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

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.

Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia

“…We used PICRUSt, a bioinformatics tool that uses marker genes, in this case 16S rRNA, to predict metagenome gene functional content. A detailed description of these methods has been published previously [25,36] …”

“…This is an extraction method frequently used for this purpose [36,41,42]. Briefly, the whole membrane filter and 500 mg of sediment or sponge were transferred to Lysing Matrix E tubes containing a mixture of ceramic and silica particles.…”

“…Seawater was sampled by filtering approximately 1 l [37,38] of seawater (collected between 1 and 3 m depth) through a Millipore ® White Isopore Membrane Filter (0.22-μm pore size). Sponges were sampled including fragments of surface and interior following previously described methods [36]. All samples were stored in 96 % EtOH [39,40] and kept cool (<4°C) after collection and during transport.…”

“…We, therefore, sampled additional specimens of S. massa from Kudingareng Keke and another site, Bone Baku. Sediment was sampled using the mini core method as previously described [35,36]. Seawater was sampled by filtering approximately 1 l [37,38] of seawater (collected between 1 and 3 m depth) through a Millipore ® White Isopore Membrane Filter (0.22-μm pore size).…”

Distribution of sediment bacterial and archaeal communities in plateau freshwater lakes

“…Archaea are currently known to be involved in a variety of biogeochemical processes, such as mineralization of organic carbon to methane (methanogenesis) (Ahila et al 2014;Chaudhary et al 2013;Polonia et al 2014), sulfate reduction (Hocking et al 2014), and ammonia oxidation (Liu et al Jingxu Zhang and Yuyin Yang contributed equally to this study.…”