The Relationship Between Microbiomes and Selective Regimes in the Sponge Genus Ircinia

Abstract

Sponges are often densely populated by microbes that benefit their hosts through nutrition and bioactive secondary metabolites; however, sponges must simultaneously contend with the toxicity of microbes and thwart microbial overgrowth. Despite these fundamental tenets of sponge biology, the patterns of selection in the host sponges' genomes that underlie tolerance and control of their microbiomes are still poorly understood. To elucidate these patterns of selection, we performed a population genetic analysis on multiple species of Ircinia from Belize, Florida, and Panama using an F _ST -outlier approach on transcriptome-annotated RADseq loci. As part of the analysis, we delimited species boundaries among seven growth forms of Ircinia. Our analyses identified balancing selection in immunity genes that have implications for the hosts' tolerance of high densities of microbes. Additionally, our results support the hypothesis that each of the seven growth forms constitutes a distinct Ircinia species that is characterized by a unique microbiome. These results illuminate the evolutionary pathways that promote stable associations between host sponges and their microbiomes, and that potentially facilitate ecological divergence among Ircinia species.

Keywords: 16S metabarcoding; RADseq; innate immunity; microbiome; sponge (Porifera).

FIGURE 1

Top: Four Panamanian growth forms were collected from three sites: Massive A pink was collected from Rhizophora prop roots at Inner Solarte, a network of mangrove hammocks; Massive A green and Massive B were collected from STRI Point, a Thalassia seagrass-dominated habitat; and Encrusting was collected from Punta Caracol, a coral patch reef. I. campana and I. strobilina specimens were also collected from STRI Point and Punta Caracol. Middle: specimens of a growth form (Ramose) and I. campana were collected from a seagrass bed on Summerland Key, Florida; two specimens of I. campana were also collected from Looe Key. Bottom: Two Belizean growth forms were collected from three sites: Sp. 1 specimens were collected from Rhizophora prop roots at the Twin Cays and from mangrove hammocks adjacent to the series of Blue Ground coral patch reefs; and Sp. 2 specimens were collected from the coral reefs at Blue Ground. Specimens of I. strobilina were collected form the same patch reef inhabited by Sp. 2 and also from the forereef at Carrie Bow Cay, and I. felix specimens were collected from the Carrie Bow Cay forereef. I. felix photo credit: Patrick Erwin (Hentschel et al., 2012). Numbers in each photograph correspond to sample size, reported as total sample size (samples in 2bRAD dataset, samples in 16S dataset), less the transcriptomic sample of the Ramose growth form. A complete sampling overview can be found in Supplementary Table 1.

FIGURE 2

(A) Plot showing the relative abundances of the 1043 OTUs that are shared between sponges and seawater, restricted to Panama and Belize. Orange dots are relative abundances in sponges, blue dots are relative abundances in seawater. Black triangles mark OTUs that correspond to vertically transmitted bacteria in I. felix (Schmitt et al., 2007). (B) Venn diagram showing the number of sponge-specific OTUs, seawater-specific OTUs, and OTUs found in both sources. OTUs in the intersection of the two sources are plotted by relative abundance in (A).

FIGURE 3

PCoA of microbiome compositions, normalized by relative abundance, for each host lineage. Ellipses are standard ellipse area (SEA). Squares are Floridian specimens (FL), circles are Panamanian specimens (PA), and triangles are Belizean specimens (BZ).

FIGURE 4

Phylogeny produced via SNAPP for the best-supported species grouping model in BFD^∗. Left: consensus tree with posterior probabilities as node labels. Right: Densitree visualization of posterior tree distribution displaying most frequent topology in blue and alternative topologies in green and red. Tip labels are colored by geography: blue for Belize, yellow for Florida, and red for Panama.

FIGURE 5

Structure plots of ancestries of neutrally evolving SNPs estimated for K = 4 and K = 5.