World Journal of Microbiology and Biotechnology

, Volume 30, Issue 2, pp 757–766 | Cite as

Molecular diversity of the ammonia-oxidizing bacteria community in disused tin-mining ponds located within Kampar, Perak, Malaysia

  • S. L. S. Sow
  • G. Khoo
  • L. K. Chong
  • T. J. Smith
  • P. L. Harrison
  • H. K. A. OngEmail author
Original Paper


Disused tin-mining ponds make up a significant amount of water bodies in Malaysia particularly at the Kinta Valley in the state of Perak where tin-mining activities were the most extensive, and these abundantly available water sources are widely used in the field of aquaculture and agriculture. However, the natural ecology and physicochemical conditions of these ponds, many of which have been altered due to secondary post-mining activities, remains to be explored. As ammonia-oxidizing bacteria (AOB) are directly related to the nutrient cycles of aquatic environments and are useful bioindicators of environmental variations, the focus of this study was to identify AOBs associated with disused tin-mining ponds that have a history of different secondary activities in comparison to ponds which were left untouched and remained as part of the landscape. The 16S rDNA gene was used to detect AOBs in the sediment and water sampled from the three types of disused mining ponds, namely ponds without secondary activity, ponds that were used for lotus cultivation and post-aquaculture ponds. When the varying pond types were compared with the sequence and phylogenetic analysis of the AOB clone libraries, both Nitrosomonas and Nitrosospira-like AOB were detected though Nitrosospira spp. was seen to be the most ubiquitous AOB as it was present in all ponds types. However, AOBs were not detected in the sediments of idle ponds. Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture indicated the highest richness of AOBs. Canonical correspondence analysis indicated that among the physicochemical properties of the pond sites, TAN and nitrite were shown to be the main factors that influenced the community structure of AOBs in these disused tin-mining ponds.


Ammonia oxidizing bacteria 16S ribosomal RNA gene Molecular diversity Disused mining ponds Physicochemical properties 



This project is supported by Tunku Abdul Rahman University and a research grant awarded by the Malaysia Toray Science Foundation (09/G23).

Supplementary material

11274_2013_1506_MOESM1_ESM.docx (2.5 mb)
Supplementary material 1 (DOCX 2535 kb)


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Copyright information

© Springer Science+Business Media Dordrecht 2013

Authors and Affiliations

  • S. L. S. Sow
    • 1
  • G. Khoo
    • 1
  • L. K. Chong
    • 2
  • T. J. Smith
    • 3
  • P. L. Harrison
    • 3
  • H. K. A. Ong
    • 4
    Email author
  1. 1.Department of Biological Science, Faculty of ScienceUniversiti Tunku Abdul RahmanKamparMalaysia
  2. 2.School of Science and EngineeringMalaysia University of Science and TechnologyPetaling JayaMalaysia
  3. 3.Biomedical Research CentreSheffield Hallam UniversitySheffieldUK
  4. 4.Department of Pre-Clinical Sciences, Faculty of Medicine and Health SciencesUniversiti Tunku Abdul RahmanKajangMalaysia

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