Evidence for Selective Bacterial Community Structuring in the Freshwater Sponge Ephydatia fluviatilis

Abstract

To understand the functioning of sponges, knowledge of the structure of their associated microbial communities is necessary. However, our perception of sponge-associated microbiomes remains mainly restricted to marine ecosystems. Here, we report on the molecular diversity and composition of bacteria in the freshwater sponge Ephydatia fluviatilis inhabiting the artificial lake Vinkeveense Plassen, Utrecht, The Netherlands. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) fingerprints revealed that the apparent diversities within the domain Bacteria and the phylum Actinobacteria were lower in E. fluviatilis than in bulk water. Enrichment of specific PCR-DGGE bands in E. fluviatilis was detected. Furthermore, sponge- and bulk water-derived bacterial clone libraries differed with respect to bacterial community composition at the phylum level. E. fluviatilis-derived sequences were affiliated with six recognized phyla, i.e., Proteobacteria, Planctomycetes, Actinobacteria, Bacteroidetes, Chlamydiae and Verrucomicrobia, in order of relative abundance; next to the uncultured candidate phylum TM7 and one deeply rooted bacterial lineage of undefined taxonomy (BLUT). Actinobacteria, Proteobacteria, and Bacteroidetes were the dominant bacterial phyla in the freshwater clone library whereas sequences affiliated with Planctomycetes, Verrucomicrobia, Acidobacteria and Armatimonadetes were found at lower frequencies. Fine-tuned phylogenetic inference showed no or negligible overlaps between the E. fluviatilis and water-derived phylotypes within bacterial taxa such as Alphaproteobacteria, Bacteroidetes and Actinobacteria. We also ascertained the status of two alphaproteobacterial lineages as freshwater sponge-specific phylogenetic clusters, and report on high distinctiveness of other E. fluviatilis specific phylotypes, especially within the Bacteroidetes, Planctomycetes and Chlamydia taxa. This study supports the contention that the composition and diversity of bacteria in E. fluviatilis is partially driven by the host organism.

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

“…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.…”

Planctomycetes and macroalgae, a striking association

“…Furthermore, their association with a great number of diverse eukaryotic organisms has been reported. These include sponges (Webster et al, 2001; Pimentel-Elardo et al, 2003; Zhu et al, 2008; Costa et al, 2013), ascidians (Oliveira et al, 2013), corals (Yakimov et al, 2006; Webster and Bourne, 2007; Duque-Alarcón et al, 2012), prawns (Fuerst et al, 1997), macrophytes (Hempel et al, 2008) and lichens (Grube et al, 2012). They were also found in sphagnum peat bogs (Kulichevskaia et al, 2006), the rock below the lichens (Bjelland et al, 2011) and in the rizosphere of several plants (Jensen et al, 2007; Zhao et al, 2010; Zhang et al, 2013).…”

Brown Rot Syndrome and Changes in the Bacterial Сommunity of the Baikal Sponge Lubomirskia baicalensis

“…Under reference condition, the L. baicalensis bacterial com-munity includes Crenarchaeota and 23 Eubacteria phyla and candidate phyla. The major bacterial phyla are Bacteroidetes, Proteobacteria, Actinobacteria, Verrucomicrobia, and Planctomycetes, which also dominate bacterial communities of other freshwater sponges such as Ephydatia fluviatilis [12], Eunapius carteri, and Corvospongilla lapidosa [73]. Moreover, Cyanobacteria and OD1 candidate phylum seem to be also very common in L. baicalensis.…”

“…In high microbial abundance (HMA) species, microorganisms can represent up to 40% of the sponge biomass [6] and show great taxonomic diversity, with up to 47 bacterial or candidate phyla recorded so far [7][8][9]. Acidobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Cyanobacteria, Proteobacteria (Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria), Verrucomicrobia, and Nitrospira phyla are the most common both in marine [4,10] and freshwater sponges [11][12][13][14]. Sponge disease outbreaks or mass mortality events have been reported for more than a century, with more than 20 events studied, sometimes affecting several species and large areas [4,[15][16][17][18][19][20][21][22][23][24][25][26][27][28].…”