Microbial Community Composition and Putative Biogeochemical Functions in the Sediment and Water of Tropical Granite Quarry Lakes
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.
KeywordsQuarry 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
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.
- 1.Allewalt JP, Bateson MM, Revsbech NP, Slack K, Ward DM (2006) Effect of temperature and light on growth of and photosynthesis by Synechococcus isolates typical of those predominating in the octopus spring microbial mat community of Yellowstone National Park. Appl Environ Microbiol 72:544–550CrossRefGoogle Scholar
- 4.Bai L, Cao C, Wang C, Xu H, Zhang H, Slaveykova VI, Jiang H (2017) Toward quantitative understanding of the bioavailability of dissolved organic matter in freshwater lake during Cyanobacteria blooming. Environ Sci Technol 51:6018–6026Google Scholar
- 10.Capone DG, Bronk DA, Mulholland MR, Carpenter EJ (2008) Nitrogen in the marine environment. Academic Press, CambridgeGoogle Scholar
- 24.Gächter R, Meyer JS, Mares A (1988) Contribution of bacteria to release and fixation of phosphorus in lake sediments. Limnol Oceanogr 33:1542–1558Google Scholar
- 26.Glass EM, Wilkening J, Wilke A, Antonopoulos D, Meyer F (2010) Using the metagenomics RAST server (MG-RAST) for analyzing shotgun metagenomes. Cold Spring Harb Protoc. https://doi.org/10.1101/pdb.prot5368
- 28.Hamdi O, Hania WB, Postec A, Bouallagui H, Hamdi M, Bonin P, Ollivier B, Fardeau M-L (2015) Aminobacterium thunnarium sp. nov., a mesophilic, amino acid-degrading bacterium isolated from an anaerobic sludge digester, pertaining to the phylum Synergistetes. Int J Syst Evol Microbiol 65:609–614CrossRefGoogle Scholar
- 29.Henderson JC (2000) The survival of a forest fragment: Bukit Timah Nature Reserve, Singapore. Forest tourism and recreation: case studies in environmental management. New York: Cabi Pub, pp 23–39Google Scholar
- 34.Kerou M, Offre P, Valledor L, Abby SS, Melcher M, Nagler M, Weckwerth W, Schleper C (2016) Proteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers. Proc Natl Acad Sci 113:E7937–E7946Google Scholar
- 49.Oksanen J, Blanchet F, Kindt R, Legendre P, O’Hara R (2016) Vegan: community ecology package. R Packag. 2.3-3Google Scholar
- 51.Otwell AE, Callister SJ, Zink EM, Smith RD & Richardson RE (2016) Comparative proteomic analysis of Desulfotomaculum reducens MI-1: insights into the metabolic versatility of a gram-positive sulfate- and metal-reducing bacterium. Front Microbiol 7:191Google Scholar
- 52.Qu J, Zhang Q, Zhang N, Shen L, Liu P (2015) Microbial community diversity in water and sediment of an eutrophic lake during harmful algal bloom using MiSeq illumina technology. Int Congr Adv Environ Res. https://doi.org/10.7763/IPCBEE
- 60.Stal LJ, Severin I, Bolhuis H (2010) The ecology of nitrogen fixation in cyanobacterial mats. In: Hallenbeck PC (ed) Recent advances in phototrophic prokaryotes. Springer, Berlin/Heidelberg, pp 31–45Google Scholar
- 61.Stieglmeier M, Klingl A, Alves RJ, Simon KM, Melcher M, Leisch N, Schleper C (2014) Nitrososphaera viennensis gen. nov., sp. nov., an aerobic and mesophilic, ammonia-oxidizing archaeon from soil and a member of the archaeal phylum Thaumarchaeota. Int J Syst Evol Microbiol 64(8):2738–2752CrossRefGoogle Scholar
- 65.Wilke A, Gerlach W, Harrison T, Paczian T, Trimble WL, Meyer F (2016) MG-RAST Manual for version 4, revisionGoogle Scholar
- 69.Keegan KP, Glass EM, Meyer F (2016) MG-RAST, a metagenomics service for analysis of microbial community structure and function. In: Martin F, Uroz S (eds) Microbial environmental genomics. Springer, Berlin/Heidelberg, pp 207–233Google Scholar
- 70.Shcherbakova VA, Laurinavichyus KS, Chuvil’skaya NA, Ryzhmanova YV, Akimenko VK (2015) Anaerobic bacteria involved in the degradation of aromatic sulfonates to methane. Appl Biochem Microbiol 51(2):209–214Google Scholar
- 71.Liu G, Ling FQ, van der Mark EJ, Zhang XD, Knezev A, Verberk JQJC, van der Meer WGJ, Medema GJ, Liu WT, van Dijk JC (2016) Comparison of particle-associated bacteria from a drinking water treatment plant and distribution reservoirs with different water sources. Sci Rep 6:20367Google Scholar