Functional equivalence and evolutionary convergence in complex communities of microbial sponge symbionts

Abstract

Microorganisms often form symbiotic relationships with eukaryotes, and the complexity of these relationships can range from those with one single dominant symbiont to associations with hundreds of symbiont species. Microbial symbionts occupying equivalent niches in different eukaryotic hosts may share functional aspects, and convergent genome evolution has been reported for simple symbiont systems in insects. However, for complex symbiont communities, it is largely unknown how prevalent functional equivalence is and whether equivalent functions are conducted by evolutionarily convergent mechanisms. Sponges represent an evolutionarily divergent group of species with common physiological and ecological traits. They also host complex communities of microbial symbionts and thus are the ideal model to test whether functional equivalence and evolutionary convergence exist in complex symbiont communities across phylogenetically divergent hosts. Here we use a sampling design to determine the phylogenetic and functional profiles of microbial communities associated with six sponge species. We identify common functions in the six microbiomes, demonstrating the existence of functional equivalence. These core functions are consistent with our current understanding of the biological and ecological roles of sponge-associated microorganisms and also provide insight into symbiont functions. Importantly, core functions also are provided in each sponge species by analogous enzymes and biosynthetic pathways. Moreover, the abundance of elements involved in horizontal gene transfer suggests their key roles in the genomic evolution of symbionts. Our data thus demonstrate evolutionary convergence in complex symbiont communities and reveal the details and mechanisms that underpin the process.

Fig. 1.

Phylogenetic relationship of the sponges used in this study based on 18S rRNA sequences. The maximum-likelihood tree is constructed with a sequence alignment length of 1,694 nt; percentage bootstrapping values (1,000 replications) greater than 50% are shown. The tree is rooted to the coral Acanthogorgia granulata (FJ643593). Sponges from the present study are shown in bold. The Axinella clades are named according to Gazave et al. (25). The photographs of C. coralliophila and R. odorabile were provided by Heidi Luter (Townsville, Australia). The photograph of C. concentrica was provided by Michael Taylor (Auckland, New Zealand).

Fig. 2.

Microbial community diversity of sponge and seawater samples. (Right) The relative abundance of the 35 most abundant OTUs (according to the sum of the relative abundance across all samples). Phylogenetic distance cutoff for OTU generation is 0.03. The size of the circle reflects the relative abundance of an OTU in a sample. (Left) Maximum-likelihood tree of the OTUs. Bootstrapping percentages greater than 50% are given (1,000 replications). The tree is rooted with the archaeal clade. Samples are clustered based on the phylogenetic relationships of their OTUs (the top 35 OTUs and the other, low-abundant OTUs) using the weighted Unifrac algorithm with 1,000 rounds of Jackknife values (in percentages) shown in nodes. “16S rRNA sequences not in OTUs” indicates reads that fail to assemble into contigs used for OTU generation.

Fig. 3.

Multidimensional scaling (MDS) plots of samples by Bray–Curtis similarity according to COG functional annotation.

Fig. 4.

Specific functions abundant in sponge-associated or planktonic microbial communities annotated with COG. The brightness (red) in the heatmap reflects the abundance (copies per genome) of a particular function in a sample. Samples are clustered by Bray–Curtis similarity and average linkage analysis.

Fig. 5.

Abundance of enzymes in the energy-producing (respiratory) pathways of nitrogen cycling. With the exception of AmoA (Pfam annotation), abundances of enzymes are obtained from SEED/Subsystem annotation (Materials and Methods). Units on the horizontal axis indicate copies per genome. Error bars show SDs.

Fig. 6.

Abundance of ELPs in seawater versus sponge samples (A–G) and in free-living versus symbiotic species in the Integrated Microbial Genomes database (accessed November 25, 2011) (H). Abundance is normalized by copies per genome of each sample. “Abundance of motifs” refers to the number of repeats; “abundance of proteins” refers to the number of proteins with the repeat; the ratio of abundance of motifs to abundance of repeats gives an estimate of the average number of motifs per protein. Error bars show SDs. Tests between each sponge and the seawater group were performed at 95% confidence interval, and significant differences are marked. *P ≤ 0.05 but > 0.01; **P ≤ 0.01.

Fig. 7.

Abundance and diversity of transposases. The brightness (red) in the heatmap reflects the abundance (copies per genome) of a particular transposase in a sample. Samples are clustered by Bray–Curtis similarity and average general algorithm. Transposase entries are clustered with Euclidian distance and complete linkage.

Fig. 8.

Abundances of CAS proteins in subfamilies.

Fig. P1.

Functional profile of microbial communities of different sponges [Cymbastela coralliophila (Cyr), Rhopaloeides odorabile (Rho), Cymbastela concentrica (Cyn), Stylissa sp. 445 (Sty), Scopalina sp. (Sco), and Tedania anhelans (Ted)] and seawater (SW). Color indicates abundance of gene functions. General categories are identified on the left, and specific names are given on the right. Samples were clustered according to their functional profile, revealing a common set of functions for sponge symbiont communities.