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Detection of ammonia-oxidizing Bacteria and Archaea within coral reef cyanobacterial mats

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Abstract

Coral-reef filamentous cyanobacterial mats are complex communities of microbes. We used DGGE and eubacterial and archaeal 16S rRNA and amoA ammonium monooxygenase subunit A primer sets to explore the presence of genes mediating nitrogen conversion within cyanobacterial mats from Hawaii. DGGE band analysis revealed the presence of halophiles such as Halococcus salifodinae and of Nitrosopumilus-like organisms. Twenty seven out of 31 clone sequences exhibited a 95 % or greater 16S rRNA gene identity with known archaeal ammonia oxidizers such as Nitrosopumilus maritimus. The presence of Archaea within those mats, as well as the co-occurrence of both ammonia-oxidizing Archaea and ammonia-oxidizing Bacteria suggests importance of the former in the cyanobacterial mat community, and suggests greater than anticipated diversity of nitrogen conversion processes and organisms in those systems.

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Acknowledgments

This work was partially supported by Grant #0314353 from the National Science Foundation to the Quality Education for Minorities (QEM) Network under which E. Cruz-Rivera served as a QEM Fellow. Cruz-Rivera would like to thank M. Rappé, D. Karl, H. Trapido-Rosenthal, T. Hemscheidt, and P. Bienfang for the use of facilities and equipment at HIMB and the University of Hawaii at Manoa, during the collection of field samples. He also acknowledges the invaluable help of B. Bruno in coordinating travel and other logistical arrangements. Sobolev was supported by the Junior Faculty Summer Research Grant from the University of Houston-Victoria Office of the Provost. Sobolev also would like to thank Ashley Chang who conducted a pilot study of Archaea in our samples. The data processing and manuscript preparation was conducted in Free Open Source Software; authors are indebted to Open Office, GIMP and the Ubuntu development community. Paige Ruschhaupt, T. Hibiya and three anonymous reviewers provided important editorial comments that improved the manuscript.

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  1. School of Arts and Sciences, University of Houston-Victoria, 3007N. Ben Wilson Dr. Rm. 109C, Victoria, TX, 77901, USA

    Dmitri Sobolev & Matthew R. Boyett

  2. Asian University for Women, 20/A M.M. Ali Road, Chittagong, Bangladesh

    Edwin Cruz-Rivera

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  1. Dmitri Sobolev
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  2. Matthew R. Boyett
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  3. Edwin Cruz-Rivera
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Correspondence to Dmitri Sobolev.

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Sobolev, D., Boyett, M.R. & Cruz-Rivera, E. Detection of ammonia-oxidizing Bacteria and Archaea within coral reef cyanobacterial mats. J Oceanogr 69, 591–600 (2013). https://doi.org/10.1007/s10872-013-0195-3

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