Sponges and Their Microbiomes Show Similar Community Metrics Across Impacted and Well-Preserved Reefs

Abstract

Sponge diversity has been reported to decrease from well-preserved to polluted environments, but whether diversity and intra-species variation of their associated microbiomes also change as function of environmental quality remains unknown. Our study aimed to assess whether microbiome composition and structure are related to the proliferation of some sponges and not others under degraded conditions. We characterized the most frequent sponges and their associated bacteria in two close areas (impacted and well-preserved) of Nha Trang Bay (Indo-Pacific). Sponge assemblages were richer and more diverse in the well-preserved reefs, but more abundant (individuals/m. transect) in the impacted environments, where two species (Clathria reinwardti and Amphimedon paraviridis) dominated. Sponge microbiomes from the polluted zones had, in general, lower bacterial diversity and core size and consequently, higher intra-species dispersion than microbiomes of sponges from the well-preserved environments. Microbial communities reflect the reduction of diversity and richness shown by their host sponges. In this sense, sponges with less complex and more variable microbiomes proliferate under degraded environmental conditions, following the ecological paradigm that negatively correlates community diversity and environmental degradation. Thereby, the diversity and structure of sponge microbiomes might indirectly determine the presence and proliferation of sponge species in certain habitats.

Keywords: contrasting environments; diversity; ecology; eutrophication; microbiomes; resilience; sponges.

FIGURE 1

(A) Bar plots of sponge species composition and abundance at the well-preserved and impacted habitats. Y-axis represents the numbers of individuals per meter of transect. (B) Venn diagram of total species richness and the species overlap between well-preserved (gray) and impacted (red) environments. ^∗ Indicates species for which microbiome has been analyzed.

FIGURE 2

Pictures of the most common sponges of the impacted (A–D) and the well-preserved (E–I) habitats: (A) Amphimedon paraviridis (greenish) and Clathria reinwardti (pinkish), (B) Clathria (Isociella) skia, (C) Mycale (Arenochalina) sp., (D) Amphimedon sulcata (in the impacted environment), (E) A. sulcata (in the well-preserved environment), (F) Neofibularia sp., (G) Antho (Antho) sp., (H) Aaptos suberitioides and (I) Monanchora unguiculata.

FIGURE 3

Heatmap of the sponge bacterial composition at the family level. Only taxa with relative abundances higher than 1% in any of the samples are shown, with abundance represented in the color temperature bar. Sponge samples (y-axis) and bacterial taxa (x-axis) are organized according to a hierarchical clustering based on Bray-Curtis dissimilarity matrices (at the level of ZOTU and family, respectively). Square colors correspond to different sponge species, and circle colors indicate the site of collection: impacted (red) or well-preserved (gray).

FIGURE 4

Box plots comparing the intra-species dispersion (A), core size (B) and Shannon diversity (C) of the sponge microbiomes between impacted (red) and well-preserved (gray) environments. Replicates of the same species are depicted in the same dot color.

FIGURE 5

Schematic representation of the sponge microbiomes in impacted and well-preserved environments. Gray fraction represents the variable community and white fraction represents the core community. Each colored dot corresponds to a single bacterial species.