Microbial Ecology

, Volume 77, Issue 1, pp 1–11 | Cite as

Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes

  • Amit Kumar
  • Daphne H. P. Ng
  • Yichao Wu
  • Bin CaoEmail author
Microbiology of Aquatic Systems


Re-naturalized quarry lakes are important ecosystems, which support complex communities of flora and fauna. Microorganisms associated with sediment and water form the lowest trophic level in these ecosystems and drive biogeochemical cycles. A direct comparison of microbial taxa in water and sediment microbial communities is lacking, which limits our understanding of the dominant functions that are carried out by the water and sediment microbial communities in quarry lakes. In this study, using the 16S rDNA amplicon sequencing approach, we compared microbial communities in the water and sediment in two re-naturalized quarry lakes in Singapore and elucidated putative functions of the sediment and water microbial communities in driving major biogeochemical processes. The richness and diversity of microbial communities in sediments of the quarry lakes were higher than those in the water. The composition of the microbial communities in the sediments from the two quarries was highly similar to one another, while those in the water differed greatly. Although the microbial communities of the sediment and water samples shared some common members, a large number of microbial taxa (at the phylum and genus levels) were prevalent either in sediment or water alone. Our results provide valuable insights into the prevalent biogeochemical processes carried out by water and sediment microbial communities in tropical granite quarry lakes, highlighting distinct microbial processes in water and sediment that contribute to the natural purification of the resident water.


Quarry lake Sediment 16S rDNA amplicon sequencing Microbial community 



Sequencing was carried out with the help of Dr. Daniela Moses and Professor Stephan Schuster using the sequencing facilities at the Singapore Centre for Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore. We thank the Singapore National Parks Board (NParks), in particular, Ms. Samantha Lai and Ms. Joanna Yeo, for their assistance in sample collection. This material is based on research/work supported by the Singapore Ministry of National Development and National Research Foundation under L2 NIC Award No. L2NICCFP1-2013-3.

Compliance with Ethical Standards

Competing Interests

The authors declare that they have no competing interests.


Any opinions, findings, and conclusions or recommendations expressed in this material are those of the authors and do not necessarily reflect the views of the L2 NIC.

Supplementary material

248_2018_1204_MOESM1_ESM.pdf (3.6 mb)
ESM 1 (PDF 3659 kb)


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Authors and Affiliations

  1. 1.School of Civil and Environmental EngineeringNanyang Technological UniversitySingaporeSingapore
  2. 2.Singapore Centre for Environmental Life Sciences EngineeringNanyang Technological UniversitySingaporeSingapore
  3. 3.College of Resources and EnvironmentHuazhong Agricultural UniversityWuhanChina

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