In what ways do viruses affect their host?
- global transfer of niche adaptation genes (i.e. AMG’s) (Rowher and Thurber, 2009).
- Modifications of the ontogeny and ecology of marine organisms
What are Auxilary Metabolic Genes?
- Genes that provide supplemental support to key steps in host metabolism of significance to phage, thereby fostering a more successful infection (Thompson et al., 2011). For example, cyanophages, encoding elements of photosynthesis, the pentose phosphate pathway (PPP), and phosphate acquisition.
- ^ phage gene products may integrate into host photosystems and contribute to host photosynthesis during infection, possibly fueling phage dNTP biosynthesis (Thompson et al., 2011). Use of ATP and NADPH from light cycle.
- The use of host-like metabolic genes by viruses is a central theme in the coevolution of viruses and their hosts, and the particular metabolic genes carried by viruses provide clues to the mechanisms of viral replication (Thompson et al., 2011).
Why is viral diversity in marine environments hard to study?
- Viruses do not have a universally conserved gene like the ribosomal DNA genes in cellular organisms (Rowher and Thurber, 2009)
- Most viral hosts are difficult to culture (Rohwer and Thurber, 2009)
When was the first evidence of diverse viral infection strategies made available?
In the early twentieth century to mid-twentieth century, based on isolation and characterization of model laboratory systems (Correa et al., 2021).
What methods determine viral diversity?
- Plaque assays: quantify the abundance of infectious units that cause lysis. host cells must be cultured. These assays are used to estimate the tires of viruses that cause the lysis of bacteria.
- Most-probable- number assays (MPNs) - used for cells that are cultivable, but cannot be grown on solid substrates, and use a series of dilutions.
- Transmission electron microscopy (TEM) - only method that provides data on both the abundance and morphology of virus-like-particles.
- Epifluorescence microscopy (EfM) - widely used. viruses are concentrated on a membrane filter, nucleic acids are stained with dye and abundance is estimated.
- Flow virometry
Are viruses more abundant than bacteria?
Yes, the abundance of viruses exceeds bacterial and archaea 15 fold. However, due to their small size, viruses represent 5% of prokaryotic biomass. Consequently, in the oceans, viral abundance decreases further offshore and deeper in the water column (Suttle, 2007)
What is the expanded rule of life view of:
Temperate phages are dormant and
do not interfere with host regulation.
Temperate phages can actively regulate
host genomes.
Such viral infection can reshape cells and their functions (for example, metabolism, regulatory
elements and communication systems) in ways that could benefit both the virus and the host.
- (Correa et al., 2021)
What is the only recognized family of marine RNA viruses?
Marnaviridae, which was founded based on discovery and characterization of the species Heterosigma akashiwo RNA virus (Vlok et al., 2019)
The order Picornavirales is comprised of what families?
Picornaviridae, Dicistroviridae, Iflaviridae, Secoviridae, Marnaviridae (Sanfac ̧on et al. 2009, 2011a), and the newly defined Polycipiviridae (King et al. 2018; Olendraite et al. 2018). (Vlok et al., 2019)
Culture-independent studies indicate that RNA viruses are _________ and metagenomics says _________
- abundant and genetically diverse
- the existence of multiple picorna-like viruses that are more similar known picornavirus isolates than to other known viruses (Culley, Lang, and Suttle 2007; Culley et al. 2014; Miranda et al. 2016; Shi et al. 2016). Vlok et la., 2019
Name some characteristics of viruses belonging to Picornavirales.
All known genomes of Picornavirales members
1. encode proteins with helicase, 3C-like protease, and RNA-dependent RNA polymerase (RdRp) domains
2. Capsid proteins with related structures, although the genome organizations can differ among viruses (Le Gall et al. 2008). Vlok et la., 2019
3. The viral proteins are expressed as one or more polyprotein(s) that are cleaved into in- dividual functional proteins and the viruses can vary in their number of genome segments and open reading frames (ORFs)
What information has ICTV relied on when classifying viruses?
- host range, replication cycle, virus particle structures and properties, serology and similarity.
What is one downfall with classifying viruses using metagnomics?
Some biological information (i.e., replication cycle, structure, etc.,) can be lacking.
What did Cook et al., 2024 find when comparing ONT, Pacbio, and Illumina sequencing technologies when reconstructing viral (phage) communities?
- Illumina sequences were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used.
- Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly.
- Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies.
Have viruses been the causative agents of coral disease?
No. But they have been implicated as coral pathogens due to 1) upregulation of viral proteins in diseased corals and presence of virus-like particles via TEM.
What do latent viruses have to do with bleaching?
Some latent viral infections can compromise the algal symbionts under environmental stress and may be involve in bleaching. (Sweet and Bythell, 2017)
Why was it hypothesized that viruses are an active part of the coral’s innate immune system? (Hint: Barr et al. 2013)
The BAM model.
– Phages can encode a population of hypervariable proteins (as seen in the human gut by Minot and colleagues). Ig-like domains of phage capsid proteins and glycan residues mediate phage-bacterium adherence.
– Barr and colleagues found that phage concentrations in the mucus are elevated, likely taking on a defense mechanism towards pathogens that enter via the coral surface mucus layer.
What is an example of mutualism between corals and viruses?
the bacteriophage-adhering-to-mucus (BAM) model.
– The authors suggest that the surface mucus layer and phages may have coevolved, with phage adherence maintained as it benefits the corals by limiting pathogenic bacteria in the mucus layer, and benefits the phage by enabling more frequent interactions with bacterial hosts.
– They posit that BAM immunity reduces bacterial pathogenesis and provides mucosal immunity.
Explain how viruses participate in this tripartite symbiosis in corals
– Corals provide shelter and hosts for the viruses
– phage protects coral by creating a ‘lytic barrier’ against potentially pathogenic bacteria.
– Viruses infect symbiotic bacteria but can become prophages. This allows bacteria to perform their ecological services to the coral without the viruses killing them. Additionally, phages can share genes with bacteria conferring increased host fitness and protection from lytic viruses.
Why might there be cellular genes present in viral metagenomes?
Can be a result of host contamination, horizontal gene transfer between viruses and their hosts, or gene transfer agents.
papers: Wood-Charlson et al., 2015; Roux et al., 2013; Canchaya et al., 2003; Monier et al., 2009; Liu et al., 2011; Lang et al., 2012;
Corals are degrading at an alarming rate due to…
Synergistic impacts of overfishing, anthropogenically derived increases in carbon dioxide levels, warming of sea surface temperatures, eutrophication, sedimentation, and pollution.
