A Model Ocean To Study Nitrogen Use

A review of: Bragg, J.G., Dutkiewicz, S., Jahn, O., Follows, M.J., Chisholm, S.W., (2010), Modeling selective pressures on phytoplankton in the global ocean, PLoS ONE, 5, 3, 9569

As our understanding and knowledge of marine microbes improves and increases, new ideas and hypotheses arise to further learn about this vast topic. However, one area that has proven difficult is in the development of a model approach capable of representing the numerous and complex processes that are present in the marine microbial systems. These processes include physical, biogeochemical and biological forces, which can influence such factors as microbial growth, population dynamics and ecological processes such as predation and species interactions. These processes are addressed in this study by the incorporation of a global numerical simulation to study marine pictophytoplankton for nitrogen use abilities. 

This model is created using the marine pictophytoplankton Prochlorococcus and Synechococcus which are dominant planktons in tropical and subtropical ecosystems respectively. Within each of these genera, are many ‘ecotypes’ consisting of populations with different habitats and nitrogen using abilities. Examples of these include some of the Synechococcus ecotypes abilities to use nitrate, nitrite and ammonium as nitrogen sources. Many Prochlorococcus ecotypes do not possess the ability to use nitrate. 

The results of this model show that tropical regions are often dominated by picophytoplankton and higher latitudes are dominated by large phytoplanktonic groups. All of the phytoplankton used in the model could originally use nitrate, nitrite and ammonium, however as the model ran, mutations occurred and produced three different types of phytoplankton, one unable to use nitrate (M1), the second unable to use nitrate and nitrite (M2) and the third was a ‘null mutant’ resembling the parent in all respects (M3).

The loss of nitrogen use abilities was witnessed to occur at different biogeographic regions depending on the organism. One of the main observations seen was the lack in abundance of the M2 mutants at higher latitudes, indicating that they were disadvantaged in these regions, this indicates that being able to use nitrogen in these regions is an extremely important ability. This results in a higher selective pressure against the M2 mutants due to the higher latitudes containing larger quantities of inorganic nitrogen.

This is a very important test regarding the ocean processes that involve marine microbes, due to the application of studying selective pressures on functional traits. The results found tend to highlight the importance of studying the physical, biogeochemical, ecological and evolutionary processes that affect microbes in the marine environment. As this is a model, there are many ways to make it a more comprehensive test, allowing for a vast amount of  further research in this area, particularly in that of the effects of differing latitudinal gradients on microbial functional traits. It also allows the marine environment to be studied in one go, which is vastly beneficial to the understanding how the differing populations of microbes survive and flourish.

Symbiotic Degradation Of Crude Oil

A review of: Hii, Y.S., Law, A.T., Shazili, N.A.M., Abdul-Rashid, M.K., Lee, C.W., (2009), Biodegradation of Tapis blended crude oil in marine sediment by a consortium of symbiotic bacteria, International Biodeterioration & Biodegradation, 63, 142-150

As the human population increases, so does its demand for fossil fuels, this raised demand has lead to larger, and more frequent transportation modes for distribution, one of the most widely used is in large ocean tankers. The increased traffic of these leads to an increased risk of oil spills in the marine environment. The spillages of oil in the world oceans is a huge threat to the marine habitat and the organisms in it. The most affected part of the habitat due to oil spills is in the sediment, and considering the importance of the habitat provided by marine sediments, this is very problematic. Oil also has a longer residential time in sediments when compared to water, and can pose long-term hazards to marine life.

The aim of this study is to provide information on the consortium of bacteria to combat oil pollution in the environment. This will be done by determining the identity of bacteria that are responsible for degrading blended crude oil. Also determining the effectiveness of the bacteria in the degradation of higher molecular weight hydrocarbons. The test was carried out by preparing flasks containing 100g sterilized sediment material along with 1g of crude oil, and adding to them the bacterial population. Bacteria were identified using direct 16S rDNA sequencing. Data analysis consisted of non-parametric analysis when data was not normally distributed and parametric analysis when data was normally distributed. A biodegradation rate was formulated and these were tested using an ANOVA test and Tukey’s test.

The results show that, under optimal conditions, the bacteria responsible for the degradation of the crude oil, P. pseudoalcaligenes, degraded 583.3mgkg^-1 of the blended crude oil from 1000mgkg^-1 oil contaminated sediment over a period of 10 days.

The identified bacteria consisting of P. pseudoalcaligenes, was found to drastically increase the degradation rate of the blended crude oil in the sediment. A symbiotic relationship was observed between the P. pseudoalcaligenes and E. citreus when the two populations are present, the degradation rate is further increased and allowed for the degradation of polycyclic aromatic hydrocarbons. These symbiotic relationships can be used to formulate bacterial consortias for degradation of crude oil compounds, these can be mixed with other isolated bacteria from different locations, however the symbiotic relationships are highly species dependent and will not be universal.

Marine Microbes as Pharmaceutical Agents

A Review of: Waters, A.L., Hill, R.T., Place, A.R., Hamann, M.T., (2010), The expanding role of marine microbes in pharmaceutical development, Current Opinion in Biotechnology, 21, 780-786

Marine microbes are a phenomenally vast group of organisms which cover many of the niches in the marine environment. These organisms are a major focus for drug discoveries and bioactive metabolites. One major area of existing study is that of invertebrate symbionts as creators of molecules that are beneficial to their hosts. This ability is desired for the creation and synthesis of molecules that are beneficial enough to enter clinical trials. Another promising area of study is that of toxins found in harmful algal blooms (HABs), which are increasing in frequency and as a result are becoming a serious hazard to the marine environment and humans alike. 

HABs are a major toxicological issue and can affect many organisms due to the build up of toxins in tissues. With 50,000-500,000 incidents per year, the biotoxins found during these blooms have been affecting humans with a 1.5% mortality rate, they also pose many economic problems due to tourism and fishing industries, an estimated $82 million per year is lost from the US economy due to the effects of HABs. However, upon studying these biotoxins, it has been discovered that they possess a unique stability in the environment including metabolic stability. This can be advantageous to humans as they could possibly be modified into functional drug compounds. An example of this is the karlotoxins, which are a serious hazard as a HAB but have allowed for the design of cholesterol targeting drugs.

Karlotoxins are produced from a toxic suite of metabolites from the dinoflagellate K. veneficum. Due to their unique properties, karlotoxins are able to be synthesised into a non toxic cholesterol pharmacore that has the potential to transport cholesterol from the arteries and into the liver or kidneys for excretion. If effective, this would result in a decrease in serum cholesterol levels and a large increase in HDL cholesterol levels. Due to current research linking cholesterol to numerous human health issues such as cancer, HIV-1, Alzheimer’s and Parkinson’s diseases, this is a very important area of study.

Marine microbes provide a great insight into what is possible for the future of human health advancements, with a multitude of uses, they may soon be essential to pharmacology. This is primarily due to their ability to produce unique compounds which can have multiple roles, these compounds cover new chemical space and allow for substantial growth in the pharmaceutical pipeline. Marine microbes also allow for improved methodologies in fermentation, biosynthesis and synthesis, allowing for new drugs to be created and supplied. Biotechnological pharmacology is certain to benefit from the use of marine microbes as both ways to make new drugs, and sources of unique chemicals that can be used in them.

The Many Isolates of VHSV In Rainbow Trout

A review of: Campbell, S., Collet, B., Einer-Jensen, K., Secombes, C.J., Snow, M., (2009), Identifying potential virulence determinants in viral haemorrhagic septicaemia virus (VHSV) for rainbow trout, Diseases of Aquatic Organisms, 86, 205-212

Viral haemorrhagic septicaemia virus (VHSV) is virus responsible for the disease viral haemorrhagic septicaemia, a disease responsible for a large loss of the rainbow trout Oncorhynchus mykiss. So far, four main genotypes have been identified which allows for genomic regions to be made for analysis. Until recently the rainbow trout that were infected by VHSV were isolated to the geographic location of the Genotype I, but due to the sourcing of food fed to farmed fish, there are many contaminations that have occurred leading to infections of other genomic regions.

The aim of the test is to determine the mortality of the four different genotypes and to analyse the sequencing data. This was done by isolating 24 fish per study group then infected with the different strains of virus intraperitoneally. A control was set up containing an inoculum. RNA was then extracted using a viral RNA kit, cDNA was then synthesised from the viral RNA using a polymerase kit. Polymerase chain reactions were then conducted on each sample to give a consensus nucleotide sequence per isolate.

Results of the mortality test show that the SE-SVA-1033 (GIb) isolates had a mortality of 75% with the majority of fish dying at between 6 and 10 days after exposure. The other three strains resulted in mortalities of 34.6% and under. These deaths also occurred at the same point as those exposed to the SE-SVA-1033 strain but the mortality was reduced. There was no mortality in the control group allowing for the test to be validated. Results of a Chi-squared analysis revealed a statistically significant difference in the mortality rates between treatments. A complete coding region for VHSV strains SE-SVA-1033 and DK-4p37 were also determined.

The results of the infection trial confirm other studies carried out on the mortality of the trout when immersion tested with the SE-SVA-1033 isolate. Observations were made when looking into the lower mortality rate isolates when inoculated, whereby the fish had significant lower mortality rates which indicates that these isolates are less  virulent. 

Further studies can be based on the findings of this test, mainly further looking into the amino acid substitutions that were identified across the genome. This change clearly has an effect upon the virulence and mortality of the virus to the rainbow trout. The exact significance of these mutations can be studied in order to view possible causes to the virulence of the VHVS isolates and as more occur, these can be cross referenced with the genomic data found.

Coral Reefs - More Danger Than Originally Thought?

A review of: Mao-Jones, J., Ritchie, K.B., Jones, L.E., Ellner, S.P., (2010), How microbial community composition regulates coral disease development, PLoS Biology, March 2010 Issue, 44-51

Coral reefs are one of the most delicate and fragile ecosystems on the planet, they are also the habitats that hold over a quarter of all marine species. These two facts result in them being of huge importance to the marine system as a whole, with one small problem facing the symbiotic dinoflagellate zooxanthellae leading to catastrophic effects to the entire ecosystem, it is for this reason that corals are constantly monitored for chemical, physical and microbial change.

Microbes pose a huge threat to corals, with infectious diseases being a leading cause for the increased worldwide coral reef decline. The effects of these diseases are worsened when coupled with the dangers of coral bleaching, caused by an increase in ocean temperatures, which can actually make corals more susceptible to microbial disease. The wide use of the Vibro spp. in tests has been extremely beneficial to understanding the risks posed by disease and possible ways to reduce this risk.

This study looks into using a model to test how the Vibro spp. in corals has an effect on spatial gradients, production of a mucus layer and the abundances of other microbial life. The model used consists of two main rules, that microbial populations are measured in units of growth limiting substrate, and that there is no external inoculation. Once these have been made, the model uses the abundance of pathogenic microbes and the abundance of antibiotic producing beneficial microbes plus antibiotics and substrate.

Results show that models can show insights into the problems that corals face, a rising temperature of oceans, causing an increased susceptibility to pathogens. There can be two states that corals face microbial, and these are the domination of pathogens, and the domination of beneficial microbes, the model can help predict changes that can occur in the balance between these two states due to a number of factors, such as an increase in temperature. However, findings of the model indicate that even if the stress of heat is removed, the corals susceptibility to pathogens can remain and this shift in balance is enough to rid the coral of the beneficial microbial community. This model is highly dependent on the assumptions of the beneficial microbes antibiotic abilities, which can cause unexpected shifts in the outcomes of the models. This is mostly due to the model being carried out int he SMC which can host much more microbial life than the natural ocean. Results show that a shift between the two states is much more favorable to go towards the direction of the pathogen as opposed to the beneficial microbes.

As this model allows for numerous factors to be tested, including factors that directly affect coral susceptibility such as poor water quality, an increase in temperature and poor quality of habitat, it is a very good model for investigating the effects of pathogens on the beneficial microbes that allow the corals to survive.

The Role of Marine Viruses and the Understanding of Nutrient Cycling

A review of: Brussaard, C.P.D., Wilhelm, S.W., Thingstad, F., Weinbauer, M.G., Bratbak, G., Heldal, M., Kimmance, S.A., Middelboe, M., Nagasaki, K., Paul, J.H., Schroeder, D.C., Suttle, C.A., Vaque, D., Wommack, K.E., (2008), Global-scale processes with a nanoscale drive: the role of marine viruses, The ISME Journal, 2, 575-578

Viruses represent the largest pool of genetic diversity and are by far the most numerous of all biotic agents on earth, with an estimated number of around 10^30 viruses in the ocean, they can take over cells in organisms varying from bacteria to sharks, to humans. However, even given this data, the extent of viruses in nanoscale processes are rarely linked to global scale biodiversity and biogeochemistry.

The poor connections between viruses and biogeochemistry is mostly due to the processes being ignored in most carbon flux models. Although much of this data is as of yet unknown, there is much room for research into completing comprehensive models including it. However, due to the findings that they accelerate the recycling of growth limiting nutrient elements in the photic zone, should they be measured as a hinderance or a stimulant to the primary production. There is much ongoing debate as to whether viruses short circuit the biological pump by releasing elements back to their dissolved phase, whether they prime the biological pump by accelerating host export from the euphotic zone, or whether they drive particle aggregation and transfer of carbon into the deep sea. They have also been hypothesized to contribute to the resilience of ecosystems.

An area where viruses are moving forward in biogeochemistry is the combination of molecular techniques such as molecular probes and viral gene expression, to allow for biodiversity, biogeochemistry and genomics to come together. With recent developments allowing for the wealth of the information of the viral genetic reservoir to be discovered using genomic tools. Although, while viruses can be key parts of biogeochemical cycles, it is in what way they do this that is an important area for study. Without the deciphering of metaviromes being required for testing, the ‘blueprints’ of the viruses actions are still locked in the viroplankton metagenomic data sets. Resulting in many viruses that are not in the genomic database having unknown functions. This would be greatly helped with a smooth communication between studies of the virus-host systems in marine microbes and viral biogeochemistry.

In future, the role of viruses can be further understood with tests such as the quantitative reverse transcription–PCR, allowing the accurate measurement of messenger RNA and the expression of the genes. Virology, especially in aquatic and marine habitats, will allow for future collection and understanding of data on the links between the virus-host systems and nutrient cycling and energy flow. With the study of a subject that is still highly debated as to whether it is a life-form in itself, is always going to be a difficult challenge, but backed up with current knowledge, there is the potential to expand our knowledge of viruses and their role in the marine environment in future to give us a greater understanding of how the worlds most important systems work.

Rising CO2 Levels - Worse Than You Thought!

A review of: Doney, S.C., Ruckelshaus, M., Emmett Duffy, J., Barry, J.P., Chan, F., English, C.A., Galindo, H.M., Grebmeier, J.M., Hollowed, A.B., Knowlton, N., Polovina, J., Rabalais, N.N., Sydeman, W.J., Talley, L.D., (2012), Climate Change Impacts on Marine Ecosystems, Annual Review of Marine Science, 4, 11 -37

The marine ecosystem is a very large, complex and delicately balanced world process, however, it is primarily driven, and largely made up of primary producing microorganisms. These are essential in all marine food webs and allow for organisms throughout these webs to survive, including humans, however, with an increase in the human population, there is a greater demand for fossil fuels, and as a result, a larger amount of CO2. This rise in atmospheric CO2, is one of the most critical problems facing our planet due to its global and irreversible effects on the environment. It is in the oceans that one of the largest threats is posed, and this is due to the nature of CO2 which can both raise temperatures of the oceans and lower its pH. This rise in temperature can also lead to the the rising of sea levels, with many coastal habitats being lost, including many of the worlds reef systems. The increase in dissolved CO2 also results in hypoxia where oxygen levels haven been lowered, this is vey problematic for higher species, but can be beneficial to some microbes. However, diatoms will suffer from this as literary tests show that the calcification process is severely hindered in the presence of raised CO2 levels. 

One of the largest problems caused by rising CO2 levels is posed to the symbiotic dinoflagellate zooxanthellae found in corals which, when occurring in the tropics, result in a boom in biodiversity density containing one quarter of all marine species. Risks posed by the rising CO2 levels are the acidification preventing normal calcification of the coral, and the rising temperatures causing bleaching due to the highly sensitive nature of the zooxanthellae. So not only is it the coral organisms that are at a very high risk, but the whole ecosystem that is based around and in them is too. Another area of coral reefs that is directly threatened, is that of the coralline algae coverings, forming a biofilm for reproductive purposes and also as a primary producing food source to other organisms.

As the marine microbes are very often the primary producers in a food web, their importance to the whole world process is of dire importance, this becomes evident when looking at the ice dominated polar systems, where a direct effect can be witnessed when zooplankton have a reduced primary production and are seen to have a knock-on effect to many species in the tropic levels above them.

In its current state, the world oceans contain many of the most delicate ecosystems to be found, this is to do with the delicate nature of many of the microbes that dive the main processes found in them. Due to the delicateness of these organisms, they are posed the largest risk by the very small changes that are predicted from the rising levels of atmospheric and dissolved CO2.