Marine viruses

Marine viruses are defined by their habitat as viruses that are found in marine environments, that is, in the saltwater of seas or oceans or the brackish water of coastal estuaries. Viruses are small infectious agents that can only replicate inside the living cells of a host organism, because they need the replication machinery of the host to do so. They can infect all types of life forms, from animals and plants to microorganisms, including bacteria and archaea.
When not inside a cell or in the process of infecting a cell, viruses exist in the form of independent particles called virions. A virion contains a genome surrounded by a capsid. The shapes of these virus particles range from simple helical and icosahedral forms for some virus species to more complex structures for others. Most virus species have virions that are too small to be seen with an optical microscope. The average virion is about one one-hundredth the linear size of the average bacterium.
A teaspoon of seawater typically contains about fifty million viruses. Most of these viruses are bacteriophages which infect and destroy marine bacteria and control the growth of phytoplankton at the base of the marine food web. Bacteriophages are harmless to plants and animals but are essential to the regulation of marine ecosystems. They supply key mechanisms for recycling ocean carbon and nutrients. In a process known as the viral shunt, organic molecules released from dead bacterial cells stimulate fresh bacterial and algal growth. In particular, the breaking down of bacteria by viruses has been shown to enhance nitrogen cycling and stimulate phytoplankton growth. Viral activity also affects the biological pump, the process which sequesters carbon in the deep ocean. By increasing the amount of respiration in the oceans, viruses are indirectly responsible for reducing the amount of carbon dioxide in the atmosphere by approximately 3 gigatonnes of carbon per year.
Marine microorganisms make up about 70% of the total marine biomass. It is estimated marine viruses kill 20% of the microorganism biomass every day. Viruses are the main agents responsible for the rapid destruction of harmful algal blooms which often kill other marine life. The number of viruses in the oceans decreases further offshore and deeper into the water, where there are fewer host organisms. Viruses are an important natural means of transferring genes between different species, which increases genetic diversity and drives evolution. It is thought viruses played a central role in early evolution before the diversification of bacteria, archaea and eukaryotes, at the time of the last universal common ancestor of life on Earth. Viruses are still one of the largest areas of unexplored genetic diversity on Earth.

Background

Viruses are now recognised as ancient and as having origins that pre-date the divergence of life into the three domains. They are found wherever there is life and have probably existed since living cells first evolved. The origins of viruses in the evolutionary history of life are unclear because they do not form fossils. Molecular techniques are used to compare the DNA or RNA of viruses and are a useful means of investigating how they arose. Some viruses may have evolved from plasmids—pieces of DNA that can move between cells—while others may have evolved from bacteria. In evolution, viruses are an important means of horizontal gene transfer, which increases genetic diversity.
Opinions differ on whether viruses are a form of life or organic structures that interact with living organisms. They are considered by some to be a life form, because they carry genetic material, reproduce by creating multiple copies of themselves through self-assembly, and evolve through natural selection. However they lack key characteristics such as a cellular structure generally considered necessary to count as life. Because they possess some but not all such qualities, viruses have been described as replicators and as "organisms at the edge of life".
The existence of viruses in the ocean was discovered through electron microscopy and epifluorescence microscopy of ecological water samples, and later through metagenomic sampling of uncultured viral samples. Marine viruses, although microscopic and essentially unnoticed by scientists until recently, are the most abundant and diverse biological entities in the ocean. Viruses have an estimated abundance of 10³⁰ in the ocean, or between 10⁶ and 10¹¹ viruses per millilitre. Quantification of marine viruses was originally performed using transmission electron microscopy but has been replaced by epifluorescence or flow cytometry.

Bacteriophages

s, often contracted to phages, are viruses that parasitize bacteria for replication. As aptly named, marine phages parasitize marine bacteria, such as cyanobacteria. They are a diverse group of viruses which are the most abundant biological entity in marine environments, because their hosts, bacteria, are typically the numerically dominant cellular life in the sea. There are up to ten times more phages in the oceans than there are bacteria, reaching levels of 250 million bacteriophages per millilitre of seawater. These viruses infect specific bacteria by binding to surface receptor molecules and then entering the cell. Within a short amount of time, in some cases just minutes, bacterial polymerase starts translating viral mRNA into protein. These proteins go on to become either new virions within the cell, helper proteins, which help assembly of new virions, or proteins involved in cell lysis. Viral enzymes aid in the breakdown of the cell membrane, and there are phages that can replicate three hundred phages twenty minutes after injection.
Bacteria defend themselves from bacteriophages by producing enzymes that destroy foreign DNA. These enzymes, called restriction endonucleases, cut up the viral DNA that bacteriophages inject into bacterial cells. Bacteria also contain a system that uses CRISPR sequences to retain fragments of the genomes of viruses that the bacteria have come into contact with in the past, which allows them to block the virus's replication through a form of RNA interference. This genetic system provides bacteria with acquired immunity to infection.
File:Lytic cycle.png|thumb|upright=2| The lytic cycle, the reproductive cycle of the bacteriophage, has six stages:

→ attachment: the phage attaches itself to the surface of the host cell

→ penetration: the phage injects its DNA through the cell membrane

→ transcription: the host cell's DNA is degraded and the cell's metabolism is directed to initiate phage biosynthesis

→ biosynthesis: the phage DNA replicates inside the cell

→ maturation: the replicated material assembles into fully formed viral phages

→ lysis: the newly formed phages are released from the infected cell to seek out new host cells
Microbes drive the nutrient transformations that sustain Earth's ecosystems, and the viruses that infect these microbes modulate both microbial population size and diversity. The cyanobacterium Prochlorococcus, the most abundant oxygenic phototroph on Earth, contributes a substantial fraction of global primary carbon production, and often reaches densities of over 100,000 cells per milliliter in oligotrophic and temperate oceans. Hence, viral infection and lysis of Prochlorococcus represent an important component of the global carbon cycle. In addition to their ecological role in inducing host mortality, cyanophages influence the metabolism and evolution of their hosts by co-opting and exchanging genes, including core photosynthesis genes.
For a long time, tailed phages of the order Caudovirales seemed to dominate marine ecosystems in number and diversity of organisms. However, as a result of more recent research, non-tailed viruses appear to dominate multiple depths and oceanic regions. These non-tailed phages also infect marine bacteria, and include the families Corticoviridae,
Inoviridae,
Microviridae and Autolykiviridae.
As of September 2023, Halomonas phage vB HmeY H4907 is the first virus isolated from the deepest part of the ocean.

Archaeal viruses

Archaean viruses replicate within archaea: these are double-stranded DNA viruses with unusual and sometimes unique shapes. These viruses have been studied in most detail in the thermophilic archaea, particularly the orders Sulfolobales and Thermoproteales. Defences against these viruses involve RNA interference from repetitive DNA sequences within archaean genomes that are related to the genes of the viruses. Most archaea have CRISPR–Cas systems as an adaptive defence against viruses. These enable archaea to retain sections of viral DNA, which are then used to target and eliminate subsequent infections by the virus using a process similar to RNA interference.

Fungal viruses

es, also known as mycophages, are viruses that infect fungi. The infection of fungal cells is different from that of animal cells. Fungi have a rigid cell wall made of chitin, so most viruses can get inside these cells only after trauma to the cell wall.

Eukaryote viruses

Marine protists

By 2015, about 40 viruses affecting marine protists had been isolated and examined, most of them viruses of microalgae. The genomes of these marine protist viruses are highly diverse. Marine algae can be infected by viruses in the family Phycodnaviridae. These are large double-stranded DNA viruses with icosahedral shaped capsids. By 2014, 33 species divided into six genera had been identified within the family, which belongs to a super-group of large viruses known as nucleocytoplasmic large DNA viruses. Evidence was published in 2014 suggesting some strains of Phycodnaviridae might infect humans rather than just algal species, as was previously believed. Most genera under this family enter the host cell by cell receptor endocytosis and replicate in the nucleus.
File:Virus cocco 2.jpg|thumb| A giant coccolithovirus, Emiliania huxleyi virus 86, infecting an Emiliania huxleyi coccolithophore
Phycodnaviridae play important ecological roles by regulating the growth and productivity of their algal hosts. Algal species such Heterosigma akashiwo and the genus Chrysochromulina can form dense blooms which can be damaging to fisheries, resulting in losses in the aquaculture industry. Heterosigma akashiwo virus has been suggested for use as a microbial agent to prevent the recurrence of toxic red tides produced by this algal species. The coccolithovirus Emiliania huxleyi virus 86, a giant double-stranded DNA virus, infects the ubiquitous coccolithophore Emiliania huxleyi. This virus has one of the largest known genomes among marine viruses. Phycodnaviridae cause death and lysis of freshwater and marine algal species, liberating organic carbon, nitrogen and phosphorus into the water, providing nutrients for the microbial loop.
The virus-to-prokaryote ratio, VPR, is often used as an indicator of the relationship between viruses and hosts. Studies have used VPR to indirectly infer virus impact on marine microbial productivity, mortality, and biogeochemical cycling. However, in making these approximations, scientists assume a VPR of 10:1, the median observed VPR in the surface ocean. The actual VPR varies greatly depending on location, so VPR may not be the accurate proxy for viral activity or abundance as it has been treated.