Composition and Predictive Functional Analysis of Bacterial Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesiaby Daniel F. R. Cleary, Nicole J. de Voogd, Ana R. M. Polónia, Rossana Freitas, Newton C. M. Gomes

Microb Ecol


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Composition and Predictive Functional Analysis of Bacterial

Communities in Seawater, Sediment and Sponges in the Spermonde Archipelago, Indonesia

Daniel F. R. Cleary1 & Nicole J. de Voogd2 &

Ana R. M. Polónia1 & Rossana Freitas1 &

Newton C. M. Gomes1

Received: 2 December 2014 /Accepted: 21 May 2015 # Springer Science+Business Media New York 2015

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.

Keywords 16S rRNAgene . KEGG orthologs .Makassar .

Ordination . Pyrosequencing


Coastal marine ecosystems influence climate, nutrient cycling and primary productivity on a global scale [1]. Despite the acknowledged importance of these ecosystems, they have been severely affected by anthropogenic disturbances. This is particularly the case with coral reef ecosystems that have been adversely affected by a number of disturbances including local perturbations such as overfishing, eutrophication and heavy metal pollution [2–4] and global disturbances related to warming such as coral bleaching [3–6]. The intensity of these disturbances is predicted to increase over the coming decades [7, 8].

Electronic supplementary material The online version of this article (doi:10.1007/s00248-015-0632-5) contains supplementary material, which is available to authorized users. * Daniel F. R. Cleary; 1 Departamento de Biologia, Centro de Estudos do Ambiente e doMar (CESAM), Universidade de Aveiro, Campus Universitário de

Santiago, 3810-193 Aveiro, Portugal 2 Naturalis Biodiversity Center, P.O. Box 9517, 2300

RA Leiden, The Netherlands

Microb Ecol

DOI 10.1007/s00248-015-0632-5

Microbes play key roles in the functioning of coral reef ecosystems [9]. Relatively little research has, however, focused on microbial communities in coral reefs when compared to other taxa such as corals or fish. In coral reef ecosystems, microbes can be found in the plankton and sediment but are also important symbionts in higher taxa such as corals and sponges. Here, we studied communities of bacteria in six coral reef biotopes in the

Spermonde Archipelago, a coral reef system off the coast of Makassar, Indonesia, and located in an area known as the coral triangle. These included two nonhost biotopes namely sediment and seawater and four host biotopes namely the sponge species Stylissa carteri and Stylissa massa (order Halichondrida: family

Dictyonellidae), Xestospongia testudinaria (order

Haplosclerida: family Petrosiidae) and Hyrtios erectus (order Dictyoceratida: family Thorectidae). Sponges are both abundant and ecologically important in coral reef ecosystems [10]. They also harbour very high microbial densities; high microbial abundance (HMA) sponges can contain 1010 bacterial cells per gram wet weight of sponge. This is orders of magnitude higher than the surrounding seawater [11–15]. In most cases, bacteria make up the lion’s share of prokaryotic diversity [15–17]. There has been a recent surge in studies of bacteria and their functions in a number of biotopes including sponges [18–20]. At present, however, relatively little is known about the functions of sponges and their bacterial symbionts in the reefs of the coral triangle, which contains the most diverse coral reefs in the world [21]. It is important, however, to have some idea of how sponges may affect the coral reef environment given that they are predicted to increase in abundance in the future [22, 23].

Unfortunately, very few bacterial symbionts of sponges have been cultured. It is, therefore, difficult to identify the functions of the majority of sponge-associated symbionts [24]. Recent advances in ‘omics’ techniques such as metatranscriptomics [18] and proxy techniques including predictive analysis using marker genes, however, now enable predictions of metagenomic functional content. In the present paper, we use a recently developed bioinformatic tool,