salinity might be a key factor shaping the AOB community composition.