Marine microbiology virues.

1.  Faculty of Science
 Department : Marine Science
 Presentaion Group-A, B, C
 Chapter Seven : Marine Viruses
 Members of the Group-C
1. Abdulahi hassan farah
2. Amal mohamed ali
3. Abdirahman mahad mahamud
4. Abdulahi Ahmed Mohamed
5. Ibrahim mohamed dirie
6. Mohamed abdullahi ahmed
7. Abukar hassan
Somali national university

2.  Viruses are non-cellular biological entities. They cannot be described as
microorganisms, but they are included in the more encompassing term
microbes. Virus particles, termed “virions,” are composed of nucleic acid
surrounded by a protein coat (capsid). A fundamental difference in the
makeup of viruses compared with cells is that viruses contain only one type
of nucleic acid, either DNA or RNA, whereas cells contain both. Also, they do
not contain ribosomes and therefore cannot synthesize proteins.
 Viral genomes can be circular, linear, or segmented; with either a DNA or
RNA genome, both of which can be either single- or double-stranded. A key
factor in the replication strategy of single-stranded viruses—used in the
Baltimore classification scheme—is whether the nucleic acid is positive or
negative sense.
Viruses are highly diverse non-
cellular microbes

3.  When viruses that infect bacteria were discovered in 1915, they were
called bacteriophages—a term meaning “bacteria-eaters.” Subsequently,
viruses that infect archaeal cells have also been discovered, but no specific
term to denote them has been coined. Therefore, the abbreviated term
“phage” is usually used to indicate viruses infecting members of either
domain. Prefixes indicating a particular host range are also used: terms
such as “vibriophages” (infecting Vibrio spp.), “cyanophages” (infecting
cyanobacteria), or “roseophages” (infecting members of the Roseobacter
clade) are used.
 Although the first marine phages were described in the 1950s, the
significance of early findings was not appreciated, and it was not until the
late 1980s that serious attention was paid to this field. The relatively slow
development of this area of research may be linked to the long-held fallacy
that microbial populations in the oceans are insignificant and that, by
association, viruses must also be unimportant.
Phages are viruses that infect
bacterial and archaeal cell

4. The classical method of enumerating infective phages and
viruses infecting protists is based on the formation of plaques
of lysis in lawns of susceptible hosts grown on agar plates
(Figure 7.3)

5.  The first step in the life cycle of phages is adsorption to the host cell
surface, which may be reversible, followed by irreversible binding to a
specific receptor on the host cell surface. For those marine phages that
have so far been propagated in cultivated bacteria, most show specificity
for particular bacterial species and sometimes for particular strains. These
findings are similar to those seen in other well-known viruses and are
usually thought to be due to the molecular specificity of virus receptors on
the host cell surface, the presence of restriction enzymes, or compatibility
of the replication processes.
 In most cases, enzymes in the tail or capsid of the phage attack the
bacterial cell wall, forming a small pore through which its nucleic acid
enters. The phage genetic material then remains in the cytoplasm or is
integrated into the host cell genome.
Life cycle of phages shows number
of distinct of stages

6.  Lytic phages take over the host cell, replicate their nucleic acid, and
cause lysis of the host cell after assembly of the virus particles.
However, another outcome is seen when phages, known as temperate
viruses, infect the cell (Figure 7.5b). The phage genome replicates along
with the host DNA, but it is not expressed. Often, the silent viral
genome is stably integrated into the bacterial genome; this latent state is
known as a prophage. In other cases, the phage genome remains in the
cytoplasm in a circular or linear form. Bacteria infected with these
phages are known as lysogenic, because under certain conditions the
bacteria enter the lytic cycle and release infective virus particles. The
mechanisms that determine whether the phage enters the lytic or
lysogenic cycle has been well studied in the lambda phage of
Escherichia coli and a few other examples, where there appears to be a
quorum-sensing like process (p.102) mediated by the phage and a
peptide signal molecule.
Lysogeny occur when the phage
genome is integrated into host cell.

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8.  Usually, a virus will lose its infectivity before showing obvious signs of degradation.
 However, since most marine viruses are studied by microscopic or flow cytometric enumeration of VLPs,
the term “virus decay” reflects the observation of a decline in numbers of VLPs
 over time in the absence of new viral production. Many of the studies of virus inactivation
 in water were originally carried out in connection with the health hazards associated with
 sewage-associated viruses (such as enteroviruses or coliphages; in waters for swimming or
 cultivation of shellfish (p.366). Subsequently, the results of these studies have been applied to
 the population dynamics of autochthonous marine viruses. A wide range of physical, chemical, and
biological factors can influence virus infectivity and decay. Different studies have
 produced various estimates of decay rates, but a value of about 1% per hour is typical in
 natural seawater kept in the dark. Visible light and ultraviolet (UV) irradiation are by far the
 most important factors influencing virus survival, and in full-strength sunlight, the decay
 rate may increase to 3–10% per hour, and in some circumstances can be as high as 80%. UV
 light has its greatest effect in the upper part of the water column but is probably still effective
 down to about 200 m in clear ocean water. Even in very turbid coastal waters, viral inactivation by light
can be observed down to several meters.
Loss of viral infectivity arises from
damage
to the nucleic acid or capsid

9.  Many studies in viral ecology have attempted to measure the effect of viruses on
microbial mortality and the rate of production of new virions. This enables
estimates of the proportion of primary and secondary production that is “turned
over” by viral lysis. It is possible to use filtration and high-speed centrifugation
to obtain a pellet of planktonic microbes, which can be embedded in resin and
sectioned for TEM. By examining such samples from various locations, it has
been found that about 1−4% of microbial cells contain mature, fully assembled
VLPs. Since VLPs can only be seen within infected host cells in the final stages
of the lytic cycle of infection—this stage usually represents about a quarter of
the life cycle—it is possible to estimate the total proportion of plankton that are
infected at any one time. Another method used in early studies of virus
production was to measure the incorporation of radioactively labeled precursors
such as 3H-thymidine, 14C-leucine, or 32P-phosphate into virus particles, which
can be separated from cells and cell debris by filtration.
Measurments of Viruses production rate
is important for quantifying viruses-
induced Mortality

10.  After adjustments for the relative abundance of host cells in the sample, the
production rate and the original percentage of infected cells can be calculated.
Each of these methods has advantages and disadvantages and no single method
gives precise estimates of virus-mediated mortality. (Obviously, these methods
cannot detect prophage-infected cells). Nevertheless, despite variability
depending on the method, location, and time of sampling, the unequivocal
conclusion from various studies is that viral mortality has a highly significant
impact on mortality of microbes that is at least as significant as grazing by
protists and zooplankton. A consensus value is that about up to 40% of marine
bacteria are killed each day by viral action. Between 20–30% of bacteria in the
oceans are probably infected by phages at any one time, and an estimated 1023
viral infections occur every second. In the case of algae, laboratory experiments
and mesocosm studies have indicated that viral infection can account for nearly
100% of mortality of bloom-forming microalgae such as E. huxleyi.
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11.  Viral infection of heterotrophic and autotrophic bacteria, archaea, fungi,
microalgae, and other protists seems to be the most important factor
influencing nutrient cycles in the oceans. This is important because it
leads to the release of massive amounts of organic material and
essential elements from these microbes into the dissolved organic pool
from where it is metabolized by heterotrophs. Because the contents of
cells lysed by viruses are rich in nitrogen and phosphorus, this “viral
shunt” speeds up the recycling of nutrients, enhances the rate of
microbial respiration, and reduces the amount of organic material
available to higher trophic levels through protistan grazing in the
microbial loop (see Figures 8.3 and 8.4). However, viral lysis is now
recognized as having more complex effects, because it leads to the
release of high molecular weight polymeric substances from cells.
Viral mortality “lubricates” the
Biological pump

12.  microalgae and other protists
 One of the most studied family of viruses is the Phycodnaviridae,
a family of large dsDNA
 viruses infecting a wide host range of freshwater and marine
algae. Although genetically
 diverse, they share some morphological similarities, with a
dsDNA-protein core usually surrounded by a lipid membrane and
a capsid (120–220 nm diameter) with icosahedral symmetry.
Genomes of several species have been obtained and range in
size from 100–560 kb.
 There are currently six genera recognized in ICTV taxonomy
Nucleocytoplasmic large DNA viruses (NCLDVs) are
important pathogens of microalgae and other
protists

13. RNA viruses also infect protists
 It is generally assumed that DNA viruses are the most dominant viruses
in the ocean, but this assumption may be influenced by methodological
constraints because RNA viruses with small genomes are more difficult
to observe and enumerate using electron microscopy or flow
cytometry, and metagenomic methods for their detection have not been
fully developed. Nevertheless, RNA viruses appear to be very diverse,
and numerous ecologically important examples occur in the major
virus groups, as shown in Table 7.1. PCR-based screening of seawater
samples using conserved sequences of the RNA-dependent RNA
polymerase gene has demonstrated that distinct groups of picorna-like
viruses are abundant, widespread, and persistent. Metagenomic
analysis based on reverse-transcribed shotgun sequencing has shown
that most sequences are unrelated to known RNA viruses. Some RNA
viruses are well-known because of their economic importance as
pathogens in marine fish and shellfish aquaculture (Chapter 11).

14. Viral mortality plays a major role in structuring
diversity of Microbial Communities
 As well as influencing microbial diversity by HGT and genetic rearrangements between host
and virus, viruses influence host diversity at ecological scales. The discovery in the 1990s that
phages are so numerous and responsible for high levels of bacterial mortality led to the
development of models to explain how this might be influencing community structure. These
approaches subsequently extended also to interactions between viruses and algae. The
probability of an encounter between a host cell and a virus is more likely at high host densities
because increased contact rates between a virus and its host are determined by their relative
abundances. Also, some viruses may be very specific, and small changes in host cell surface
receptors or replication processes could make them resistant to infection by a particular virus
genotype (but note the earlier discussion suggesting that some phages probably have a broad
host range). The density dependence and host range factors mean that viruses should
preferentially infect the most common hosts: abundant hosts are more susceptible and rare
hosts are less susceptible.
 Therefore, viruses may control excessive proliferation of hosts that have an advantage in
nutrient acquisition and growth, encouraging a high diversity in the host population so that less
competitive, but virus-resistant, microbes survive. This has been developed into a
mathematical model termed the “kill the winner” hypothesis,

15. Marine viruses show enormous genetic
diversity
 As with other microbial groups, the application of culture-independent methods has led to major
advances in our understanding of the level of diversity of marine viruses. One of the problems in the
study of viral diversity is that there is no universal marker like the ribosomal RNA genes used for
other microbes. However, some success has been made by using representative signature genes that
are sufficiently conserved to be used as markers of particular viral groups. For example, extensive
virus diversity studies focused on the variation in the sequences of structural proteins, such as the
g20 capsid protein gene in cyanophages or the major capsid protein (MCP) in phycodnaviruses.
Primers for parts of the viral DNA or RNA polymerase genes are also used in PCR amplification
reactions for phycodnaviruses,.
 Major advances in the study of viral diversity were also made possible using high-throughput
metagenomic sequencing. The genome sequences of a large number of cultured marine phages have
been obtained, providing insight into metabolic functions and replication strategies. In addition,
direct sequencing of environmental samples is helping us to understand the extent of viral diversity
and biogeography in their natural setting.
 New developments in single-cell genomics and metagenome assembled genomes (p.56) of viruses
is leading to vast increases in the amount of sequence data, which in turn catalyzes further
exploration of viral diversity.

16. Viromes are creators of genetic diversity and
exchange
 As noted previously, besides affecting microbial population dynamics, viruses influence
diversity in the marine environment because of genetic exchange. Analysis of viral metagenomes
(viromes) has unexpectedly revealed numerous genes involved in metabolic pathways,
indicating that they are a reservoir of genetic information, which is important in the evolution
and adaptation of their hosts to different ecological niches. Lysogeny of bacteria by temperate
phages may lead to the introduction and expression of new genes into a host and excision of a
prophage can lead to transduction of genes to new hosts. In addition, a process known as
generalized transduction can occur, in which the enzymes responsible for packaging viral DNA
into the capsid may mistakenly incorporate host DNA.
 These virions are defective and cannot induce a lytic infection, but DNA can be passed from one
host to another and may recombine with the DNA of the recipient host. We have known for some
time that viruses are vectors for HGT, but we now know that this has powerful effects on the
evolution of both the microbial hosts and the viruses. Genetic information is moved by viruses
from organism to organism and throughout the biosphere. As discussed in Box 7.2, genes
encoding entire metabolic pathways may move between viruses and their hosts. Unlike defective
phages, which are “genuine” virions that are empty or have mistakenly packaged host DNA,
another class of virus-like entities called gene transfer agents (GTAs) has recently been
discovered in Rhodobacter and some other members of the Alphaproteobacteria.

17. Conclusions
 This chapter has illustrated the rapid pace at which the field of marine
virology is moving. Viruses have emerged to take “center stage” in marine
ecology and biogeochemical processes, through their effects on plankton
composition and production. On a more fundamental level, recent
metagenomic studies and the genomic analysis of isolated viruses have
revealed that they provide an unprecedented reservoir of genetic diversity
and play a major role in the evolution of life. The discovery of extensive
gene transfer and the metabolic effects of viral infection provides important
insights into evolution and adaptation to environmental change. Viruses
feature again in the next three chapters, which include further discussion of
their involvement in nutrient cycles, in specific biogeochemical cycles, and
as disease agents of marine organisms other than microbes.