Dynamics, diversity, and roles of bacterial transmission modes during the first asexual life stages of the freshwater sponge Spongilla lacustris

Abstract

Background: Sponge-associated bacteria play important roles in the physiology of their host, whose recruitment processes are crucial to maintain symbiotic associations. However, the acquisition of bacterial communities within freshwater sponges is still under explored. Spongilla lacustris is a model sponge widely distributed in European rivers and lakes, producing dormant cysts (named gemmules) for their asexual reproduction, before winter. Through an in vitro experiment, this study aims to describe the dynamics of bacterial communities and their transmission modes following the hatching of these gemmules.

Results: An overall change of bacterial β-diversity was observed through the ontology of the juvenile sponges. These temporal differences were potentially linked, first to the osculum acquisition and the development of a canal system, and then, the increasing colonization of the Chlorella-like photosymbionts. Gemmules hatching with a sterilized surface were found to have a more dispersed and less diverse microbiome, revealing the importance of gemmule epibacteria for the whole holobiont stability. These epibacteria were suggested to be vertically transmitted from the maternal tissues to the gemmule surface. Vertical transmission through the incorporation of bacterial communities inside of the gemmule, was also found as a dominant transmission mode, especially with the nitrogen fixers Terasakiellaceae. Finally, we showed that almost no ASVs were shared between the free-living community and the juveniles, suggesting that horizontal recruitment is unlikely to happen during the first stages of development. However, the free-living bacteria filtered are probably used as a source of nutrients, allowing an enrichment of copiotrophic bacteria already present within its microbiome.

Conclusions: This study brings new insight for a better understanding of the microbiome acquisition during the first stages of freshwater sponge development. We showed the importance of epibacterial communities on gemmules for the whole holobiont stability, and demonstrated the near absence of recruitment of free-living bacteria during the first stages.

Keywords: Freshwater sponge; Gemmule; Holobiont; Horizontal acquisition; Microbiome; Ontogeny; Vertical transmission.

Fig. 1

Workflow summarizing the experimental design of the study. Abbreviations EM for epibiotic microbiome, and FB for free-living bacteria

Fig. 2

Dynamics of the α-diversity (Shannon index) of the bacterial communities associated with the gemmules (t₀) and the in vitro juvenile sponges (t₁ to t₆). Lowercase indices (from a to f) indicate the results from the Wilcoxon pairwise tests comparing ± EM samples within each time. Abbreviations EM for epibiotic microbiome, and FB for free-living bacteria

Fig. 3

β-diversity of the bacterial communities (Bray-Curtis distances). A NMDS plot performed with all samples represented according to their sample type and sampling time. B NMDS plots performed for each sampling time of the in vitro juveniles, separately, with samples represented according to their treatments. Abbreviations EM for epibiotic microbiome, and FB for free-living bacteria

Fig. 4

Phylogenetical heat trees performed with juvenile sponges samples collected at t₁ and representing the taxa significantly and differentially abundant between the + EM and -EM treatments, within + FB (A) and -FB samples (B). For each taxon, (i) the colors of their associated nodes correspond to the log2 fold change between the ratio of the mean relative abundance within each treatment, (ii) the size of the nodes corresponds to the relative abundance of each taxon. Abbreviations EM for epibiotic microbiome, and FB for free-living bacteria

Fig. 5

Dynamics of number of ASVs shared between gemmules/in vitro juveniles and in situ adult sponges. Abbreviations EM for epibiotic microbiome, and FB for free-living bacteria

Fig. 6

Illustration summarizing the potential transmission modes and the dynamics of the epibacterial community during the first life stages of the asexual cycle of Spongilla lacustris. The gemmule formed within the maternal tissue, encapsulate undifferentiated dormant cells: the thesocytes. Three transmission modes can be considered during the gemmule formation: (1 A) a vertical transmission of bacteria inside of the gemmule (e.g. Terasakiellaceae that might be associated with the thesocytes); (1B) a vertical transmission of bacteria on the gemmule surface within its biofilm (e.g. Hydrogenophaga), increasing the overall α-diversity; (1 C) a horizontal acquisition of ambient bacteria which are not directly associated with the maternal tissues (e.g. potential particle-attached planktonic colonizers). Stage 0: following its planktonic phase, the gemmule is in contact with a substrate, and (2) the epibacteria from the gemmule biofilm can colonize this new surface. These epibacteria (e.g. Bacteroidota such as Flavobacterium) might enhance the settlement of the gemmule and promote its hatching. Stage 1 to 2: the gemmule is hatching, with the thesocytes emerging out of the micropyle, together with the bacteria initially inside (3). The bacteria from the gemmule surface play an important role for the whole stability of the juvenile holobiont (4). Stage 3 to 4: the juvenile is developing its canal system and forming an osculum, while (5) the filtered free-living bacteria (FB) are used as a source of nutrients allowing an enrichment of copiotroph bacteria (6). Stage 5 and beyond: the increasing colonization of Chlorella-like symbionts, is associated with a shift of bacterial composition (7). Adult stage of S. lacustris: the tissues are forming a new generation of gemmules before winter. The different elements of the illustration are not to scale