Viruses- Instead, the progeny virus can be released out

Viruses-
what we know so far
A virus is a small particle with RNA
or DNA genetic material which can be single or double stranded and is generally
about 20-200nm in length. The infectious virus particle is composed of a
nucleic acid surrounded by a protein shell (Lodish et al., 2000). Viruses need a host to reproduce and multiply as
they cannot do it by themselves. With almost every cellular organism being
vulnerable to infection by a vast array of viruses, this makes viruses one of
the most diverse and dangerous entities on earth. Viruses use the hosts exposed
cellular structures as a method to attach and enter the organism, while using
passive transport to come in contact with a host (Fuhrman, 1999).

The
three major types of reproduction in viruses are: Lytic infection, chronic
infection and lysogeny. Lytic infection is when the host cell is penetrated by
a lytic phage. A nucleic acid is injected into the cell which encourages the
host cell to produce multiple progeny viruses. The cell will then burst causing
the death of the cell, which allows the process to start once again as the
virus particles that are released can infect other cells of the host (Clyde and
Glaunsinger, 2010). Chronic infection does not result in the fatality of the
cell. Instead, the progeny virus can be released out of the cell through
budding or extrusion over numerous generations (Fuhrman, 1999). Lysongeny (also
referred to as the lysogenic cycle) is when the host cell can carry the cell of
the virus in a relatively stable state. The nucleic acid of the virus is
reproduced with the genome of the host cell and is called a prophage. However,
a stressful event to the host cell can trigger a change from the lysogenic
cycle to lytic infection (Guttman, 2001).

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Viruses
are abundant in every environment on earth from high up in the atmosphere to
the deepest depths of the ocean. Approximately 71% of the earth is covered by
water, of which 96.5% is in the ocean where the true power of viruses can be
seen. Viruses have the highest abundance of any other life form in the ocean,
occurring at approximately ten billion per litre of water with a vast range of
genetic diversity (Fuhrman, 1999). Microorganisms make up 90% of the biomass in
the ocean and are essential to nutrient and energy cycles. Yet, approximately
20% of this living biomass is lost to viruses every day (Suttle, 2007). Viruses
however to do not just affect microorganisms, they can impact almost every
lifeform in the ocean such as bacteria, archaea and eukaryotic organisms (Rohwer
and Thurber, 2009).

The
development of methods to estimate the abundance and diversity of viruses in
the ocean has proved to be quite difficult for researchers. It was once thought
that the quantity of viruses in the ocean was linked to prokaryotic abundance
and activity but researchers have now found dissimilarity occurring between
them in different marine environments.  Researchers
have also found it difficult to quantify the exact effects that viruses have on
heterotrophic and autotrophic communities in the ocean (Suttle, 2007). However
in recent years our knowledge of the vast range of viruses in the marine
environment has grown by using metagenomics processes. The relationship between
viruses and the organisms that they effect appears to limit and control the
genetic diversity of viruses in that area (Suttle, 2007). Recent studies have
revealed that viruses are capable of manipulating entire life histories and
future evolution of the organism that have infected, which shows that they are
of major importance in the marine food web. Since viruses can impact bacteria,
archaea and eukaryotic communities, they have the ability to change the
composition of almost any organism in our oceans (Rohwer and Thurber, 2009).

The bacterial virus “phage”
was discovered by Frederick W. Thwort in 1915 and also discovered by Félix d’Hérelle in 1917 in
France, independently of each other. Some say that d’Hérelle’s claims
that he had no knowledge of Thworts earlier discovery when he published his
work in 1917 are false (Duckworth,
1976). In 1979 Francisco Torella and Richard Morita discovered that there are
many morphological similarities between phage and marine viral particles and that
they are extremely abundant in the ocean with approximately 10 million occurring
in every millilitre of water. In the 1990’s, a lot of research was put into diversity
and abundance of marine phage and the ecological effect these viruses have on
marine plankton communities. Research showed that viruses and protists gave
major contributions to the global biogeochemical cycle. Soon, the very first
marine viral genomes were sequenced and developed what we know today as metagenomics
to characterize the different types of DNA and RNA viruses in the water (Rohwer
and Thurber, 2009). The timeline shown in the figure below shows the major
events that have occurred in the research of marine viruses.

Figure
1. from Rohwer and Thurber, 2009.

 

Abundance
of viruses

It
is difficult to locate a paper talking about marine virology which does not
state the sheer abundance of viruses in our oceans. In the late 1980’s, the discovery
of the magnitude of viruses in our oceans brought interest into the study of
marine virology (BØrsheim et al.,
1990). For several decades, the effect that viruses had on certain marine organisms
was studied rather than the effect that they had on ecological systems as a
whole (Fuhrman and Suttle, 1993). Viruses were not seen to be ecologically
important in the marine food web, until the late 1980’s where the true abundance
of viruses in the marine environment was discovered.  Before then researchers knew that there was a
presence of viruses in the ocean, but it was not thought that they were
abundant enough to have significant impacts on the ecology there. What was once
a topic of just curiosity, was now a topic vital to be studied in depth in
order to understand the physical and biological effects that viruses have in
our ocean (Suttle and Fuhrman, 2010).

In
just one litre of surface seawater, there is approximately 1010 virus-like
particles. This would mean that virus-like particles occur more often in the
water than bacteria and archea, which are the second largest biological entity
in our oceans (Wommack and Colwell, 2000). This easily makes viruses the largest
group of predators in our oceans, rivers and lakes. Even though viruses are only
a very small size of 20-200nm in length, they still make up the oceans second
biggest biomass (Lodish et al., 2000).
They are second only to the total biomass of prokaryotes occuring in the water
(Suttle, 2005).  

The
quantification of viruses occurring in the marine environment has shown that
virioplankton is the most abundant plankton class, which can vary drastically
between season and geographical position (Wommack and Colwell, 2000). Viruses
tend to follow the same general abundance occurrences as bacteria. They usually
occur in the greatest amount at the euphotic zone (layer in ocean closest to
the surface with enough light to allow photosynthesis to occur) and will continue
to decrease in abundance at increasing depth. Viral abundance is usually
greater in coastal regions rather than oligotrophic (nutrient poor) open ocean
waters (Marchant et al., 2000). Their general abundance patterns are also
similar to bacteria with the fact that sea ice can contain a higher amount of
viruses than the water lying beneath it.

Viruses
are sensitive to ecological changes that can occur in the water, for example
algal blooms. In one particular study, the abundance of viruses was noted
during a spring diatom bloom. The population size of viruses varied throughout,
with 5 × 105 occurring before the bloom and 1.3 × 107 viruses
ml?1 occurring one week after the peak of the bloom. A high concentration
of viral particles was observed in a mucus layer encircling dead diatoms after
the collapse of the bloom. Approximately 23% of the entire virus population
were joined to the diatoms. This shows that viruses are active components of
the microbial food web, and not just inactive species as once thought (Bratbak et al., 1990). Fluctuations in the concentration
of viruses can also occur due to lysis of host cells causing viral particles to
be released into the water. These concentration changes can occur in a matter
of minutes (Bratbak et al., 1996).
Virus abundance is most often linked to the concentration of prokaryotes in an
area, which indicates that most viruses infect bacteria and archaea. Viruses
with an approximate diameter of 60nm usually dominate the virus population (Cochlan
et al., 1993).

In
recent years, the processes for estimating the abundance of viruses in the ocean
has moved from transmission electron microscopy to epifluorescence microscopy
and flow cytometry. Transmission electron microscopes were used in order to visualise
the viral particles. Special processes are needed in order to get a
concentrated level of viral particles from water (Fuhrman, 1999). The use of a
transmission electron microscope (TEM) was adapted from the use of an electron
microscope, which was the first method of virus quantification and counting
published (Sharp, 1949). If the use of a TEM was applied rather than an
electron microscope back then, research in this area and the high abundance of
viral particles in water would have been discovered up to 40 years earlier. This
could have changed the development of biological oceanography, which has only
moved within the last two decades towards microbiological research (Fuhrman,
1999). Epifluorescence microscopy uses an epifluorescence microscope with a
high intensity light that passes through the sample being examined and
magnifies it. Several thousand samples are taken from oceans all over the world
in order to quantify and estimate the abundance of viruses (Breitbart, 2011).

As
the use of a transmission electron microscope (TEM) can be quite expensive,
alternative methods such as staining viruses with SYBR green can be used. This
method is a lot quicker and less expensive, and can even be used while out in
the field (Noble and Fuhrman, 1998). Samples taken from the water can be viewed
in time as little as one hour using a fluorescence microscope. The results are usually
very alike to those you get when using a TEM. Below is an example of the kind
of image you would get while looking at viruses dyed with SYBR green using a
fluorescence microscope.

Figure
2. from Fuhrman, 1999.

As
well as counting the amount of viruses from a given sample, the size and
distribution of these different shapes and forms of viruses has also become an
area of interest in recent studies. Viruses can occur in a variety of different
shapes and sizes (Proctor, 1997). A marine sample taken can reveal the extent
of the variety of different shapes that viruses can have using pulsed field
electrophoresis. The different size and abundance of viruses you get in a
sample depend on the location the sample was taken, the season and
environmental conditions. The typical sample usually contains up to 40
different shapes of viruses (Fuhrman, 1999).

Diversity
of viruses
It has become clear only in recent
years that viruses obtain a huge range of genetic and morphological diversity. Although
they are the most abundant biological entities in our oceans, the knowledge into
the diversity that viruses have is quite limited (Rohwer and Edwards, 2002). The
shape of the virus can give us insight into what and who the virus will impact.
Recent studies have shown that communities of viruses of similar genetic structure
can have a huge geographical range in the marine environment (Kellogg et al., 1995). Below are examples of the
types of shapes in which viruses can occur that impact bacteria.

Figure
3. taken from Suttle, 2005.

Above
in picture (a) is an example a virus with a contractile, quite rigid and thick
tail. Examples of this type of virus include the myoviridae family which currently
has 93 recognised species. These types of viruses are regularly isolated from
water samples taken and have a vast variety of hosts that they can infect.
Picture (b) is a virus with a very short non contractile tail. These types of
viruses typically have a small range of hosts that they can infect and are not
isolated from water samples as frequently as those with contractile tails.
Examples of this type of virus include the podoviridae family which currently has
50 recognised species (King et al.,
2011).
Picture (c) is a virus with a long, flexible contractile tail. These viruses
are similar to those in picture (a) as they can often be isolated from water
samples taken and can also infect a vast variety of hosts. An example of this
type of virus include the siphoviridae family which currently has 313
recognised species. These types of viruses have the ability to replicate into
the genome of the host and be passed from one generation to the next (Suttle,
2005).

The
morphology of viruses can indicate selection difficulties which face virus
populations. Viruses which have the ability to infect a large quantity of hosts
can exploit increased host populations in an area, for example the myoviridae
family. In comparison to this, viruses in the siphoviridae family can integrate
into the genome of the host and be passed from one generation to the next (King
et al., 2011). This would indicate
that although viruses in the myoviridae family have a higher rate of
reproduction, viruses in the siphoviridae family have much more extensive
generation times. The morphological and genetic diversity of viruses still has
much more to be discovered and studied in depth. Recent studies have proved it
difficult to culture prokaryotes which occur most often in the ocean, so the
viruses viewed are not likely to be the most superior (Suttle, 2005).

Several
studies of waters along the coast and sediment indicate that there are up to 5
thousand different virus genotypes in 200 litres of sea water and often over a
million occurring in 1kg of sediment. Sequences of water samples have shown
several new genotypes are emerging each time, suggesting that we are only just
beginning to discover all the types of viral life in the marine environment.
The diversity occurring in viral communities is huge, with the vast majority of
genotypes discovered making up less than 0.01% of the population (Breitbart et al., 2002). The true genetic
diversity of viral communities is shown as up to 80% of the viruses seen were
not alike any previously recorded in databases (Breitbart and Rohwer, 2005).

Culture
based studies of bacteriophages are frequently done using a technique called
plaquing. This involves a host cell being grown in a liquid culture, a sample
with the phage intending to infect the host being added to this culture and the
two mixed together. This mixture of the two is then placed into agar and put on
plate of media. The loose agar allows the phage to diffuse through it and
infect bacteria. A clear area called a “plaque” soon appears where
bacteriopahges in the agar have infected host cells. This technique for culture
based studies of bacteriopahges have proven that any marine microbial host can
be infected by one or more viruses (Breitbart and Rohwer, 2005).

Culture
independent studies are difficult because no single genome appears in all
viruses. Techniques using PCR amplification have shown that many microorganisms
in the marine environment are part of uncultured groups, which makes study into
virus biodiversity quite challenging. However, within particular virus
families, “signature genes” can be recognised and used to put viruses into
certain taxonomic groups. These “signature genes” are extremely useful when
trying to categorise cultured and culture independent viral diversity (Rohwer
and Edwards, 2002). The majority of viruses discovered in studies belong to
particular subgroups of viruses and only a few found are cultured isolates. (Breitbart
and Rohwer, 2005). Studies by Short and Suttle, 2005 have shown the viruses which
infect similar hosts can have huge geographical ranges and be distributed in a
large amount of varying environments (Short and Suttle, 2005).