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

  • Microbiology of Aquatic Systems
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Abstract

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.

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Acknowledgments

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.

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Authors and Affiliations

  1. Department of Biology, CESAM, Universidade de Aveiro, Campus Universitário de Santiago, 3810-193, Aveiro, Portugal

    Ana R. M. Polónia, Daniel F. R. Cleary, Leticia N. Duarte & Newton C. M Gomes

  2. Naturalis Biodiversity Center, P.O. Box 9517, 2300 RA, Leiden, The Netherlands

    Nicole J. de Voogd

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  1. Ana R. M. Polónia
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  2. Daniel F. R. Cleary
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  3. Leticia N. Duarte
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  5. Newton C. M Gomes
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Correspondence to Ana R. M. Polónia.

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Polónia, A.R.M., Cleary, D.F.R., Duarte, L.N. et al. Composition of Archaea in Seawater, Sediment, and Sponges in the Kepulauan Seribu Reef System, Indonesia. Microb Ecol 67, 553–567 (2014). https://doi.org/10.1007/s00248-013-0365-2

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