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Tropical Soil Bacterial Communities in Malaysia: pH Dominates in the Equatorial Tropics Too

  • Soil Microbiology
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Abstract

The dominant factors controlling soil bacterial community variation within the tropics are poorly known. We sampled soils across a range of land use types—primary (unlogged) and logged forests and crop and pasture lands in Malaysia. PCR-amplified soil DNA for the bacterial 16S rRNA gene targeting the V1–V3 region was pyrosequenced using the 454 Roche machine. We found that land use in itself has a weak but significant effect on the bacterial community composition. However, bacterial community composition and diversity was strongly correlated with soil properties, especially soil pH, total carbon, and C/N ratio. Soil pH was the best predictor of bacterial community composition and diversity across the various land use types, with the highest diversity close to neutral pH values. In addition, variation in phylogenetic structure of dominant lineages (Alphaproteobacteria, Beta/Gammaproteobacteria, Acidobacteria, and Actinobacteria) is also significantly correlated with soil pH. Together, these results confirm the importance of soil pH in structuring soil bacterial communities in Southeast Asia. Our results also suggest that unlike the general diversity pattern found for larger organisms, primary tropical forest is no richer in operational taxonomic units of soil bacteria than logged forest, and agricultural land (crop and pasture) is actually richer than primary forest, partly due to selection of more fertile soils that have higher pH for agriculture and the effects of soil liming raising pH.

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Acknowledgments

This work was supported by a Brain Gain grant from the Government of Malaysia and by SNU new faculty research grant to JM Adams. BM Tripathi was supported by the Graduate Scholarship for Excellent Foreign Students Program, SNU, South Korea.

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Authors and Affiliations

  1. Department of Biological Sciences, Seoul National University, Gwanak, Seoul, 151, Republic of Korea

    Binu M. Tripathi, Mincheol Kim, Dharmesh Singh, Larisa Lee-Cruz, Jongsik Chun & Jonathan M. Adams

  2. Division of Forest Biotechnology, Forest Research Institute of Malaysia (FRIM), Kepong, Malaysia

    Ang Lai-Hoe

  3. INTROP, Universiti Putra Malaysia, Serdang, Malaysia

    A. N. Ainuddin, Rusea Go & Jonathan M. Adams

  4. Institute of Bioscience, Faculty of Biotechnology and Biomolecular Sciences, Universiti Putra Malaysia, Serdang, Malaysia

    Raha Abdul Rahim

  5. Department of Land Management, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Malaysia

    M. H. A. Husni

Authors
  1. Binu M. Tripathi
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  2. Mincheol Kim
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  3. Dharmesh Singh
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  10. Jongsik Chun
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Correspondence to Jonathan M. Adams.

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Tripathi, B.M., Kim, M., Singh, D. et al. Tropical Soil Bacterial Communities in Malaysia: pH Dominates in the Equatorial Tropics Too. Microb Ecol 64, 474–484 (2012). https://doi.org/10.1007/s00248-012-0028-8

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  • DOI: https://doi.org/10.1007/s00248-012-0028-8

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