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Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring

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Abstract

Microbial nitrification is a key process in the nitrogen cycle in the continental shelf ecosystems. The genotype compositions and abundance of the ammonia monooxygenase gene, amoA, derived from ammonia-oxidizing archaea (AOA) and bacteria (AOB) in two size fractions (2–10 and 0.2–2 µm), were investigated in the East China Sea (ECS) in May 2008 using PCR-denaturing gradient gel electrophoresis (DGGE) and quantitative PCR (qPCR). Four sites were selected across the continental shelf edge: continental shelf water (CSW), Kuroshio branch water (KBW), transition between CSW and KBW (TCSKB) and coastal KBW (CKBW). The gene copy numbers of AOA-amoA were higher than those of AOB-amoA in ECS. The relative abundance of amoA to the total 16S rRNA gene level reached approximately 15% in KBW and CKBW for the free-living fraction of AOA, whereas the level was less than 0.01% throughout ECS for the AOB. A cluster analysis of the AOA-amoA-DGGE band pattern showed distinct genotype compositions in CSW in both the size fractions and in the surface of the TCSKB and KBW. Sequences of the DGGE bands were assigned to two clades. One of the clades exclusively consisted of sequences derived from the 2–10-µm fraction. This study revealed that AOA-amoA abundance dominated over AOB-amoA throughout the ECS, whereas the genotype composition of AOA-amoA were distributed heterogeneously across the water masses. Additionally, this is the first report showing the distribution of AOA-amoA genotypes characteristic to particle-associated AOA in the offshore of the East China Sea.

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Acknowledgements

We appreciate the efforts of the captain and crews of the R/V Tansei-Maru in facilitating sample collection for this study. We also thank to H. Endo for assistance. We also acknowledge support from the Hong Kong RGC (GRF661610 and 661911) and a HKUST Post-Doctoral Fellowship (PDF) matching fund; the Ministry of Education, Culture, Sports, Science and Technology, Japan for the Study of Kuroshio Ecosystem Dynamics for Sustainable Fisheries; and the JSPS Grant-in-Aid for Scientific Research on Innovative Areas (24121004).

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Authors and Affiliations

  1. Department of Biology, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong SAR, Hong Kong

    Takafumi Kataoka & Hongbin Liu

  2. Faculty of Environmental Earth Science, Hokkaido University, Kita-ku, Sapporo, 060-0810, Japan

    Takafumi Kataoka, Koji Suzuki, Tomohisa Irino, Masanobu Yamamoto & Seigo Higashi

  3. Faculty of Marine Science and Technology, Fukui Prefectural University, Gakuen-cho 1-1, Obama, 917-0003, Japan

    Takafumi Kataoka

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  1. Takafumi Kataoka
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Correspondence to Takafumi Kataoka.

Additional information

Communicated by Harald Huber.

The nucleotide sequences of amoA determined in this study have been deposited in the DNA Data Bank of Japan (DDBJ) nucleotide sequence database under Accession Numbers AB666167–AB666221.

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Kataoka, T., Suzuki, K., Irino, T. et al. Phylogenetic diversity and distribution of bacterial and archaeal amoA genes in the East China Sea during spring. Arch Microbiol 200, 329–342 (2018). https://doi.org/10.1007/s00203-017-1442-6

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