Species-specific viromes in the ancestral holobiont Hydra

Abstract

Recent evidence showing host specificity of colonizing bacteria supports the view that multicellular organisms are holobionts comprised of the macroscopic host in synergistic interdependence with a heterogeneous and host-specific microbial community. Whereas host-bacteria interactions have been extensively investigated, comparatively little is known about host-virus interactions and viral contribution to the holobiont. We sought to determine the viral communities associating with different Hydra species, whether these viral communities were altered with environmental stress, and whether these viruses affect the Hydra-associated holobiont. Here we show that each species of Hydra harbors a diverse host-associated virome. Primary viral families associated with Hydra are Myoviridae, Siphoviridae, Inoviridae, and Herpesviridae. Most Hydra-associated viruses are bacteriophages, a reflection of their involvement in the holobiont. Changes in environmental conditions alter the associated virome, increase viral diversity, and affect the metabolism of the holobiont. The specificity and dynamics of the virome point to potential viral involvement in regulating microbial associations in the Hydra holobiont. While viruses are generally regarded as pathogenic agents, our study suggests an evolutionary conserved ability of viruses to function as holobiont regulators and, therefore, constitutes an emerging paradigm shift in host-microbe interactions.

Figure 1. The relative abundance of viral types and the bacterial class hosts of associating viruses to various Hydra species.

A) Predicted host range of each Hydra associated virome, including eukaryotic and prokaryotic viruses. B) Predicted bacterial host range for the bacteriophages associating with Hydra species. The order in each column is equivalent to the order in the legend.

Figure 2. The Hydra viromes.

The relative abundance and diversity of viral families associating with Hydra species in non-stressed and heat-stressed conditions reveals that each species of Hydra associates with a unique community of viruses. Results display the relative abundances of families of identified viruses (TBLASTX, E-value threshold ≤10⁻⁵) associating with the different species of Hydra under both non-stressed and heat-stressed conditions for all viral families (A), for prokaryotic viruses (B), and for eukaryotic viruses (C). The order of the viral family in each column is equivalent to the order of the viral family in the legend.

Figure 3. Hydra species harbor specific viral communities.

Viromes were cross-assembled into one file using MIRA and then each virome was compared to the cross-assembled file using crAss. A) CrAss Wootters formula cladogram output of each Hydra species virome. B) CrAss Wootters formula cladogram output of each Hydra species under non-stressed (NS) and heat-stressed (HS) conditions. The viral family in each pie chart is listed in the legend.

Figure 4. Examples of viral families found in the isolation of viruses from Hydra species.

After viral isolation, a subsample of viruses were absorbed on a carbon-formar TEM grid, negatively stained with 2% uranyl acetate, and visualized by transmission electron microscopy at 40000X. Many viral families have been identified, including bacteriophages A) Myoviridae, B) Siphoviridae, C) Inoviridae (arrows point towards Inoviridae virion), and D) Podoviridae, as well as eukaryotic viral families E) Herpesviridae, and F) Phycodnaviridae. Tissue bound G) Herpesviridae and H) Baculoviridae. The bar in each panel is 50 nm.

Figure 5. Assembled sequence coverage of prokaryotic and eukaryotic viruses from Hydra viromes.

A) Assembled sequence of Myoviridae Burkholderia Phage KS14 from wild-caught H. vulgaris non-stressed virome. B) Assembled sequence of Siphoviridae Staphylococcus prophage phiPV83 from wild-caught H. vulgaris heat-stressed virome. C) Assembled sequence of Inoviridae Ralstonia Phage RSM1 from H. vulgaris (AEP) heat-stressed virome. D) Assembled sequence of Podoviridae Burkholderia phage BcepIL02 from wild-caught H. vulgaris non-stressed virome. E) Assembled sequence of Herpesviridae Cercopithecine Herpesvirus 5 from H. vulgaris (AEP) non-stressed virome. F) Assembled sequence of Phycodnaviridae Paramecium bursaria Chlorella Virus 1 from H. viridissima non-stressed virome. Each bar in the top part of each panel indicates an open reading frame from the viral sequence. Green bars indicate known gene function. Yellow bars indicate putative gene function. Red bars indicate unknown gene function. The bottom part of each panel indicates the depth of coverage for each assembled viral sequence.

Figure 6. Effects of Hydra-associating viruses on metabolic subsystems.

Relative abundances of sequences assigned to each cellular metabolic subsystem by MG-RAST. Assembled sequences were submitted to MG-RAST and TBLASTX was used to compare to a metabolic subsystem SEED database (E-value threshold ≤10⁻⁵). A) Values show the percent relative abundance of each SEED category assignment for each virome with respect to their effect on metabolism, genetic processing, and cellular regulation. The order of the subsystem in each column is equivalent to the order of the subsystem in the legend. B) Percent changes with heat-stress for each Hydra species of the three general groupings from (A). C) Percent changes with heat-stress for each Hydra species from three specific subsystems in (A).