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

Abstract

In this study, we used a 16S rRNA gene barcoded pyrosequencing approach to sample bacterial communities from six biotopes, namely, seawater, sediment and four sponge species (Stylissa carteri, Stylissa massa, Xestospongia testudinaria and Hyrtios erectus) inhabiting coral reefs of the Spermonde Archipelago, South Sulawesi, Indonesia. Samples were collected along a pronounced onshore to offshore environmental gradient. Our goals were to (1) compare higher taxon abundance among biotopes, (2) test to what extent variation in bacterial composition can be explained by the biotope versus environment, (3) identify dominant (>300 sequences) bacterial operational taxonomic units (OTUs) and their closest known relatives and (4) assign putative functions to the sponge bacterial communities using a recently developed predictive metagenomic approach. We observed marked differences in bacterial composition and the relative abundance of the most abundant phyla, classes and orders among sponge species, seawater and sediment. Although all biotopes housed compositionally distinct bacterial communities, there were three prominent clusters. These included (1) both Stylissa species and seawater, (2) X. testudinaria and H. erectus and (3) sediment. Bacterial communities sampled from the same biotope, but different environments (based on proximity to the coast) were much more similar than bacterial communities from different biotopes in the same environment. The biotope thus appears to be a much more important structuring force than the surrounding environment. There were concomitant differences in the predicted counts of KEGG orthologs (KOs) suggesting that bacterial communities housed in different sponge species, sediment and seawater perform distinct functions. In particular, the bacterial communities of both Stylissa species were predicted to be enriched for KOs related to chemotaxis, nitrification and denitrification whereas bacterial communities in X. testudinaria and H. erectus were predicted to be enriched for KOs related to the toxin-antitoxin (TA) system, nutrient starvation and heavy metal export.

Bacterial Community Composition and Potential Driving Factors in Different Reef Habitats of the Spermonde Archipelago, Indonesia

“…Barott et al (2011) showed clear difference in bacterial community composition of different types of algae and corals. Another recent study from the Spermonde Archipelago confirmed this for a variety of reef sponges (Cleary et al, 2015). The production of specific carbohydrates and antibiotics very likely plays an important role in shaping those stable host-specific microbial communities (Ritchie, 2006; Rosenberg et al, 2007).…”

“…To date, there are only two studies of the Spermonde Archipelago that have focused on bacterial diversity of settlement tile biofilms (Sawall et al, 2012) and bacterial communities from different reef habitats, specifically within sponges and the functional role of the associated bacteria (Cleary et al, 2015). Our study now further examines the relationship between bacterial communities, habitats, and water quality gradients in the Spermonde Archipelago, and additionally includes mucus of the common hard corals genus Fungia as an important bacterial habitat (Wild et al, 2004; Allers et al, 2008).…”

Specialized Microbiome of a Halophyte and its Role in Helping Non-Host Plants to Withstand Salinity

“…Other endophytic bacterial traits predicted by PICRUSt include phosphate solubilization, auxin synthesis and nitrogen fixation features, all of which have been strongly correlated with plant growth. Admittedly, these results can be viewed as supportive as the analysis by PICRUSt does not provide data on actual gene expression in the sample45. The relatively high NSTI scores in root samples indicate not only a degree of uncertainty in the prediction of said gene(s) relevance, but also the novelty of microbes in the endosphere.…”

Sustaining Rare Marine Microorganisms: Macroorganisms As Repositories and Dispersal Agents of Microbial Diversity

“…One of the most striking examples is the study from Webster et al (2010; Figure 2A ) where bacterial genera such as Iamia , Nitrosococcus , or Trichodesmium shift from less than 0.8% relative abundance in open water to 16.9, 10.8, and 8.3% of the total abundance in sponge microbiota, respectively. These examples are only a small part of the studies reporting such an OTUs abundance shift between seawater or sediment and the sponge microbiota (Lee et al, 2011; Jackson et al, 2012; Cuvelier et al, 2014; O’Connor-Sánchez et al, 2014; Polónia et al, 2014; Reveillaud et al, 2014; Cleary et al, 2015; de Voogd et al, 2015; see Supplementary Figures for more examples).…”