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Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia

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Abstract

In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

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Acknowledgments

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

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Authors and Affiliations

  1. Department of Biological Science, Faculty of Science, Universiti Tunku Abdul Rahman, Jalan Universiti, Bandar Barat, Kampar, 31900, Perak, Malaysia

    S. L. S. Sow & G. Khoo

  2. School of Science and Engineering, Malaysia University of Science and Technology, GL33, Ground Floor, Block C, Kelana Square, 17, Jalan SS 7/26, Petaling Jaya, 47301, Selangor, Malaysia

    L. K. Chong

  3. Biomedical Research Centre, Sheffield Hallam University, Howard Street, Sheffield, S1 1WB, United Kingdom

    T. J. Smith & P. L. Harrison

  4. Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Lot PT 21144, Jalan Sungai Long, Bandar Sungai Long, Cheras, 43000, Kajang, Selangor, Malaysia

    H. K. A. Ong

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  1. S. L. S. Sow
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  2. G. Khoo
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  3. L. K. Chong
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  4. T. J. Smith
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Correspondence to H. K. A. Ong.

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Sow, S.L.S., Khoo, G., Chong, L.K. et al. Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia. World J Microbiol Biotechnol 30, 2645–2653 (2014). https://doi.org/10.1007/s11274-014-1687-z

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  • DOI: https://doi.org/10.1007/s11274-014-1687-z

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