Microbial Ecology

, Volume 76, Issue 3, pp 610–624 | Cite as

Bacterial Communities Inhabiting the Sponge Biemna fortis, Sediment and Water in Marine Lakes and the Open Sea

  • Daniel F. R. ClearyEmail author
  • Ana R. M. Polónia
  • Nicole J. de Voogd
Microbiology of Aquatic Systems


Marine lakes are small bodies of landlocked seawater that are isolated from the open sea and have been shown to house numerous rare and unique taxa. The environmental conditions of the lakes are also characterised by lower pH and salinity and higher temperatures than generally found in the open sea. In the present study, we used a 16S rRNA gene barcoded pyrosequencing approach and a predictive metagenomic approach (PICRUSt) to examine bacterial composition and function in three distinct biotopes (sediment, water and the sponge species Biemna fortis) in three habitats (two marine lakes and the open sea) of the Berau reef system, Indonesia. Both biotope and habitat were significant predictors of higher taxon abundance and compositional variation. Most of the variation in operational taxonomic unit (OTU) composition was related to the biotope (42% for biotope alone versus 9% for habitat alone and 15% combined). Most OTUs were also restricted to a single biotope (1047 for B. fortis, 6120 for sediment and 471 for water). Only 98 OTUs were shared across all three biotopes. Bacterial communities from B. fortis, sediment and water samples were, however, also distinct in marine lake and open sea habitats. This was evident in the abundance of higher bacterial taxa. For example, the phylum Cyanobacteria was significantly more abundant in samples from marine lakes than from the open sea. This difference was most pronounced in the sponge B. fortis. In line with the compositional differences, there were pronounced differences in predicted relative gene count abundance among biotopes and habitats. Of particular interest was the predicted enrichment in B. fortis from the marine lakes for pathways including DNA replication and repair and the glutathione metabolism. This may facilitate adaptation of host and microbes to life in ‘stressful’ low pH, low salinity and/or high temperature environments such as those encountered in marine lakes.


Anchialine lakes Cyanobacteria Indonesia pH 



We are grateful to the Indonesian State Ministry of Research and Technology (RISTEK) for providing research permits. We thank the following people for their help in various ways: Leontine Becking, Rossana Freitas, Suharsono, Y. Tuti, E.Oberhauser, R. Suhr and the staff of Nabucco Island Dive Resort.

Funding Information

The research was sponsored by the Indonesian Institute of Sciences (LIPI) and funded by the Portuguese Foundation for Science and Technology, FCT, project LESS CORAL, PTDC/AAC-AMB/115304/2009. Ana R.M. Polónia was supported by a postdoctoral scholarship [SFRH/BPD/117563/2016] funded by FCT, Portugal (QREN-POPH Type 4.1—Advanced Training, subsidised by the European Social Fund and national funds MCTES). Thanks are also due, for the financial support to CESAM [UID/AMB/50017], to FCT/MEC through national funds and co-funding by FEDER, within the PT2020 Partnership Agreement and Compete 2020.

Supplementary material

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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  • Daniel F. R. Cleary
    • 1
    Email author
  • Ana R. M. Polónia
    • 1
  • Nicole J. de Voogd
    • 2
  1. 1.Department of Biology, CESAMUniversidade de AveiroAveiroPortugal
  2. 2.Naturalis Biodiversity CenterLeidenThe Netherlands

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