Microbiome changes through the ontogeny of the marine sponge Crambe crambe

Abstract

Background: Poriferans (sponges) are highly adaptable organisms that can thrive in diverse marine and freshwater environments due, in part, to their close associations with internal microbial communities. This sponge microbiome can be acquired from the surrounding environment (horizontal acquisition) or obtained from the parents during the reproductive process through a variety of mechanisms (vertical transfer), typically resulting in the presence of symbiotic microbes throughout all stages of sponge development. How and to what extent the different components of the microbiome are transferred to the developmental stages remain poorly understood. Here, we investigated the microbiome composition of a common, low-microbial-abundance, Atlantic-Mediterranean sponge, Crambe crambe, throughout its ontogeny, including adult individuals, brooded larvae, lecithotrophic free-swimming larvae, newly settled juveniles still lacking osculum, and juveniles with a functional osculum for filter feeding.

Results: Using 16S rRNA gene analysis, we detected distinct microbiome compositions in each ontogenetic stage, with variations in composition, relative abundance, and diversity of microbial species. However, a particular dominant symbiont, Candidatus Beroebacter blanensis, previously described as the main symbiont of C. crambe, consistently occurred throughout all stages, an omnipresence that suggests vertical transmission from parents to offspring. This symbiont fluctuated in relative abundance across developmental stages, with pronounced prevalence in lecithotrophic stages. A major shift in microbial composition occurred as new settlers completed osculum formation and acquired filter-feeding capacity. Candidatus Beroebacter blanensis decreased significatively at this point. Microbial diversity peaked in filter-feeding stages, contrasting with the lower diversity of lecithotrophic stages. Furthermore, individual specific transmission patterns were detected, with greater microbial similarity between larvae and their respective parents compared to non-parental conspecifics.

Conclusions: These findings suggest a putative vertical transmission of the dominant symbiont, which could provide some metabolic advantage to non-filtering developmental stages of C. crambe. The increase in microbiome diversity with the onset of filter-feeding stages likely reflects enhanced interaction with environmental microbes, facilitating horizontal transmission. Conversely, lower microbiome diversity in lecithotrophic stages, prior to filter feeding, suggests incomplete symbiont transfer or potential symbiont digestion. This research provides novel information on the dynamics of the microbiome through sponge ontogeny, on the strategies for symbiont acquisition at each ontogenetic stage, and on the potential importance of symbionts during larval development.

Keywords: 16S rRNA gene; Demospongiae; Life cycle; Porifera; Symbionts; Vertical transmission.

Fig. 1

Pictures of all the Crambe crambe ontogenetic stages analysed (A–D) and ultrastructural images of their tissue and associated microbes E–G. A Adult individual of Crambe crambe in the field. B Brooded larvae (arrows) within the maternal tissue and free-swimming larva (inset). Scale bar: 1 mm for embryos and 0.5 mm for the free-swimming larva (inset). C. Settled juvenile without an osculum (JNO). Scale bar: 1 mm. D Settled juvenile with an osculum (JO). Note the osculum in the upper part of the juvenile sponge (arrow). Scale bar: 1 mm. E Mesohyl in the adult sponge showing a variety of symbionts (arrows), with a bacterium morphotype more abundant than the others (s). F Larval flagellated epithelium showing very few symbionts (arrows) in the intercellular medium, except for a common bacterial morphotype (s), which also occurrs in the adult (E). G Mesohyl of a juvenile with osculum showing few symbionts (arrows), with a common bacterium morphotype (s) similar to that occurring in adults and larvae (E and F)

Fig. 2

Microbial Taxonomic composition in C. crambe during different developmental stages: Barplots showing the taxonomic composition at class level for each sample, grouped by ontogenetic stage. In the legend; A Archaea, B Bacteria

Fig. 3

Alpha and Beta microbial diversity within different developmental stages of C. crambe: A. Cluster dendogram based on Bray–Curtis dissimilarity matrices of microbial communities in the ontogenetic cycle of the sponge C. crambe. Each colour depicts a developmental stage and sampling dates are indicated in brackets. B. Box plot showing alpha diversity measures of C. crambe ontogenetic stages using Shannon diversity index. C. Principal coordinate analysis (PCoA) plot based on Bray–Curtis dissimilarity index of the microbial composition across the different C. crambe ontogenetic phases (indicated by different colours). Shapes on the figure legend correspond to different adult individuals. Variation explained by the first two axes is indicated as %

Fig. 4

Crambe crambe Offspring similarity: Boxplots of Bray–Curtis distances of specified interactions: A Adult-Adult, Brooded larvae-Brooded larvae, Adult-Brooded larvae, B Brooded larvae comparing siblings between them and with non-siblings and C Parents and brooded larvae comparing adults and their own larvae, and adults with non-related larvae

Fig. 5

ASVs shared between ontogenetic stages in C. crambe. A Venn diagram showing all the interactions. B Upset plot showing inclusive intersections between consecutive stages analysed. Set size corresponds to core community values (assessed at 70% of replicates) and bars represent the size (no. ASVs) of the indicated intersections in the matrix ordered by decreasing values. C–H Relative abundance and composition of each consecutive developmental stages in C. crambe, and across all the stages (H). Taxonomic composition is indicated at class level. On top of each panel, number of shared ASVs that account for the plotted relative abundance in each intersection

Fig. 6

Differentially abundant microbes within C. crambe developmental stages A Differentially abundant (DA) ASVs across the reproductive cycle of the sponge C. crambe. Values represent the number of ASVs identified at higher relative abundances in the comparison between the consecutive ontogeny phases. Abundances and taxonomy of DA ASVs for each comparison can be found in Additional files 5–9 and 18. B Heatmap of the most abundant DA ASVs among the different ontogenetic stages of C. crambe, with log transformed abundances represented in the colour temperature bar. Microbial ASVs are organized according to a hierarchical clustering based on Bray–Curtis Dissimilarity matrices. Sponge samples (x-axis) are coloured according to stage and sampling date