Fungi found in Mediterranean and North Sea sponges: how specific are they?

Abstract

Fungi and other eukaryotes represent one of the last frontiers of microbial diversity in the sponge holobiont. In this study we employed pyrosequencing of 18S ribosomal RNA gene amplicons containing the V7 and V8 hypervariable regions to explore the fungal diversity of seven sponge species from the North Sea and the Mediterranean Sea. For most sponges, fungi were present at a low relative abundance averaging 0.75% of the 18S rRNA gene reads. In total, 44 fungal OTUs (operational taxonomic units) were detected in sponges, and 28 of these OTUs were also found in seawater. Twenty-two of the sponge-associated OTUs were identified as yeasts (mainly Malasseziales), representing 84% of the fungal reads. Several OTUs were related to fungal sequences previously retrieved from other sponges, but all OTUs were also related to fungi from other biological sources, such as seawater, sediments, lakes and anaerobic digesters. Therefore our data, supported by currently available data, point in the direction of mostly accidental presence of fungi in sponges and do not support the existence of a sponge-specific fungal community.

Keywords: Fungi; Malasseziales; Marine sponge; Symbiosis; Yeast.

Figure 1. Relative abundance of sponge, fungal and “other eukaryotic” 18S rRNA gene sequences for sample types from the North Sea (A–D) and Mediterranean Sea (E–I).

The triplicate samples per sponge species are pooled and the numbers within the pie diagrams represent the number of sequences obtained for the sample type. The numbers in parentheses indicate the number of fungal reads obtained for each sample type. WNS, North Sea water; WMS, Mediterranean seawater.

Figure 2. Relative abundance of fungal phyla found in the cumulative sponge and seawater samples.

Figure 3. Heatmap of fungal OTUs in North Sea sponges and Mediterranean Sea sponges.

OTUs that were only found in seawater and singletons are not shown. Taxonomic affiliation is shown at phylum level and order level whenever possible. Some OTUs (in red) were re-classified based on Bayesian phylogenetic analysis (see also Fig. 4). WNS, North Sea water; P, Halichondria panicea; X, Haliclona xena; M, Suberites massa; WMS, Mediterranean seawater; F, Petrosia ficiformis; A, Aplysina aerophoba. Numbers 1, 2 and 3 refer to different individuals of the sponge species.

Figure 4. Bayesian phylogram of Ascomycota OTUs found in sponges based on 18S rRNA gene sequences.

Other sequences included are (i) their nearest neighbors, and (ii) 18S rRNA sequences published by Simister et al. (2012) and Baker et al. (2009). Numbers in parentheses after the sample type indication refer to the absolute numbers of reads that were included in the corresponding OTU per sample (34 P(0/0/4) WMS(2) F(4/0/0) means that 4 reads of P3, 2 reads of Mediterranean seawater and 4 reads of F1 are included in OTU34). The NCBI genbank accession number is the last descriptor for each branch. Grey boxes indicate sponge-specific clusters (SSC) as defined by Simister et al. (2012). Yellow boxes represent yeasts. Taxonomic groups marked with an asterisk (*) indicate non-formal taxonomic classification (i.e., fungal environmental clade LKM11 is not a phylum, but a group assigned for environmental fungal-like sequences; Lara, Moreira & López-García, 2010). The numbers above or below the branches correspond to posterior probability (PP) values of the Bayesian analysis. Nodes with PP values of <50 are not indicated.

Figure 5. Bayesian phylogram of Basidiomycota OTUs found in sponges based on 18S rRNA gene sequences.

For additional information see the legend of Fig. 4.