Ontogenetic Changes in the Bacterial Symbiont Community of the Tropical Demosponge Amphimedon queenslandica: Metamorphosis Is a New Beginning

Abstract

Vertical transmission of bacterial symbionts, which is known in many species of sponge (Porifera), is expected to promote strong fidelity between the partners. Combining 16S rRNA gene amplicon sequencing and electron microscopy, we have assayed the relative abundance of vertically-inherited bacterial symbionts in several stages of the life cycle of Amphimedon queenslandica, a tropical coral reef sponge. We reveal that adult A. queenslandica house a low diversity microbiome dominated by just three proteobacterial OTUs, with a single gammaprotebacterium clearly dominant through much of the life cycle. This ontogenetic perspective has revealed that, although vertical transmission occurs very early in development, the inherited symbionts do not maintain proportional dominance of the bacterial community at every developmental stage. A reproductive bottleneck in the A. queenslandica life cycle is larval settlement, when a free-swimming pelagic larva settles out of the water column onto the benthos and completes metamorphoses into the sessile body plan within just 3-4 days. During this dramatic life cycle transition, an influx of environmentally-derived bacteria leads to a major reorganization of the microbiome, potentially challenging the fidelity and persistence of the vertically-inherited symbiotic relationships. However, dominance of the primary, vertically-inherited symbionts is restored in adult sponges. The mechanisms underlying ontogenetic changes in the bacterial community are unknown, including how the dominance of the primary symbionts is restored in the adult sponge-does the host or symbiont regulate this process? Using high-resolution transcriptional profiling in multiple stages of the A. queenslandica life cycle combined with this natural perturbation of the microbiome immediately following larval settlement, we are beginning to identify candidate host genes associated with animal-bacterial crosstalk. Among the sponge host genes upregulated during the times of active microbiome assembly, there is an enrichment of genes potentially involved in innate immunity, including scavenger receptors, and of genes containing eukaryote-like domains, which have elsewhere Fieth et al.Sponge Microbiome Changes through Lifecycle been implicated in host-symbiont interactions. Intriguingly, we also see an enrichment of sponge genes arising from ancient horizontal transfer events from bacteria, which raises the possibility that host-bacterial associations in the evolutionary past may help to regulate host-bacterial associations in the ecological present.

Host genetics and geography influence microbiome composition in the spongeIrcinia campana

“…Horizontal transmission of microbes from the environment also contributes to the sponge microbiome (Fieth et al, 2016;Maldonado & Riesgo, 2009;Sipkema et al, 2015;Turon et al, 2018). As such, ecological interactions with seawater microbes could be key in shaping the microbiome.…”

“…Similarly, relatively few microbial taxa are shared across the phylum, and host species is a key determinant of microbiome composition (Blanquer, Uriz, & Galand, 2013;Pita, Turon, López-Legentil, & Erwin, 2013;Schmitt et al, 2012;Thomas et al, 2016;Turon, Cáliz, Garate, Casamayor, & Uriz, 2018). This strong association is thought to be driven by a combination of vertical transmission of microbial associates (i.e., parent to offspring transmission) and horizontal transmission of seawater microbes to highly selective host environments (Fieth, Gauthier, Bayes, Green, & Degnan, 2016;Thacker & Freeman, 2012;Turon et al, 2018).…”

Modelling sponge-symbiont metabolism

“…This large requirement for, but low abundance of, nitrogen in the environment may be a driving factor for the apparent fast pumping rates in A. queenslandica, especially since their most abundant symbiotic bacteria appear unable to fix nitrogen . This is congruent with the low microbial abundance (LMA) status of this sponge (Feith et al, 2016) that implies A. queenslandica needs to process large volumes of water to meet its nitrogen requirements from particulate matter (Hentschel et al, 2003;Weisz et al, 2007b).…”

“…Deep transcriptomic sequencing of 82 developmental stages is available (Anavy et al, 2014) and was recently used to enhance the original gene identification and annotation (Fernandez-Valverde et al, 2015). A. queenslandica was identified as a LMA sponge by 16S amplicon sequencing and EM imaging (Feith et al, 2016). The LMA status of A. queenslandica is an advantage for metabolic modelling, as it presents a system where the identification of who is able to do what is simplified when compared to the complex microbiome of a HMA sponge.…”

The characterization of larval homology: transcriptomic insights into the origin and evolution of animal life cycles

“…This enrichment can be rationalized with known prevalence of the cell turnover events (Alexander et al 2014), such as the phagocytosis of apoptosed larval cells during metamorphosis in A. queenslandica (Sogabe et al 2016), that have also been described in other sponge species (Bergquist andGlasglow 1986, Funayama 2013). Additionally, the enrichment of the GO term for vesicle-mediated transport may also reflect histological evidence for the digestion and transport of bacterial cells associated with the maintenance of symbiont communities during metamorphosis via vesicle-mediated phagocytosis (Fieth et al 2016). …”