First insight into the viral community of the cnidarian model metaorganism Aiptasia using RNA-Seq data

Abstract

Current research posits that all multicellular organisms live in symbioses with associated microorganisms and form so-called metaorganisms or holobionts. Cnidarian metaorganisms are of specific interest given that stony corals provide the foundation of the globally threatened coral reef ecosystems. To gain first insight into viruses associated with the coral model system Aiptasia (sensu Exaiptasia pallida), we analyzed an existing RNA-Seq dataset of aposymbiotic, partially populated, and fully symbiotic Aiptasia CC7 anemones with Symbiodinium. Our approach included the selective removal of anemone host and algal endosymbiont sequences and subsequent microbial sequence annotation. Of a total of 297 million raw sequence reads, 8.6 million (∼3%) remained after host and endosymbiont sequence removal. Of these, 3,293 sequences could be assigned as of viral origin. Taxonomic annotation of these sequences suggests that Aiptasia is associated with a diverse viral community, comprising 116 viral taxa covering 40 families. The viral assemblage was dominated by viruses from the families Herpesviridae (12.00%), Partitiviridae (9.93%), and Picornaviridae (9.87%). Despite an overall stable viral assemblage, we found that some viral taxa exhibited significant changes in their relative abundance when Aiptasia engaged in a symbiotic relationship with Symbiodinium. Elucidation of viral taxa consistently present across all conditions revealed a core virome of 15 viral taxa from 11 viral families, encompassing many viruses previously reported as members of coral viromes. Despite the non-random selection of viral genetic material due to the nature of the sequencing data analyzed, our study provides a first insight into the viral community associated with Aiptasia. Similarities of the Aiptasia viral community with those of corals corroborate the application of Aiptasia as a model system to study coral holobionts. Further, the change in abundance of certain viral taxa across different symbiotic states suggests a role of viruses in the algal endosymbiosis, but the functional significance of this remains to be determined.

Initial virome characterization of the common cnidarian lab modelNematostella vectensis

“…Similarly, we identified in Nematostella dataset 37.2% viral sequences which belong to the Picorna-Calici clade, although the vast majority of them are classified here as "other viruses" due to the applied ICTV classification. On the contrary, E. pallida had more diverse viral community composition, in which among 40 identified viral families Picornaviridae constitute only 9.87% [16]. Moreover, we did not observe any viruses with obvious homology shared between N. vectensis and E. pallida.…”

“…None of the identified sequences of Iridoviridae representatives was neither mapped in Artemia libraries, nor amplified from Artemia cDNA, which confirms that these dsDNA viruses are actively expressed and specific to Nematostella, or organisms comprising this holobiont, rather than food derived. Interestingly, members of Iridoviridae family were missing from all viromes available for other sea anemones species: E. pallida [16], Actinia equina [52] and Bolocera sp [4]. It seems plausible that such a major difference in the viral community composition between sea anemones might stem from the very distinct environmental conditions of these marine animals and therefore, a different ensemble of neighboring viral species.…”

“…Herpesviruses have been previously associated with other cnidarian species [3,58,59] and with Symbiodinium microadriaticum found in corals [14]. Given that E. pallida is also a host to several members of Symbiodinium family [60] and the contribution of Herpesviridae decreases in aposymbiotic state when compared to a fully symbiotic Exaiptasia (8.1% and 12.9%, respectively) [16], it is possible that this viral family is associated with the presence of these symbionts and hence, not found in sea anemone species which do not harbor zooxanthellae.…”

“…Among cnidarians, much focus has been placed on deciphering the composition and significance of virome of corals (reviewed in [13]), their photosynthetic dinoflagellate symbionts from the Symbiodinium genus [14,15], and their symbiotic sea anemone proxy Exaiptasia pallida (formerly called Aiptasia pallida) [16], mainly due to the environmental significance of the coral reef ecosystems. Members of coral virome have been suggested to play a role in some coral diseases [17,18], and a general increase of viral abundance has been observed during bleaching (loss of dinoflagellate symbionts) of several coral species [19][20][21].…”

Reading the Book of Life – Omics as a Universal Tool Across Disciplines

“…The exact same dataset was used by Brüwer et al (2017), who in silico detected a diverse viral community associated with the dinoflagellate and observed differential viral gene expression upon heat treatment. As in this example, nextgeneration sequencing often contains "by-catch" of hostassociated microorganisms and viruses, which may be assessed separately (see also Levin et al 2017;Brüwer and Voolstra 2018; Brüwer and Voolstra within the abstracts related to this chapter).…”