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Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples

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Abstract

Research on anammox (anaerobic ammonium oxidizing) bacteria is important due to their biogeochemical and industrial application significance since the first discovery made over two decades ago. By coupling NH4+ and NO2− biochemically to form N2 gas, anammox bacteria contribute significantly to global marine and terrestrial nitrogen balance (responsible for 50, 9~40, and 4~37% of the nitrogen loss for marine, lakes, and paddy soil) and are also useful in energy-conserving nitrogen removal in wastewater treatment. PCR-based detection and quantification of anammox bacteria are an easy, essential, and widely accessible technique used ubiquitously for studying them in many environmental niches. In this article, we make a summary on practical applications of 16S rRNA and functional gene PCR primers, including hydrazine dehydrogenase (Hzo), nitrite reductase (NirS), hydrazine synthase (Hzs), and cytochrome c biogenesis proteins (Ccs) in detection of them. PCR primer performances in both practical applications and tests in silico are also presented for comparison. For detecting general and specific anammox bacterial groups, selection of appropriate PCR primers for different environmental samples and practical application guidance on choice of appropriate primer pairs for different purposes are also offered. This article provides practical information on selection and application of PCR technique in detection of anammox bacteria from the diverse environments to further promote convenient applications of this technique in research and other purposes.

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Funding

This study was funded by the Key Project of Department of Education of Guangdong Provice (No. 2017KZDXM071) (ML), the Science and Technology Innovation Committee  Shenzhen City (No. JCYJ20170818091727570) (ML); General Research Fund (Grant No. 701913) (J-DG); and Theme-based Research Scheme Project (Grant No. T21-711/16-R) (J-DG).

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  1. Zhichao Zhou and Qiaoyan Wei contributed equally to this work.

Authors and Affiliations

  1. Laboratory of Environmental Microbiology and Toxicology, School of Biological Sciences, The University of Hong Kong, Pokfulam Road, Hong Kong SAR, Hong Kong, People’s Republic of China

    Zhichao Zhou, Yuchun Yang & Ji-Dong Gu

  2. Institute for Advanced Study, Shenzhen University, Shenzhen, 518060, People’s Republic of China

    Qiaoyan Wei & Meng Li

  3. Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, People’s Republic of China

    Qiaoyan Wei

  4. State Key Laboratory in Marine Pollution, City University of Hong Kong, Tat Chee Avenue, Kowloon, Hong Kong, SAR, People’s Republic of China

    Ji-Dong Gu

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  1. Zhichao Zhou
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  2. Qiaoyan Wei
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  3. Yuchun Yang
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  4. Meng Li
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  5. Ji-Dong Gu
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Correspondence to Meng Li or Ji-Dong Gu.

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Zhou, Z., Wei, Q., Yang, Y. et al. Practical applications of PCR primers in detection of anammox bacteria effectively from different types of samples. Appl Microbiol Biotechnol 102, 5859–5871 (2018). https://doi.org/10.1007/s00253-018-9078-2

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  • DOI: https://doi.org/10.1007/s00253-018-9078-2

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