Bacterial community composition and predicted functional ecology of sponges, sediment and seawater from the thousand islands reef complex, West Java, Indonesia

Abstract

In the present study, we assessed the composition of Bacteria in four biotopes namely sediment, seawater and two sponge species (Stylissa massa and Xestospongia testudinaria) at four different reef sites in a coral reef ecosystem in West Java, Indonesia. In addition to this, we used a predictive metagenomic approach to estimate to what extent nitrogen metabolic pathways differed among bacterial communities from different biotopes. We observed marked differences in bacterial composition of the most abundant bacterial phyla, classes and orders among sponge species, water and sediment. Proteobacteria were by far the most abundant phylum in terms of both sequences and Operational Taxonomic Units (OTUs). Predicted counts for genes associated with the nitrogen metabolism suggested that several genes involved in the nitrogen cycle were enriched in sponge samples, including nosZ, nifD, nirK, norB and nrfA genes. Our data show that a combined barcoded pyrosequencing and predictive metagenomic approach can provide novel insights into the potential ecological functions of the microbial communities. Not only is this approach useful for our understanding of the vast microbial diversity found in sponges but also to understand the potential response of microbial communities to environmental change.

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

“…The relative abundance of the most dominant OTU in each sample was highest in both Stylissa species and lowest in sediment. This result reflects similar findings of these biotopes in coral reefs of Jakarta, Indonesia [54].…”

“…Importantly, our data confirms that both LMA Stylissa species maintain a bacterial community that is similar to, but still distinct from, the surrounding seawater and includes highly abundant OTUs that were absent in all other biotopes including seawater. This result is in line with de Voogd et al [54] who found the same for S. massa in Jakarta and Moitinho-Silva et al [72] who found the same for S. carteri in the Red Sea.…”

“…The predicted contribution of Deltaproteobacteria to both nitrification and denitrification is in line with similar findings for S. massa in Jakarta [54] and highlights the potential importance of this class and OTU-1 in particular to nitrogen cycling with Stylissa species. In other marine environments, Deltaproteobacteria have also been shown to play a key role in the nitrogen cycle.…”

Distinctive Feature of Microbial Communities and Bacterial Functional Profiles in Tricholoma matsutake Dominant Soil

“…Recently, Langille et al [22] developed the software Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt), which analyzes microbial function by combining phylogenetic analyses and genome database data to predict functional profiles. To date, PICRUSt has contributed to our understanding of microbial functional profiles in the animal gut [23], human mouth [24], ocean [25], and soil [26]. …”

Sponge-associated actinobacterial diversity: validation of the methods of actinobacterial DNA extraction and optimization of 16S rRNA gene amplification

“…One striking characteristic of sponges is their association with a remarkable array of microorganisms, such as archaea (Preston et al 1996;Radax et al 2012;Turque et al 2010), bacteria (Hentschel et al 2001;Hentschel et al 2012;Montalvo and Hill 2011;Radwan et al 2010;Richardson et al 2012;Schmitt et al 2011;Webster and Hill 2001) including actinobacteria (Abdelmohsen et al 2014a) and cyanobacteria (Alex et al 2012;Thacker and Starnes 2003), unicellular algae (Annenkova et al 2011;He et al 2014;Hentschel et al 2012;Wecker et al 2015) and fungi (Gopi et al 2012;Maldonado et al 2005). These microorganisms are reported to comprise between 35 and 40 % of the total tissue volume in some sponge species Taylor et al 2007;Vacelet and Donadey 1977) and exceed a density of 10 9 microbial cells/ml of sponge tissue (de Voogd et al 2015;Webster and Hill 2001). The extraordinary high abundance and diversity of microorganisms in sponges has led to ecological questions on their role and how the association is established and maintained.…”