Expanding our Understanding of the Seaweed Holobiont: RNA Viruses of the Red Alga Delisea pulchra

Abstract

Marine seaweeds are holobionts comprised of the macroalgal hosts and their associated microbiota. While the composition of the bacterial component of seaweed microbiomes is increasingly studied, almost nothing is known about the presence, diversity and composition of viruses in macroalgae in situ. In this study, we characterize for the first time the viruses associated with a red macroalga, Delisea pulchra. Using transmission electron microscopy we identified diverse morphotypes of virus-like particles in D. pulchra ranging from icosahedral to bacilliform to coiled pleomorphic as well as bacteriophages. Virome sequencing revealed the presence of a diverse group of dsRNA viruses affiliated to the genus Totivirus, known to infect plant pathogenic fungi. We further identified a ssRNA virus belonging to the order Picornavirales with a close phylogenetic relationship to a pathogenic virus infecting marine diatoms. The results of this study shed light on a so far neglected part of the seaweed holobiont, and suggest that some of the identified viruses may be possible pathogens for a host that is already known to be significantly impacted by bacterial infections.

Keywords: alga; disease; fungi; macroalga; metaorganism; pathogen; seaweed; viromes.

FIGURE 1

Different morphotypes of virus like particles could be observed in both individuals. Icosahedral viral particles with a diameter of 40 nm (A,D) and another size class with a diameter of 30 nm (E). Bacilliform to coiled pleomorphic forms (B,C) were detected as well as bacteriophages (F).

FIGURE 2

RNA virome composition. Taxonomic classification of viral contigs based on significant blastx and tblastx results with an e-value cut off of smaller than 10^-5 from two different D. pulchra individuals (A,B). The viral abundance is based on the coverage of each contig as a relative quantitative measure.

FIGURE 3

(A–C) Comparison between the Asterionellopis glacialis (“Agla”) RNA virus and the D. pulchra RNA virus. (A) The genomes of both viruses encode two polyproteins, one replication associated and one structural polyprotein. (B) Protein domain analysis using SMART (Simple Modular Architecture Research Tool) and sequence alignment of the replication associated polyprotein shows a similar structural organization consisting of RNA helicase or replication associated protein AAA, transmembrane proteins (blue boxes) and RdRP. Low complex regions are shown in pink. (C) Protein domain analysis and sequence alignment of the structural polyprotein shows four structural protein domains Rhv, DicistroVP4, Calici coat, and CRPV capsid. The Calici coat domain overlaps with the second Rhv domain of the Agla RNA virus. Sequences of conserved protein domains are highlighted in boxes.

FIGURE 4

Maximum-likelihood phylogenetic tree of D. pulchra associated Picornavirales based on the RdRp amino acid sequence compared to environmental sequences (AY285750-AY285768) of virioplankton communities of geographically diverse regions (Culley et al., 2003) and to the families Iflaviridae, Picornaviridae, Dicistroviridae, and Secoviridae. NCBI accession numbers are shown in brackets. The scale bar represents 20% of amino acid changes between close relatives.

FIGURE 5

Maximum-likelihood phylogenetic tree of D. pulchra associated Totiviridae based on the RdRp amino acid sequence compared to the genus Victorivirus and Totivirus. NCBI accession numbers are shown in brackets. The scale bar represents 20% of amino acid changes between close relatives.