User:Viralhgt

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Marine viral - Mediated Horizontal Gene Transfer: impact on prokaryotic diversity and the potential for speciation
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Outline
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'1.0. Introduction - a glass full of viruses'' '''

2.0. Prokaryotic diversity vs. biodiversity

2.1. Microbial genetic analysis & genome complexity '2.1.1. Virus impact on bacterial communities and diversity''  3.0. Horizontal Gene Transfer (HGT)    ''3.1.  Horizontal Gene Transfer: mechanisms 3.1.2. Cyanophages and the acquisition of photosynthetic genes 3.2. The Stable core, the variable shell: The Complexity Hypothesis''  4.0. Conclusions: viral - mediated HGT, evolution, and the potential for speciation '''

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1.0.	 A glass full of viruses
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The global oceans, acting like a grapefruit, is full of new and surprising discoveries with each layer revealed. Within the past century, numerous discoveries have resulted from detailed analysis of every layer of the oceans from the euphotic zone in the epipelagic to the endless depths of the marine abyss. From this, a greater understanding of the radical dynamics our oceanic ecosystems have resulted and further discoveries continue with technological advances and inquisitive minds. Within the past half century, oceanography has taken great leaps with the discovery of the ubiquitous distribution of bacterial, and more recently, viral biomasses in the world oceans. Viruses have been deemed to dominate the world with abundances ranging from 10^30 – 10^31 virus – like particles (VLP) in the oceans (5 – 25 times higher than the bacterial abundance (Fuhrman, 1999). Amounting to such a high abundance and a wide distribution, VLPs act as a key factor controlling numerous marine biogeochemical processes simultaneously.  Typically numbering 10 billion VLPs per liter and most likely infecting all microcellular organisms, VLP presence will have impacts on: oceanic nutrient cycling, biological system respiration, particulate – size distributions and sinking rates, bacterial and algal community diversity & abundance, and the transfer and exchange of genetic material through various prokaryotic and eukaryotic communities, influencing diversity and evolution (Fuhrman, 1999).  Functioning as catalysts of nutrient cycles by means of mass microbial mortality, VLPs accelerate the transformation of nutrients from particulate organic matter (POM) to dissolved organic matter (DOM) allowing for incorporation into the microbial loop, resulting in the increase of carbon respiration while decreasing the efficiency of carbon transfer to higher trophic levels (Suttle, 2005). Viral – mediated cell lysis converts particulate organic carbon (POC) into dissolved organic carbon (DOC), influencing global carbon cycling as more carbon is respired, and is significant as the sinking of POC contributes to a net transfer of ~ 3 Gtonnes of Carbon between the surface and deep ocean depths (Suttle, 2005). Furthermore, because nutrients are largely organically bound, cell lysis can affect the pathway of nutrient cycling such as the release of iron, fulfilling a major portion of the requirements of many organisms (Suttle, 2005). Additionally, frequent measurements and estimates near surface waters indicate that viral lysis can remove ~ 20 – 40% of the standing stock of prokaryotes each day, approximately equivalent to the rate of grazing (Suttle, 2007). More importantly, viral infection, lysis and gene transfer mediates and maintains prokaryotic community diversity (Suttle, 2007). Despite the exact method of how viruses regulate microbial diversity being relatively unknown (Suttle, 2007), viral interactions with marine microbes does have a significant impact on prokaryotic diversity and biodiversity. This paper article analyzes the mechanics and influence of marine viruses on the prokaryotic bacterial community, emphasizing the importance of viral – mediated horizontal gene transfer (HGT) in regulating bacterial diversity as well as the potential for HGT causing prokaryotic speciation.

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2.0. Prokaryotic diversity vs. biodiversity
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The global oceanic system houses ~ 10^29 prokaryotic cells, yet the partitioning of these cells into explicit species asks the question of how many species of prokaryotes there are there in the oceans (Pedros-Alio, 2006). It is generally agreed among the scientific community that the greater majority of microbial diversity remains unknown, however Pedros-Alio (2006) has proposed that this unknown diversity is largely hidden in the form of novel metabolisms (e.g. photoheterotrophy). Despite great uncertainty, this ‘unknown – diversity’ is currently being explored by various techniques. Methods such as DNA – DNA hybirdization and 16S – rDNA analysis have resulted in a new understanding of the vast diversity in marine prokaryotes. An estimate of ~ 10^6 taxons of microbial species, through cloning and sequencing techniques, has been made for the entire oceans yet there is still numerous micro – diversity among bacterial assemblages (Pedros-Alio, 2006). One must note that molecular surveys predominantly overestimate the microbial diversity as genetic sequencing, more often then not, claims the findings of new gene sequences (Pedros-Alio, 2006). Despite 16S – rDNA analysis being the main method of estimating microbial diversity (Weinbauer and Rassoulzadgen, 2004), the gene sequences analyzed may already belong to an already described organism(s), whose genes have not yet been sequenced (Pedros-Alio, 2006). Thus, there is implication that the diversity found from molecular surveys my not reflect the diversity of a true species (Pedros-Alie, 2006). A distinction must be made between microbial diversity and biodiversity. Microbial diversity is the abundance and distribution of microbial genetically encoded information (Weinbauer and Rassoulzadgen, 2004) or the components that are active and abundant at one particular time and place, also known as the core diversity (Pedros-Alio, 2004) (e.g. endemic species) whereas microbial biodiversity is the total microbial genetic information (Pedros-Alio, 2004) i.e. structural and functional diversity (Weinbauer and Rassoulzadgen, 2004), in the oceans. The majority of the already classified taxa of microbial species would fall under the core diversity group while the occasional species (varying temporally and/or spatially) act as a diversity seed bank and together, would complete the microbial biodiversity (Pedros-Alio, 2006).

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2.1. Prokaryotic genetic analysis & genome complexity
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16S – rRNA analysis, a technique assessing species richness, is based on the observation that a threshold of 97% similarity of the entire 16S – rRNA gene (common for in all prokaryotes) will match the 70% DNA – DNA hybridization, where there is ~ 96% sequence similarity, used to distinguish differing species (Weinbauer and Rassoulzadegan, 2004). Despite this, 16S – rRNA analysis alone, is not sufficient to describe differing species however, this technique does allow determination for the number of phylotypes in an environment, permitting estimates of prokaryotic species richness (Weinbauer and Rassoulzadgen, 2004). Current estimates of prokaryotic species richness range from a few to 160 species in a sample of one or two to 10 – 30 liters of seawater, with a maximum possible richness of 163 species per water sample (estimated on the basis of log – normal species abundance curves) (Weinbauer and Rassoulzadgen, 2004). An example in the Sargasso Sea, using results from the Sorcerer II expedition has identified 1.2 million genes, inferring the presence of at least 1,800 bacterial species and has generated ~ 6.5 million sequencing reads (Gross, 2007). Using these findings, a geographically diverse environmental genomic data set of 6.3 billion base pairs has been made (Gross, 2007). In spite of advancements in genomic investigations, prokaryotic genome complexity in the pelagic system is basically unknown (Weinbauer and Rassoulzadgen, 2004). Assuming a maximum of 163 species or genome equivalents in a sample of seawater, and using the genome size of E.coli, the maximum genomic complexity of prokaryotes would be 6.7 x 10^8 base pairs in a given water sample, leading to the genome complexity of the entire ocean being slightly < 8.2 x 10^12 bp (Weinbauer and Rassoulzadgen, 2004). The preceding estimate is very uncertain due to the amount of unknown bacterial diversity and genetic variation within this diversity.

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2.1.1. Virus impacts on bacterial communities & diversity
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Recent findings of tight correlations in VLP abundances and bacterial abundances have deemed marine viruses to have an active role in the community (Suttle, 2005) as well as having a dramatic effect on bacterial abundance and composition. Along with regulating the species abundance and composition in bacterial communities through mass mortality of dominating species, marine viruses act as prominent vectors in the mobility and transfer of genetic material. Virus – host interactions include: true parasitism – chronic infection without killing the host, predation – lytic infection killing the host, and mutualistic interaction – phage conversion, conferring new metabolic traits to the host, impacting the parameters of species diversity: species richness, species evenness, and species difference (taxonomic relatedness) (Weinbauer and Rassoulzadge, 2004). Through these interactions, there is redistribution and transfer of genetic material by differing mechanisms of horizontal gene transfer (HGT).

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3.0. Horizontal Gene Transfer
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HGT for short, horizontal transfer of genes is the acquisition of genetic material by one organism from another without being its progeny (Weinbauer, 2004). Transfer of genes may have various effects on the new hosts. Transfer of genes may affect the hosts membrane proteins, give new metabolic properties to the host as well increasing the host resistance to certain chemicals, all allowing greater adaptability of various strains of oceanic bacteria to differing physical/chemical stresses (Weinbauer, 2004). Confirmed by Paul (1999), stating that HGT can introduce fully functional, complex metabolic capabilities immediately upon integration. Bateriophages act as an important element for mobile DNA and act as a spark for short – term bacterial evolution (Canchaya et. al. 2003). HGT is a common process, often with many bacteria having multiple phages causing infection (Canchaya et. al. 2003). Acting as the most efficient gene – transfer particles, tailed phages are able to densely compact phage DNA, for insertion into a various bacterial hosts (Canchaya et. al. 2003). An average of 35% of marine bacteria contain a functional viral genome, which when combined with a total viral infection of 35% of the worlds ocean along with the mass abundance of prokaryotic bacterial biomass, it is estimated that 4 x 10^28 bacterial cells in the worlds ocean carries a viral functional genome (Weinbauer, 2004).

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3.1. Horizontal Gene Transfer: mechanisms
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There are two major mechanisms of viral HGT, both falling under the classification of transformation – the genetic alteration of a cell from the uptake, incorporation and expression of foreign genetic material. Transduction, a phage – mediated transfer of genetic material is separated into generalized and specialized transduction. During generalized transduction, the host genetic material is packed ‘mistakenly’ along with the viral genome into the capsids or temperate phages, while specialized transduction occurs during cell lysis when the host sequence is excised along with the phage sequence before being packaged into the phage capsid (Weinbauer, 2004). Conjugation is the transfer of genetic material through direct cellular contact, becoming significant during mass cell lysis events (Weinbauer, 2004). During cell lysis, genetic material is released and dispersed into the water column, contributing to the free DNA pool, which could come into direct contact with other bacterial cells (Weinbauer, 2004). Conjugation generally mediates the transfer of genes responsible for accessory functions (e.g. UV resistance, expanded metabolic capabilities – xenobiotic degradation, etc.) and is the most promiscuous mechanism of gene transfer (Paul, 1999).

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3.1.2. Cyanophages and the acquisition of photosynthetic genes
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To determine the evolutionary role of marine viruses in the evolution of bacteria and other prokaryotes, genetic analysis of numerous phage samples have identified cellular metabolic genes (e.g. phosphate sensing genes, photosynthetic and stress response, and carbon metabolism and pigment biosynthesis genes) in marine viral genomes (Comeau and Hatful, 2008). Further studies have found that viral genomes consist of numerous genes similar to genes from differing taxa, spanning across differing domains, confirming the high likelihood of horizontally transferred genes, and strengthened by findings of genomic islands in cyanobacteria, flanked with viral – like signature sequences (Comeau and Hatfall, 2008). Sullivan et. al. (2003) produced results signifying viral – mediated HGT as being primarily responsible for many differences in the genomes of closely related prochlorococcus and synechococcus species. Despite the prior groups having greater than 96% identity in 16S – rRNA analysis, the groups displayed high microdiversity in the form of 10 well – defined subgroups (Sullivan et. al. 2003). In fact numerous studies have all lead to the same conclusion that genomes of phages contain variable numbers of host – like photosynthetic genes which have functional roles during infection, impacting the evolution of the host as well as the phage (Lindell et. al. 2004). Utilizing phylogenetic reconstructions, based on the infected amino acid sequences of psbA and psbD, resulted in the finding of phage and host gene sequences being clustered together, inferring horizontal acquisition from a host cell (Hambly and Suttle, 2005). Furthermore, the differences in the genetic organization of the photosynthetic genes between the differing synechococcus hosts and their respective phages imply the occurrence of multiple HGT events, signifying that viral – mediated HGT is an ongoing process (Hambly and Suttle, 2005). Despite the growing evidence of marine viruses transferring and distributing genes of unique function (i.e. photosynthesis), viral – mediated HGT is not without its borders. From cyanophage samples, containing photosynthetic genes, it is viewed that these genes are non – conserved genes, outside the core of conserved genes, and lack sufficient resistance to HGT (Sullivan et. al. 2003).

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3.2. The stable core, the variable shell: the Complexity Hypothesis
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It is clear that HGT events are a common occurrence in the marine environment. However, the frequency of intraphyla HGT greatly exceeds interphyla HGT events and due to this, HGT, in the long run, is regarded as a weak force in comparison with natural selection, in terms of evolutionary significance (Zhaxybayeva et. al. 2006). With regards to intraphyla HGT, individual viruses and hosts have a higher probability of encountering each other as they occur in similar environments, there is less phyla – specific constraints, limiting successful HGT events, and interphyla differences between the virus and host cells present divergences in genome organization (e.g. wrong receptor site) as well as in the machinery of gene expression and regulation, preventing successful HGT (Zhaxybayeva et. al. 2006). In combination with the lack of successful interphyla HGT events, the function of the gene also poses as another barrier for successful viral HGT. As confirmed by Sullivan et. al. (2003), rates of successful HGT events are very high for operational genes, relative to informational genes (ribosomal genes responsible for transcription and translation). This is due to the nature of conserved (informational) and non – conserved (operational) genes, with non – conserved operational genes being less critical to biophysical interactions, hence is more readily transferred vs. conserved core genes (Sullivan et. al. 2003). With this, Sullivan et. al. (2003) suggest the relation between the potential of evolution and resistance to HGT: the probability of successful HGT increases with decreasing conservation of amino acid sequences in the gene product. This is affirmed by findings of limited successful HGT events for proteins with a conserved primary structure (Lindell et. al. 2004). A fairly new proposed theory explaining the lack of successful HGT of conserved core genes is the Complexity Hypothesis. This hypothesis states that not all genes are equally likely to be successfully transferred and there is preferential for successful HGT according to gene function (i.e. complex genes – genes responsible for transcription and translation are much less likely to be transferred than simple, metabolic genes) (Jain et. al. 1999). As an example, translation in prokaryotic organisms requires the coordinated assembly of at least 100 gene products, large and small ribosomal subunits, numerous tRNA and mRNA as well as sequence initiation and termination factors (Lindell et. al. 2004). Reinforced by observations from Lawrence (1997), genes providing for central metabolic functions are least likely to be found in operons and hence to be horizontally transferred (Lawrence, 1997). Operons are typically comprised of genes providing for unusual metabolic functions (e.g. chemical resistance), and can effectively invade many genomes (Lawrence, 1997), thus explaining the higher rate of successful HGT events for the variable operational genes. Similarly, an oxygenic photosynthetic system requires the investment in a large number of proteins, pigments coefactors, and trace elements for effective functionality (Lindell et. al. 2004). Hence, this fairly new hypothesis states that it is the complexity of gene product requirements and interactions that greatly restricts the success of HGT for conserved core informational genes (Lindell et. al. 2004).

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4.0. Conclusions: viral – mediated HGT, evolution, and potential for speciation
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With the ample and continually growing amount of evidence of viral activity in the mobility and transfer of genetic material, the influence of viruses on marine bacterial communities is now undeniable. Despite the majority of evidence opposing the likelihood of interspecific transfer of complex informational core genes, this phenomenon does occur, with very low probabilities however. Personally, I would think that given enough time, along with the high frequency of viral – mediated HGT events occurring simultaneously throughout the world oceans, there is potential for interphyla speciation. In addition, the higher rates of intraphyla HGT events vs. interphyla HGT events may cause greater evolutionary changes within certain bacterial phylas thus causing a greater divergence of physiological and genetic characteristics between differing phylas, contributing to greater potential for speciation in the long run.

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References Cited
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•	Canchaya C, Fournous G, Chennoufi C, Dillman ML, and Brussow H. “Phage as agents of lateral gene transfer”. Current Opinions in Microbiology, vol       6(4) : 417 – 424. 2003.

•	Comeau AM and Hatfull GF. “Exploring the prokaryotic viriosphere”. Research in Microbiology, vol 159(5) : 306. 2008.

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•	Gross L. “Oceanic metagenomics: Untapped bounty: Sampling the seas to survey microbial diversity”. PLOS Biology, vol 5(3) : e85. 2007.

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•	Lindell D, Sullivan MB, Johnson ZL, Tolonen AC, Rohwer F, and Chisholm W. “Transfer of photosynthetic genes to and from prochlorococcus viruses”. Proc Natl. Acad Sci USA, vol 101(30) : 11013 – 11018. 2004.

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•	Sullivan MB, Waterberry JB, and Chisholm SW. “Cyanophages infecting the oceanic cyanobacterium prochlorococcus”. Nature, vol 424(6952) : 1047. 2003.

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•	Weinbauer MG. “Ecology of prokaryotic viruses”. FEMS Microbiology Reviews, vol 28(2) : 127 – 181. 2004.

•	Zhaxybayeva O, Gogarten P, Charlehois RL, Doolittle WF, and Papke RT. “Phylogenetic analysis of cyanobacterial genomes: quantification of horizontal gene transfer events”. Genome Research, vol 16(9) : 1099 – 1108. 2006.