How to survive iron depletion

A review of Kupper, H., Šetlík, I., Seibert, S., Prášil, O., Šetlikova, E., Strittmatter, M., Levitan, O., Lohscheider, J., Adamska, I. & Berman-Frank, I., (2008), Iron limitation in the marine cyanobacterium Trichodesmium reveals new insights into regulation of photosynthesis and nitrogen fixation, New Phytologist, Vol. 179 Pg. 784-798

This is a post based on the paper reviewed in the seminar by myself and Sara Puddy.

Trichodesmium is a nonheterocystous diazotrophic cyanobacterium, which unlike most photosynthesising, nitrogen-fixing organisms uses the Mehler Cycle as a mechanism to protect the oxygen-sensitive nitrogenise. It does this by rapidly reducing oxygen back to water as soon as it is produced, thus preventing it from inactivating nitrogenise.

Trichodesmium is found in tropic and subtropic oligotrophic waters which are characterised by period pulses of iron supply and reduced iron availability between the pulse events. This means it is highly prone to iron deficiency due to its high demand of iron, both for nitrogen-fixation and photosynthesis. Therefore it is important for the Trichodesmium to have a survival strategy in order to overcome the periods of iron-depletion and the authors explore the techniques it uses for this. This was done by analysing two cultures of Trichodesmium, an iron-replete and an iron-limited culture, where the iron was slowly diluted out.

They found that the iron-replete culture grew healthily and displayed normal functions. However in the iron-limited culture, the filaments, containing cells for nitrogen-fixation, had fragmented and shortened. This is believed to be a survival strategy, as it increases the surface/volume quotient, allowing increased uptake of iron and other nutrients. This strategy is believed to be the evolutionary adaptation of programmed cell death.

They also found that photosynthesis activity was maintained throughout iron depletion and instead nitrogen-fixation had decreased significantly and after 9 days of diluting the iron, nitrogen-fixation per volume, decreased to 25% compared to the iron-replete culture and further down to 10% after another 3 days. This is because nitrogen-fixation is an energetically and iron-expensive process, so instead the energy was used for photosynthesis. Infact, pigments and proteins, specifically keto-carotenoids, associated with photosynthesis had actually increased in the iron-limited culture, some which were only a minor component in the iron-replete culture. Nitrogenase was also degraded to yield an emergency supply of iron and nitrogen for the remaining metabolism.

They also observed that although photosynthesis activity is maintained there is modification of PSI, PSII and phycobilisomes, and a reduction in carbon assimilation efficiency, in order to adapt to the lack of iron levels needed to maintain the normal process.

The study shows that Trichodesmium can survive short-term iron depletion by reducing nitrogen-fixation to compensate for the lack of iron, but that the cells can only survive in this state for approximately 3 weeks. Interestingly, they found that shortly before the cells died, there was a rapid increase in nitrogen-fixation. This was a last resort, as nitrogen starvation in cells had become too severe and so it was necessary to degrade other iron-containing proteins in order to assemble more nitrogenise. It is believed that this was done using an unknown type of restructuring of the phycobilisomes.

Another aspect of this process that is not well researched is the ability to assemble nitrogenise, as normally this requires previous nitrogen-fixation to have taken place, which is not the case for the iron-depleted culture. It is believed that an isoform of phycoerythrin (part of the phycobiliprotein family) is used, which contains more chromophores per amount of protein backbone, helping the cells synthesise nitrogenise.

This paper is a really good basis for further research. It presents us with many different processes which are yet to be investigated and also explores an interesting survival technique, one which perhaps could explain the mechanisms of other nitrogen-fixing organisms in their productivity and survival.

better summary than seminar!

Unicellular cyanobacteria with a new mode of life: the lack
of photosynthetic oxygen evolution allows nitrogen fixation
to proceed.

The reactions of N2 - fixation catalyzed by the O2-sensitive nitrogenase and photosynthetic O2-evolution are incompatible. Most filamentous cyanobacteria that perform N- fixation during the day develop specialized cells, called heterocysts, that do not evolve O2 photosynthetically. Some of the unicellular cyanobacteria separate the two processes by performing N- fixation in darkness and photosynthetic O2-evolution and CO2- fixation during the day. However, few other unicellular cyanobacteria can fix both CO2 and N2 in light.

A group of unicellular N - fixing cyanobacteria of the oceanic picoplankton have revealed a new mode of life. These organisms, termed UCYN-A, were discovered by amplification of the nitrogenase gene (nifH) and are characterized by their 16S rRNA gene sequences. UCYN-A cells have nitrogenase gene arrangement and composition similar to those of Cyanothece sp. ATCC 51142 and of the spheroid bodies of Rhopalodia gibba.

The lack of genes coding for phycocyanin, phycoerythrin or associated linkers, the Calvin-Benson cycle and for photosystem II suggests that UCYN-A cyanobacteria cannot synthesize organic carbon by photosynthesis but are strictly dependent on extracellular sources. The cells apparently meet their energy demand by cyclic photophosphorylation. UCYN-A does contain complete metabolic pathways such as glycolysis however and possess transporters for sugars and dicarboxylic
acids. The authors are therefore tempted to assume that they assimilate dicarboxylic acids, sugars and/or amino acids from ocean waters, as other non-photosynthetic bacteria.

Another possibility is that the UCYN-A cells might be able to cleave pyruvate, but the fate of the remaining two electrons (of NADH) remains uncertain. The authors consider a symbiosis where a fermentative end product such as malate is rapidly consumed by other microorganisms, which could symbiotically supply the missing amino acids to UCYNA. But no organism accompanying UCYN-A has been detected as yet. The review then makes comparisons and takes the reader through the logic of the relatedness of the cyanobacteria to the endosymbiotic spheroid bodies of R. gibba and the acetate photoassimilating green alga Chlamydobotrys sp. of the Volvocales.

It remains to be shown whether acetate or any other chemically simple organic carbon source is sufficiently available in the oligotrophic regions of the open oceans to sufficiently allow growth of the N-fixing picoplankton. However the low population density and small size of UCYN-A requires three orders of magnitude less organic carbon than that which could theoretically be provided by Prochlorococcus. The authors concluding remarks said that the catabolism of organic carbon is not fully understood in UCYN-A. Photoassimilation of acetate, as in the alga Chlamydobotrys, is only one of the possibilities that may happen in their carbon metabolism. Nature may hide further microorganisms with entirely new modes of life.

Replication of the Mimivirus - no nucleus necessary!

This post is a review of the paper discussed by Lee Hutt and myself in Friday’s seminar.

Poxviruses are considered to be unique because of their ability to replicate only in the cytoplasm of their host cell, outside of the nucleus. This paper explores this strategy and its discovered use within the Acanthamoeba infecting Mimivirus. As has been previously discussed in posts by Lee and myself, the Mimivirus is one of the largest and most complex viruses, boasting a 1.2Mb genome. The knowledge of this virus is ever adapting and evolving as new techniques are implemented, with most recent being the rise in known gene number from 917 to 1018. The Mimivirus has raised a lot of debate and questioning concerning the relationship between viruses and single celled organisms. Most of this interest has spiked from the discovery of the virus possessing genes for nucleotide and amino acid synthesis. The virus is as large as several bacteria, has a bigger genome than many and contains genetic information that was previously unknown and thought not possible for viruses. This paper and many recent others generally highlight the underestimation of the ability of viruses.

This paper explores the evolution of the Mimivirus to perform cytoplasmic replication. Since the nucleus provides an optimal, ready-made site for viral replication, the use of the cytoplasm for this function is extremely unusual and maybe even unnecessary. However, the Mimivirus has turned to building large and elaborate replication ‘factories’ within the cytoplasm of its host,
operating seemingly independently. This brings into question our current understanding of the infection strategies of other large DNA viruses of the NCLDV clade. Some works have suggested that this may be made possible by ‘leakage’ of nuclear enzymes. This has been proven for replication of the Vaccinia virus, however this is not yet the case for the Mimivirus.

This paper also applies methods which we have recently been familiarised with such as fluorescent in situ hybridisation, immunofluorescence and general image processing and microscopy. New techniques have allowed researchers to thoroughly investigate the infection cycle of the Mimivirus, presenting the previously mentioned independent replication ‘factories’.

This paper is of great importance in furthering research and knowledge of the Mimivirus. It shows how current techniques can be applied to explore infection strategies, highlights the evolution of the Mimivirus and its relatives, and also opens up a wide range of questions concerning our basic knowledge of viruses, their current status, their evolution and their future.

A review of:
Mutsafi, Y., Zauberman, N., Sabanay, I. and Minsky, A., 2010. Vaccinia-like cytoplasmic replication of the giant Mimivirus. Proc. Natl. Acad. Sci. U. S. A, 107, pp. 5978-5982.

Zooxanthellae: not just for corals!

I thought it might be nice to have a change of symbiosis...!

Symbioses are often not well understood due to an incomplete knowledge of the costs and benefits incurred by each of the symbiotic partners. This holds true in the case of Cliona tropical reef sponges and their zooxanthellar symbionts. Like corals, they maintain an intracellular population of Symbiodinium within their pinacoderm (outer layer), which is believed to be a mutualistic relationship similar to that of corals. However, even coral-zooxanthellae relationships are not completely understood and it is hoped that studies such as this may help unravel the complexities generally.

Hill (1996) provided support for a sponge-zooxanthellae mutualism by finding that symbiotic sponges had higher growth rates than non-symbiotic species; and that when shaded, the symbiotic species growth rate was reduced, suggesting that the Symbiodinium provide extra energy for the sponge. However, due to a lack of further research the suggested mutualism may not necessarily be the case.

In this study 3 experiments were carried out to ascertain whether or not the relationship is mutualistic, and also whether depth would play a part due to decreasing light levels. Firstly, carbon and nitrogen (labelled with organismal uptake specific markers) were traced through the symbionts. Secondly, sponges were transplanted to different habitats to examine the effects of light on ¹³C and ¹⁵N isotopes; and thirdly bulk ¹³C and ¹⁵N ratios were taken from sponges at different depths.

The findings provided evidence for a mutualism as the labelled carbon was traced from the zooxanthellae (as only they could uptake it) through the pinacoderm to the choanosome where it could be metabolised by the sponge. However, this mutualism may be questioned as the labelled nitrogen could not be traced. It could be that sponges exploit the zooxanthellae, although perhaps it is more likely that this process is just more complicated than expected as it is one of the main advantages to the zooxanthellae symbiotic lifestyle.

Depth also affected the symbiosis as stable isotope analysis revealed that the carbon contributed by the zooxanthellae decreased with depth, as did the zooxanthellae population. Consequently the sponges at depth had switched to a more heterotrophic feeding mechanism. However, this is an energetically expensive process and not always possible, so to make up for the lack of ‘free’ carbon, some sponges use their stored resources, which explains the loss of mass and health of some sponges in the experiments.

This shows how important the symbiosis is to the sponges’ and also demonstrates how such relationships can determine species ecology; as sponge distribution must be, at least partially, dependent on the conditions needed to maximise their intracellular zooxanthellae populations. This may also be significant evolutionarily as, if this relationship is as important to the hosts as it seems, they may become totally dependent upon it, as in the case of Riftia worms, changing both their physiology and evolution. However, although the authors conclude a mutualism here, they do not show evidence of nitrogen passing to the zooxanthellae, which leads me to wonder what they are benefitting from? More in-depth analysis is clearly needed here, as in the case of corals, to determine whether a nutritional advantage is even the main benefit for zooxanthellae in these relationships.

A review of: Jeremy B. Weisz, Andrew J. Massaro, Blake D. Ramsby and Malcolm S. Hill (2010) Zooxanthellar Symbionts Shape Host Sponge Trophic Status Through Translocation of Carbon. Biol. Bull. 219: 189–197

Nutrient uptake in corals: what is more important pH or temperature?

A review of the paper by Godinot, C. ,Houlbrèque, F. , Grover, R. ,Ferrier-Pagès, C. (2011) Coral Uptake of Inorganic Phosphorus and Nitrogen Negatively Affected by Simultaneous Changes in Temperature and pH, Plos one, volume 6, issue 9, e25024

Ocean acidification is an important aspect of climate change and just within the 20^th century the pH levels of the sea has dropped from 8.21 to 8.10 and is predicted to drop another 0.5 units in the next century. A decrease of pH is already known to affect the oceans carbon cycle and calcification of corals, and must also influence the other nutrient cycles such as phosphorous and nitrogen. The symbiotic dinoflagellates within corals (Symbiodinium) play an important part within coral nutrition and provide the coral with essential nutrients nitrogen and phosphorous in the form of amino acids. The ocean pH should therefore affect this process and the uptake of nutrients. The aim of this study is to test to see if the pH and temperature affect nutrient uptake in the coral Stylophora pistillata. This is important as nutrient depleted corals are known to be more susceptible to bleaching by expelling their dinoflagellate symbiont.

Colonies of S. pistillata were collected from the red sea and nubbins were cut off and kept in laboratory tanks. Three experiments were run alongside each other for 10 days: 1) three pH’s (8.1, 7.8 and 7.5) at standard 26°C, 2) three temperatures (26, 28 and 33°C) at standard pH 8.1, 3) three pH’s at “warm” 33 °C. After ten days, the nutrient uptake was studied by monitoring the nutrient levels in the water of a contained beaker containing nutrient enriched water. Measurements of photosynthesis and respiration were also taken using respirometric chambers and a diving PAM. Finally, chlorophyll, protein and zooxanthellae concentrations were measured and statistical analyses including t-tests and ANOVA were carried out.

There was found to be no effect of pH or temperature on zooxanthellae, protein or chlorophyll densities or on the rate of respiration. However, the rate of photosynthesis was affected by temperature and the combination of temperature and pH, but not by pH alone. It decreased twofold when the coral was exposed to temperature of 33°C or when kept at pH 7.8. There was no combined effect of pH and temperature. When the temperature was raised to 29°C , the uptake rate of ammonium increased 5-fold, however at 33°C there was a severe decrease. At 33°C and a low pH corals even excreted nitrate instead of absorbing. Phosphate was the only nutrient that was affected by a combination of pH and temperature and the uptake decreased four fold from pH 8.1 to 7.5.

This results show that short term ocean acidification has no major effect on nutrient uptake whereas an elevated temperature does. An elevated temperature increases the uptake of phosphorous, however corals cannot use the phosphorous without nitrogen, which is actually excreted during periods of high temperature. There was also a decrease of photosynthesis at 33°C, due to damages in the PSII in the zooxanthellae from thermal stress.

Despite such strong patterns in this paper, the results are converse to other papers such as Anthony et al 2008, but are similar to others. These variances may be due to other factors such as irradiance levels, showing that this is a complicated relationship and cannot be fully explained by simple experiments. However, if these results are the truth, it shows that climate change will severely effect nutrient supply to the both the dinoflagellate and the host coral, and can therefore alter the susceptibility of coral reefs to bleaching.

Is climate change affecting the microbial distribution and carbon cycling in the Australian Southern Ocean?

A review of: Potential climate change impacts on microbial distribution and carbon cycling in the Australian Southern Ocean. Evans et al. Deep-Sea Research II, 58, 2001, p.2150-2161.

Climate change effects on ecosystems have the potential to dramatically alter carbon cycling throughout the land, oceans and the atmosphere. It is important to understand how these processes work, especially within oceans, as they have some of the largest processes within the Carbon cycle. Microbial communities promote the transfer of atmospheric carbon to the deep oceans via the biological pump, and it is the effect on this pump that is of concern when discussing climate change. Changes can be easily observed in microbial plankton as they have short generation times and respond easily to temperature changes and ocean currents.

The sub-Antartica Zone (SAZ) of the Southern ocean is characterised by high levels of nitrate but low levels of silicate and chlorophyll. It is of specific importance as it is a major sink of atmospheric C0^­₂ due to the composition of the microbial plankton present_. If oceanic currents change due to climate change then an influx of tropical waters into the SAZ may occur. The result will be a change in the microbial assemblage. These biogeographical changes have already been documents in other areas making it likely the same effects will be observed here.

There were 5 distinct biogeographical regions identified by the SAZ-Sense survey. The Polar frontal zone, the Sub-Tropical zone and three regions within the SAZ. The microbial communities found in each region corresponded to the assemblage expected from the physio-chemical properties of the regions. Statistical analysis showed that salinity temperature and No_x availability, explained the microbial variation with Fe availability also being important.

Comparing the differences between these regions allows predictions to be made about the future microbial assemblages and any changes that may occur. this information will be a key tool in predicting the effect of climate change on the biological pump in certain areas of the ocean.

Under the assumption that the SAZ was previously homogenous, the contrast between the three regions can be accredited to the intrusion of the East-Australian current (EAC), South-Easterly into the SAZ, resulting in higher inputs of warmer, more saline and Fe rich waters. The Fe arrives via increased Aeolian dust deposition from Australia plains and increased movement of shelf sedimentary Fe, moved by the stronger EAC. This has the effect of changing the microbial community.

Higher primary production was observed in the regions affected by the EAC. This is not only due to the higher availability of nutrients such as Fe but due to the increased stability of the water column. This occurs because the sub-Antarctic water and sub-tropical waters have very different density profiles due to salinity and temperature differences. It has been previously reported that shallow stable surface layers lead to an increase in cyanobacteria and other phytoplankton.

Associated with this higher production were higher levels of bacteria, bacteriophages and viruses. Viruses are believed to account for a much higher rate of bacteria mortality in the Eastern waters affected by the EAC. Up to 40% bacteria mortality is due to viruses. This creates high levels of DOM which then stimulates higher bacteria abundance and activity.

The poleward intrusion of the EAC over the last 62 years has been increasing and predictions suggest that it will continue to get worse. The reason for this is wind-driven and circulation changed caused by human induced climate change. This results in the Southward extension of the ranges of cyanobacteria and therefore the bacteria and viruses associated with the ecosystem.

Due to the low silica present the previously observed dominance of smaller autotrophs over larger diatoms will likely result in higher importance of the microbial loop. The export of particulate carbon to the deep ocean from diatoms will be reduced in favour of higher production of smaller cells that are then subject to predation my microzooplankton. The higher levels of virus lysis will cause higher levels of DOM over particulate, providing nutrients for substrate dwelling heterotrophs therefore making the system more regenerative.

The increased viral lysis will cause higher rates of respiration in the euphotic zone and reduce the transfer of carbon to higher trophic levels, thereby reducing the effect of the biological pump.

The poleward intrusion of the EAC over the last 62 years has been increasing and predictions suggest that it will continue to get worse. The reason for this is wind-driven and circulation changed caused by human induced climate change. This results in the Southward extension of the ranges of cyanobacteria and therefore the bacteria and viruses associated with the ecosystem.

If these predictions are true then the fate of the SAZ is that it will have a reduced capacity to act as a sink for atmospheric C0₂. This positive feedback mechanism will therefore increase the effect of climate change in the future.

Enough to include viruses to the tree of life?

A review of: Reasons to include viruses in the tree of life. Hegde NR, Maddur MS, Kaveri SV, Bayry J. Comment on Nature Reviews Microbiology. 2009 Apr;7(4):306-11

As we all are aware there is a debate which has been on-going for decades, Are viruses alive? There has been a previous post by Nikie Pontefract on Ten Reasons to Exclude Viruses from the tree of life, this paper although very short raises opinions for why viruses should be included in the tree of life as a direct response to Moreira and Lopez-Garcia’s paper (2009). As I was one of the people who also reviewed this paper for the seminar I decided it would be a good idea to review a paper which was pro viruses being classified as living organisms.

This paper selects but a few of the main points raised by Moreira and Lopez-Garcia (2009) and uses them to turn and suggest reasons why viruses should be included in the tree of life.

In the original article they stated that viruses are not alive because they are polyphyletic this means that they derive from more than one ancestral type, however this paper they suggest that because of the rapid evolution of viruses it would make sense that they are polyphyletic. This is only one example used but the authors do explain a more plausible comparisons being between viruses and spermatozoa or ova neither of which would survive without a host, the most interesting point raised by the authors was Darwin’s theory of ‘survival of the fit test’: those organisms that cannot adapt to a particular condition become extinct. The authors remind us that non-living organisms do not follow this theory and if viruses are non-living then they should not be able to adapt to a particular condition. This is not true for most viruses as they constantly mutate to adapt, Human immunodeficiency virus being an example of this.

This paper does show some valid reasons for why viruses should be included but too few, in my opinion this was a very rushed article just to get an opposing opinion out there. It does not unfortunately take the time like Moreira and Lopez-Garcia (2009) to formulate an equally lengthy or informative read which is a shame because it would have been very interesting……

Further Refrence: Moreira and Lopez-Garcia. Ten Reasons to exclude viruses from the tree of life. Nature. Vol 7. 2009.