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2011-04-04T19:37:16Z

Farhad:

<center>'''The Effect of Metabolic Processes on Bacterial Richness and Diversity '''</center>

The term biodiversity was broadly defined as “life on earth” in 1986. However, a more specific definition of biodiversity is variation in species based on multiple factors in genetic, taxonomic, and ecological levels. In the taxonomic level biodiversity is defined as richness (11). Scientists have not been able to determine the cause of change in biodiversity and richness in animals, plants, and most importantly bacteria until recently. The Statistical examination of species richness based on latitude formed in 1950's and became more developed as time passed. According to Fuhrman, J. A. who conducted a recent research on diversity gradient in planktonic marine bacteria, planktonic diversity and richness increase from poles towards tropics due to increase in temperature (3). The pattern of increase in biodiversity has been approved by many researchers; however, there is discrepancy in terms of what causes these changes in biodiversity and richness. This paper explains different hypotheses about the patterns of biodiversity and richness in micro species including planktons which led to Fuhrman’s discovery, explains that increase in temperature boosts molecular evolution and metabolic rates of species and increases biodiversity, suggests light as an important factor for the growth and richness of photosynthetic prokaryotes, suggests improvements to Fuhrman’s methodology, ARISA (automated ribosomal intergenic spacer analysis) in calculating bacterial diversity. Although the work done my Fuhrman provides a good explanation for planktonic change in diversity from poles toward the equator, I think temperature alone does not provide the sole explanation for the species diversity and other factors, such as, nutrients has to be considered.
In 1966, Pianka provided a number of hypotheses such as area and time hypotheses which became the bases for the further explorations in species biodiversity and richness and their relations to geographical regions (11). Area hypothesis has been approved through many studies and shows that the relationship between the number of observed species and the area of the sampling is universal and true for all organisms (3). The time hypothesis is divided to ecological and evolutionary components. The first one, states that species exist in particular habitats but they did not have enough time to spread within these regions, and the later states that in some regions species have not have enough time to evolve yet, but as the time goes, new species will evolve and become more diverse. These hypotheses can explain regional but not latitudinal gradient in diversity since rich diversity still can be found in glacier regions (9). Later, these hypotheses gave rise to the newer hypotheses about species richness. Willing et al. provided more recent hypotheses for latitudinal gradients: ambient energy hypotheses, and evolutionary speed hypotheses. Ambient energy hypothesis is based on solar energy effects on physical environment through temperature. This hypothesis concludes that polar regions, despite tropical regions, have less favorable condition ideal for the growth of most organisms (11). In addition, there is more variation in season and living conditions in higher latitudes in contrast to tropical regions which are more stable and less variable. In comparison to lower latitudes, higher latitudes are associated with colder more extreme winters, lower annual average temperature, and shorter seasonal growth which create more unfavorable environments for organisms. On the other hand, for the organisms, it is more physiologically costly to live in higher latitudes compared to lower latitudes since "the ambient temperature in polar regions is outside the thermal neutral zone of many organisms for the majority of the year” (11). According to another hypothesis, at the certain depth, the diversity between communities’ increase as the distance between them increase. For instance, a study for deep see bacteria shows that the community similarity decreases over a 1000-km distance at 1000m depth in Atlantic ocean and over 3500-km distance in 3000m depth in the pacific ocean which clearly shows that bacterial communities are not similar at ocean depth. These differences may be due to the difference in regional temperature, since different depths and distances of the ocean have different temperature due to factors like upwelling and their latitudinal location (2). These hypotheses are led to more recent hypotheses, namely, evolutionary speed hypothesis, which states the richness of species closer to the tropical area is higher since higher temperature increases evolutionary rate. In tropical regions, this increase in evolutionary rate is due to faster speciation rate, which in turn, is due to higher mutation rates, shorter generation times, and higher selection pressure (11). According to Mittelbach et al. based on 'evolutionary speed' hypotheses, environmental temperature affects the kinetic rate of biological processes and the effect is strongest in tropical area were the temperature is relatively higher. The relevance between the temperature and energy can be explained through Boltzmann--Arrhenius formula, which explains the relation between the energy flux and evolutionary rate and defines mass-specific metabolic rate, ''B'' (Jsec1g1) as ''B'' =''Boe''^(-E/kT), in which, E represents energy and T, the absolute temperature (K). Therefore, the higher the temperature, the higher the metabolic rate will be (1). Mittelbach further states that the increase in metabolic rate leads to higher mutation rate and considered to be an important factor to cause molecular evolution of new taxa (6).
Fuhrman supports Mittelbach’s hypothesis based on temperature, since based on his studies, the marine environments that are rich in biodiversity are mostly the ones with higher temperature (3). In his research, Fuhrman mostly considers near-surface planktonic marine bacteria since these organisms are most closely associated with solar energy. He states that his discovery on increase in richness and diversity from poles toward equator is due to elevated level of metabolic processes such as dispersal, rate of reproduction, species interaction, adaptive evolution, speciation, and mutation due to increase in temperature. Although a specific amount of genetic variation causes the same amount of morphological and ecological changes, these changes happen with exponentially higher rates in the warmer tropical regions because of higher mutation rates and shorter generation time (1). A study on foraminifera shows that to produce a certain level of evolutionary change, 1.8 x 10^13 J/g of energy must be fluxed to cause a substitution per nucleotide, and this energy is substantially higher in tropical regions relative to temperate and polar regions(1). Furthermore, fossil records also indicate that speciation rates increase as we go from poles toward the tropics. Based on these fossil records, the speciation rates are significantly lower in temperate regions relative to the habitats in tropical latitudes. Based on Another study on foraminifera, in which, data was collected from sea-surface and depth of 200m based on small ribosomal rRNA-encoding DNA from arctic to tropical waters, temperature is linearly related to the logarithm of the rate of neutral molecular evolution. The depth analysis on foraminifera’s population shows that foraminifera in deeper depth has less molecular evolution rates since the temperature is lower in higher depths. Therefore, the thermal state of habitats affects DNA evolutionary rates of foraminifera (1). Foraminifera’s diversity can be used as a reliable source to study biodiversity since there is a broad fossil record of foraminifera’s communities. The broad distribution of Foraminifera from poles to tropics and its close grazing relation to bacteria enables us to understand bacterial diversity and richness (1). Therefore, the kinetic metabolism of organisms has strong influence on their biodiversity (3). In my opinion, although evolutionary speed hypotheses provides an in depth explanation for different patterns of biodiversity and richness in different latitudes of oceans, the area, time hypothesis and the effect of light also have to be considered. Different areas of the ocean have different bacterial richness and biodiversity in different seasons and climatic conditions. Furthermore, the effect of light itself has to be considered as an important factor to affect photosynthetic bacteria’s metabolic activities. Cyanobacteria bacteria rely mostly on light for their metabolic activities. Since different latitudes in the ocean receive different intensities and wavelengths of light, it is expected to observe different patterns of biodiversity among photosynthetic planktons. According to a study by Hewson et al. light affects gene expression. The study compares light and dark phases in bacterial activity and states that light level affects transcription of genes that are involved in nutrient transport and acquisition, cellular growth and metabolism. For example, after exposing to light during the day and dark phase at night, it became apparent that transcripts from Prochloroccocus were involved in photosynthesis (psa and psb photosystem genes) and their level of activity was affected by light exposure (6). Moreover, this study shows that photosystems I and II metabolic rate vary geotropically and based on light level. A later study also expressed that the metabolic rate of C1, oxidative phosphorylation and photosynthesis genes are more highly expressed during the day compared to the night, which can inform us that light has an important effect in the metabolic rate of bacteria (6). According to Schwalbach et. al, who conducted three experiments on the effects of light on bacterial communities using ARISA ( automated ribosomal intergenic spacer analysis) technique to measure bacterial richness, plastid-containing organisms and cyanobacteria are very sensitive to light and the removal or decreasing the intensity of light reduce their survival since they can not withstand viral lyses or protist grazing (10). However, some groups of phototrophic bacteria (Anoxygenic Proteobacterias such as Roseobacter, SAR11 and SAR86) which contain bacteriochlorophyll pigments show also mixotrophic behavior and can fix Carbon dioxide to sustain up to 20% of their energy demand. Therefore, the effect of light on bacterial richness can only be considered valid if we consider cyanobacteria and photosynthetic bacteria in which, light is the only source of energy (10). It is crucial though to imply appropriate techniques to count bacterial richness and diversity based proposed hypothesis.
Operational taxonomic units (OUT’s) are defined based on different 16S-23S rRNA spacer sequence lengths and differ 98% from each other (3). These taxonomic units are used in ARISA technique which is used by Fuhrman in order to estimate bacterial richness. According to a recent research, ARISA technique is a reliable technique that can be used to count bacterial diversity, however, there are some corrections required to use ARISA in some cases (5). This study which considered 722 complete genomes revealed that about 8 percent of bacterial strains do no give a PCR fragment using the primers of ARISA which leads to over estimation of bacterial richness. Although the overall relation between the number of bacteria and the number of fragments stays linear, in higher richness of bacteria this linear relationship disappears because of saturation of <nowiki>bind fragments. This study suggests where the number of the bind fragment lengths is between 10 and 116, a correction with the formula “[correctedspecies-level OTU richness] ¼ 0.8_ [lengthbased OTU richness]_ 6.7” should be used (5). </nowiki>Xavier et. al has came up with a more recent test to measure bacterial and phytoplankton richness in the ocean based on small ribosomal DNA subunit sequences. This technique is based on liquid bead array technology in which taxon-specific oligonucleotide probes are joined to specific beads and then get fluorescent labels. These fluorescent-labeled beads then are complimentary based pared to the end PCR products (7). The beads-PCR combinations are measured through flow cytometry. This method is very efficient since it can measure hundreds of samples of bacteria as well as eukaryotes in a short time period, and enables us to rapidly alter the bead and probe types. It has been used to detect bacterial pathogens and diversity of phytoplankton types and also bacterial richness in coastal areas. Since this method measures both bacterial and eukaryotes richness, it can also be used to study the interactions and dynamics between different organisms in the ocean and also the factors that affect these dynamics (7). Fuhrman’s results show that bacterial richness was negatively correlated with latitude and positively with temperature. The comparison between his data from the poles and equator shows clear difference in richness, however, between the two, the correlation with richness was not very strong (3). Therefore, through the use of newer techniques, more accurate results can be achieved.
To conclude, many hypotheses based on the biodiversity of marine planktons and bacteria state that the biodiversity and richness increase from poles towards the equator. Although there is not a single explanation for the change in biodiversity, according to Fuhrman, temperature can be assumed as one of the main causes of these changes from polar to tropical regions since it affects the metabolic processes and the level of speciation. In the case of phototrophic bacteria, in addition to the effects temperature, light appears to play the most important role since it causes the expression of the genes involved in metabolic processes and induce them. Furthermore, efficient techniques are critical to achieve accurate estimations of bacterial diversity and richness. One of the most reliable methods after ARISA is the liquid bead array technology which enables scientists to measure high bacterial diversity in a short time. In my opinion although Fuhrman’s explanation on bacterial diversity based on temperature is valid, however, other factors should not be neglected. Gilbert, J. A. et al. believes that three factors: phosphate, silicate and temperature are all responsible for bacterial diversity (4). Temperature and light can increase the metabolic processes and the rate of speciation, however, without enough nutrients and appropriate environmental conditions new species will not be able to survive and reproduce.

<center>References </center>
1. Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. ''Proc. Natl. Acad. Sci. U. S. A.''''' 103''', 9130-9135 (2006).
2. Fuhrman, J. A. Microbial community structure and its functional implications. ''Nature''''' 459''', 193-199 (2009).
3. Fuhrman, J. A.'' et al''. A latitudinal diversity gradient in planktonic marine bacteria. ''Proc. Natl. Acad. Sci. U. S. A.''''' 105''', 7774-7778 (2008).
4. Gilbert, J. A.'' et al''. The seasonal structure of microbial communities in the Western English Channel. ''Environ. Microbiol.''''' 11''', 3132-3139 (2009).
5. Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P. & Zehr, J. P. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. ''Environ. Microbiol.''''' 12''', 1940-1956 (2010).
6. Kovacs, A., Yacoby, K. & Gophna, U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. ''Res. Microbiol.''''' 161''', 192-197 (2010).
7. Mayali, X., Palenik, B. & Burton, R. S. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. ''Environ. Microbiol.''''' 12''', 975-989 (2010).
8. Mittelbach, G. G.'' et al''. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. ''Ecol. Lett.''''' 10''', 315-331 (2007).
9. Rohde, K. Latitudinal Gradients in Species-Diversity - the Search for the Primary Cause. ''Oikos''''' 65''', 514-527 (1992).
10. Schwalbach, M. S., Brown, M. & Fuhrman, J. A. Impact of light on marine bacterioplankton community structure. ''Aquat. Microb. Ecol.''''' 39''', 235-245 (2005).
11. Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: Pattern, process, scale, and synthesis. ''Annual Review of Ecology Evolution and Systematics''''' 34''', 273-309 (2003).

File:The effects of Metabolic Processes on Bacterial Diversity and Richnesspdf.pdf

2011-04-04T18:02:28Z

Farhad: uploaded a new version of "File:The effects of Metabolic Processes on Bacterial Diversity and Richnesspdf.pdf"

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2011-04-04T06:45:42Z

Farhad:

Thread:User talk:Farhad/Overwrote Documentation page/reply

2011-04-04T06:30:28Z

Farhad: Reply to Overwrote Documentation page

Hi, can you please tell me how to upload my file into wiki page, I am really confused. It doesn't tranfer my essay in the same format when I copy and paste.

Documentation

2011-04-04T06:21:16Z

Farhad:

The Effect of Metabolic Processes on Bacterial Richness and Diversity B (Jsec1g1) as B =Boe^(-E/kT), in which, E represents energy and T, the absolute temperature (K). Therefore, the higher the temperature, the higher the metabolic rate will be (1). Mittelbach further states that the increase in metabolic rate leads to higher mutation rate and considered to be an important factor to cause molecular evolution of new taxa (6).
Fuhrman supports Mittelbach’s hypothesis based on temperature, since based on his studies, the marine environments that are rich in biodiversity are mostly the ones with higher temperature (3). In his research, Fuhrman mostly considers near-surface planktonic marine bacteria since these organisms are most closely associated with solar energy. He states that his discovery on increase in richness and diversity from poles toward equator is due to elevated level of metabolic processes such as dispersal, rate of reproduction, species interaction, adaptive evolution, speciation, and mutation due to increase in temperature. Although a specific amount of genetic variation causes the same amount of morphological and ecological changes, these changes happen with exponentially higher rates in the warmer tropical regions because of higher mutation rates and shorter generation time (1). A study on foraminifera shows that to produce a certain level of evolutionary change, 1.8 x 10^13 J/g of energy must be fluxed to cause a substitution per nucleotide, and this energy is substantially higher in tropical regions relative to temperate and polar regions(1). Furthermore, fossil records also indicate that speciation rates increase as we go from poles toward the tropics. Based on these fossil records, the speciation rates are significantly lower in temperate regions relative to the habitats in tropical latitudes. Based on Another study on foraminifera, in which, data was collected from sea-surface and depth of 200m based on small ribosomal rRNA-encoding DNA from arctic to tropical waters, temperature is linearly related to the logarithm of the rate of neutral molecular evolution. The depth analysis on foraminifera’s population shows that foraminifera in deeper depth has less molecular evolution rates since the temperature is lower in higher depths. Therefore, the thermal state of habitats affects DNA evolutionary rates of foraminifera (1). Foraminifera’s diversity can be used as a
reliable source to study biodiversity since there is a broad fossil record of foraminifera’s communities. The broad distribution of Foraminifera from poles to tropics and its close grazing relation to bacteria enables us to understand bacterial diversity and richness (1). Therefore, the kinetic metabolism of organisms has strong influence on their biodiversity (3). In my opinion, although evolutionary speed hypotheses provides an in depth explanation for different patterns of biodiversity and richness in different latitudes of oceans, the area, time hypothesis and the effect of light also have to be considered. Different areas of the ocean have different bacterial richness and biodiversity in different seasons and climatic conditions. Furthermore, the effect of light itself has to be considered as an important factor to affect photosynthetic bacteria’s metabolic activities. Cyanobacteria bacteria rely mostly on light for their metabolic activities. Since different latitudes in the ocean receive different intensities and wavelengths of light, it is expected to observe different patterns of biodiversity among photosynthetic planktons. According to a study by Hewson et al. light affects gene expression. The study compares light and dark phases in bacterial activity and states that light level affects transcription of genes that are involved in nutrient transport and acquisition, cellular growth and metabolism. For example, after exposing to light during the day and dark phase at night, it became apparent that transcripts from Prochloroccocus were involved in photosynthesis (psa and psb photosystem genes) and their level of activity was affected by light exposure (6). Moreover, this study shows that photosystems I and II metabolic rate vary geotropically and based on light level. A later study also expressed that the metabolic rate of C1, oxidative phosphorylation and photosynthesis genes are more highly expressed during the day compared to the night, which can inform us that light has an important effect in the
metabolic rate of bacteria (6). According to Schwalbach et. al, who conducted three experiments on the effects of light on bacterial communities using ARISA ( automated ribosomal intergenic spacer analysis) technique to measure bacterial richness, plastid-containing organisms and cyanobacteria are very sensitive to light and the removal or decreasing the intensity of light reduce their survival since they can not withstand viral lyses or protist grazing (10). However, some groups of phototrophic bacteria (Anoxygenic Proteobacterias such as Roseobacter, SAR11 and SAR86) which contain bacteriochlorophyll pigments show also mixotrophic behavior and can fix Carbon dioxide to sustain up to 20% of their energy demand. Therefore, the effect of light on bacterial richness can only be considered valid if we consider cyanobacteria and photosynthetic bacteria in which, light is the only source of energy (10). It is crucial though to imply appropriate techniques to count bacterial richness and diversity based proposed hypothesis.
Operational taxonomic units (OUT’s) are defined based on different 16S-23S rRNA spacer sequence lengths and differ 98% from each other (3). These taxonomic units are used in ARISA technique which is used by Fuhrman in order to estimate bacterial richness. According to a recent research, ARISA technique is a reliable technique that can be used to count bacterial diversity, however, there are some corrections required to use ARISA in some cases (5). This study which considered 722 complete genomes revealed that about 8 percent of bacterial strains do no give a PCR fragment using the primers of ARISA which leads to over estimation of bacterial richness. Although the overall relation between the number of bacteria and the number of fragments stays linear, in higher richness of bacteria this linear relationship disappears because of saturation of
bind fragments. This study suggests where the number of the bind fragment lengths is between 10 and 116, a correction with the formula "[correctedspecies-level OTU richness] ¼ 0.8_ [lengthbased OTU richness]_ 6.7" should be used (5). Xavier et. al has came up with a more recent test to measure bacterial and phytoplankton richness in the ocean based on small ribosomal DNA subunit sequences. This technique is based on liquid bead array technology in which taxon-specific oligonucleotide probes are joined to specific beads and then get fluorescent labels. These fluorescent-labeled beads then are complimentary based pared to the end PCR products (7). The beads-PCR combinations are measured through flow cytometry. This method is very efficient since it can measure hundreds of samples of bacteria as well as eukaryotes in a short time period, and enables us to rapidly alter the bead and probe types. It has been used to detect bacterial pathogens and diversity of phytoplankton types and also bacterial richness in coastal areas. Since this method measures both bacterial and eukaryotes richness, it can also be used to study the interactions and dynamics between different organisms in the ocean and also the factors that affect these dynamics (7). Fuhrman’s results show that bacterial richness was negatively correlated with latitude and positively with temperature. The comparison between his data from the poles and equator shows clear difference in richness, however, between the two, the correlation with richness was not very strong (3). Therefore, through the use of newer techniques, more accurate results can be achieved.
To conclude, many hypotheses based on the biodiversity of marine planktons and bacteria state that the biodiversity and richness increase from poles towards the equator. Although there is not a single explanation for the change in biodiversity, according to Fuhrman, temperature can be assumed as one of the main causes of these changes from
polar to tropical regions since it affects the metabolic processes and the level of speciation. In the case of phototrophic bacteria, in addition to the effects temperature, light appears to play the most important role since it causes the expression of the genes involved in metabolic processes and induce them. Furthermore, efficient techniques are critical to achieve accurate estimations of bacterial diversity and richness. One of the most reliable methods after ARISA is the liquid bead array technology which enables scientists to measure high bacterial diversity in a short time. In my opinion although Fuhrman’s explanation on bacterial diversity based on temperature is valid, however, other factors should not be neglected. Gilbert, J. A. et al. believes that three factors: phosphate, silicate and temperature are all responsible for bacterial diversity (4). Temperature and light can increase the metabolic processes and the rate of speciation, however, without enough nutrients and appropriate environmental conditions new species will not be able to survive and reproduce.
References
1. Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U. S. A. 103, 9130-9135 (2006).
2. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
3. Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 7774-7778 (2008).
4. Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132-3139 (2009).
5. Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P. & Zehr, J. P. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ. Microbiol. 12, 1940-1956 (2010).
6. Kovacs, A., Yacoby, K. & Gophna, U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiol. 161, 192-197 (2010).
7. Mayali, X., Palenik, B. & Burton, R. S. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ. Microbiol. 12, 975-989 (2010).
8. Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10, 315-331 (2007).
9. Rohde, K. Latitudinal Gradients in Species-Diversity - the Search for the Primary Cause. Oikos 65, 514-527 (1992).
10. Schwalbach, M. S., Brown, M. & Fuhrman, J. A. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39, 235-245 (2005).
11. Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: Pattern, process, scale, and synthesis. Annual Review of Ecology Evolution and Systematics 34, 273-309 (2003).
The term biodiversity was broadly defined as "life on earth" in 1986. However, a more specific definition of biodiversity is variation in species based on multiple factors in genetic, taxonomic, and ecological levels. In the taxonomic level biodiversity is defined as richness (11). Scientists have not been able to determine the cause of change in biodiversity and richness in animals, plants, and most importantly bacteria until recently. The Statistical examination of species richness based on latitude formed in 1950's and became more developed as time passed. According to Fuhrman, J. A. who conducted a recent research on diversity gradient in planktonic marine bacteria, planktonic diversity and richness increase from poles towards tropics due to increase in temperature (3). The pattern of increase in biodiversity has been approved by many researchers; however, there is discrepancy in terms of what causes these changes in biodiversity and richness. This paper explains different hypotheses about the patterns of biodiversity and richness in micro species including planktons which led to Fuhrman’s discovery, explains that increase in temperature boosts molecular evolution and metabolic rates of species and increases biodiversity, suggests light as an important factor for the growth and richness of photosynthetic prokaryotes, suggests improvements to Fuhrman’s methodology, ARISA (automated ribosomal intergenic spacer analysis) in calculating bacterial diversity. Although the work done my Fuhrman provides a good explanation for planktonic change in diversity from poles toward the equator, I think temperature alone does not provide the sole explanation for the species diversity and other factors, such as, nutrients has to be considered.
In 1966, Pianka provided a number of hypotheses such as area and time hypotheses which became the bases for the further explorations in species biodiversity and richness and their relations to geographical regions (11). Area hypothesis has been approved through many studies and shows that the relationship between the number of observed species and the area of the sampling is universal and true for all organisms (3). The time hypothesis is divided to ecological and evolutionary components. The first one, states that species exist in particular habitats but they did not have enough time to spread within these regions, and the later states that in some regions species have not have enough time to evolve yet, but as the time goes, new species will evolve and become more diverse. These hypotheses can explain regional but not latitudinal gradient in diversity since rich diversity still can be found in glacier regions (9). Later, these hypotheses gave rise to the newer hypotheses about species richness. Willing et al. provided more recent hypotheses for latitudinal gradients: ambient energy hypotheses, and evolutionary speed hypotheses. Ambient energy hypothesis is based on solar energy effects on physical environment through temperature. This hypothesis concludes that polar regions, despite tropical regions, have less favorable condition ideal for the growth of most organisms (11). In addition, there is more variation in season and living conditions in higher latitudes in contrast to tropical regions which are more stable and less variable. In comparison to lower latitudes, higher latitudes are associated with colder more extreme winters, lower annual average temperature, and shorter seasonal growth which create more unfavorable environments for organisms. On the other hand, for the organisms, it is more physiologically costly to live in higher latitudes compared to lower latitudes since "the ambient temperature in polar regions is outside the thermal neutral zone of many
organisms for the majority of the year" (11). According to another hypothesis, at the certain depth, the diversity between communities’ increase as the distance between them increase. For instance, a study for deep see bacteria shows that the community similarity decreases over a 1000-km distance at 1000m depth in Atlantic ocean and over 3500-km distance in 3000m depth in the pacific ocean which clearly shows that bacterial communities are not similar at ocean depth. These differences may be due to the difference in regional temperature, since different depths and distances of the ocean have different temperature due to factors like upwelling and their latitudinal location (2). These hypotheses are led to more recent hypotheses, namely, evolutionary speed hypothesis, which states the richness of species closer to the tropical area is higher since higher temperature increases evolutionary rate. In tropical regions, this increase in evolutionary rate is due to faster speciation rate, which in turn, is due to higher mutation rates, shorter generation times, and higher selection pressure (11). According to Mittelbach et al. based on 'evolutionary speed' hypotheses, environmental temperature affects the kinetic rate of biological processes and the effect is strongest in tropical area were the temperature is relatively higher. The relevance between the temperature and energy can be explained through Boltzmann--Arrhenius formula, which explains the relation between the energy flux and evolutionary rate and defines mass-specific metabolic rate,B (Jsec1g1) as B =Boe^(-E/kT), in which, E represents energy and T, the absolute temperature (K). Therefore, the higher the temperature, the higher the metabolic rate will be (1). Mittelbach further states that the increase in metabolic rate leads to higher mutation rate and considered to be an important factor to cause molecular evolution of new taxa (6).
Fuhrman supports Mittelbach’s hypothesis based on temperature, since based on his studies, the marine environments that are rich in biodiversity are mostly the ones with higher temperature (3). In his research, Fuhrman mostly considers near-surface planktonic marine bacteria since these organisms are most closely associated with solar energy. He states that his discovery on increase in richness and diversity from poles toward equator is due to elevated level of metabolic processes such as dispersal, rate of reproduction, species interaction, adaptive evolution, speciation, and mutation due to increase in temperature. Although a specific amount of genetic variation causes the same amount of morphological and ecological changes, these changes happen with exponentially higher rates in the warmer tropical regions because of higher mutation rates and shorter generation time (1). A study on foraminifera shows that to produce a certain level of evolutionary change, 1.8 x 10^13 J/g of energy must be fluxed to cause a substitution per nucleotide, and this energy is substantially higher in tropical regions relative to temperate and polar regions(1). Furthermore, fossil records also indicate that speciation rates increase as we go from poles toward the tropics. Based on these fossil records, the speciation rates are significantly lower in temperate regions relative to the habitats in tropical latitudes. Based on Another study on foraminifera, in which, data was collected from sea-surface and depth of 200m based on small ribosomal rRNA-encoding DNA from arctic to tropical waters, temperature is linearly related to the logarithm of the rate of neutral molecular evolution. The depth analysis on foraminifera’s population shows that foraminifera in deeper depth has less molecular evolution rates since the temperature is lower in higher depths. Therefore, the thermal state of habitats affects DNA evolutionary rates of foraminifera (1). Foraminifera’s diversity can be used as a
reliable source to study biodiversity since there is a broad fossil record of foraminifera’s communities. The broad distribution of Foraminifera from poles to tropics and its close grazing relation to bacteria enables us to understand bacterial diversity and richness (1). Therefore, the kinetic metabolism of organisms has strong influence on their biodiversity (3). In my opinion, although evolutionary speed hypotheses provides an in depth explanation for different patterns of biodiversity and richness in different latitudes of oceans, the area, time hypothesis and the effect of light also have to be considered. Different areas of the ocean have different bacterial richness and biodiversity in different seasons and climatic conditions. Furthermore, the effect of light itself has to be considered as an important factor to affect photosynthetic bacteria’s metabolic activities. Cyanobacteria bacteria rely mostly on light for their metabolic activities. Since different latitudes in the ocean receive different intensities and wavelengths of light, it is expected to observe different patterns of biodiversity among photosynthetic planktons. According to a study by Hewson et al. light affects gene expression. The study compares light and dark phases in bacterial activity and states that light level affects transcription of genes that are involved in nutrient transport and acquisition, cellular growth and metabolism. For example, after exposing to light during the day and dark phase at night, it became apparent that transcripts from Prochloroccocus were involved in photosynthesis (psa and psb photosystem genes) and their level of activity was affected by light exposure (6). Moreover, this study shows that photosystems I and II metabolic rate vary geotropically and based on light level. A later study also expressed that the metabolic rate of C1, oxidative phosphorylation and photosynthesis genes are more highly expressed during the day compared to the night, which can inform us that light has an important effect in the
metabolic rate of bacteria (6). According to Schwalbach et. al, who conducted three experiments on the effects of light on bacterial communities using ARISA ( automated ribosomal intergenic spacer analysis) technique to measure bacterial richness, plastid-containing organisms and cyanobacteria are very sensitive to light and the removal or decreasing the intensity of light reduce their survival since they can not withstand viral lyses or protist grazing (10). However, some groups of phototrophic bacteria (Anoxygenic Proteobacterias such as Roseobacter, SAR11 and SAR86) which contain bacteriochlorophyll pigments show also mixotrophic behavior and can fix Carbon dioxide to sustain up to 20% of their energy demand. Therefore, the effect of light on bacterial richness can only be considered valid if we consider cyanobacteria and photosynthetic bacteria in which, light is the only source of energy (10). It is crucial though to imply appropriate techniques to count bacterial richness and diversity based proposed hypothesis.
Operational taxonomic units (OUT’s) are defined based on different 16S-23S rRNA spacer sequence lengths and differ 98% from each other (3). These taxonomic units are used in ARISA technique which is used by Fuhrman in order to estimate bacterial richness. According to a recent research, ARISA technique is a reliable technique that can be used to count bacterial diversity, however, there are some corrections required to use ARISA in some cases (5). This study which considered 722 complete genomes revealed that about 8 percent of bacterial strains do no give a PCR fragment using the primers of ARISA which leads to over estimation of bacterial richness. Although the overall relation between the number of bacteria and the number of fragments stays linear, in higher richness of bacteria this linear relationship disappears because of saturation of
bind fragments. This study suggests where the number of the bind fragment lengths is between 10 and 116, a correction with the formula "[correctedspecies-level OTU richness] ¼ 0.8_ [lengthbased OTU richness]_ 6.7" should be used (5). Xavier et. al has came up with a more recent test to measure bacterial and phytoplankton richness in the ocean based on small ribosomal DNA subunit sequences. This technique is based on liquid bead array technology in which taxon-specific oligonucleotide probes are joined to specific beads and then get fluorescent labels. These fluorescent-labeled beads then are complimentary based pared to the end PCR products (7). The beads-PCR combinations are measured through flow cytometry. This method is very efficient since it can measure hundreds of samples of bacteria as well as eukaryotes in a short time period, and enables us to rapidly alter the bead and probe types. It has been used to detect bacterial pathogens and diversity of phytoplankton types and also bacterial richness in coastal areas. Since this method measures both bacterial and eukaryotes richness, it can also be used to study the interactions and dynamics between different organisms in the ocean and also the factors that affect these dynamics (7). Fuhrman’s results show that bacterial richness was negatively correlated with latitude and positively with temperature. The comparison between his data from the poles and equator shows clear difference in richness, however, between the two, the correlation with richness was not very strong (3). Therefore, through the use of newer techniques, more accurate results can be achieved.
To conclude, many hypotheses based on the biodiversity of marine planktons and bacteria state that the biodiversity and richness increase from poles towards the equator. Although there is not a single explanation for the change in biodiversity, according to Fuhrman, temperature can be assumed as one of the main causes of these changes from
polar to tropical regions since it affects the metabolic processes and the level of speciation. In the case of phototrophic bacteria, in addition to the effects temperature, light appears to play the most important role since it causes the expression of the genes involved in metabolic processes and induce them. Furthermore, efficient techniques are critical to achieve accurate estimations of bacterial diversity and richness. One of the most reliable methods after ARISA is the liquid bead array technology which enables scientists to measure high bacterial diversity in a short time. In my opinion although Fuhrman’s explanation on bacterial diversity based on temperature is valid, however, other factors should not be neglected. Gilbert, J. A. et al. believes that three factors: phosphate, silicate and temperature are all responsible for bacterial diversity (4). Temperature and light can increase the metabolic processes and the rate of speciation, however, without enough nutrients and appropriate environmental conditions new species will not be able to survive and reproduce.
References
1. Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U. S. A. 103, 9130-9135 (2006).
2. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
3. Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 7774-7778 (2008).
4. Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132-3139 (2009).
5. Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P. & Zehr, J. P. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ. Microbiol. 12, 1940-1956 (2010).
6. Kovacs, A., Yacoby, K. & Gophna, U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiol. 161, 192-197 (2010).
7. Mayali, X., Palenik, B. & Burton, R. S. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ. Microbiol. 12, 975-989 (2010).
8. Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10, 315-331 (2007).
9. Rohde, K. Latitudinal Gradients in Species-Diversity - the Search for the Primary Cause. Oikos 65, 514-527 (1992).
10. Schwalbach, M. S., Brown, M. & Fuhrman, J. A. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39, 235-245 (2005).
11. Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: Pattern, process, scale, and synthesis. Annual Review of Ecology Evolution and Systematics 34, 273-309 (2003).
B (Jsec1g1) as B =Boe^(-E/kT), in which, E represents energy and T, the absolute temperature (K). Therefore, the higher the temperature, the higher the metabolic rate will be (1). Mittelbach further states that the increase in metabolic rate leads to higher mutation rate and considered to be an important factor to cause molecular evolution of new taxa (6).
Fuhrman supports Mittelbach’s hypothesis based on temperature, since based on his studies, the marine environments that are rich in biodiversity are mostly the ones with higher temperature (3). In his research, Fuhrman mostly considers near-surface planktonic marine bacteria since these organisms are most closely associated with solar energy. He states that his discovery on increase in richness and diversity from poles toward equator is due to elevated level of metabolic processes such as dispersal, rate of reproduction, species interaction, adaptive evolution, speciation, and mutation due to increase in temperature. Although a specific amount of genetic variation causes the same amount of morphological and ecological changes, these changes happen with exponentially higher rates in the warmer tropical regions because of higher mutation rates and shorter generation time (1). A study on foraminifera shows that to produce a certain level of evolutionary change, 1.8 x 10^13 J/g of energy must be fluxed to cause a substitution per nucleotide, and this energy is substantially higher in tropical regions relative to temperate and polar regions(1). Furthermore, fossil records also indicate that speciation rates increase as we go from poles toward the tropics. Based on these fossil records, the speciation rates are significantly lower in temperate regions relative to the habitats in tropical latitudes. Based on Another study on foraminifera, in which, data was collected from sea-surface and depth of 200m based on small ribosomal rRNA-encoding DNA from arctic to tropical waters, temperature is linearly related to the logarithm of the rate of neutral molecular evolution. The depth analysis on foraminifera’s population shows that foraminifera in deeper depth has less molecular evolution rates since the temperature is lower in higher depths. Therefore, the thermal state of habitats affects DNA evolutionary rates of foraminifera (1). Foraminifera’s diversity can be used as a
reliable source to study biodiversity since there is a broad fossil record of foraminifera’s communities. The broad distribution of Foraminifera from poles to tropics and its close grazing relation to bacteria enables us to understand bacterial diversity and richness (1). Therefore, the kinetic metabolism of organisms has strong influence on their biodiversity (3). In my opinion, although evolutionary speed hypotheses provides an in depth explanation for different patterns of biodiversity and richness in different latitudes of oceans, the area, time hypothesis and the effect of light also have to be considered. Different areas of the ocean have different bacterial richness and biodiversity in different seasons and climatic conditions. Furthermore, the effect of light itself has to be considered as an important factor to affect photosynthetic bacteria’s metabolic activities. Cyanobacteria bacteria rely mostly on light for their metabolic activities. Since different latitudes in the ocean receive different intensities and wavelengths of light, it is expected to observe different patterns of biodiversity among photosynthetic planktons. According to a study by Hewson et al. light affects gene expression. The study compares light and dark phases in bacterial activity and states that light level affects transcription of genes that are involved in nutrient transport and acquisition, cellular growth and metabolism. For example, after exposing to light during the day and dark phase at night, it became apparent that transcripts from Prochloroccocus were involved in photosynthesis (psa and psb photosystem genes) and their level of activity was affected by light exposure (6). Moreover, this study shows that photosystems I and II metabolic rate vary geotropically and based on light level. A later study also expressed that the metabolic rate of C1, oxidative phosphorylation and photosynthesis genes are more highly expressed during the day compared to the night, which can inform us that light has an important effect in the
metabolic rate of bacteria (6). According to Schwalbach et. al, who conducted three experiments on the effects of light on bacterial communities using ARISA ( automated ribosomal intergenic spacer analysis) technique to measure bacterial richness, plastid-containing organisms and cyanobacteria are very sensitive to light and the removal or decreasing the intensity of light reduce their survival since they can not withstand viral lyses or protist grazing (10). However, some groups of phototrophic bacteria (Anoxygenic Proteobacterias such as Roseobacter, SAR11 and SAR86) which contain bacteriochlorophyll pigments show also mixotrophic behavior and can fix Carbon dioxide to sustain up to 20% of their energy demand. Therefore, the effect of light on bacterial richness can only be considered valid if we consider cyanobacteria and photosynthetic bacteria in which, light is the only source of energy (10). It is crucial though to imply appropriate techniques to count bacterial richness and diversity based proposed hypothesis.
Operational taxonomic units (OUT’s) are defined based on different 16S-23S rRNA spacer sequence lengths and differ 98% from each other (3). These taxonomic units are used in ARISA technique which is used by Fuhrman in order to estimate bacterial richness. According to a recent research, ARISA technique is a reliable technique that can be used to count bacterial diversity, however, there are some corrections required to use ARISA in some cases (5). This study which considered 722 complete genomes revealed that about 8 percent of bacterial strains do no give a PCR fragment using the primers of ARISA which leads to over estimation of bacterial richness. Although the overall relation between the number of bacteria and the number of fragments stays linear, in higher richness of bacteria this linear relationship disappears because of saturation of
bind fragments. This study suggests where the number of the bind fragment lengths is between 10 and 116, a correction with the formula "[correctedspecies-level OTU richness] ¼ 0.8_ [lengthbased OTU richness]_ 6.7" should be used (5). Xavier et. al has came up with a more recent test to measure bacterial and phytoplankton richness in the ocean based on small ribosomal DNA subunit sequences. This technique is based on liquid bead array technology in which taxon-specific oligonucleotide probes are joined to specific beads and then get fluorescent labels. These fluorescent-labeled beads then are complimentary based pared to the end PCR products (7). The beads-PCR combinations are measured through flow cytometry. This method is very efficient since it can measure hundreds of samples of bacteria as well as eukaryotes in a short time period, and enables us to rapidly alter the bead and probe types. It has been used to detect bacterial pathogens and diversity of phytoplankton types and also bacterial richness in coastal areas. Since this method measures both bacterial and eukaryotes richness, it can also be used to study the interactions and dynamics between different organisms in the ocean and also the factors that affect these dynamics (7). Fuhrman’s results show that bacterial richness was negatively correlated with latitude and positively with temperature. The comparison between his data from the poles and equator shows clear difference in richness, however, between the two, the correlation with richness was not very strong (3). Therefore, through the use of newer techniques, more accurate results can be achieved.
To conclude, many hypotheses based on the biodiversity of marine planktons and bacteria state that the biodiversity and richness increase from poles towards the equator. Although there is not a single explanation for the change in biodiversity, according to Fuhrman, temperature can be assumed as one of the main causes of these changes from
polar to tropical regions since it affects the metabolic processes and the level of speciation. In the case of phototrophic bacteria, in addition to the effects temperature, light appears to play the most important role since it causes the expression of the genes involved in metabolic processes and induce them. Furthermore, efficient techniques are critical to achieve accurate estimations of bacterial diversity and richness. One of the most reliable methods after ARISA is the liquid bead array technology which enables scientists to measure high bacterial diversity in a short time. In my opinion although Fuhrman’s explanation on bacterial diversity based on temperature is valid, however, other factors should not be neglected. Gilbert, J. A. et al. believes that three factors: phosphate, silicate and temperature are all responsible for bacterial diversity (4). Temperature and light can increase the metabolic processes and the rate of speciation, however, without enough nutrients and appropriate environmental conditions new species will not be able to survive and reproduce.
References
1. Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U. S. A. 103, 9130-9135 (2006).
2. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
3. Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 7774-7778 (2008).
4. Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132-3139 (2009).
5. Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P. & Zehr, J. P. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ. Microbiol. 12, 1940-1956 (2010).
6. Kovacs, A., Yacoby, K. & Gophna, U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiol. 161, 192-197 (2010).
7. Mayali, X., Palenik, B. & Burton, R. S. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ. Microbiol. 12, 975-989 (2010).
8. Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10, 315-331 (2007).
9. Rohde, K. Latitudinal Gradients in Species-Diversity - the Search for the Primary Cause. Oikos 65, 514-527 (1992).
10. Schwalbach, M. S., Brown, M. & Fuhrman, J. A. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39, 235-245 (2005).
11. Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: Pattern, process, scale, and synthesis. Annual Review of Ecology Evolution and Systematics 34, 273-309 (2003).
The term biodiversity was broadly defined as "life on earth" in 1986. However, a more specific definition of biodiversity is variation in species based on multiple factors in genetic, taxonomic, and ecological levels. In the taxonomic level biodiversity is defined as richness (11). Scientists have not been able to determine the cause of change in biodiversity and richness in animals, plants, and most importantly bacteria until recently. The Statistical examination of species richness based on latitude formed in 1950's and became more developed as time passed. According to Fuhrman, J. A. who conducted a recent research on diversity gradient in planktonic marine bacteria, planktonic diversity and richness increase from poles towards tropics due to increase in temperature (3). The pattern of increase in biodiversity has been approved by many researchers; however, there is discrepancy in terms of what causes these changes in biodiversity and richness. This paper explains different hypotheses about the patterns of biodiversity and richness in micro species including planktons which led to Fuhrman’s discovery, explains that increase in temperature boosts molecular evolution and metabolic rates of species and increases biodiversity, suggests light as an important factor for the growth and richness of photosynthetic prokaryotes, suggests improvements to Fuhrman’s methodology, ARISA (automated ribosomal intergenic spacer analysis) in calculating bacterial diversity. Although the work done my Fuhrman provides a good explanation for planktonic change in diversity from poles toward the equator, I think temperature alone does not provide the sole explanation for the species diversity and other factors, such as, nutrients has to be considered.
In 1966, Pianka provided a number of hypotheses such as area and time hypotheses which became the bases for the further explorations in species biodiversity and richness and their relations to geographical regions (11). Area hypothesis has been approved through many studies and shows that the relationship between the number of observed species and the area of the sampling is universal and true for all organisms (3). The time hypothesis is divided to ecological and evolutionary components. The first one, states that species exist in particular habitats but they did not have enough time to spread within these regions, and the later states that in some regions species have not have enough time to evolve yet, but as the time goes, new species will evolve and become more diverse. These hypotheses can explain regional but not latitudinal gradient in diversity since rich diversity still can be found in glacier regions (9). Later, these hypotheses gave rise to the newer hypotheses about species richness. Willing et al. provided more recent hypotheses for latitudinal gradients: ambient energy hypotheses, and evolutionary speed hypotheses. Ambient energy hypothesis is based on solar energy effects on physical environment through temperature. This hypothesis concludes that polar regions, despite tropical regions, have less favorable condition ideal for the growth of most organisms (11). In addition, there is more variation in season and living conditions in higher latitudes in contrast to tropical regions which are more stable and less variable. In comparison to lower latitudes, higher latitudes are associated with colder more extreme winters, lower annual average temperature, and shorter seasonal growth which create more unfavorable environments for organisms. On the other hand, for the organisms, it is more physiologically costly to live in higher latitudes compared to lower latitudes since "the ambient temperature in polar regions is outside the thermal neutral zone of many
organisms for the majority of the year" (11). According to another hypothesis, at the certain depth, the diversity between communities’ increase as the distance between them increase. For instance, a study for deep see bacteria shows that the community similarity decreases over a 1000-km distance at 1000m depth in Atlantic ocean and over 3500-km distance in 3000m depth in the pacific ocean which clearly shows that bacterial communities are not similar at ocean depth. These differences may be due to the difference in regional temperature, since different depths and distances of the ocean have different temperature due to factors like upwelling and their latitudinal location (2). These hypotheses are led to more recent hypotheses, namely, evolutionary speed hypothesis, which states the richness of species closer to the tropical area is higher since higher temperature increases evolutionary rate. In tropical regions, this increase in evolutionary rate is due to faster speciation rate, which in turn, is due to higher mutation rates, shorter generation times, and higher selection pressure (11). According to Mittelbach et al. based on 'evolutionary speed' hypotheses, environmental temperature affects the kinetic rate of biological processes and the effect is strongest in tropical area were the temperature is relatively higher. The relevance between the temperature and energy can be explained through Boltzmann--Arrhenius formula, which explains the relation between the energy flux and evolutionary rate and defines mass-specific metabolic rate,B (Jsec1g1) as B =Boe^(-E/kT), in which, E represents energy and T, the absolute temperature (K). Therefore, the higher the temperature, the higher the metabolic rate will be (1). Mittelbach further states that the increase in metabolic rate leads to higher mutation rate and considered to be an important factor to cause molecular evolution of new taxa (6).
Fuhrman supports Mittelbach’s hypothesis based on temperature, since based on his studies, the marine environments that are rich in biodiversity are mostly the ones with higher temperature (3). In his research, Fuhrman mostly considers near-surface planktonic marine bacteria since these organisms are most closely associated with solar energy. He states that his discovery on increase in richness and diversity from poles toward equator is due to elevated level of metabolic processes such as dispersal, rate of reproduction, species interaction, adaptive evolution, speciation, and mutation due to increase in temperature. Although a specific amount of genetic variation causes the same amount of morphological and ecological changes, these changes happen with exponentially higher rates in the warmer tropical regions because of higher mutation rates and shorter generation time (1). A study on foraminifera shows that to produce a certain level of evolutionary change, 1.8 x 10^13 J/g of energy must be fluxed to cause a substitution per nucleotide, and this energy is substantially higher in tropical regions relative to temperate and polar regions(1). Furthermore, fossil records also indicate that speciation rates increase as we go from poles toward the tropics. Based on these fossil records, the speciation rates are significantly lower in temperate regions relative to the habitats in tropical latitudes. Based on Another study on foraminifera, in which, data was collected from sea-surface and depth of 200m based on small ribosomal rRNA-encoding DNA from arctic to tropical waters, temperature is linearly related to the logarithm of the rate of neutral molecular evolution. The depth analysis on foraminifera’s population shows that foraminifera in deeper depth has less molecular evolution rates since the temperature is lower in higher depths. Therefore, the thermal state of habitats affects DNA evolutionary rates of foraminifera (1). Foraminifera’s diversity can be used as a
reliable source to study biodiversity since there is a broad fossil record of foraminifera’s communities. The broad distribution of Foraminifera from poles to tropics and its close grazing relation to bacteria enables us to understand bacterial diversity and richness (1). Therefore, the kinetic metabolism of organisms has strong influence on their biodiversity (3). In my opinion, although evolutionary speed hypotheses provides an in depth explanation for different patterns of biodiversity and richness in different latitudes of oceans, the area, time hypothesis and the effect of light also have to be considered. Different areas of the ocean have different bacterial richness and biodiversity in different seasons and climatic conditions. Furthermore, the effect of light itself has to be considered as an important factor to affect photosynthetic bacteria’s metabolic activities. Cyanobacteria bacteria rely mostly on light for their metabolic activities. Since different latitudes in the ocean receive different intensities and wavelengths of light, it is expected to observe different patterns of biodiversity among photosynthetic planktons. According to a study by Hewson et al. light affects gene expression. The study compares light and dark phases in bacterial activity and states that light level affects transcription of genes that are involved in nutrient transport and acquisition, cellular growth and metabolism. For example, after exposing to light during the day and dark phase at night, it became apparent that transcripts from Prochloroccocus were involved in photosynthesis (psa and psb photosystem genes) and their level of activity was affected by light exposure (6). Moreover, this study shows that photosystems I and II metabolic rate vary geotropically and based on light level. A later study also expressed that the metabolic rate of C1, oxidative phosphorylation and photosynthesis genes are more highly expressed during the day compared to the night, which can inform us that light has an important effect in the
metabolic rate of bacteria (6). According to Schwalbach et. al, who conducted three experiments on the effects of light on bacterial communities using ARISA ( automated ribosomal intergenic spacer analysis) technique to measure bacterial richness, plastid-containing organisms and cyanobacteria are very sensitive to light and the removal or decreasing the intensity of light reduce their survival since they can not withstand viral lyses or protist grazing (10). However, some groups of phototrophic bacteria (Anoxygenic Proteobacterias such as Roseobacter, SAR11 and SAR86) which contain bacteriochlorophyll pigments show also mixotrophic behavior and can fix Carbon dioxide to sustain up to 20% of their energy demand. Therefore, the effect of light on bacterial richness can only be considered valid if we consider cyanobacteria and photosynthetic bacteria in which, light is the only source of energy (10). It is crucial though to imply appropriate techniques to count bacterial richness and diversity based proposed hypothesis.
Operational taxonomic units (OUT’s) are defined based on different 16S-23S rRNA spacer sequence lengths and differ 98% from each other (3). These taxonomic units are used in ARISA technique which is used by Fuhrman in order to estimate bacterial richness. According to a recent research, ARISA technique is a reliable technique that can be used to count bacterial diversity, however, there are some corrections required to use ARISA in some cases (5). This study which considered 722 complete genomes revealed that about 8 percent of bacterial strains do no give a PCR fragment using the primers of ARISA which leads to over estimation of bacterial richness. Although the overall relation between the number of bacteria and the number of fragments stays linear, in higher richness of bacteria this linear relationship disappears because of saturation of
bind fragments. This study suggests where the number of the bind fragment lengths is between 10 and 116, a correction with the formula "[correctedspecies-level OTU richness] ¼ 0.8_ [lengthbased OTU richness]_ 6.7" should be used (5). Xavier et. al has came up with a more recent test to measure bacterial and phytoplankton richness in the ocean based on small ribosomal DNA subunit sequences. This technique is based on liquid bead array technology in which taxon-specific oligonucleotide probes are joined to specific beads and then get fluorescent labels. These fluorescent-labeled beads then are complimentary based pared to the end PCR products (7). The beads-PCR combinations are measured through flow cytometry. This method is very efficient since it can measure hundreds of samples of bacteria as well as eukaryotes in a short time period, and enables us to rapidly alter the bead and probe types. It has been used to detect bacterial pathogens and diversity of phytoplankton types and also bacterial richness in coastal areas. Since this method measures both bacterial and eukaryotes richness, it can also be used to study the interactions and dynamics between different organisms in the ocean and also the factors that affect these dynamics (7). Fuhrman’s results show that bacterial richness was negatively correlated with latitude and positively with temperature. The comparison between his data from the poles and equator shows clear difference in richness, however, between the two, the correlation with richness was not very strong (3). Therefore, through the use of newer techniques, more accurate results can be achieved.
To conclude, many hypotheses based on the biodiversity of marine planktons and bacteria state that the biodiversity and richness increase from poles towards the equator. Although there is not a single explanation for the change in biodiversity, according to Fuhrman, temperature can be assumed as one of the main causes of these changes from
polar to tropical regions since it affects the metabolic processes and the level of speciation. In the case of phototrophic bacteria, in addition to the effects temperature, light appears to play the most important role since it causes the expression of the genes involved in metabolic processes and induce them. Furthermore, efficient techniques are critical to achieve accurate estimations of bacterial diversity and richness. One of the most reliable methods after ARISA is the liquid bead array technology which enables scientists to measure high bacterial diversity in a short time. In my opinion although Fuhrman’s explanation on bacterial diversity based on temperature is valid, however, other factors should not be neglected. Gilbert, J. A. et al. believes that three factors: phosphate, silicate and temperature are all responsible for bacterial diversity (4). Temperature and light can increase the metabolic processes and the rate of speciation, however, without enough nutrients and appropriate environmental conditions new species will not be able to survive and reproduce.
References
1. Allen, A. P., Gillooly, J. F., Savage, V. M. & Brown, J. H. Kinetic effects of temperature on rates of genetic divergence and speciation. Proc. Natl. Acad. Sci. U. S. A. 103, 9130-9135 (2006).
2. Fuhrman, J. A. Microbial community structure and its functional implications. Nature 459, 193-199 (2009).
3. Fuhrman, J. A. et al. A latitudinal diversity gradient in planktonic marine bacteria. Proc. Natl. Acad. Sci. U. S. A. 105, 7774-7778 (2008).
4. Gilbert, J. A. et al. The seasonal structure of microbial communities in the Western English Channel. Environ. Microbiol. 11, 3132-3139 (2009).
5. Hewson, I., Poretsky, R. S., Tripp, H. J., Montoya, J. P. & Zehr, J. P. Spatial patterns and light-driven variation of microbial population gene expression in surface waters of the oligotrophic open ocean. Environ. Microbiol. 12, 1940-1956 (2010).
6. Kovacs, A., Yacoby, K. & Gophna, U. A systematic assessment of automated ribosomal intergenic spacer analysis (ARISA) as a tool for estimating bacterial richness. Res. Microbiol. 161, 192-197 (2010).
7. Mayali, X., Palenik, B. & Burton, R. S. Dynamics of marine bacterial and phytoplankton populations using multiplex liquid bead array technology. Environ. Microbiol. 12, 975-989 (2010).
8. Mittelbach, G. G. et al. Evolution and the latitudinal diversity gradient: speciation, extinction and biogeography. Ecol. Lett. 10, 315-331 (2007).
9. Rohde, K. Latitudinal Gradients in Species-Diversity - the Search for the Primary Cause. Oikos 65, 514-527 (1992).
10. Schwalbach, M. S., Brown, M. & Fuhrman, J. A. Impact of light on marine bacterioplankton community structure. Aquat. Microb. Ecol. 39, 235-245 (2005).
11. Willig, M. R., Kaufman, D. M. & Stevens, R. D. Latitudinal gradients of biodiversity: Pattern, process, scale, and synthesis. Annual Review of Ecology Evolution and Systematics 34, 273-309 (2003).

File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc

2011-04-04T06:00:05Z

Farhad: uploaded a new version of "File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc"

File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc

2011-04-04T05:54:52Z

Farhad: uploaded a new version of "File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc": Reverted to version as of 05:42, 4 April 2011

File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc

2011-04-04T05:53:15Z

Farhad: uploaded a new version of "File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc"

File:The effects of Metabolic Processes on Bacterial Diversity and Richness.doc

2011-04-04T05:42:25Z

Farhad:

File:The issue is that for a long time scientists where not able to determine the cause of change in biodiversity by in animals.doc

2011-04-04T05:16:57Z

Farhad:

Thread:User talk:Farhad/Delete Notice on Course:Bacterial Richness/reply

2011-03-14T23:28:36Z

Farhad: Reply to Delete Notice on Course:Bacterial_Richness

Hi there,
Yes, I believe I made it by mistake. The only "bacterial richness" text that I need is supposed to be under the course 475(please don't delet this one)project.

Course:EOSC 475/ResearchProject

2011-03-05T04:23:17Z

Farhad:

=== March 2nd, 2011

Some of you seem to be a bit confused about the annotated bibliography, so there is some info that might help:

The annotated bibliography should consist of references from the primary literature (i.e. articles from scientific journals) that you will use as resources for your Wiki. The format of these should be the citation, followed by a few sentences explaining the significance of the paper to the topic you are presenting. The annotated bibliography will be part of your Wiki page. I have included an example below.
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467-468. This manuscript is the first to report concentrations of viruses in seawater in excess of 10 million viruses per mL, and showed that these high abundances occurred in a variety of freshwater and marine environments.

A minimum of 10 references is needed for the annotated bibliography.

Caroline your TA :)

== EOSC475 Wiki page==

There is a requirement to produce a Wiki page on an aspect related to this course; you must produce an in-depth and critical examination of a topic that stems from a scientific paper related to the content of the course.

A list of suggested papers is on the WIKI (see below)
; '''Only one student can sign up for each paper and others can be selected but must be approved'''.
The project will make up 25% of the final grade.

It will be an ongoing process with progress evaluated on:

'''Friday, January 28''', (Research Project topic due),

'''Friday, March 4''' (Research Project outline and annotated bibliography due),and

'''Friday, April 1''' (Research Project final submission)

Plagiarism will result in a grade of 0 (see http://www.vpacademic.ubc.ca/integrity/policies.htm).

A few things are expected for your Wiki Project:

1. The topic should be related to paper in Marine Microbiology. Click here for paper list: http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Ideas

2. The research project should be a CRITICAL review. So, include your opinion in the research project. Do not only review the paper.

3. Most, if not all, of your cited literature should be primary literature, which are peer-review scientific papers. Do not use websites or books, including encyclopedias, as references.

4. The length of the Wiki page should be about 10 pages.

If you have any questions about the wiki project please contact me (Caroline) at cchenard@eos.ubc.ca.

== EOSC475 - Wiki Project Launchpad Page ==

In order to keep the Research Projects for the students gathered within one subsection of this Wiki, we would like each student to create a link on this page (below) to their project. By keeping them here together, everyone can easily find each other's work. If you are curious about why we have chosen the wiki space for the Research Projects, it has to do with the affordances of the space. A wiki environment easily supports multipage, collaborative and hypertextual writing, something that feels a bit constrained within a weblog space. In this wiki space, you will be able to author multiple pages and create inter-textual links as well as links out to other materials that may be relevant to your work.

== Creating your top-level Wiki Project page ==

'''Step 1'''

Think of a good, short title for your research project. You will need to use CamelCase, which is a wiki syntax for words with capital letters joined together without a space. If I were writing about marine viruses, for example, I might use a link title: MarineViruses

'''Step 2'''

Look at the URL for this page up in the address bar in your browser. Depending on your browser it should look something like this:

[[File:Wiki4.jpg]]

You will need to create a new page on this wiki by adding in the name of the page you want to create. So, using my example again, I type in the following:

[[File:Wiki2.jpg]]

'''Make sure that you put a "/" in before you type in your new title, as that will put your page within the subsection of the ResearchProject page.'''

Type in the title of the page that you want to create and hit return on your keyboard.

'''Step 3'''

Mediawiki will come up with a screen that tells you that the page does not yet exist (unless, of course, it already does in which case you will need to come up with another, unique name), and you will have the option to edit the page.

[[File:Wiki3.jpg]]

Click on Edit page and then proceed to put in a couple bits of text to claim your space.

'''Step 4'''

Take note of the URL that appears in your browser address bar when you view your newly created page. That will be the URL for the top-level page of your Research Project. If you end up writing on multiple pages, just use the same process as described in the steps above to create subsection pages within your own page.

'''You only need to go on to Step 5 when you are ready to publish the URL for your Research Project. Please do so when you are ready for other students to have a link to your project.'''

'''Step 5'''

Add your top-level page to the list below and that way everyone will be able to find your work right from this landing page. You can, of course, add your name beside your link so that people can see who is authoring which Research Projects. For links within this Wiki server, you can use the portion of the URL after the "title=" You can also use the full URL if you prefer. Please place a link to your project in the list below.

''' Wiki projects:'''

* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRichness Farhad Mohaddes
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Vvulnificus#Vibrio_vulnificus]Kevin's Wiki
http://wiki.ubc.ca/Course:EOSC_475/Researchprojectexample Research Project Example

* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/DeepSeaPhototroph Emily Aitken's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/SargassoBacterioplankton Genetic diversity in Sargasso Sea bacterioplankton] Carrie Wan's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineViruses Anna-lize Mattam's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialMortality Viruses and protists cause similar bacterial mortality] Roya Elahi's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/AnammoxBacteria Anaerobic ammonium oxidation by anammox bacteria in the Black Sea] - Tysha Bell's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/GiantVirus A Giant Virus in Amoebae] - Emily Chen's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineGenome Functional metagenomic profiling of nine biomes] - Ashley Smith's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/CyanobacteriaNFixation Cyanobacteria & Oceanic Nitrogen Fixation] - David Rowen's Wiki
* [[Course:EOSC_475/ResearchProject/MpVintheMedSea|MpV in the Med. Sea]] - Tyler Nelson's Wiki
*[[Course:EOSC_475/ResearchProject/ImpactsOfMarineViruses|Impacts of Marine Viruses]] - Dara Lo's Wiki
* [[Course:EOSC_475/ResearchProject/PathogenicityIsland|Pathogenicity Islands]] - Julia Wai's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/iron - Taewook Kim's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealAbundance - Lauren Proteau's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealEvolutionAndDiversity: Archaeal Evolution and Diversity] Kevin Han's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRhodopsin Bacterial rhodopsin: evidence for a new type of phototrophy in the sea] Henry Liu's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/MarineCommunityGenomics Marine Community Genomics ]- Trevor Leggat's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/HydrothermalGeochemistry - Aaron Yeung
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/PicornalikeViruses High diversity of unknown picorna-like viruses in the sea] - Sam Soufi's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/SulphurFluxOceanicPhytoplankton - Brad Reid's Wiki

'''Reference:'''
Dobson, T., and Miller, J. (2009). ETEC540 - Research Project Launchpad Page. Retrieved from the UBC wiki on Dec. 21, 2009: http://wiki.ubc.ca/Course:ETEC540/2009WT1/Assignments/ResearchProject

Course:EOSC 475/ResearchProject

2011-03-05T04:21:05Z

Farhad:

=== March 2nd, 2011

Some of you seem to be a bit confused about the annotated bibliography, so there is some info that might help:

The annotated bibliography should consist of references from the primary literature (i.e. articles from scientific journals) that you will use as resources for your Wiki. The format of these should be the citation, followed by a few sentences explaining the significance of the paper to the topic you are presenting. The annotated bibliography will be part of your Wiki page. I have included an example below.
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467-468. This manuscript is the first to report concentrations of viruses in seawater in excess of 10 million viruses per mL, and showed that these high abundances occurred in a variety of freshwater and marine environments.

A minimum of 10 references is needed for the annotated bibliography.

Caroline your TA :)

== EOSC475 Wiki page==

There is a requirement to produce a Wiki page on an aspect related to this course; you must produce an in-depth and critical examination of a topic that stems from a scientific paper related to the content of the course.

A list of suggested papers is on the WIKI (see below)
; '''Only one student can sign up for each paper and others can be selected but must be approved'''.
The project will make up 25% of the final grade.

It will be an ongoing process with progress evaluated on:

'''Friday, January 28''', (Research Project topic due),

'''Friday, March 4''' (Research Project outline and annotated bibliography due),and

'''Friday, April 1''' (Research Project final submission)

Plagiarism will result in a grade of 0 (see http://www.vpacademic.ubc.ca/integrity/policies.htm).

A few things are expected for your Wiki Project:

1. The topic should be related to paper in Marine Microbiology. Click here for paper list: http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Ideas

2. The research project should be a CRITICAL review. So, include your opinion in the research project. Do not only review the paper.

3. Most, if not all, of your cited literature should be primary literature, which are peer-review scientific papers. Do not use websites or books, including encyclopedias, as references.

4. The length of the Wiki page should be about 10 pages.

If you have any questions about the wiki project please contact me (Caroline) at cchenard@eos.ubc.ca.

== EOSC475 - Wiki Project Launchpad Page ==

In order to keep the Research Projects for the students gathered within one subsection of this Wiki, we would like each student to create a link on this page (below) to their project. By keeping them here together, everyone can easily find each other's work. If you are curious about why we have chosen the wiki space for the Research Projects, it has to do with the affordances of the space. A wiki environment easily supports multipage, collaborative and hypertextual writing, something that feels a bit constrained within a weblog space. In this wiki space, you will be able to author multiple pages and create inter-textual links as well as links out to other materials that may be relevant to your work.

== Creating your top-level Wiki Project page ==

'''Step 1'''

Think of a good, short title for your research project. You will need to use CamelCase, which is a wiki syntax for words with capital letters joined together without a space. If I were writing about marine viruses, for example, I might use a link title: MarineViruses

'''Step 2'''

Look at the URL for this page up in the address bar in your browser. Depending on your browser it should look something like this:

[[File:Wiki4.jpg]]

You will need to create a new page on this wiki by adding in the name of the page you want to create. So, using my example again, I type in the following:

[[File:Wiki2.jpg]]

'''Make sure that you put a "/" in before you type in your new title, as that will put your page within the subsection of the ResearchProject page.'''

Type in the title of the page that you want to create and hit return on your keyboard.

'''Step 3'''

Mediawiki will come up with a screen that tells you that the page does not yet exist (unless, of course, it already does in which case you will need to come up with another, unique name), and you will have the option to edit the page.

[[File:Wiki3.jpg]]

Click on Edit page and then proceed to put in a couple bits of text to claim your space.

'''Step 4'''

Take note of the URL that appears in your browser address bar when you view your newly created page. That will be the URL for the top-level page of your Research Project. If you end up writing on multiple pages, just use the same process as described in the steps above to create subsection pages within your own page.

'''You only need to go on to Step 5 when you are ready to publish the URL for your Research Project. Please do so when you are ready for other students to have a link to your project.'''

'''Step 5'''

Add your top-level page to the list below and that way everyone will be able to find your work right from this landing page. You can, of course, add your name beside your link so that people can see who is authoring which Research Projects. For links within this Wiki server, you can use the portion of the URL after the "title=" You can also use the full URL if you prefer. Please place a link to your project in the list below.

''' Wiki projects:'''

* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRichness] Farhad Mohaddes
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Vvulnificus#Vibrio_vulnificus]Kevin's Wiki
http://wiki.ubc.ca/Course:EOSC_475/Researchprojectexample Research Project Example

* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/DeepSeaPhototroph Emily Aitken's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/SargassoBacterioplankton Genetic diversity in Sargasso Sea bacterioplankton] Carrie Wan's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineViruses Anna-lize Mattam's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialMortality Viruses and protists cause similar bacterial mortality] Roya Elahi's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/AnammoxBacteria Anaerobic ammonium oxidation by anammox bacteria in the Black Sea] - Tysha Bell's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/GiantVirus A Giant Virus in Amoebae] - Emily Chen's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineGenome Functional metagenomic profiling of nine biomes] - Ashley Smith's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/CyanobacteriaNFixation Cyanobacteria & Oceanic Nitrogen Fixation] - David Rowen's Wiki
* [[Course:EOSC_475/ResearchProject/MpVintheMedSea|MpV in the Med. Sea]] - Tyler Nelson's Wiki
*[[Course:EOSC_475/ResearchProject/ImpactsOfMarineViruses|Impacts of Marine Viruses]] - Dara Lo's Wiki
* [[Course:EOSC_475/ResearchProject/PathogenicityIsland|Pathogenicity Islands]] - Julia Wai's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/iron - Taewook Kim's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealAbundance - Lauren Proteau's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealEvolutionAndDiversity: Archaeal Evolution and Diversity] Kevin Han's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRhodopsin Bacterial rhodopsin: evidence for a new type of phototrophy in the sea] Henry Liu's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/MarineCommunityGenomics Marine Community Genomics ]- Trevor Leggat's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/HydrothermalGeochemistry - Aaron Yeung
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/PicornalikeViruses High diversity of unknown picorna-like viruses in the sea] - Sam Soufi's Wiki

'''Reference:'''
Dobson, T., and Miller, J. (2009). ETEC540 - Research Project Launchpad Page. Retrieved from the UBC wiki on Dec. 21, 2009: http://wiki.ubc.ca/Course:ETEC540/2009WT1/Assignments/ResearchProject

Course:EOSC 475/ResearchProject

2011-03-05T04:19:15Z

Farhad:

=== March 2nd, 2011

Some of you seem to be a bit confused about the annotated bibliography, so there is some info that might help:

The annotated bibliography should consist of references from the primary literature (i.e. articles from scientific journals) that you will use as resources for your Wiki. The format of these should be the citation, followed by a few sentences explaining the significance of the paper to the topic you are presenting. The annotated bibliography will be part of your Wiki page. I have included an example below.
Bergh O, Børsheim KY, Bratbak G, Heldal M (1989) High abundance of viruses found in aquatic environments. Nature 340:467-468. This manuscript is the first to report concentrations of viruses in seawater in excess of 10 million viruses per mL, and showed that these high abundances occurred in a variety of freshwater and marine environments.

A minimum of 10 references is needed for the annotated bibliography.

Caroline your TA :)

== EOSC475 Wiki page==

There is a requirement to produce a Wiki page on an aspect related to this course; you must produce an in-depth and critical examination of a topic that stems from a scientific paper related to the content of the course.

A list of suggested papers is on the WIKI (see below)
; '''Only one student can sign up for each paper and others can be selected but must be approved'''.
The project will make up 25% of the final grade.

It will be an ongoing process with progress evaluated on:

'''Friday, January 28''', (Research Project topic due),

'''Friday, March 4''' (Research Project outline and annotated bibliography due),and

'''Friday, April 1''' (Research Project final submission)

Plagiarism will result in a grade of 0 (see http://www.vpacademic.ubc.ca/integrity/policies.htm).

A few things are expected for your Wiki Project:

1. The topic should be related to paper in Marine Microbiology. Click here for paper list: http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Ideas

2. The research project should be a CRITICAL review. So, include your opinion in the research project. Do not only review the paper.

3. Most, if not all, of your cited literature should be primary literature, which are peer-review scientific papers. Do not use websites or books, including encyclopedias, as references.

4. The length of the Wiki page should be about 10 pages.

If you have any questions about the wiki project please contact me (Caroline) at cchenard@eos.ubc.ca.

== EOSC475 - Wiki Project Launchpad Page ==

In order to keep the Research Projects for the students gathered within one subsection of this Wiki, we would like each student to create a link on this page (below) to their project. By keeping them here together, everyone can easily find each other's work. If you are curious about why we have chosen the wiki space for the Research Projects, it has to do with the affordances of the space. A wiki environment easily supports multipage, collaborative and hypertextual writing, something that feels a bit constrained within a weblog space. In this wiki space, you will be able to author multiple pages and create inter-textual links as well as links out to other materials that may be relevant to your work.

== Creating your top-level Wiki Project page ==

'''Step 1'''

Think of a good, short title for your research project. You will need to use CamelCase, which is a wiki syntax for words with capital letters joined together without a space. If I were writing about marine viruses, for example, I might use a link title: MarineViruses

'''Step 2'''

Look at the URL for this page up in the address bar in your browser. Depending on your browser it should look something like this:

[[File:Wiki4.jpg]]

You will need to create a new page on this wiki by adding in the name of the page you want to create. So, using my example again, I type in the following:

[[File:Wiki2.jpg]]

'''Make sure that you put a "/" in before you type in your new title, as that will put your page within the subsection of the ResearchProject page.'''

Type in the title of the page that you want to create and hit return on your keyboard.

'''Step 3'''

Mediawiki will come up with a screen that tells you that the page does not yet exist (unless, of course, it already does in which case you will need to come up with another, unique name), and you will have the option to edit the page.

[[File:Wiki3.jpg]]

Click on Edit page and then proceed to put in a couple bits of text to claim your space.

'''Step 4'''

Take note of the URL that appears in your browser address bar when you view your newly created page. That will be the URL for the top-level page of your Research Project. If you end up writing on multiple pages, just use the same process as described in the steps above to create subsection pages within your own page.

'''You only need to go on to Step 5 when you are ready to publish the URL for your Research Project. Please do so when you are ready for other students to have a link to your project.'''

'''Step 5'''

Add your top-level page to the list below and that way everyone will be able to find your work right from this landing page. You can, of course, add your name beside your link so that people can see who is authoring which Research Projects. For links within this Wiki server, you can use the portion of the URL after the "title=" You can also use the full URL if you prefer. Please place a link to your project in the list below.

''' Wiki projects:'''
http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRichness Farhad Mohaddes
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/Vvulnificus#Vibrio_vulnificus]Kevin's Wiki
http://wiki.ubc.ca/Course:EOSC_475/Researchprojectexample Research Project Example

* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/DeepSeaPhototroph Emily Aitken's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/SargassoBacterioplankton Genetic diversity in Sargasso Sea bacterioplankton] Carrie Wan's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineViruses Anna-lize Mattam's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialMortality Viruses and protists cause similar bacterial mortality] Roya Elahi's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/AnammoxBacteria Anaerobic ammonium oxidation by anammox bacteria in the Black Sea] - Tysha Bell's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/GiantVirus A Giant Virus in Amoebae] - Emily Chen's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/MarineGenome Functional metagenomic profiling of nine biomes] - Ashley Smith's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/CyanobacteriaNFixation Cyanobacteria & Oceanic Nitrogen Fixation] - David Rowen's Wiki
* [[Course:EOSC_475/ResearchProject/MpVintheMedSea|MpV in the Med. Sea]] - Tyler Nelson's Wiki
*[[Course:EOSC_475/ResearchProject/ImpactsOfMarineViruses|Impacts of Marine Viruses]] - Dara Lo's Wiki
* [[Course:EOSC_475/ResearchProject/PathogenicityIsland|Pathogenicity Islands]] - Julia Wai's Wiki
* http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/iron - Taewook Kim's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealAbundance - Lauren Proteau's Wiki
* [http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/ArchaealEvolutionAndDiversity: Archaeal Evolution and Diversity] Kevin Han's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/BacterialRhodopsin Bacterial rhodopsin: evidence for a new type of phototrophy in the sea] Henry Liu's Wiki
*[http://wiki.ubc.ca/Course:EOSC_475/MarineCommunityGenomics Marine Community Genomics ]- Trevor Leggat's Wiki
*http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/HydrothermalGeochemistry - Aaron Yeung
*[http://wiki.ubc.ca/Course:EOSC_475/ResearchProject/PicornalikeViruses High diversity of unknown picorna-like viruses in the sea] - Sam Soufi's Wiki

'''Reference:'''
Dobson, T., and Miller, J. (2009). ETEC540 - Research Project Launchpad Page. Retrieved from the UBC wiki on Dec. 21, 2009: http://wiki.ubc.ca/Course:ETEC540/2009WT1/Assignments/ResearchProject

Course:EOSC 475/ResearchProject/Ideas

2011-01-23T02:55:39Z

Farhad:

'''
'''Please sign up your name under the paper you are interested to critique. Only one person for each paper'''.

1. Ammerman,JW, Fuhrman, JA, Hagstrom, A, Azam, F. 1984. Bacterioplankton growth in seawater: Growth kinetics and cellular characteristics in seawater cultures. Marine Ecology Progress Series. 18:31-39.

'''Student name:'''

2. Angly, F. et al. 2006. The marine viromes of four oceanic regions. PLOS Biology 4: e368

'''Student name:'''

3. Azam, F, Fenchel, T, Field, JG, Gray, JS, Meyer-Reil, LA, Thingstad, F. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series. 10:257-263.

'''Student name:Yasmin Taheri

4. Beatty, J.T., et al. 2005. An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proceedings of the National Academy of Sciences. 102:9306-9310.

'''Student name:Emily Aitken

5. Beja, O et al. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Applied and Environmental Microbiology. 68:335-345.

'''Student name:'''

6. Beja,O, et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:1902-1906.

'''Student name:'''

7. Bergh,O, Borsheim, KY, Bratbak, G, Heldal, M 1989. High abundance of viruses found in aquatic environments. Nature. 340:467-468.

'''Student name:Dara Lo

8. Boetius,A et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626.

'''Student name:'''

9. Brussaard CPD. 2004. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70: 1506-1513.

'''Student name:'''

10. Burns,BP, Goh, F, Allen, M, Neilan, BA. 2004. Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay,Australia. Environmental Microbiology. 6:1096-1101.

'''Student name:'''

11. Cerda-Cuellar, M, Jofre, J, Blanch AR. 2000. A selective medium and a specific probe for detection of Vibrio vulnificus. Appl. Environ.Microbiol 66:855-859.

'''Student name: Kevin Tsai'''

12. Choi,JW, Sherr, EB, Sherr, BF. 1996. Relation between presence-absence of a visible nucleoid and metabolic activity in bacterioplankton cells. Limnology and Oceanography. 41:1161-1168.

'''Student name:'''''''''Bold text''''''Bold text''''''

13. Church, MJ, Hutchins, DA, Ducklow, HW. 2000. Limitation of bacterial growth by dissolved organic matter and iron in the Southern Ocean. Applied and Environmental Microbiology. 66:455-466.

'''Student name:'''Janice Setijadi

14. Culley, AI, Lang, AS, Suttle, CA. 2003. High diversity of unknown picorna-like viruses in the sea. Nature. 424:1054-1057.

'''Student name:'''

15. Czyz,A, Jasiecki, J, Bogdan, A, Szpilewska, H, Wegrzyn, G. 2000. Genetically modified Vibrio harveyi strains as potential bioindicators of mutagenic pollution in marine environments. Applied and Environmental Microbiology. 66:599-605.

'''Student name:'''

15. Czyz, A, Wrobel, B, Wegrzyn G. 2000. Vibrio harveyi bioluminescence plays a role in stimulation of DNA repair Microbiology 146:283-288

'''Student name:'''

16. Dang,H, Lovell CR. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ.Microbiol. 66:467-475

'''Student name:'''

17.Davis,PG, Sieburth, JM. 1984. Estuarine and oceanic microflagellate predation of actively growing bacteria: estimation by frequency of dividing-divided bacteria. Marine Ecology Progress Series. 19:237-246.

'''Student name:'''

18. DeLong,E.F. 1992. Archaea in coastal marine environments. PNAS 89: 5685-5689.

'''Student name:'''

19. DeLong,EF, et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311:496-503.

'''Student name:''' Trevor Leggat

20. Dinsdale,EA et al. 2007. Functional metagenomic profiling of nine biomes. Nature 452:629-32.

'''Student name:''' Ashley Smith

21. Ducklow,HW, Hill, SM. 1985. The growth of heterotrophic bacteria in the surface waters of warm core rings. Limnology and Oceanography. 30:239-259.

'''Student name:'''

22.Fenchel, T, Finlay BJ. 2004. The ubiquity of small species: Patterns of local and global diversity. Bioscience 54: 777-784.

'''Student name:'''

23. Fuhrman,JA, McCallum K, Davis, AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 59:1294-1302.

'''Student name:'''

24.Fuhrman,JA, Noble RT. 1995. Viruses and protists cause similar bacterial mortality in coastal seawater. Limnol Oceaogr 40: 1236-1242

'''Student name:'''

25. Fuhrman,JA et al. 2008. A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105: 7774-7778.

'''Student name:'''FARHAD MOHADDES

26. Ghai,R et al. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. The ISME Journal. 4:1154-1166.

'''Student name:'''

27. Giovannoni, SJ, Britschgi, TB, Moyer, CL. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 60-63.

'''Student name:'''

28. Giovannoni, SJ, et al. 2005. Genome Streamlining in a cosmopolitan oceanic bacterium.Science 309:1242-1245

'''Student name:'''

29. Gonzalez,JM, Sherr,, EB, Sherr, BF. 1990. Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56:583-589.

'''Student name:'''

30.Hallam,SJ et al. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science. 305:1457-1462.

'''Student name:'''

31. Hewson,I. et al. 2009. Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat Limnol Oceanogr 54:1981-1994.

'''Student name:'''

32. Howard,EC et al. 2006. Bacterial taxa that limit sulfur flux from the ocean.Science 314: 649-652.

'''Student name:'''

33. Hutchinson,GE. 1961. The paradox of the plankton. American Naturalist. 95:137-145.

'''Student name:'''Karina Gurdzhyan

34. Jedani,KE, Stroeher, UH, Manning, PA. 2000. Distribution of IS1358 and linkage to rfb-related genes in Vibrio anguillarum. Microbiology. 146:323-331.

'''Student name:'''

35. Jiang,SC, Matte, M, Matte, G, Huq, A, Colwell, RR. 2000. Genetic diversity of clinical and environmental isolates of Vibrio cholerae determined by amplified fragment length polymorphism fingerprinting. Applied and Environmental Microbiology. 66:148-153.

'''Student name:''' Melissa Wood

36. Joint,I, Doney, SC, Karl, DM. 2011. Will ocean acidification affect marine microbes? The ISME Journal. 5:1-7.

'''Student name:''' Laura Tamblyn

37. Karaolis,DKR, et al. 1999. A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 300:375-379.

'''Student name:''' Julia Wai

39. Karner, MB, DeLong, EF, Karl, DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. 2001. Nature. 409:507-510.

'''Student name:'''

40.Kuypers, MMM, et al. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:609-611.

'''Student name:''' Tysha Bell

41. La Scola, B, et al. 2003. A giant virus in amoebae. Science. 299:2033.

'''Student name:''' Emily Chen

42. LaMontagne,MG, Leifer, I, Bergmann, S, Van De Werfhorst, LC, Holden, PA. 2004.Bacterial diversity in marine hydrocarbon seep sediments. Environmental Microbiology. 6:799-808.

'''Student name:'''

43. Li,WKW, et al. 1983. Autotrophic picoplankton in the tropical ocean. Science 219:292-295.

'''Student name:'''

44. Martin,JH et al. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature. 371:123-129.

'''Student name:'''37950052

45. Massana, R, Castresana, J, Balague, V, Guillou, L, Romari, K, Groisillier, A,Valentin, K, Pedros-Alio, C. 2004. Phylogenetic and ecological analysis of novel marine stramenopiles. Applied and Environmental Microbiology. 70:3528-3534.

'''Student name:'''

46. Moran,MA et al. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.

'''Student name:'''

47. Moraru,C, Lam, P, Fuchs, PL, Kuypers, MMM, and Amann, R. 2010. GeneFISH- an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environmental Microbiology. 12:3057-3073.

'''Student name:'''

48. Morris, RM, Rappe, MS, Connon,SA, Vergin, KL, Siebold, WA, Carlson, CA, Giovannoni, SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature.420:806-810.

'''Student name:'''

49.Moisander, PH, et al. 2010. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science, 327:1512-1514.

'''Student name:'''

50. Mussmann,M et al. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PloS Biology 5:1923-1937.

'''Student name:'''

51. Nagasaki, K, Tarutani, K,Yamaguchi, M. 1999. Cluster analysis on algicidal activity of HaV clones and virus sensitivity of Heterosigma akashiwo (Raphidophyceae). Journal of Plankton Research. 21:2219-2226.

'''Student name:'''

52. Pomeroy,LR. 1974. The ocean's food web, a changing perspective. Bioscience.24:499-504.

'''Student name:'''

53. Riemann,L, Steward, GF, Azam, F, 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl.Environ.Microbiol 66, 578-587

'''Student name:'''Jina Choi

54. Rocap,G et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424:1042-1047.

'''Student name:'''

55. Rohwer,F, Seguritan, V, Azam, F, Knowlton, N. 2002. Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series. 243:1-10.

'''Student name: Andrea Brown

56. Sharon,I et al. 2007. Viral photosynthetic reaction center genes and transcripts in the marine environment. The ISME Journal. 1:492-501.

'''Student name:'''

57. Short,CM, Suttle, CA. 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71:480-486

'''Student name:'''

58. Sogin, M.L. et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proceedings of the National Academy of Sciences USA 103:12115–12120.

'''Student name:'''Ari Shamash

59. Strzepek,RF, Maldonado, MT, Higgins, JL, Hall, J, Safi, K, Wilhelm, SW, Boyd, PW.2005. Spinning the “Ferrous Wheel”: the importance of the microbial community in an iron budget during the FeCycle experiment. Global Biogeochemical Cycles. 19.

'''Student name:'''

60.Venter,JC et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304:66-74.

'''Student name:'''

61. Walsh,D et al. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 326:578-582.

'''Student name:'''

62. Wilson,KM, Schembri, MA, Baker, PD, Saint, CP. 2000. Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of species-specific PCR. Applied and Environmental Microbiology. 66:332-338.

'''Student name:'''

63. Wilson,WH, et al. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science. 309:1090-1092.

'''Student name:'''

64. Zehr,JP, et al. 2001. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature. 412:635-638.

'''Student name: Saba Marzara'''

65. Zingone,A, Sarno, D, Forlani, G. 1999. Seasonal dynamics in the abundance of Micromonas pusilla (Prasinophyceae) and its viruses in the Gulf of Naples(Mediterranean Sea). Journal of Plankton Research. 21:2143-2159.

'''Student name:'''Tyler Nelson

66. Zweifel,UL, Hagstrom, A. 1995. Total counts of marine bacteria include a large fraction of non-nucleoid containg bacteria (ghosts). Applied and Environmental Microbiology. 61:2180-2185.

'''Student name:'''

Course:EOSC 475/ResearchProject/Ideas

2011-01-16T04:21:58Z

Farhad:

'''
'''Please sign up your name under the paper you are interested to critique. Only one person for each paper'''.

1. Ammerman,JW, Fuhrman, JA, Hagstrom, A, Azam, F. 1984. Bacterioplankton growth in seawater: Growth kinetics and cellular characteristics in seawater cultures. Marine Ecology Progress Series. 18:31-39.

'''Student name:'''

2. Angly, F. et al. 2006. The marine viromes of four oceanic regions. PLOS Biology 4: e368

'''Student name:'''

3. Azam, F, Fenchel, T, Field, JG, Gray, JS, Meyer-Reil, LA, Thingstad, F. 1983. The ecological role of water-column microbes in the sea. Marine Ecology Progress Series. 10:257-263.

'''Student name:

4. Beatty, J.T., et al. 2005. An obligately photosynthetic bacterial anaerobe from a deep-sea hydrothermal vent. Proceedings of the National Academy of Sciences. 102:9306-9310.

'''Student name:Emily Aitken

5. Beja, O et al. 2002. Comparative genomic analysis of archaeal genotypic variants in a single population and in two different oceanic provinces. Applied and Environmental Microbiology. 68:335-345.

'''Student name:'''

6. Beja,O, et al. 2000. Bacterial rhodopsin: evidence for a new type of phototrophy in the sea. Science. 289:1902-1906.

'''Student name:'''

7. Bergh,O, Borsheim, KY, Bratbak, G, Heldal, M 1989. High abundance of viruses found in aquatic environments. Nature. 340:467-468.

'''Student name:'''

8. Boetius,A et al. 2000. A marine microbial consortium apparently mediating anaerobic oxidation of methane. Nature 407:623-626.

'''Student name:'''

9. Brussaard CPD. 2004. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70: 1506-1513.

'''Student name:'''

10. Burns,BP, Goh, F, Allen, M, Neilan, BA. 2004. Microbial diversity of extant stromatolites in the hypersaline marine environment of Shark Bay,Australia. Environmental Microbiology. 6:1096-1101.

'''Student name:'''

11. Cerda-Cuellar, M, Jofre, J, Blanch AR. 2000. A selective medium and a specific probe for detection of Vibrio vulnificus. Appl. Environ.Microbiol 66:855-859.

'''Student name:'''

12. Choi,JW, Sherr, EB, Sherr, BF. 1996. Relation between presence-absence of a visible nucleoid and metabolic activity in bacterioplankton cells. Limnology and Oceanography. 41:1161-1168.

'''Student name:'''Farhad Mohaddes

13. Church, MJ, Hutchins, DA, Ducklow, HW. 2000. Limitation of bacterial growth by dissolved organic matter and iron in the Southern Ocean. Applied and Environmental Microbiology. 66:455-466.

'''Student name:'''Janice Setijadi

14. Culley, AI, Lang, AS, Suttle, CA. 2003. High diversity of unknown picorna-like viruses in the sea. Nature. 424:1054-1057.

'''Student name:'''

15. Czyz,A, Jasiecki, J, Bogdan, A, Szpilewska, H, Wegrzyn, G. 2000. Genetically modified Vibrio harveyi strains as potential bioindicators of mutagenic pollution in marine environments. Applied and Environmental Microbiology. 66:599-605.

'''Student name:'''

15. Czyz, A, Wrobel, B, Wegrzyn G. 2000. Vibrio harveyi bioluminescence plays a role in stimulation of DNA repair Microbiology 146:283-288

'''Student name:'''

16. Dang,H, Lovell CR. 2000. Bacterial primary colonization and early succession on surfaces in marine waters as determined by amplified rRNA gene restriction analysis and sequence analysis of 16S rRNA genes. Appl. Environ.Microbiol. 66:467-475

'''Student name:'''

17.Davis,PG, Sieburth, JM. 1984. Estuarine and oceanic microflagellate predation of actively growing bacteria: estimation by frequency of dividing-divided bacteria. Marine Ecology Progress Series. 19:237-246.

'''Student name:'''

18. DeLong,E.F. 1992. Archaea in coastal marine environments. PNAS 89: 5685-5689.

'''Student name:'''

19. DeLong,EF, et al. 2006. Community genomics among stratified microbial assemblages in the ocean's interior. Science. 311:496-503.

'''Student name:'''

20. Dinsdale,EA et al. 2007. Functional metagenomic profiling of nine biomes. Nature 452:629-32.

'''Student name:'''

21. Ducklow,HW, Hill, SM. 1985. The growth of heterotrophic bacteria in the surface waters of warm core rings. Limnology and Oceanography. 30:239-259.

'''Student name:'''

22.Fenchel, T, Finlay BJ. 2004. The ubiquity of small species: Patterns of local and global diversity. Bioscience 54: 777-784.

'''Student name:'''

23. Fuhrman,JA, McCallum K, Davis, AA. 1993. Phylogenetic diversity of subsurface marine microbial communities from the Atlantic and Pacific Oceans. Appl Environ Microbiol. 59:1294-1302.

'''Student name:'''

24.Fuhrman,JA, Noble RT. 1995. Viruses and protists cause similar bacterial mortality in coastal seawater. Limnol Oceaogr 40: 1236-1242

'''Student name:'''

25. Fuhrman,JA et al. 2008. A latitudinal diversity gradient in planktonic marine bacteria. PNAS 105: 7774-7778.

'''Student name:'''

26. Ghai,R et al. 2010. Metagenome of the Mediterranean deep chlorophyll maximum studied by direct and fosmid library 454 pyrosequencing. The ISME Journal. 4:1154-1166.

'''Student name:'''

27. Giovannoni, SJ, Britschgi, TB, Moyer, CL. 1990. Genetic diversity in Sargasso Sea bacterioplankton. Nature 345 60-63.

'''Student name:'''

28. Giovannoni, SJ, et al. 2005. Genome Streamlining in a cosmopolitan oceanic bacterium.Science 309:1242-1245

'''Student name:'''

29. Gonzalez,JM, Sherr,, EB, Sherr, BF. 1990. Size-selective grazing on bacteria by natural assemblages of estuarine flagellates and ciliates. Appl Environ Microbiol 56:583-589.

'''Student name:'''

30.Hallam,SJ et al. 2004. Reverse methanogenesis: testing the hypothesis with environmental genomics. Science. 305:1457-1462.

'''Student name:'''

31. Hewson,I. et al. 2009. Metagenomic potential of microbial assemblages in the surface waters of the central Pacific Ocean tracks variability in oceanic habitat Limnol Oceanogr 54:1981-1994.

'''Student name:'''

32. Howard,EC et al. 2006. Bacterial taxa that limit sulfur flux from the ocean.Science 314: 649-652.

'''Student name:'''

33. Hutchinson,GE. 1961. The paradox of the plankton. American Naturalist. 95:137-145.

'''Student name:'''Karina Gurdzhyan

34. Jedani,KE, Stroeher, UH, Manning, PA. 2000. Distribution of IS1358 and linkage to rfb-related genes in Vibrio anguillarum. Microbiology. 146:323-331.

'''Student name:'''

35. Jiang,SC, Matte, M, Matte, G, Huq, A, Colwell, RR. 2000. Genetic diversity of clinical and environmental isolates of Vibrio cholerae determined by amplified fragment length polymorphism fingerprinting. Applied and Environmental Microbiology. 66:148-153.

'''Student name:'''

36. Joint,I, Doney, SC, Karl, DM. 2011. Will ocean acidification affect marine microbes? The ISME Journal. 5:1-7.

'''Student name:''' Laura Tamblyn

37. Karaolis,DKR, et al. 1999. A bacteriophage encoding a pathogenicity island, a type-IV pilus and a phage receptor in cholera bacteria. Nature 300:375-379.

'''Student name:'''

39. Karner, MB, DeLong, EF, Karl, DM. 2001. Archaeal dominance in the mesopelagic zone of the Pacific Ocean. 2001. Nature. 409:507-510.

'''Student name:'''

40.Kuypers, MMM, et al. 2003. Anaerobic ammonium oxidation by anammox bacteria in the Black Sea. Nature 422:609-611.

'''Student name:''' Tysha Bell

41. La Scola, B, et al. 2003. A giant virus in amoebae. Science. 299:2033.

'''Student name:'''

42. LaMontagne,MG, Leifer, I, Bergmann, S, Van De Werfhorst, LC, Holden, PA. 2004.Bacterial diversity in marine hydrocarbon seep sediments. Environmental Microbiology. 6:799-808.

'''Student name:'''

43. Li,WKW, et al. 1983. Autotrophic picoplankton in the tropical ocean. Science 219:292-295.

'''Student name:'''

44. Martin,JH et al. 1994. Testing the iron hypothesis in ecosystems of the equatorial Pacific Ocean. Nature. 371:123-129.

'''Student name:'''37950052

45. Massana, R, Castresana, J, Balague, V, Guillou, L, Romari, K, Groisillier, A,Valentin, K, Pedros-Alio, C. 2004. Phylogenetic and ecological analysis of novel marine stramenopiles. Applied and Environmental Microbiology. 70:3528-3534.

'''Student name:'''

46. Moran,MA et al. 2004. Genome sequence of Silicibacter pomeroyi reveals adaptations to the marine environment. Nature 432:910-913.

'''Student name:'''

47. Moraru,C, Lam, P, Fuchs, PL, Kuypers, MMM, and Amann, R. 2010. GeneFISH- an in situ technique for linking gene presence and cell identity in environmental microorganisms. Environmental Microbiology. 12:3057-3073.

'''Student name:'''

48. Morris, RM, Rappe, MS, Connon,SA, Vergin, KL, Siebold, WA, Carlson, CA, Giovannoni, SJ. 2002. SAR11 clade dominates ocean surface bacterioplankton communities. Nature.420:806-810.

'''Student name:'''

49.Moisander, PH, et al. 2010. Unicellular cyanobacterial distributions broaden the oceanic N2 fixation domain. Science, 327:1512-1514.

'''Student name:'''

50. Mussmann,M et al. 2007. Insights into the genome of large sulfur bacteria revealed by analysis of single filaments. PloS Biology 5:1923-1937.

'''Student name:'''

51. Nagasaki, K, Tarutani, K,Yamaguchi, M. 1999. Cluster analysis on algicidal activity of HaV clones and virus sensitivity of Heterosigma akashiwo (Raphidophyceae). Journal of Plankton Research. 21:2219-2226.

'''Student name:'''

52. Pomeroy,LR. 1974. The ocean's food web, a changing perspective. Bioscience.24:499-504.

'''Student name:'''

53. Riemann,L, Steward, GF, Azam, F, 2000. Dynamics of bacterial community composition and activity during a mesocosm diatom bloom. Appl.Environ.Microbiol 66, 578-587

'''Student name:'''

54. Rocap,G et al. 2003. Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature. 424:1042-1047.

'''Student name:'''

55. Rohwer,F, Seguritan, V, Azam, F, Knowlton, N. 2002. Diversity and distribution of coral-associated bacteria. Marine Ecology Progress Series. 243:1-10.

'''Student name:'''

56. Sharon,I et al. 2007. Viral photosynthetic reaction center genes and transcripts in the marine environment. The ISME Journal. 1:492-501.

'''Student name:'''

57. Short,CM, Suttle, CA. 2005. Nearly identical bacteriophage structural gene sequences are widely distributed in both marine and freshwater environments. Appl Environ Microbiol 71:480-486

'''Student name:'''

58. Sogin, M.L. et al. 2006. Microbial diversity in the deep sea and the underexplored “rare biosphere.” Proceedings of the National Academy of Sciences USA 103:12115–12120.

'''Student name:'''

59. Strzepek,RF, Maldonado, MT, Higgins, JL, Hall, J, Safi, K, Wilhelm, SW, Boyd, PW.2005. Spinning the “Ferrous Wheel”: the importance of the microbial community in an iron budget during the FeCycle experiment. Global Biogeochemical Cycles. 19.

'''Student name:'''

60.Venter,JC et al. 2004. Environmental genome shotgun sequencing of the Sargasso Sea. Science. 304:66-74.

'''Student name:'''

61. Walsh,D et al. 2009. Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones. Science. 326:578-582.

'''Student name:'''

62. Wilson,KM, Schembri, MA, Baker, PD, Saint, CP. 2000. Molecular characterization of the toxic cyanobacterium Cylindrospermopsis raciborskii and design of species-specific PCR. Applied and Environmental Microbiology. 66:332-338.

'''Student name:'''

63. Wilson,WH, et al. 2005. Complete genome sequence and lytic phase transcription profile of a Coccolithovirus. Science. 309:1090-1092.

'''Student name:'''

64. Zehr,JP, et al. 2001. Unicellular cyanobacteria fix N2 in the subtropical North Pacific Ocean. Nature. 412:635-638.

'''Student name:'''

65. Zingone,A, Sarno, D, Forlani, G. 1999. Seasonal dynamics in the abundance of Micromonas pusilla (Prasinophyceae) and its viruses in the Gulf of Naples(Mediterranean Sea). Journal of Plankton Research. 21:2143-2159.

'''Student name:'''Tyler Nelson

66. Zweifel,UL, Hagstrom, A. 1995. Total counts of marine bacteria include a large fraction of non-nucleoid containg bacteria (ghosts). Applied and Environmental Microbiology. 61:2180-2185.

'''Student name:'''