User:Alombard.9/sandbox

Topic: How have bacteria and phages evolved with each other to either become more resistant to the others’ effect or to have a greater infection influence?

Annotated Bibliography
Buckling, A. and Rainey, P. B. (2002). Antagonistic coevolution between a bacterium and a bacteriophage. Proc. R. Soc. Lond. 269 1494 931-936; doi:10.1098/rspb.2001.1945 1471-2954 The coevolution between parasites and their host cells can be considered antagonistic. This antagonistic coevolution holds a strong influence over how one is able to control the other’s population and vice versa. Thanks to this, both bacteria and their phage counterparts have differentiated rapidly in an attempt to become resistant/better at infecting.

Koskella, B. and Brockhurst, M. A. (2014), Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiology Reviews. doi: 10.1111/1574-6976.12072 The coevolution between bacteria and phages has a large impact on microbial communities in an ecological and evolutionary sense. This coevolution makes it easy for variation in populations to be maintained, as they are constantly changing from generation to generation.

Lenski, R. E. and Levin, B. R. (1985). Constraints on the Coevolution of Bacteria and Virulent Phage: A Model, Some Experiments, and Predictions for Natural Communities. The American Naturalist Vol. 125, No. 4 pp. 585-602 This study was conducted to see how quickly the genes in phages and in their host cells are able to mutate. It was found that the mutation rate is directly related to many environmental factors including, but not limited to, population density and habitat size. The Escherichia coli B that was worked with managed to develop a resistance to phage T4. The phage did not mutate to a point where it became a threat to the bacteria again.

Morgan, A. D., Bonsall, M. B. and Buckling, A. (2010), Impact of Bacterial Mutation Rate on Coevolutionary Dynamics Between Bacteria and Phages. Evolution, 64: 2980–2987. doi: 10.1111/j.1558-5646.2010.01037.x In this article, it is hypothesized that phages must adapt more rapidly than their bacterial host counterparts, else they would go extinct as the bacteria are able to mutate quickly. An experiment was done using a mutator bacteria and a wild-type bacteria and the same phage for both. Initially, both groups coevolved with the phage but then the mutator bacteria quickly went ahead and the phage was unable to keep up.

Stern, A. and Sorek, R. (2011), The phage-host arms race: Shaping the evolution of microbes. Bioessays, 33: 43–51. doi: 10.1002/bies.201000071 This article is primarily about the ways in which bacteria are able to resist the effect of phages. The mechanisms employed can be found in many types of bacteria, suggesting they are evolutionary traits that will lead to finding when these mechanisms were first developed.

Article Found For 10/1
https://en.wikipedia.org/wiki/Phage_ecology#Phage_community_ecology

Sentence added: Bacteria have developed mechanisms that prevent phage from having an effect on them, which has led to this evolutionary arms race between the phage and their host bacteria.

Three suggestions:

Suggestions
It may be a good idea to include more information on the relationship between phage and bacteria, as it is so important. Also in the "historical overview" section or in the "studying phage ecology" section I think it would be beneficial to talk about how research into phages has really taken off in recent years. Finally, in the "Phage Ecosystem Ecology" section you mention that ecologists are concerned about how phages impact the carbon cycle. Instead of stopping there, maybe go a little more in depth as it sounds like an important issue.

FINAL DRAFT OF PAPER
Bacteria are found everywhere and are generally thought of as the most common organism in existence. However, most people are unfamiliar with the fact that bacteriophages outnumber bacteria immensely, by a factor of about 10:1 (Stern and Sorek 2011). Whether or not phages should be considered organisms or not is another topic entirely. Regardless, bacteriophages are extremely abundant even though little is known about them in the grand scheme of things.

Simply put, a bacteriophage is a virus to a bacterium. They are quite simple in structure, consisting of a head with the phage DNA, a sheath, and tail fibers. When bacteriophages interact with a host bacterial cell, one of two things can happen. Either the cell will lyse or the phage DNA will become incorporated into the bacterial DNA and the host cell will continue to replicate. These two processes are called the lytic and lysogenic cycles, respectively. A temperate phage can use both of these cycles to reproduce. The lytic cycle involves a phage attaching to a host cell, then injecting its DNA into the cell where it will replicate, creating new phages that eventually cause the cell to burst (Koskella and Brockhurst 2014). In either case, the phage is benefitting while the bacterial host cell is harmed in some way, whether it be that it dies or that its offspring now end up with the phage DNA (Clokie et al. 2011). Interest in studying bacteriophages has grown in more recent years as they have the potential to advance medicine greatly when it comes to fighting bacterial infections. A specific type of bacteriophage is not able to infect just any type of bacteria. They are specific to a certain kind or just a couple of types of bacteria. This is important because it means that eventually, phage therapy can be used to get rid of unwanted bacteria without destroying any of the “good” bacteria, as many antibiotics do (Gomez and Buckling 2011). This would require more research than has been done so far, but there is progress being made. The relationship between bacteria and these phages obviously presents a problem to the bacteria (Buckley and Rainey 2002). So in order to combat this, bacteria adapt to be phage resistance, which puts pressure on the phages to develop stronger effects on the bacteria. This leads to what can be a called a “phage-host arms race” (Stern and Sorek 2011). The two develop a relationship that can be described by the Red Queen hypothesis that states organisms must constantly adapt and evolve in order to survive (Lenski and Levin 1985). This relationship is important to understand, especially now as phages are being used more and more for medicinal purposes. Bacteria have developed multiple defense mechanisms to fight off the effects of bacteriophages (Stern and Sorek 2011). Angus Buckley and P. B. Rainey carried out a study to observe the resistance of certain bacteria to phages. They ended up plating bacterial colonies where phage were already present, and if they bacterial colonies were able to grow, there was no hindrance by the phages and the bacteria could be considered resistant (Buckley and Rainey 2002). However, if clear spots, or holes in the colony were to appear, then a little bit of resistance would be said to exist, but the phage still managed to effect the bacteria. A completely lysed plate would look almost clear with some slight webbing, which really would look like a pattern of thin lines on the plate due to the lysed bacteria creating clear circles. The most common of these defense mechanisms is called the restriction-modification (RM) system. In this system, foreign DNA trying to enter the bacterial host is restricted by endonucleases that recognize specific base pairs within the DNA, while the DNA of the cell is protected from restriction due to methylase (Stern and Sorek 2011). Work done by Ludo Pagie and Paulien Hogeweg went even further to show how RM systems have evolved to keep up with the ever-changing bacteria and bacteriophages. In general, these RM types differ in the nucleotide sequences that they recognize (Pagie and Hogeweg 2000). However, there is an occasional slip where the endonuclease misses the DNA sequence of the phage and the phage DNA is able to enter the cell anyway, becoming methylated and protected against the endonuclease. This accident is what can spur the evolution of the RM system (Pagie and Hogeweg 2000). The RM system does not work for too long, though. Phages can acquire or use the enzyme from the host cell to protect its own DNA or they can even have proteins that dismantle the enzyme that is meant to restrict the phage DNA (Stern and Sorek 2011). A third option is for the phage to throw in some different base pairs into its DNA, thereby confusing the enzyme. No matter the method, it becomes an ongoing battle between the phage and host. Another mechanism employed by bacteria is referred to as CRISPR. This stands for “clustered regularly interspersed palindromic repeats” which basically means that the immunity to phages by bacteria has been acquired via adding spacers of DNA that are identical to that of the DNA from the phage. Some phages have been found to be immune to this mechanism as well. In some way or another, the phages have managed to get rid of the sequence that would be replicated. A third way that bacteria have managed to escape the effects of bacteriophages is by abortive infection. This is a last resort option- when the host cell has already been infected by the phage. This method is not ideal for the host cell, as it still leads to its death. The redeeming feature of this mechanism is the fact that it interferes with the phage processes and prevents it from then moving on to infect other cells (Stern and Sorek 2011). Each of these mechanisms increases the genetic diversity of both phage and host (Buckley and Rainey 2002, Koskella and Brockhurst 2014). While it may seem as though everything the phage does harms the host bacterial cell and that the relationship is solely antagonistic (Buckley and Rainey 2002), there is at least one benefit. During the lysogenic cycle when a phage incorporates its DNA into that of the host cell, the host cell is introduced to new genes. It is possible that some of the new genes may be beneficial in the long run to the host cell (Stern and Sorek 2011). The coevolution of both phage and host is a rapid process when it comes to an evolutionary time scale (Buckley and Rainey 2002). This is due to the fact that both organisms reproduce very quickly and can therefore develop such mechanisms of defense and offense at a faster rate. This fast replication also makes this relationship easier to study as it requires much less time than other organisms like fish or plants. One question that may be present is, how can we know that there has been some sort of evolutionary change? Yes it sounds like it would work in theory, but is that what actually happens? In Buckley and Rainey’s experiment, they determined evolutionary change by comparing the most recent generations of phage and bacteria they used to an “ancestral” species. (As in, the beginning forms of both). In each case, the phage and bacteria had become more resistant/infective than the ancestral species. Could this also be the case in the natural world? Buckley worked with Gomez to test just that. Instead of creating an unnatural laboratory experiment, they worked solely in sterile soil which is a little closer to where the bacteria would be found naturally. Every few days a sample was taken and plated and the resistance was determined. The findings they had were slightly different in that bacteria were most resistant to what they determined to be “contemporary” phages, while the phage were least infective to those phages. That is to say there is still a coevolutionary process, but it is not limitless (Buckley and Gomez 2011). Mutations are another factor that play into this host-arms race. Both bacteria and phages have a fairly high mutation rate, so that coupled with their speedy reproduction can carry along coevolution at a steady rate (Lenski and Levin 1985). The populations of bacteria and bacteriophages in the world are constantly changing. Selective pressures from each other drive this coevolutionary force that creates a phage-host arms race. The Red Queen hypothesis describes this relationship as both types of organisms must constantly adapt and evolve in order to survive and produce offspring. Evolutionary changes can arise from adaptations that use enzymes to carry out certain processes and mutations that allow for greater resistance or infection ability. The world of bacteriophages is so vast and the implications of their interactions with other organisms still have yet to fully be determined, but it is a work in progress. In order to gain more knowledge about phages in general, a program has been set up in multiple universities across the United States called SEA PHAGES program which stands for Science Education Alliance- Phage Hunters Advancing Genomics and Evolutionary Science. It gives students the opportunity to work in a controlled laboratory setting while doing real research and discovering new types of bacteriophages. More and more researchers are recognizing the importance of bacteriophages and their potential benefits to society. It is possible that one day, the most common treatment for bacterial infections will be phage treatment as opposed to antibiotics.

References Buckling, A. and Rainey, P. B. 2002. Antagonistic coevolution between a bacterium and a bacteriophage. Proc. R. Soc. Lond. 269: 931-936; doi:10.1098/rspb.2001.1945. Clokie, M. R.; Heaphy, S.; Millard, A. D.; Letarov, A. V. 2011. Phages in nature. Bacteriophage. 1 (1): 31-45; doi: 10.4161/bact.1.1.14942. Gomez, P. and Buckling, A. 2011. Bacteria-phage antagonistic coevolution in soil. Science. 322: 106-109; doi: 10.1126/science.1198767 Koskella, B. and Brockhurst, M. A. 2014. Bacteria–phage coevolution as a driver of ecological and evolutionary processes in microbial communities. FEMS Microbiology Reviews. doi: 10.1111/1574-6976.12072. Lenski, R. E. and Levin, B. R. 1985. Constraints on the coevolution of bacteria and virulent phage: A model, some experiments, and predictions for natural communities. The American Naturalist. 125 (4): 585-602. Morgan, A. D.; Bonsall, M. B.; and Buckling, A. 2010. Impact of bacterial mutation rate on coevolutionary dynamics between bacteria and phages. Evolution. 64: 2980–2987; doi: 10.1111/j.1558-5646.2010.01037.x Pagie, L., Hogeweg, P. 2000. Individual- and population-based diversity in restriction-modification systems. Bulletin of Mathematical Biology. 62:759-774; doi: 10.1006/bulm.2000.0177 Stern, A. and Sorek, R. 2011. The phage-host arms race: Shaping the evolution of microbes. Bioessays. 33: 43–51; doi: 10.1002/bies.201000071 Woolhouse, M. E. J.; Webster, J. P.; Domingo, E.; Charlesworth, B.; and Levin, B.R. 2002. Biological and biomedical implications of the co-evolution of pathogens and their host. Nature Genetics. 32 (4): 569-577.

Edits to Phage Ecology article
https://en.wikipedia.org/wiki/Phage_ecology#Phage_community_ecology

Relationship with bacteria
The interaction of phage with bacteria is the primary concern of phage community ecologists. Bacteria have developed mechanisms that prevent phage from having an effect on them, which has led to this evolutionary arms race between the phage and their host bacteria. Bacterial resistance to phage puts pressure on the phage to develop stronger effects on the bacteria. The Red Queen hypothesis describes this relationship, as the organisms must constantly adapt and evolve in order to survive. This relationship is important to understand as phage are now being used for more practical and medicinal purposes.

Bacteria have developed multiple defense mechanisms to fight off the effects of bacteriophage. In experimentation, amount of resistance can be determined by how much of a plate (generally agar with bacteria, infected with phage) ends up being clear. The clearer, the less resistant as more bacteria have been lysed. The most common of these defense mechanisms is called the restriction-modification system (RM system). In this system, foreign DNA trying to enter the bacterial host is restricted by endonucleases that recognize specific base pairs within the DNA, while the DNA of the cell is protected from restriction due to methylase. RM systems have evolved to keep up with the ever-changing bacteria and phage. In general, these RM types differ in the nucleotide sequences that they recognize. However, there is an occasional slip where the endonuclease misses the DNA sequence of the phage and the phage DNA is able to enter the cell anyway, becoming methylated and protected against the endonuclease. This accident is what can spur the evolution of the RM system. Phage can acquire or use the enzyme from the host cell to protect their own DNA, or sometimes they will have proteins that dismantle the enzyme that is meant to restrict the phage DNA. Another option is for the phage to insert different base pairs into its DNA, thereby confusing the enzyme.

Another mechanism employed by bacteria is referred to as CRISPR. This stands for “clustered regularly interspersed palindromic repeats” which means that the immunity to phages by bacteria has been acquired via adding spacers of DNA that are identical to that of the DNA from the phage. Some phage have been found to be immune to this mechanism as well. In some way or another, the phage have managed to get rid of the sequence that would be replicated.

A third way that bacteria have managed to escape the effects of bacteriophage is by abortive infection. This is a last resort option- when the host cell has already been infected by the phage. This method is not ideal for the host cell, as it still leads to its death. The redeeming feature of this mechanism is the fact that it interferes with the phage processes and prevents it from then moving on to infect other cells.