Scientific Writing


Vifian, Brian

Science Blog


The idea that iron might be a limiting nutrient in the vast open ocean has gained popularity as of late. One of the reasons for this is the result of responsible scientific research performed by oceanographers based out of Moss Landing Marine Labs.


In order to understand the importance of iron to living organisms we have to go back in evolution, way back, 2 billion years back. The earth was a very different place then. Oxygen was scarce and iron was plentiful, but something was about to change. Enter ferrodoxin, the light harvesting molecule, and with it the glory and doom of photosynthesis. In many respects the dramatic legacy of geo-engineering really took off here when a lowly prokaryote discovered the magic energy of solar radiation and literally changed the course of nature for all time. Most predecessors would die, poisoned by the toxic, caustic oxygen it and its kin were spewing out into the atmosphere. Iron solidified itself as indispensible to life and has been ever since. But in a cruel twist of fate, of which nature has an elicit desire to perpetuate, iron has been stripped away from the oceans due to life’s affinity for its multiuse, half full valence shell. All manner of proteins have at their center, like the chocolaty goodness of a tootsie pop, a lone iron atom seemingly holding it all together.

It was this importance that led researchers to wonder if iron wasn’t playing a much larger role in controlling phytoplankton growth rates in the already nutrient poor central and southern Pacific Ocean, far away from shore and the source of land derived iron entering the ocean. So much in fact, they began to wonder if the relationship between iron and carbon in the biosphere might be a predictor of climate variability due to their utilization en mass by phytoplankton. Crazy stuff. But it gets better. What if phytoplankton were sequestering iron out of the atmosphere by releasing dimethylsulfide gas which would combine with iron(II) ions floating around in the clouds, keeping them soluble until they fell back down into the ocean and the waiting phytoplankton below? Well this is one of the proposed models researchers would like to further test to help explain the major cycles of climate. It will also help us understand what effects we as human beings, through our apparent, however mostly unconscious geo-engineering activities that we regularly engage in while producing our energy and food, are having on the timing and intensity of these cycles.

What we can now say with certainty, due to the efforts of responsible research, is that iron is indeed the limiting nutrient for phytoplankton growth in the central and southern Pacific Ocean. We know this because of an experiment involving iron fertilization, which means soluble iron was spread out into the ocean over a relatively small area and measurements were taken to determine the growth rate, concentration and species makeup of the subsequent bloom of phytoplankton. The results showed a drastic increase in concentrations of larger sized phytoplankton such as diatoms, which need sufficient nutrients in order to keep from sinking.

Here is where we get to the crux of the geo-engineering through iron fertilization of the oceans debate. The idea is if we dump a very small and affordable amount of iron into the open ocean, diatoms will grow, sequester CO2 out of the atmosphere, run out of nutrients and sink to the bottom of the ocean where that carbon will stay for a thousand years. But there are many questions still to be answered. What will really happen to the sequestered CO2? The oceans have roughly a thousand year turnover of surface water so what we sink to the bottom today will want to come back up eventually. What happens then? What if we bloom phytoplankton that release toxins? These experiments have indeed shown that species of the diatom genus Psuedo-nitzschia were common in the blooms and their toxin, domoic acid, was produced in concentrations that could kill sea lions and other large vertebrates.

Obviously there is a lot more work to be done before we can be sure of the effects of iron fertilization and whether or not it is a feasible and more importantly, scientifically viable tool for controlling or at least having an anthropomorphically positive influence on our climate. So it is of great concern when opportunists like Russ George start dumping iron into the ocean promising carbon sequestration and increased productivity to well intentioned people in order to turn a quick profit. Any dedicated oceanographer will tell you this is wholly irresponsible and potentially extremely dangerous. All progress has the risk of the unknown, but it is the stupidity of greedy ignorance that will kill us all.

The longer I study biology the more I realize it is a microbial world and all of the living things we can see with our naked eyes are mere extensions of their impetus and vitality. It behooves us to acknowledge this lest we pass with the closing of another epoch as quiet memories in still fossils waiting patiently for the microbial world to coalesce into some other species with a suitable intelligence to dig us up and ask why.



Brian Vifian

Research Paper Analysis


1. The Whale Pump




In this paper, Roman and McCarthy argue that cetaceans, and to a lesser extent birds, provide a mechanism by which carbon and nitrogen are recycled through the euphotic zone in opposition of the biological pump that drives the carbon/nitrogen flux downward via sinking fecal material of zooplankton and phytoplankton decay. This “whale pump” mechanism is described as a feed deep/defecate shallow behavior that is exhibited by many whales, pinnipeds and to lesser extent seabirds. The biological pump is thought to be driven primarily by intact copepod fecal pellets sinking out of the euphotic zone largely due to their diel migration below the mixed layer, thus transporting carbon and nitrogen sequestered at the surface trough primary production to the bottom of the ocean at a faster rate than thermohaline circulation alone.

The whale pump hypothesis was introduced to explain the discrepancy in observed primary production in the Gulf of Maine and the apparent lack of nitrogen entering the system from advection and adjacent waters needed to sustain that production.




The authors collected 16 fecal plume samples and measured particulate organic nitrogen (PON) and NH4+ concentrations and compared these to non-plume controls. Secondly, they collected fecal samples and placed them into incubation chambers aboard the ship lab and tracked the change in PON and NH4+ over time.

Marine Mammal consumption rates were estimated using BMRs similar to Barlow et al. 2008. FMR was then calculated based on work by Kjed and colleagues suggesting a slightly higher coefficient of 3.0 be multiplied by BMR due to their observations of increased feeding rates in fin whales and sei whales during summer months. Similar arguments for the consumption rates of pinnipeds were used. The FMR was then adjusted to reflect the percentage of crustaceans in each species’ diet. Those species that migrate were adjusted according to the estimated proportion of their annual diet that comes from the gulf.

Nitrogen Excretion rates were then estimated based on mass, consumption rate and group averaged assimilation efficiencies, which were estimated to be around 20%. Average marine mammal body mass, residence time, and population size were gathered for the dominant cetacean species from previous surveys from Kenney et al. as well as Trites and Pauly. Historic population densities from before the massive whaling efforts of the 19th century were taken from Lotze et al. and used to calculate the historical nitrogen flux.




The authors found that measured NH4+ in fecal plumes ranged from 0.4 to 55.5 umol kg-1 while non-plume samples were less than 0.1 umol kg-1showing the association of increased NH4+ and fecal plumes. The incubation experiment showed a positive correlation between PON concentration and net NH4+ production rates, which indicate particulate fecal material as the N source. NH4+ production rates were not affected by initial NH4+ concentrations further implicating the fecal material as the N source and not another dissolved N compound such as urea.

Based on their calculations of the mammalian crustacean consumption and defecation rates, the authors conclude that approximately 2.3 x 104 metric tons of N are recycled to the surface in a year. That number surpasses all river inputs combined and nearly equals coastal point source inputs, however the input from the atmosphere is larger than all other sources combined. The results of the historical N flux show that cetaceans would provide the bulk of N to the euphotic zone due to their greater densities and the lack of pollution as well as less atmospheric N fixed microbially.

In conclusion, Roman and McCarthy find that in the Gulf of Maine, the whale pump is a major contribution to increased primary and secondary productivity due to their recycling of N from feeding on crustaceans involved in the biological pump below the mixed layer and then depositing fecal material at the surface thus resupplying N to the euphotic zone that would likely be lost in the fallout of crustacean fecal pellets.

The whale pump is most effective during summer months when N is depleted due to the strong stratification of the water column and can account for the observed levels of primary production as well as the inefficiency of the Gulf of Maine as a carbon sink. The authors go on to speculate that this system provides not only a positive primary production feedback loop, but that it also encourages aggregate feeding behaviors of both the mammals and crustaceans involved, thus having the profound effect of increasing the overall productivity of the Gulf of Maine at the expense of sequestering atmospheric carbon. The authors encourage that this be taken into account in managing fisheries in the future as certain cetacean densities increase due to their ongoing protection.




One question that comes to my mind is what are the effects of this process on the productivity of the ocean basin under the gulf? What comes back up does not go back down due to trophic conversion inefficiencies but I wonder if any of the overall increased productivity finds its way to the bottom over the course of the year. It is clear from the paper that if the biological pump relies on crustacean fecal pellets being dropped off below the mixed layer, and whales are diving down and eating those crustaceans and defecating back at the surface, then that certainly would have a negative effect on the downward N/C flux.

That assumes that the percentage of crustaceans eaten by whales in the gulf is comprised primarily of those that exhibit the diel migration behavior involved in the biological pump. Also, if the biological pump is based off the idea that tiny fecal pellets can sink through the water column with sufficient speed as to remain at least partially undissolved and unmetabolized, then the authors needed to show that indeed mammal feces does not behave in the same way when released at the surface and that close to 80% is converted to NH4+ before any of the particulate descends below the mixed layer. While they showed that this process was at work, they did not show to my satisfaction that only 20% was lost to the flux of fecal material out of the mixed layer.


Top Predators in the Southern Ocean: A Major Leak in Biological Carbon Pump




This paper was written in response to the idea that primary productivity in the Southern Ocean may be increased with the addition of iron to water with sufficient nitrogen to induce a phytoplankton bloom and therefore sequester and deposit atmospheric CO2 via the biological carbon pump. The authors argue that the Southern Ocean is a poor carbon sink due to the respiration of birds and mammals, which they argue are the most influential predators in the ecosystem.




The authors constructed an Antarctic food web model based on broad averages of trophic conversion rates of carbon. Trophic levels were grouped into phytoplankton, microbes, zooplankton, fish and squid, and birds and mammals. Conversion coefficients between trophic levels were calculated using assimilation efficiency and gross growth efficiency with the assumption that all growth of any group is ultimately consumed by the next trophic level. Other assumptions include: negligible sinking of algal cells and DOC production during photosynthesis, a 0.87:0.13 split of photosynthetically fixed C consumption between zooplankton and the microbial loop, all microbial fecal material is consumed by zooplankton, krill and copepods are equal in biomass and production, there are no trophic transitions within groups, and finally that coastal measurements better represent the ecosystem of the Southern Ocean than those taken from pelagic waters.




The authors found that of the annual amount of CO2 fixed by phytoplankton, 5.0 to 22.5% is respired back to the atmosphere by birds and mammals, thus representing a potential inefficiency of the Southern Ocean as a carbon sink. They also suggest this model be applied to other ocean systems to account for mammal and bird respiration in the overall C flux.




The simplified model of carbon flux presented by Huntley et al. is based on several assumptions. Overall I can understand their concern that predator respiration rates are not accounted for when calculating carbon flux via the biological pump, however some of the assumptions being made are rather gross and if subjected to scrutiny may lack sufficient logic in their application to the Southern Ocean as a whole.

(1) In a eutrophic, highly productive system such as the near ice spring and summer environment of the Antarctic, the authors make a point to emphasize that the phytoplankton community is dominated by large organisms like diatoms but then argue that the rate of sinking algal cells and DOC production is negligible and that indeed all phytoplankton growth is consumed. This seems counter intuitive considering bloom cycles and producer/grazer population dynamics that would suggest a less efficient group clearance rate. (2) The reduced role of the microbial loop, including heterotrophic plankton and other micro zooplankton, is based off of coastal measurements and the authors make the assertion that these measurements are better representative of Southern Ocean dynamics than those taken from pelagic waters. While this model may serve the near shore environment well, it does not address the ocean at large and this is a major flaw in their application of this model to the larger system. (3) The broad groupings of multiple trophic levels within a category overestimates the C flux between all groups. (4) Zooplankton is split into copepods and krill, which are assumed to be equal in biomass and production rates. This is another highly variable assumption that can drastically change the calculation of C flux because it directly effects the ratio of C consumed by birds and mammals which breathe CO2 directly back into the atmosphere, to that consumed by fish and squid which is dissolved back into the water.



Moloney brings up several of the same concerns as I have. They include: (1) Phytoplankton respiration is not accounted for in the overall C flux, which increases the percentage of heterotrophic contribution. (2) The microbial loop is underestimated for several reasons. The diversity of microbes and the lack of trophic transfers within the loop seems largely oversimplified. Even in our highly productive California coastal system, the contribution of previously unknown microplankton is a dominant force and to consider their lack in the entire Southern Ocean as indicated by near ice measurements is obtuse.

In the Huntley et al. response, they argue that their coastal, near ice measurements are better representatives of the entire Southern Ocean than all pelagic measurements taken at higher latitudes. They go on to say that the near ice coastal ecosystem of the Antarctic is characterized by a suppressed microbial loop with few heterotrophs, and low rates of protozoan grazing as evidenced by direct measurements. They also state that there is a large amount of particle flux out of the euphotic zone, which would indicate to me that the heavy production of large diatoms was creating a large particulate C flux out of the system that is not accounted for in their model!

When considered in all, I can see that each side has a model that describes the environments each are most intimately involved in studying, the near ice and the pelagic Antarctic waters. Both sides are making assumptions about the Southern Ocean as a whole based on what they have seen in parts of it. Considering that the ocean is dynamic and contains both of these habitats, it would be wise to combine these models when trying to apply them to the system at large. What seems to be lost here is that any iron supplementation is likely to occur in the environment described by Moloney with the whole idea being to create blooms of diatoms that would overwhelm all predators and sink a good portion of C in dying algal cells to the bottom of the ocean. Secondly, siliceous sediments under areas of high diatom productivity suggest a far less than 95% transfer of primary productivity to the bellies of zooplankton.



2. Mesozooplankton influences on the microbial food web


As it is now known that phytoplankton in warm, oligotrophic regions of the open ocean are dominated by <2um cells. This tiny cell size is too small for mesozooplankton to feed on directly. It is assumed that there are intermediate trophic levels responsible for linking the two by consuming the picophytoplankton and then being consumed by the larger t mesozooplankton. Calbet and Landry designed a size dependent exclusion experiment to study the magnitude of these lower trophic level interactions.

The experiments were performed onboard a research vessel at sea 100km north of the Hawaiian Islands and samples were collected from the deep chlorophyll maximum (DCM) around 110m depth and from surface waters. The authors later show that there was no significant difference in the results of their experiments when comparing those involving surface water or DCM water.


Microbial food web interactions


To establish which size fractions of consumers were most responsible for picoplankton grazing, the authors filtered DCM water through varying pore sized filters of 1, 2, 5, 8, and 20um. Four replicates were performed per size fraction. The experimental flasks were then incubated under 1% surface irradiance to try and lessen the effect of nutrient supplementation from the excretions of zooplankton. Subsamples were taken before and after a 24hr incubation and heterotrophic bacteria and Prochloroccus sp. population abundances were enumerated using a flow cytometer. Net bacterial growth rates were calculated assuming exponential rates of increase or decrease.


The results in fig. 1 show the effect of size class exclusion on picoplankton net growth rate in doubling per day. Removal of the >20um size class had little effect on heterotrophic bacteria (HBACT) or Prochlorococcus sp. suggesting that ambient concentrations of microzooplankton had little direct impact on these picoplankton. However when the 5-20um size class was excluded there was a substantial decrease in bacterial net growth rates with Prochlorococcus sp. showing a drastic drop of -0.6 d-1. Net growth rates returned to near control levels when everything >2um was excluded. What this suggests is that the 5-20um size fraction is consuming the 2-5um organisms, which in turn are consuming the <2um bacterioplankton.


Initial Grazing Experiments


The impacts of micro- and mesozooplankton on net growth rates of total and <2um Chl a were compared in this experiment. There were three size classes of filtered DCM water- <2um, <60um, and <200um. In the <60um treatment, a control was compared to samples with and added 0.4 mg dry weight L -1 of live microzooplankton between 60 and 200um, collected and sorted from a plankton tow. The <200um treatment received 2.1 mg L-1 dry weight of mezozooplankton >200um and so included both micro- and mesozooplankton. Nitrate was added to all experimental bottles to override the differences in zooplankton excretion among treatments. Again 1% irradiance was used over a 14hr incubation time after which Chl a was extracted with acetone and measured using a Turner flourometer.

In addition, to assess the predatory pressure and possible prey selection of mesozooplankton feeding on microzooplankton, incubations of surface water were treated with varying concentrations of microzooplankton with and without the presence of mesozooplankton. The retained animals were then enumerated and ingestion rates were calculated.


Fig. 2 shows that net growth of picophytoplankton was positive in the <2um treatment at 0.3 doublings per day, while both of the controls in the <60 and <200um filtered treatments showed a drastic decrease to -0.5 per day indicating a strong negative impact from the absence of microzooplankton. Interestingly, total Chl a showed an increased net growth rate in the <60um control but a strong decrease in the <200um control indicating a strong grazing effect of microzooplankton on phytoplankton in the 2-60um range. The addition of microzooplankton in the <60um treatment and the subsequent negative total Chl a net growth rate reinforces this. There was a marked increase in net growth rate of <2um Chl a in the presence of microzzoplankton >60um indicating their consumption of bacteriovores that were feeding on the picophytoplankton. The addition of mesozooplankton >200um showed a similar response for <2um Chl a as found in the <60um treatment while total Chl a showing an increase rather than a decrease in net growth rate. This indicates the mesozooplankton are consuming some of the microzooplanton thus removing some of the grazing pressure on >2um phytoplankton.


The Trophic Cascade


In this series of experiments, the researchers tried to quantify the effects of zooplankton on the lower trophic levels. The setup was similar to the direct grazing experiment except here the concentrations of grazers were varied and their effect on Chl a, heterotrophic bacteria (HBACT), and nanoheterotrpophs (HNAN). A nutrient broth was added to each bottle again to compensate for varied excretion levels by grazers. Chl a and HBACT were measured as described previously while HNAN were enumerated with an epiflourescent microscope after being DAPI stained.

The results showed that increased grazer biomass did not significantly alter the picophytoplankton abundance while the >2um phytoplankton abundance showed a positive response in net growth rate, indicating little direct trophic interactions between larger grazers and picophytoplankton. Heterotrophs in the <5um size class showed increases in net growth rates in response to increased grazer biomass while those larger than 5um showed a decrease indicating they were eating the <5um organisms while the larger grazers were feeding on them.


2001 Study


This time around the researchers concentrated only on the interactions within the microbial web essential zooming in on the interactions of those organisms less than 20um. They also compared samples from both the DCM and the mixed layer over the course of a year to try and find seasonal variations. The results of this series of experiments confirmed their original findings in that the removal of successively smaller consumers and the subsequent increases and decreases in net bacterial growth are indicative of a trophic cascade in within the <20um size class.

They also found however that while the overall abundance of picoplankton growth is rather consistent throughout the year, the reasons alternate between nutrient limitation and grazing pressure. They found that heterotrophic flagellates in the 2-5um size class vary in their abundance throughout the year and may be the drivers of the oscillation between grazing and nutrient limitation pressures on picoplankton.



Hydrogen is an energy source for hydrothermal vent symbioses


It has been known that bacterial symbiosis accounts for much of the primary production of energy at deep sea hydrothermal vents (Corliss et al. 1979). Two sources of chemically derived energy have been identified: methane oxidation (Childress et al. 1986), and sulfur oxidation (Cavanaugh et al. 1981). Although there are many potential sources of chemically derived energy that can be found at these vents sites, no others have been identified as part of a symbiotic biochemical system. The authors of this research article have asked whether hydrogen can be added to that list and if so, to what extent can we expect to find pervasiveness of its use.

The authors chose hydrogen to study because in its molecular form it is a good electron donor with a higher potential energy yield when compared to both methane and sulfur (Amend et al. 2001). The target organism was Bathymodiolus puteoserpentis, a mussel found in high concentrations at the Logatchev vent site on the Mid-Atlantic Ridge (MAR). This is an ultramafic-hosted vent site with characteristically high concentrations of hydrogen. Comparison sites were also studied further south along the MAR. These were basalt-hosted sites characterized by low hydrogen and high sulfur and methane levels.

Bathymodiolus mussels are known to contain two types of symbiotic chemoautotrophic bacteria in their gills, each carrying out methane and sulfur oxidization respectively (Duperron et al.2006). It was the prediction of the authors that one of these bacteria symbionts was also capable of oxidizing hydrogen to the energy benefit of the host.

The authors indentify group 1 NiFe hydrogenases, membrane bound respiratory enzymes that extract electrons from hydrogen molecules for use in energy synthesis (Vignais et al. 2007), as the link between hydrogen oxidation and energy production. In Bathymodiolus puteoserpentis this enzyme is encoded in the hupL gene. A phylogenetic analysis was performed using a MAFFT alignment and calculated in ARB. This analysis showed a related sequence to other NiFe hydrogenases found in bacteria that are known to use hydrogen as an energy source, thus confirming the genetic potential of hydrogen as an energy source for Bathymodiolus puteoserpentis. This was also confirmed for Bathymodiolus mussels that were sampled from basalt-hosted vent sites with low (<0.1 µM) concentrations of hydrogen.

Samples were also taken from mussels of a different species that were located near cold seeps. The hupL gene could not be amplified from these samples indicating that these mussels lacked the enzymes necessary for hydrogen oxidation.

Samples were collected with an ROV and incubated immediately after being brought aboard the research vessel at sea. In order to measure the hydrogen uptake, samples were taken in each individual mussel from the gills, and the foot, where there are no symbionts. As controls, seawater alone, the foot, which has no symbionts, and boiled gill samples were used. The samples were placed in sterile seawater in glass vials and inverted to limit seepage through the seal. Hydrogen was then added to the vials and the change in head space concentration was measured over time by gas chromatography. Hydrogen uptake was shown to be coupled with CO2 fixation, and thus energy production, by incubating gill tissue with seawater containing 14C-bicarbonate. Control tissues were incubated with sulfides present. Both showed equivalent 14C uptake indicating that indeed hydrogen consumption was resulting in energy production in Bathymodiolus puteoserpentis.

In order to test the relationship of hydrogenase gene expression and hydrogen concentration in situ, the authors repeated the hydrogen uptake experiment with successively higher concentrations of hydrogen. It was found that for each 100 ppm increase in partial pressure, there was a 135 nmol/h/(g wet weight) for samples at Logatchev.

In addition to hosting methane and sulfur oxidizing bacteria, Bathymodiolus mussels from the MAR are also often infected by a gammaproteobacteria parasite that targets gill cell nuclei. To determine which type of bacteria were using the hydrogen, the authors used three methods: genome sequencing of the symbionts, single gene fluorescence in situ hybridization (geneFISH) and immunohistochemistry, the latter two combined with 16rRNAFISH.

The authors used geneFISH, which is a method that allows simultaneous observations of single genes and rRNA thus linking function and identity at the single cell level. Their observations showed that signals from the geneFISH targeted hupL gene overlapped with the 16SrRNA signals from the sulfur oxidizing symbionts. By combining these two genetic methods with immunohistochemistry, the authors solidified the sulfur oxidizing symbiont as the agent of the hydrogen uptake rather than the methane oxidizing symbiont.

This was done by creating and administering a polyclonal antiserum for the NiFe hydrogenase from C. necator (74%amino acid identity to the B. puteoserpentis symbiont hupL gene), which was used to detect hydrogenase expression in single symbiont cells of B. puteoserpentis. At this single cell level, the authors observed an overlap of signals produced from the anti-hydrogenase antibody in the gill bacteriocytes and the FISH signals from the sulfur-oxidizing symbiont but not the methane-oxidizing symbiont.

The authors report a potential uptake rate by a single Logatchev mussel with a gill weight of 5g in 50µM dissolved hydrogen of up to 435µmol H2/h. The authors also report that given the estimated population at the site of 250,000 – 500,000 adult mussels, a total of 200mol H2/h could be consumed.

Based on these findings, the authors conclude that these mussels are a significant hydrogen sink at these hydrothermal vents.



Considering the great potential of hydrogen as an energy source and its use by other micro-organisms, posing the question of whether it is utilized by symbionts of organisms found in hydrogen rich environments such as ultramafic-hosted vent sites was intriguing and logical progression of study. It was also intriguing to see that mussels at basalt-hosted vent sites retained the ability to oxidize hydrogenase even though hydrogen levels are quite low, suggesting its use is wide spread amongst B. puteoserpentis and related species. It was interesting to note that mussels around cold seeps, which share a common and evolutionarily recent ancestor with hydrothermal vent site specific mussels, do not have the hupL gene, and based on the authors phylogenetic analysis suggests that gene was lost due to multiple habitat specific gene loss events.

The inherent challenge of studying hydrothermal vents is alleviating the discrepancy of pressure between the laboratory on the research vessel and in situ. To counter this, and to add to the validity of the experimental results, the researchers performed an H2 concentration analysis in situ. This was done with an ROV equipped with a mass spectrometer to measure the H2 concentration in the mussel habitats. This was compared with temperature as a way to trace the dilution of hydrothermal fluids as they flowed away from the vent and eliminate the dispersion/dilution effect from the biological uptake by the mussels. Measurements were taken directly over the vent for baseline and then at various distances away from the source vent to beyond the mussel bed.

This study was accurately presented. The methods and materials used were detailed and explicit. It seems reasonably certain that if reproduced, the results would be verified. This study paves the way for future research into deep sea symbiosis study.

The study does not conclude that symbionts in other mussels or organisms are using hydrogen to harness energy. However, it has been shown that hydrogen is abundant at many vent sites, and there are other organisms with symbionts that carry the hupL genes such as the shrimp, Rimicaris exoculata, and the giant sea worm Riftia pachyptila, which occurs in the Pacific Ocean. It would appear that indeed hydrogen oxidation is a prevalent form of energy synthesis in the deep ocean. Further study is warranted to identify other organisms that may be using hydrogen for energy and perhaps it will be discovered that other molecules are being exploited as well.


Petersen JM, Zielinski FU, Pape T, Seifert R, Moraru C, Amann R, Hourdez S, Girguis PR, Wankel SD, Barbe V, Pelletier E, Fink D, Borowski C, Bach W, Dubilier N. Hydrogen is an energy source for hydrothermal vent symbioses. Nature. 2011 Aug 10;476(7359):176-80. doi: 10.1038/nature10325. PubMed PMID: 21833083.



Induced Plant Defense:


Chemical Deterrence, Parasitoid and Predatory Recruitment




By Brian G. Vifian







In the plant world mobility is in short supply. It is therefore important that plants have some mechanisms to protect themselves from the mobile organisms that pose a threat to their ability to grow and reproduce. This paper is a short summary of some of the important induced defense responses in plants triggered by herbivory, with special attention given to the association of various ant species and Acacia trees.

Induced defense mechanisms in plants are triggered in some way by the activities of the offending organism. Often in the case of insect herbivory, the response is triggered by chemicals present in the insect’s saliva. In cases of infection, metabolic byproducts of the infectious agent can trigger the response. These chemicals induce the production of two main categories of compounds: salicylates and jasmonates, which include derivatives of salycilic acid and jasmonic acid. The production of these two classes of compounds is common in plant defense mechanisms across many species (Runyon et. al., 2010). They are produced in the first step of mediated pathways that result in three categories of defense responses: chemical deterrence, parasitoid recruitment and predatory recruitment.

Salicylate – Mediated Response

Salicylic acid has been shown to be an important hormone in plant defense and has generally been attributed to responses to pathogens (Loake and Grant, 2007). The response involves the activation of pathogenic resistant genes. It also triggers what is called the hypersensitive response which is characterized by the rapid self destruction of infected plant cells in order to halt the spread of infection (Halim et. al., 2006).

Jasmonate – Mediated Response

Jasmonic acid is generally associated with herbivory in the context of plant defense. Jasmonic acid is also important in pollen maturation, flower production, root growth and photosynthesis. In defense, the common pathway is initiated by chemicals found in the herbivore’s saliva or as a product of physical damage to plant tissue (Wasternack, 2007). Linolenic acid is released from the cell membrane and enters octodecanoid pathway which then produce jasmonic acid. Systemin is an intermediary compound produced in herbivore damaged cells as a result of the saliva that travels to undamaged cells where it activates the production of jasmonic acid. The production of jasmonic acid can initiate resistance pathways and the expression of defense genes. Some of the defense chemicals that are produced include proteinase inhibitors, which inhibit the digestion of proteins in the herbivore, defense-related volatile compounds, such as ethylene, and secondary metabolites, such as morphine, terpenes, active phenolics and phytoalexins (Turner et. al., 2002). Some of the defense related volatile compounds have been shown to repel herbivores and attract organisms that either prey directly on the herbivores or parasitize them.

Parasitoid Recruitment

In cases where parasitoid recruitment is involved, the response is species specific. Particular chemicals present in the herbivore’s saliva trigger a specific transduction pathway that results in the production of a volatile compound that attracts a specific organism that parasitizes the herbivore. Generally both the herbivore and its parasitic counterpart are insects. The watery digestive saliva of aphids has been shown to induce a parasitoid recruitment response in wheat. The parasite Aphidius avenae, has been shown to be attracted to wheat plants that are infested with aphids and wheat plants treated with chemicals found in aphid saliva (Yong Liu et. al., 2009). In a field study published in 2009, Poelman et. al., showed that variations in environment and herbivorous caterpillar species induced species specific variations in parasitoid recruitment. This indicates the plants ability to respond specifically to a range of herbivore species.

Predatory Recruitment

One of the most studied mutulistic relationships involving predator recruitment by plants is that of colonial ants and various tree species such as Acacia sp., and Macaranga sp.. In these types of associations, the trees produce a food body that attracts colonial ants. The ants, to varying degrees, protect the tree from other herbivorous insects. There is an interesting interplay between the food body composition and the ant species associated with the tree over the lifetime of the tree. This is why it is an induced response and not just something the tree keeps consistent. There is wide range of compounds found in food bodies. Carbohydrates, lipids, proteins, and amino acids are all present in varying quantities. These variations in quantity and composition have been shown to favor different ant species (Heil et. al. 2004).

In a study published in 2010, involving Acacia drepanolobium, Palmer et. al., looked at the tree’s association with four species of symbiotic ants over the course of the tree’s lifetime. What they found was that the four species varied greatly in the benefits they offer the tree versus the cost. The ants are in competition with one another for the sole occupation of the tree and generally follow a hierarchical dominance transition over time ending with the most dominant species occupying the tree last. The benefits the tree receives in terms of herbivore defense vary greatly with the most dominant species allowing the most herbivory which would occur later in the tree’s life. The same dominant ant species however was the least demanding in terms of food body consumption. One ant species was aggressive at protection but also sterilized the tree by destroying floral meristems.

What the researchers concluded was that the temporal transitions of ant species and their subsequent behaviors had a positive effect on tree survivability, even though individual species of ant had specific negative impacts. The reasoning is such that for each stage of the tree’s life, the ant species that associates with it has a net benefit for both. For example, when the tree is young it doesn’t put a lot of energy into reproduction and this is the time when it is associated with the ant species that destroys the floral meristems but is an aggressive defender against other herbivores. When the tree is older it is occupied by dominant species that does little to defend the tree from herbivores but does keep the other species of ants at bay. This results in the tree producing less foliage and more reproductive tissue. Also the dominant ant species consumes little nectar from the food bodies which also conserves energy for reproduction. Trees in this stage inhabited by this species of ant had much higher reproductive success.

Given the multi-partner mutualism and the sequential nature of the associations and benefits over the life of the tree and the intricate make up of the nectar excreted from the fruiting bodies, it seems highly likely that the Acacia sp. and other long lived plants have the ability to fine tune their attractants to specify symbionts on the basis of temporal needs.


Plants display a variety of defense mechanisms that are highly reactive to stimulus in the environment, specifically in response to herbivores. These mechanisms include: chemical deterrence, which can range from proteinase inhibitors which inhibit enzymes from digesting proteins, to the release of volatile compounds that deter herbivores, parasitoid recruitment, and predatory recruitment. These mechanisms are induced through various methods and activate transduction pathways that lead to defense gene expression, defense chemical production, and volatile compounds used to signal other plants, herbivore parasites and predators. Given the complicated associations of mutualistic partners, future study of the dynamics of these interactions over time is needed to fully understand the induced mechanisms of plant defense.






Works Cited

Degen, Thomas, et al. “Differential Performance and Parasitism of Caterpillars on Maize Inbred Lines with Distinctly Different Herbivore-Induced Volatile Emissions.” Plos One 7.10 (2012): e47589. Web.

Escalante-Perez, Maria, et al. “Poplar Extrafloral Nectaries: Two Types, Two Strategies of Indirect Defenses Against Herbivores.” Plant Physiology 159.3 (2012): 1176-91. Web.

Halim VA, et al. “The Role of Salicylic Acid and Jasmonic Acid in Pathogen Defense.” Plant Biology 8:307–313 (2006).

Handa, Chihiro, et al. “Change in Biomass of Symbiotic Ants Throughout the Ontogeny of a Myrmecophyte, Macaranga Beccariana (Euphorbiaceae).” Journal of Plant Research 126.1 (2013): 73-9. Web.

Heil, M., et al. “Main Nutrient Compounds in Food Bodies of Mexican Acacia Ant-Plants.” Chemoecology 14.1 (2004): 45-52. Web.

Kersch, M. F., and C. R. Fonseca. “Abiotic Factors and the Conditional Outcome of an Ant-Plant Mutualism.” Ecology 86.8 (2005): 2117-26. Web.

Klemola, Tero, et al. “Larval Parasitism Rate Increases in Herbivore-Damaged Trees: A Field Experiment with Cyclic Birch Feeding Moths.” Oikos 121.10 (2012): 1525-31. Web.

Koepke, Diana, et al. “Species-Specific Responses of Pine Sesquiterpene Synthases to Sawfly Oviposition.” Phytochemistry 71.8-9 (2010): 909-17. Web.

Linsenmair, KE, et al. “Adaptations to Biotic and Abiotic Stress: Macaranga-Ant Plants Optimize Investment in Biotic Defence.” Journal of experimental botany 52.363 (2001): 2057-65. Web.

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Loake G and Grant M. “Salicylic Acid in Plant Defense – The Players and

Protagonists.” Plant Biology 10:466–472 (2007)

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Transduction and Action in Plant Stress Response, Growth and

Development.” Ann Bot 100:681–697 (2007).

Critique of the Annual Review
Marine Fungi: Their Ecology and Molecular Diversity
Brian Vifian





Fungi are integral components in terrestrial ecosystems. Having the ability to break down cellulose, lignin, and other hard to digest materials, allows these organisms to carry out key roles as decomposers. While research has identified tens of thousands of distinct species of terrestrial fungi, with those numbers being estimated at less than five percent of extant fungal diversity, fungal species identified in marine habitats have been less than forthcoming. This may either be the result of sampling or identification biases, or simply due to the fact that fungi do not contribute significantly to marine ecosystems.


This article, written by Thomas A. Richards et. al. was published in the Annual Review of Marine Sciences in 2012. The article addresses this fundamental question: Do fungi contribute significantly to marine ecosystems? Drawing from some very exciting and recent research in fungal genetics, the authors paint a vivid picture of fungal diversity in both species and lineage.

Most species of fungi have been identified by isolation and growth in culture. This inherently leads to a bias toward those species that are easily identified and cultivated. One way to isolate and identify fungal species involves sampling environmental substrate, or simply collecting water in particular habitats, and then lysing the cells that the sample contains revealing naked DNA. The DNA is then subjected to amplification by means of polymerase chain reaction (PCR) and species identification is the result of matching sections of DNA known to be species specific. The sections of DNA used for the majority of samples in this review were small subunit rDNA (SS rDNA). The efficacy of this process is limited by the resistance of some fungal species to the lysing process and the lack of overall genetic knowledge of fungi. The authors drew from this molecular data as well as existing clone libraries to form a comprehensive phylogenic tree of marine fungal evolutionary diversity based on the most current data. From this data it was also possible to test the various hypotheses of fungal origins.

From their analysis it was shown that, thus far, marine fungal diversity represents a very small percentage of overall fungal diversity. Yet, this diversity was doubled from previous methods of identification.

Of those marine fungi identified, intrafungal diversity was high, incorporating chytrids, multicellular types, and filamentous hyphal types. These various types inhabited diverse environments from mangrove stands to deep sea sediments and hydrothermal vent sites. Also, many types were found to parasitize fish, coral, algae, and other marine animals while some species were found to exist in mutualistic partnerships with almost all sponges and some alga.

Of the major divisions of fungi, marine forms seem to be dominated by the Dikarya yeast group. This is consistent with terrestrial fungi. Furthermore, it was also shown that the evolutionary pathways of marine fungi are quite convoluted, represented by both deep and shallow branching lineages. This suggests that there have been multiple land-sea, sea-land adaptation events over the course of fungal evolution. Finally the genetic analysis identified many pseudo fungi that share morphology, and occupy similar ecological and trophic roles, suggesting a potentially high degree of competition between the two groups.


The analysis of this review of marine fungi is indeed comprehensive. The authors’ use of genetic and clone libraries was exhaustive and complete, incorporating the most recently collected and published data. Like Mr. Holmes snatching up the smallest of clues, computer generated analyses of small subunit rDNA gives us a vivid yet limited view into the mysteries of fungal evolution.

The authors were explicit in noting the limitations of sampling and PCR biases against fungal cells. Due to the tough chitin exoskeleton, many species were surely overlooked in the DNA sequencing process because the cells failed to lyse. Also, the PCR amplification process most certainly selected against certain fungal species that did not accept the given markers and subsequently avoided amplification. These biases most likely caused an underestimation of species diversity.

Despite sampling biases, the research shows marine fungi are represented by a diversity of forms. There are species that live near the surface and feed off the detritus supplied by mangrove stands and marine algae. However, the density and ecological importance of these species is as yet unknown. Few fungal species are found in open water devoid of nutrient rich substrates, yet those that are there are likely to be parasitic, feeding off of swimming animals and free floating algae.

The authors describe in detail the deep ocean fungal species that inhabit various niches within hydrothermal vent communities as well as open seafloor sediments. Those living in anoxic and anaerobic habitats function as denitrifiers, contributing to the cycling of nitrogen. Again it is unclear to what extent their contribution is significant. The deep ocean presents its own list of sampling problems. In addition, as of yet there has been little success in culturing fungi from these environments, which severely limits the DNA cache from which accurate analyses, such as the one done in this review, can be facilitated.

Using their constructed fungal phylogenic tree, the authors proficiently describe the myriad of evolutionary pathways. They state that as with terrestrial habitats, marine fungi are primarily of the Dikarya group. However, and perhaps more interesting, there are many novel species that branch deep below the Dikarya radiation. This suggests an evolutionarily early colonization of the seas. While terrestrial radiation of fungi closely follows that of plants, the question remains whether the most distant of relatives originated on land, in freshwater, or in the oceans.

One hypothesis suggests, as all terrestrial life owes its origins to the sea, that the earliest fungal forms came onto land as some sort of mutualistic partner of microbes that would eventually evolve into plants. Nonetheless, it can be said with a degree of certainty that there have been multiple colonization events both from the sea and to the sea by fungal species throughout time.

The discovery of diverse fungal analogs in marine environments may give us a clue as to why marine fungi have not proliferated in the sea as they have on land, despite a relative abundance of suitable habitats. The relationship of marine fungal analogs and their terrestrial true fungal counterparts is much like the relationship between multi continental mammals and Australian marsupials.

Due to their isolation, marsupials on the island continent have filled symmetrical ecological roles that placental mammals have filled on other continents. Morphologically and trophically similar, these mammalian analogs have been allowed to occupy these roles that mammals have since occupied on the remaining intermittently conjoined landmasses at the expense of marsupial ancestors.

The authors’ hypothesis for fungal analogs gnaws at a similar bit and could explain the relative absence of marine fungi. If these fungal analogs are already occupying ecological roles normally left to true fungi in terrestrial environments, and for some reason have an edge in the competition, then it would be difficult indeed for a true fungal radiation to occur as it has on land. That competitive edge may be found in the stark contrast in exoskeletal morphology and their associated feeding methods. True fungi have a tough exoskeleton made of chitin, which facilitates their method of feeding by means of external enzymatic digestion and absorption. Analogous fungi lack an exoskeleton of chitin, which facilitates their method of feeding involving phagotrophy, where the absence of a rigid exoskeleton allows the fungal cell to ingest large pieces of food which are then broken down by enzymes within the cell. Given the ease of enzyme dispersion in water, it may be an important advantage to do your digestion on the inside.

While this review has an overall logically consistent narrative describing the evolution and subsequent importance of fungi to marine habitats, there are some subtopics which have contradictory conclusions. This in and of itself is not problematic as the narrative is summarized rather succinctly in the final conclusions. However, when following the logic behind the origins of fungi, the contradictory conclusions of different research models lack immediate resolution within the subtopic’s particular section. As stated this is a minor calamity rectified in the final conclusions.

There are some questions that remain unanswered that require further study are identified by the authors. Who are the key players in detrital decomposition in marine habitats? Do fungal analogs in fact out-compete their true fungal counterparts, and if so, by what means? These questions get to the heart of marine fungal evolution and subsequent importance in ocean environments.

Word Count: 1496

Works Cited

Richards, Thomas A., et al. “Marine Fungi: Their Ecology and Molecular Diversity.” Annual Review of Marine Science 4.1 (2012): 495-522. Web. 5/13/2012 12:43:50 AM.


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