An Interplay between Viruses and Bacteria Associated with the White Sea Sponges Revealed by Metagenomics

• Published in: Life
• Main Authors: Anastasiia Rusanova, Victor Fedorchuk, Stepan Toshchakov, Svetlana Dubiley, Dmitry Sutormin
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI AG 2021
• Subjects: sponge-associated communities; 16S metagenomics; shot-gun metagenomics; metavirome; phage-host interaction; bacterial antiphage defense system; Science; Q; White Sea
• Online Access: https://doi.org/10.3390/life12010025; https://doaj.org/article/1b9bf58693eb4c0babb73a8ae7ccedeb

Sponges are remarkable holobionts harboring extremely diverse microbial and viral communities. However, the interactions between the components within holobionts and between a holobiont and environment are largely unknown, especially for polar organisms. To investigate possible interactions within and between sponge-associated communities, we probed the microbiomes and viromes of cold-water sympatric sponges Isodictya palmata (n = 2), Halichondria panicea (n = 3), and Halichondria sitiens (n = 3) by 16S and shotgun metagenomics. We showed that the bacterial and viral communities associated with these White Sea sponges are species-specific and different from the surrounding water. Extensive mining of bacterial antiphage defense systems in the metagenomes revealed a variety of defense mechanisms. The abundance of defense systems was comparable in the metagenomes of the sponges and the surrounding water, thus distinguishing the White Sea sponges from those inhabiting the tropical seas. We developed a network-based approach for the combined analysis of CRISPR-spacers and protospacers. Using this approach, we showed that the virus–host interactions within the sponge-associated community are typically more abundant (three out of four interactions studied) than the inter-community interactions. Additionally, we detected the occurrence of viral exchanges between the communities. Our work provides the first insight into the metagenomics of the three cold-water sponge species from the White Sea and paves the way for a comprehensive analysis of the interactions between microbial communities and associated viruses.