Microbial Ecology

, Volume 67, Issue 3, pp 553–567 | Cite as

Composition of Archaea in Seawater, Sediment, and Sponges in the Kepulauan Seribu Reef System, Indonesia

  • Ana R. M. Polónia
  • Daniel F. R. Cleary
  • Leticia N. Duarte
  • Nicole J. de Voogd
  • Newton C. M Gomes
Microbiology of Aquatic Systems


Coral reefs are among the most diverse and productive ecosystems in the world. Most research has, however, focused on eukaryotes such as corals and fishes. Recently, there has been increasing interest in the composition of prokaryotes, particularly those inhabiting corals and sponges, but these have mainly focused on bacteria. There have been very few studies of coral reef Archaea, despite the fact that Archaea have been shown to play crucial roles in nutrient dynamics, including nitrification and methanogenesis, of oligotrophic environments such as coral reefs. Here, we present the first study to assess Archaea in four different coral reef biotopes (seawater, sediment, and two sponge species, Stylissa massa and Xestospongia testudinaria). The archaeal community of both sponge species and sediment was dominated by Crenarchaeota, while the seawater community was dominated by Euryarchaeota. The biotope explained more than 72 % of the variation in archaeal composition. The number of operational taxonomic units (OTUs) was highest in sediment and seawater biotopes and substantially lower in both sponge hosts. No “sponge-specific” archaeal OTUs were found, i.e., OTUs found in both sponge species but absent from nonhost biotopes. Despite both sponge species hosting phylogenetically distinct microbial assemblages, there were only minor differences in Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways. In contrast, most functional pathways differed significantly between microbiomes from sponges and nonhost biotopes including all energy metabolic pathways. With the exception of the methane and nitrogen metabolic pathway, all energy metabolic pathways were enriched in sponges when compared to nonhost biotopes.


Sponge Archaea Basic Local Alignment Search Tool Seawater Sample Archaeal Community 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This research was supported by the Portuguese Foundation for Science and Technology (FCT) under grant PTDC/AAC-AMB/115304/2009 (LESS CORAL) and a PhD Fellowship SFRH/BD/33391/2008. Samples were collected under a Scientific Research Permit issued by the Indonesian State Ministry for Research and Technology (Kementerian Riset Dan Teknologi Republik Indonesia – RISTEK #268/SIP/FRP/SM/VII/2011). We thank the Indonesian Institute of Sciences (PPO – LIPI) for their support and especially Dr Yos Tuti.

Supplementary material

248_2013_365_MOESM1_ESM.pdf (150 kb)
ESM 1 (PDF 150 kb)
248_2013_365_MOESM2_ESM.pdf (777 kb)
ESM 2 (PDF 777 kb)
248_2013_365_MOESM3_ESM.docx (13 kb)
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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  • Ana R. M. Polónia
    • 1
  • Daniel F. R. Cleary
    • 1
  • Leticia N. Duarte
    • 1
  • Nicole J. de Voogd
    • 2
  • Newton C. M Gomes
    • 1
  1. 1.Department of Biology, CESAMUniversidade de AveiroAveiroPortugal
  2. 2.Naturalis Biodiversity CenterLeidenThe Netherlands

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