Recently, the US National Public Radio published a story on biofuels and nitrous oxide.  I think that it is an excellent description of the reasons that researchers such as myself and others research nitrous oxide.  If you want to hear the full story, click on the link below:

http://www.npr.org/templates/story/story.php?verified=true&storyId=112288478#commentBlock

A recent article in Macleans  (http://www2.macleans.ca/2009/07/28/our-universities-can-be-smarter/4/) makes the argument that there should only be 5 major research institutions in the country.  The remaining universities should train undergraduates and feed their best students to U of A, UBC, Toronto, UM and McGill.  There are so many problems with this that I won’t even attempt to address it.  Instead, I’ve included a post by ‘eddycurrent’ in response to the Maclean’s article.  It is an excellent decoding of the big 5 president’s request:

Eddy Current Writes

I am a faculty member at a Canadian university which is not one of the self proclaimed “Big Five”. Obviously these five presidents would want their universities to receive special treatment. It would make their work more rewarding and most likely easier. I hope their plea, and this article, fall on deaf ears.

I conclude with a statement of personal experience. I was offered a faculty position at one of the Big Five, but turned it down to remain at one of the Lesser Eight (by which I mean the rest of the Canadian G13 universities - which in itself is a kind of self-proclaimed Winners Circle). There are many great things going on in the Lesser Eight, and some crap. The same is true of the Big Five. The question is, is the great to crap ratio better or worse in the Big Five. Would they willing to compare these ratios in a Big Five vs Lesser Eight winner-takes-all competition right now? If they come up short, would they stand aside for the Lesser Eight, volunteer to focus on undergraduate education, and strongly support a program to make the Lesser Eight “Harvards of the North”?

I agree completely.  Transparent competition, resources and commitment to all students (undergraduates and graduates) is the key to a respectful and successful system.

Excitement breeds imagination.  The blind passion of excitement often leads to intuitive leaps of imagination that can lead scientists into new and innovative fields of inquiry.  As a scientist who works in Antarctica, I can attest to this excitement not only in myself but also in my graduate students.  They arrive in Antarctica with eyes as wide a saucers and minds wide open to new ideas.  However, as they step foot on the continent, they bring Canada.

These young Canadian scientists bring -40°C winters, January thaws, quinzees, migrating caribou, seals lounging on the ice looking out for polar bears and the history of the Hudson Bay company men.   As they stay on Antarctic, our Métis, First Nation and Inuit culture surfaces and they view the landscape unlike any other people can.  Canadian’s live and thrive under conditions as hostile and extreme as what is routinely encountered in Antarctica.  As such, Canadian’s don’t view Antarctica as a hostile, foreign land but as a long forgotten home and thus, we are not there to conquer but to nuture.

In turn, Antarctica brings to Canada a level of excitement and innovation that is only possible for extreme explorers. It attracts technical entrepreneurs who are interested in science and risk taking. These students thrive on taking science out of the classroom and into the world.  Students such as these will found Canada’s next high-tech commercial success story.

Canada needs to be working in Antarctica because we are unique in the world.  Our Nation’s history was forged in the North and I believe our future will be as well.  By working in the South, we can demonstrate our national expertise in Polar Regions, confirm our National identity as a polar people and inform our northern science. This will help affirm our northern sovereignty claims and stimulate our innovation economy by providing unique opportunities to the best of our science cadre.

Sam Banerjee has just won the U of S Robson Bursary.  This bursary recognizes academic achievementin an area related to land and resource management with an emphasis on sustainability and ecologically sound management practices.  Sam’s Ph.D. research is focussing on how geospatial relationships of microorganisms influences processes linked to greenhouse gas production in Canada’s Arctic.  His recent work has been investigating at what scale processes are important.  Or in other words, if you are trying to link genes, greenhouse gases with long term geomorphology, should your samples be spaced at less than one meter apart or perhaps several 100 meters apart.  His results are an integral part of the IPY-CiCAT program as it attempts to provide remote sensing experts with the on the ground information they need so that Canada can accurately estimate greenhouse gas emissions under a variety of climate change scenarios.

Congratulations Sam!

A recent article by Dr. Gan’s group in Environmental Science and Technology (DOI: 10.1021/es802966z) investigates how available phenanthreneis to bacteria.  What the group did was measure phenanthrene degradation and also calculate the amount of phenanthrene freely dissolved in soil pore water.  To measure the amount of phenanthrene in pore water, they used solid phase microextraction fibers.  Importantly they checked many of the assumptions about SPMEs and their ability to measure freely dissolved phenanthrene.  Once they did this, they found that the freely dissolved concentration of phenanthrene could only predict the initialy 144 h of degradation but after that was not predictive at all.  This suggests that microorganisms can access phenanthrene directly from soil without the phenanthrene dissolving into pore water.  This is not a brand new observation by Dr. Gan’s group has been able nicely pin it down and also investigate the influence of other soil factors like organic carbon and surface area on bacterial use of phenanthrene.

Why do we care about this?  The concept of chemical activity versus bioaccessibility hinges on this very same issue.  Chemical activity can be linked to the freely dissolved chemical concentration in pore water.  In contrast, bioaccessibility is an estimate of how much of a contaminant an organism can access. One good rule of thumb put forward by Reichenberg and Mayer (2006) is that bioaccessibility is required  when organisms can specifically access a chemical whereas chemical activity is more important for passive uptake systems.  Typically for bacteria we think of them as passive systems for polyaromatic hydrocarbons.  The toxicity of PAHs to organisms is often thought to be due to non-polar narcosis in which the PAHs disrupt the lipid membrane (nitrifiers are an important exception to this).   Based on this recent publication by Dr. Gan, we are going to need to rethink this idea. If microorganisms can specifically uptake the toxicants, then we need some sort of estimate of bioaccessibilty for microorganisms.  This will allow us to modify site specific clean up scenarios to protect biogeochemical cycling at impacted sites.

So, if you are like our lab and use HPLC technology, then you know there is an acetonitrile shortage.  Acetonitrile is a by produce of the automative industry.  As you may have heard, this industry is in free fall and as a result acetonitrile has increased in price 6 to 8 fold and normally can’t be bought.  This is a problem becuase acetonitrile is the solvent of choice for most HPLC applications.  Thus, one can think of HPLC’s as running on acetonitrile.

Luckily, I work in an academic environment so I can change solvents.  Others who need to work with certified methods are stuck and can try to save acetonitrile usage by switching to smaller columns.  If you are going to change solvents, there are two major things to consider.  The first is that other solvents like methanol absorve in the UV spectrum which can pose a problem for UV/VIS detectors.  The second is that methanol has a slightly different polarity than acetonitrile and also results in higher backpressure.  Luckily, Thermo has posted an excellent user guide for replacing acetonitrile with other solvents. Today we are going to try to replace our PAH HPLC method that is acetonitrile based with a methanol based method. PAHs are detected using a fluorescence detector so the UV absorbance of methanol is not a big concern.  Hopefully it will go well and tommorrow I can post the results in case others need to change their PAH methods over.

It is funny that as scientists we normally don’t primarily think of ourselves as consumers and thus are somewhat disconnected from the overall economy.  The acetonitrile shortage is a good example of how interconnected our economy actually is.

Recently the University of Saskatchewan has decided that it needs to increase its graduate enrollment substantially.  It has asked the Department of Soil Science to have 50 graduate students enrolled in its graduate programs. On average the University has a ratio of 2 M.Sc. for every 1 Ph.D.  Currently in Soil Science, we have 38 graduate students, 19 M.Sc. and 19 Ph.D.  There are 12 tenured faculty in the department which means that the University expects the Department to supervise on average 4.1 students (Appendix D:  CGSR Strategic Plan).  This means that we need to teach an additional 12 students.

It has been suggested that we radically need to re-think our teaching strategies.  That is, we should offer a strong non-thesis based program which would be completely course based.  In my opinion, this is not a great option.  Graduate students are not trained but rather mentored.  When I consider my relationships with Brian, Alexis, Wai, Sam, Kyle, and Juliska, I am reminded of my martial arts training.  A black belt is merely an indication that you are a serious student.  Similarily, my Ph.D. merely indicates that I have learned how to learn.  Thus, I try to train my students how to learn.  In turn, they try to train me how to think.

This is why graduate students are so valuable to society, to companies and to the world.  Not because they are highly trained soil scientists and toxicologists.  But rather because they have learned how to grasp difficult concepts, apply original solutions and then evaluate these solutions through sophisticated and rigorous analyses.

It is difficult to imagine how one would do this in a course based approach. Each one of the students who works with me is different.  They are all very smart and creative.  But each in their own way.  This is not a trivial motherhood statement but rather a close observation of how my students achieve their Ph.D.  A graduate student typically faces a data storm. By this I mean a vast amount of conflicting data points that overlap and need to be organized into a coherent story.  Alone they face the unknown and somehow craft a conceptual masterpiece from disparate data.  I am always reminded of Mickey Mouse in Fantasia as the Sorcerer’s Apprentice.  Every one of my students is a Sorcerer’s Apprentice.  My job is to make sure the broom doesn’t run amok.

I know of no way to teach this in a course.  Instead, what is needed is a dedicated, very smart student and a dedicated, very smart professor.  Then, one has a good graduate experience and everyone learns something, society, student and professor.   I don’t think we should change this.  We have great students and professors in our department.  We are one of the best Departments of Soil Science in the country and internationally recognized.  Lets not mess up a good thing.

Approximately 50 soil scientists were brought together by Greg Henry to participate in the International Polar Year Project, Climate Change Effects on Canadian Arctic Tundra Ecosystems; Interdisciplinary and Multi-Scale Assessments.  Our goal in this project was to provide an assessment of Canadian Arctic soils.

About half Canada has permafrost, permanently frozen soil, and this permafrost dramatically changes how soils, plants and animals respond and contribute to climate change. We are investigating how these soils differ from one another in their responses and why they differ.  A key response is the storage of carbon because these permafrost soils hold 25% of the carbon sequestered in the terrestrial biosphere.  As a group, we have explored how these soils store, release and process carbon.  We knew that these carbon storage processes were controlled by nitrogen and thus, we also explored how nitrogen processing differed.  Our work in 2008, highlighted the ultimate importance of water for these soils.  Water affected how plants provided nitrogen to the soil; water affected how large organisms in the soil freed up this nitrogen and carbon for further storage and water affected how these soils released greenhouse gas back to the atmosphere.  Most surprisingly, we found that soils that had little water were most susceptible to climate change.  Our work highlighted that the vast desert that sits on the top of Canada, the Polar Desert, may be rapidly changing in response to climate change.  The sustainability of this change is not yet known and we worry that many fragile Arctic soils, such as the dunes and deserts, may be under threat.

The nitrogen cycle, controls carbon sequestration.  A key component of the nitrogen cycle in the Arctic is bryophytes which provide ammonia, which in turn is transformed to nitrate and used by plants.  As expected, bryophytes were controlled by moisture and needed phosphorus for maximum efficiency.  However, the normal organisms convert the nitrogen provided by bryophytes to a form available to the rest of the ecosystem, were absent.  The organisms, autotrophic ammonia oxidizers, were found at very low levels across the Arctic.  Instead, it appears that heterotrophic or archael ammonia oxidizers are the critical organisms in Canada’s Arctic.  This is important because heterotrophic and archael oxidizers respond very rapidly to increases in temperature whereas autotrophic oxidizers do not.  Thus, work in 2009 will focus on identifying what is the key group as this will be essential for predictions on how Arctic systems respond to climate change.

Most of Canada’s carbon is locked in the Arctic soils.  A key activity in 2008 was the collection of samples we need to estimate the Arctic soil carbon storage and if it was declining or increasing over the last 20 years.  This was a two step process, first we estimated soil carbon losses and/or gains over a long time period and then we estimated the variability associated with carbon storage in these soils.  These results are currently being linked to the Canadian Soil Carbon project.

All of our research teams report the same dependency in Arctic systems.  Response and contribution to climate change is highly dependent on plant species present in that soil. In other words, while moisture and temperature are important and have over the long term altered plant communities and soil types.  Current responses are linked intimately to the plant present at the sampling location.  As a group, we wish to highlight this observation as it suggests that invasive species in Arctic climes may have a significant influence on carbon cycling in Canada’s Arctic.

Contaminants become “trapped” in soil over time because of various chemical and biological processes (e.g., aging, weathering, sequestration, adsorption, degradation, etc.). Trapped contaminants are not readily available for uptake into soil organisms and do not cause even if it is detectible by chemical methods. Therefore, contaminant concentration can exceed established safety standards but represent minimal risk to soil organisms if the contaminant is trapped.

Growing earthworms in contaminated soil is a common method to evaluate the toxic effects of contaminants in soil; however, this process is time consuming. Alternatively, contaminant concentration in soil can be determined by chemical extraction and analysis. This approach is fast, but harsh chemical extractions often over estimate the risk because contaminants trapped in soil may be extracted as well thereby suggesting danger when there is none. Arguably, it is better safe (i.e., over estimating potential danger) than sorry; however, cleaning up soils that pose no actual danger wastes resources that can be used to remediate real problem areas. We designed the Simulated Earthworm Gut (SEG) to mimic the earthworm’s gastrointestinal fluid composition under the theory that soil contaminants that are extractable by the SEG would be representative of the contaminant exposure that an earthworm would experience.

Wai Ma

Petroleum hydrocarbons (PHC) are the most common type of pollutant in polar regions.  The occurrence of PHC spills has a widespread geographic distribution throughout the Canadian Arctic and Circumpolar North, as well as several reported spills at various Antarctic research stations primarily located along the coast of Antarctica.  Due to the widespread and common occurrence of PHC spills in polar regions, much effort has been put forth in the area of bioremediation in cold regions.  As the technology emerges for cleaning up these contaminated sites, new questions associated with the clean up of these sites also arises.  How clean is clean enough?  What is the most sensitive part of the ecosystem?  What biological activity should be monitored to ensure that the ecosystem is being protected?  Do the environmental properties associated with polar regions increase the sensitivity of the ecosystem?  The ecotoxicity of petroleum hydrocarbon spills in polar regions is a growing concern and thus is a focal point for soil toxicology research in our lab group.

The environmental conditions that may increase the sensitivity of polar ecosystems to contaminants include sub-zero temperatures and limited liquid water content.  In polar regions, the amount of liquid water in the soil varies dramatically with the change in soil temperature.  However, even when the soil is frozen, a small amount of liquid water remains in the soil, which allows microorganisms living in the soil to remain biologically active.  The activity of these microorganisms is important, as they supply the nutrients required for plant growth, plants in turn supplies the food for primary consumers, and primary consumers supply the food for secondary consumer.  Therefore, you can see that if there are detrimental effects to soil microorganisms, the effects could manifest themselves up the food chain.  Thus it is important to protect the very basic function and structure of the soil ecosystem. We evaluated the toxicity of PHC soil contamination at an Antarctic research station by examining the effects on microorganisms.  We found that the most sensitive indicator of soil contamination was community composition (the number of different species living in the soil), followed by soil respiration and nitrification activity.  Changes in liquid water content did not seem to affect the toxicity of PHC to the soil microorganisms but it did increase the variability of the measured parameters.

Alexis Schafer