Coral-associated marine fungi form novel lineages and heterogeneous assemblages

Abstract

Coral stress tolerance is intricately tied to the animal's association with microbial symbionts. The most well-known of these symbioses is that between corals and their dinoflagellate photobionts (Symbiodinium spp.), whose genotype indirectly affects whether a coral can survive cyclical and anthropogenic warming events. Fungi comprise a lesser-known coral symbiotic community whose taxonomy, stability and function is largely un-examined. To assess how fungal communities inside a coral host correlate with water temperature and the genotype of co-occurring Symbiodinium, we sampled Acropora hyacinthus coral colonies from adjacent natural pools with different water temperatures and Symbiodinium identities. Phylogenetic analysis of coral-associated fungal ribosomal DNA amplicons showed a high diversity of Basidiomycetes and Ascomycetes, including several clades separated from known fungal taxa by long and well-supported branches. Community similarity did not correlate with any measured variables, and total fungal community composition was highly variable among A. hyacinthus coral colonies. Colonies in the warmer pool contained more phylogenetically diverse fungal communities than the colder pool and contained statistically significant 'indicator' species. Four taxa were present in all coral colonies sampled, and may represent obligate associates. Messenger RNA sequenced from a subset of these same colonies contained an abundance of transcripts involved in metabolism of complex biological molecules. Coincidence between the taxonomic diversity found in the DNA and RNA analysis indicates a metabolically active and diverse resident marine fungal community.

Figure 1

Best of 100 maximum likelihood trees of non-singleton coral-fungi OTUs. The tree used a previously published phylogeny as a constraining reference, and was augmented with 497 sequences, which were the top BLAST matches of OTUs downloaded from NCBI nr/nt database. Superimposed on the phylogeny are color-coded cladistic information (inner ring) and sequence source (outer ring). Basidiomycetes are designated with warm colors, Ascomycetes with cool. Uninterrupted black bars on the outer ring indicate clusters of A. hyacinthus fungi, which are more closely related to other coral fungi than to previously sequenced species. The 11 taxa that were found in >90% of the corals are indicated with black pushpins. A larger image with legible labels is provided as supplementary information. Sequences lacking a taxonomic color-code belong to lineages absent in this study.

Figure 2

Box and whisker plots of alpha diversity of A. hyacinthus fungi communities. Boxes contain the upper and lower quartiles, and the median is displayed as the band within. The outlier (open circle) is >1.5 times the interquartile range, and whiskers display the extent of non-outlier values. Phylogenetic diversity was significantly higher in the warm pools (t-test, P= 0.003). Box plots sharing a letter (above) do not significantly differ in a Tukey post hoc test of an analysis of variance analysis, although phylogenetic diversity of the fungal communities associated with D clade from the warm pool were marginally higher than those associated with C clade from the cold pool (P=0.06). There were no significant differences in taxonomic diversity among variables.

Figure 3

Order-level taxonomic diversity of mRNA contigs is broadly congruent with that of DNA amplicon OTUs for most orders, although several orders were exclusive, or nearly so, to one method over the other. All orders shown here, except the Hymenochaetales, had at least a single draft genome deposited in NCBI Genbank at the time of writing. The abundance shown here is a measure of diversity, neither transcript nor DNA copy numbers were measured directly.

Figure 4

Diversity of generic Gene Ontogeny (GO) terms to which fungal transcripts were assigned. The top 20 percentile of 173 terms are shown here.