Archives for category: scientific life article

After a long hiatus, I have returned to Ground to Sky! I have been very busy, dealing with finalising two research publications and spending every lunchtime in the university music practice rooms but now I am pleased to return to this blog. In this article I will provide a brief discussion of my latest research paper to be published. The (open access) paper is available online here.

The work that I will describe took place during my PhD and was located at West Sedgemoor in the (currently terribly flooded) Somerset Levels and Moors. This land is very low lying, and floods every winter as it is part of the floodplain of the River Parrett. This seasonal cycle creates a unique habitat for wetland birds, and the site is managed by the RSPB for their conservation. West Sedgemoor is a system of small fields that are separated by a series of interconnected drainage ditches. These are managed by the RSPB to ensure that the conditions are always good for wetland birds. Part of the management of West Sedgemoor involves short term grazing during the autumn months by young beef cattle. As part of my study into the greenhouse gas emissions from these seasonally waterlogged peatlands, I was interested to see how the cattle’s urine stimulated production of greenhouse gases inside the soil and their emission as the field went from dry to flooded.


West Sedgemoor

To measure the greenhouse gas emissions (I was looking at carbon dioxide, CO2, methane, CH4 and nitrous oxide, N2O), I used ‘flux chambers’. These are boxes that are dug into the soil. A lid is put on the box and you wait a while for the gas to accumulate inside the box and take samples during this time. You can then calculate the emission of the gas from the rate of change of the gas inside the box. To measure greenhouse gases in the soil, I used ‘soil atmosphere collectors’. These are silicone tubes that are porous. Air from in the soil moves into these collectors as if they were a large soil pore and you can then take samples from the air inside through a cap accessible from the surface. Dipwells were used to measure the depth of the water-table from the surface.


Equipment in the field.

Before we could start sampling, we needed some cattle urine. Although cattle were to be loose in the field at the time of sampling, we did not want them getting close to the equipment and actually we didn’t want them to pee near it either! For a controlled experiment, we needed to be sure that every plot (with box, soil atmosphere collector and dipwell) received the same amount of urine. This would be impossible letting the cows loose in the area, so we used urine from cows at the University of Reading farms and fenced the equipment away from the cows in the field. There were ten plots, five to be treated with the urine and five to act as controls and be treated only with water. This allowed us to be sure that it was the urine that caused any changes in the soil and not just the act of the soil getting wet. The experiment ran between September and November in 2010.


This graph shows the effect of cattle urine and water application on CO2 emissions. There was a large emission of CO2 from the urine treated plots on the day that the cattle urine was applied. This is due to ‘hydrolysis’ of the urea in the urine when it impacts the soil. Bacteria make an enzyme called ‘urease’ which is found very commonly in soils and is catalyses the hydrolysis process. Despite this initial CO2 release, there was not much increase in CO2 due to the urine addition over the full period and there was no significant difference at all in CO2 in the soil atmosphere between urine treated and water treated plots.


Here we look at the methane in the cattle urine plots and can see there was a substantial reduction in the methane a few days after applying urine. We are not sure what caused this; it is a very unusual finding. It happened in 3 of the 5 urine treated plots and none of the control plots. Overall, however, adding cattle urine increased the amount of methane that came out of the soil during the experiment. As you can see, the control plots remained sinks of methane – that is, soil bacteria were taking methane from the atmosphere and using it to metabolise. This is called methane oxidation. In the plots treated with urine, this activity was prevented as a result of the urine contents. This supports other studies for this is a known effect of adding urea to soils. Under the soil surface there was also evidence of increased methane in the urine treated soil relative to the controls.

n2oThe most profound effect of adding cattle urine to the peat soil was shown for nitrous oxide, N2O. Here we see that throughout the experiment, the urine caused large increase in N2O compared to the control. This peaked 12 days after application, following rainfall. This shows how important soil moisture and water-table can be in determining what happens to added nutrients in soil. Under the soil surface, the differences between control and urine treated plots were even more interesting.

n2oWhen you look at the above figure, notice the numbers on the y axis. On day 2 after the urine was applied, you could already see the difference in production of N2O in the urine treated soils. By the twelth day, the production in the control soils was dwarfed entirely, with production at 20cm depth dominating. By Day 56, the field was entirely flooded and N2O concentrations were very high. We believe that the reason why this happened so strongly at 20cm was due to the fact that the peat soil was covered by a layer of clay. Clay soils, when saturated, are not very good at letting air pass through them and therefore N2O that was produced at levels lower than 20cm, will also get trapped here.

For more information on this experiment, please see the full paper. This is only a short summary of all of the results that were presented there. But what does this mean for managing greenhouse gases in peat soils? Well, N2O and CH4 emissions will get worse after cattle have been on the field and they will get especially worse if the field then floods. This implies that if you are concerned about the greenhouse gas balance of the field, grazing cattle earlier rather than later is likely to reduce the emissions after the field floods. However, there are far more things to balance than just the greenhouse gas emissions; for example, managing the feed supply for the cattle, managing the field grass level and, in the case of RSPB West Sedgemoor, managing the land for wetland birds. Balancing all of these demands and best practice is never an easy task and will require a carefully considered compromise.

I will write again at Ground to Sky shortly, and will attempt to reduce the long time span between blog entries. Next time, I will write about using trace gases to help us to understand where greenhouse gas emissions come from, in particular the use of carbon monoxide as a tracer for fossil-fuel carbon dioxide in cities.

No matter where you are in your research from starting out and seeking the gap in the knowledge, to rounding off that last few touches to a journal article, there will come a time when your desk looks like this.


Perhaps your desk doesn’t look like this, and you are tidy in the way you read papers, perhaps reading them all on digital devices (honourable undertaking that I haven’t yet mastered – I dislike sitting down to read at length if the thing I’m reading is not printed in black on white paper). But no matter how you read, or what your desk looks like, we all reach the point where the mountain accumulates and threatens to bury you under an endless web of “author publications,” “paper citations” and “cited by.” Here follows a few pointers from my experience on literature searching, reading journal articles and citation management.  It’s really advice for beginning environmental science PhD students, but it might be valuable to others interested in research methods.

Literature searching

When embarking on a new topic, the easiest way to find information is through a keyword search. You can do this simply on abstract database sites like Web of Science. If you’re using one of these it’s worth restricting the search to the last 5 years for an initial investigation. The latest papers will tell you the state of the research environment for your chosen topic right now. They can help you identify the current knowledge gaps and by going through a few of them you can usually identify a few common papers.  By looking at the papers they all cite, you will eventually find your way to the seminal works in your field and possibly review articles.  Seminal papers (highly cited) can identify the key authors in this specialism. By looking at this author’s other work and following the “cited by” web from the seminal papers, it is easy to gain a very quick impression of the literature in your chosen field.  Review articles can be very helpful but bear in mind unless you are interested in first principles, generally the more recent a review article, the more useful it will be to new research.

When literature searching in an expansive topic, the question will soon arise “how far back in time is too far back?” and/or “how remotely related to my research is too remotely related?” The days of limited access and hidden texts in vaults is gone. Today scientists have easy access to reams of information dating back to the turn of the 20th century and beyond.  For an initial literature search, I would advise not casting the net too far back.  In the early stages of a project, the most important thing you can do is find out what people are doing right now, and how your proposed project can fit in to the current body of literature.  When you are deeper into your project, perhaps devising methodologies for experimentation and statistical analysis this is when older/less related studies can be helpful.  At these stages, keyword searching for specific techniques can be very useful, and don’t discount the use of textbooks and manuals.  During my PhD viva, I was accused of re-inventing the wheel somewhat when I failed to cite papers from the late 1980s and early 1990s that had used a similar technique.  This was not out of disrespect, it was due to not looking far enough back down the chain of literature to identify these early papers.  This is how sometimes a reliance on the most recent papers can catch you out – if the papers do not cite these older methodologies and results then how will you find out about them?  I have learnt to cast the net wider and further back when considering experimental design by other researchers in a given field.  In the latter stages of a research project, seeking out comparable results and items to discuss can easily turn into yet another expansive search. In my PhD, I ended up citing papers from atmospheric chemistry and microbiology sources, despite my main focus being soil physics.  It’s easy to forget in your specialism that environmental science is a systems science subject and as such you may need to draw in discussion from a wider range of source material than you might have initially thought.

Finally DON’T restrict your literature search to the peer-reviewed journals. There is a wealth of information to be found online, using Google (consultancy reports, governmental reports, white papers…) and offline in books and magazine publications. Wikipedia, even though you’ll never cite it, can give you the lowdown on a new topic very quickly and provide invaluable keywords for database searches. Though you will streamline and academise your sources later on (particularly when writing up!) you shouldn’t restrict sources of information at the early stages.

Reading scientific papers

When confronted with 25 pages of tightly arranged font, equations and figures, it is excusable to feel daunted (especially if there are 20 more to follow).  The first thing to ask is: how much of this do I need to read to get the messages I need at my current research stage?  There will always be the papers that you’ll read from end to end; seminal papers, review articles (relevant sections) and the most recent work in your field.  You’ll end up coming back to many of these papers time and again, to look at different sections. So there’s really no need to go through each one with a fine tooth comb. Instead: (the following assumes you’ll always read the full abstract first – recommended in any case)

  • If you are beginning a project, focus your reading on the introduction, discussion and conclusions.  Find out the justifications for their research, the aims of their research, what they found out and what they suggest doing next.  Delving to deep into the methods and results can waste time at this stage, there’ll be a lot to get through and you can keep reference to the most useful papers to read in depth later.
  • When developing your methodologies focus on the methods sections (funnily enough). Follow method citations even if the paper itself is outside of your field. You might not be interested in the results of the cited paper at all, just the method they used to get those results. Whatever you do, don’t look at the paper and go “oh, ‘Journal of Cattle Management’, that’s not relevant to my research” when the authors have used an experimental or statistical method that could be.
  • When you have results you’ll probably want to compare them to others in the literature. You can identify results in abstracts much of the time (numerical abstracts are quite ‘in’ nowadays if you compare to abstracts from 20/30 years ago). Looking at results sections of relevant papers can also give you a great deal of information on how best to visualise your own data and the types of statistical analyses that are most useful.
  • Writing up and discussion stages.  Joy, this is the fun part. Sit yourself down and conduct another thorough literature search on your own observations. Has anybody found this before? How did they explain it? Be prepared – you might end up outside of your primary subject area again. Prepare to let this stage hoover up your time. Think of yourself as the Sherlock Holmes of the literature. Have you exhausted all leads? All possible explanations from the papers you know of?  Keep an eye on introductions, results and discussion sections.
  • Conclusions, finalising writing up, preparing papers. Well done. Now be prepared to do another literature search. Years have probably passed by now (sorry but it’s true!) since you searched your main keywords right at the beginning. You don’t want your last cited paper to be from 2 years ago. If you’ve kept abreast of the literature throughout, well done! If not, the 2013 papers in your subject area are calling you.

Citation management

I think it’s nearly enough about this. Writing about literature searching is almost as wearing as doing it. The last thing I want to do is highly recommend to all new researchers that you use a citation management system.  I let my university’s inability to provide the software for free to a student’s personal computer to put me off use of this software. As a result I wrote a thesis and managed all 300+ references manually. That is, by hand. That is, checking the reference list and the text match up and no mistakes have been made, slowly, tediously. I am still doing so in the papers relating to my PhD topic as I have no reference manager set up. Copy-and-paste is no way to go about this while sensible options are available.

Now I am staff, I have a staff computer and so I can have citation management software installed. My platform of choice is EndNote, which also has a web-based version to cite on the move!  There are also free web-based programs (i.e. Mendeley) which I haven’t used but seems pretty good to me (but anything would seem pretty good to someone who processed their PhD citations manually. If there is one thing you take away from this blog article it is not to do that).

Good luck in all your literature searching and reading endeavours!

In my next ‘life in environmental science’ article, I’ll talk about the topic I introduced earlier: environmental science as a system science discipline.  Using my research career thus far and its progress from soil to atmospheric science as an example, I’ll show how the many strands of earth and environmental science are highly interrelated. The next article on Ground to Sky will return to the science, and I will be discussing current thinking on how we can cool down our hot cities.


It was a cool but bright day in October, and I took a few steps back from my equipment to take a photograph. You can see from the picture here the variation in grass quality from the near to middle distance. The equipment had been fenced off during the cattle grazing period of the farm calendar. Ironic really, because if you look close at the photograph you can see that the grass inside the markers on the closest side is dark green. The grass here is enriched with cattle urine, that myself and my PhD supervisor had sprinkled down on the grass inside the markers with watering cans whilst bemused cattle looked on from over the electric fence.

The white boxes allowed me to measure the release of greenhouse gases from the field surface. Next to the boxes, some porous tubes were buried in the soil. By measuring the greenhouse gas concentrations inside those tubes I was able to determine some of the key biological production and physical transport processes and see how these changed when the soil had been subject to addition of the cattle urine. Along with measurements of soil chemistry, moisture and temperature, an overall picture could be developed of what heppened in that soil to create the observed greenhouse gases at the surface and how these things changed over time.

Controlled field experiments like these are crucial if we are to understand the effects that changing land use can have on the natural environment. Today, computers become ever more powerful. Processors and memory that once filled whole rooms can now fit into the palm of your hand. And scientists have capitalised on this new technology; something that was once a dream has become a feasible reality: modelling the Earth’s complex environmental system and making inferrences about how this system might change into the future. Now we move ever closer to being able to enter into a computer how many cattle we put on our field and being told the amount of fertilisation that will occur, a value for how much nitrogen might make it into nearby waterways and the effect that the cattle will have on the greenhouse gas balance of your piece of land.

This might sound highly ambitious, and it is. Yet these models continue to appear and are in continuous development and improvement; researchers validate these models using measurements from the field and look at improving understanding of processes and process interaction so that the amount of uncertainty in our estimates may be reduced (JULES land surface model, ECOSSE carbon model). Models are known by scientists to be a tool in development, a simplification of complex systems to allow us to search for missing information in the knowledge base and give us clues as to how a known process might change in the future as human activity or natural variation alters land use, biodiversity or climate. Issues arise when model data is misreported or uncertainty in the models is not adequately described. It’s important to always remember that models (particularly the largest and most complex) can have missing or inadequately described processes (Stephens and Bony, Science, 2013 (paytoview) ; Carbon Brief, 2013 (free commentary)). In order to ensure that models are telling us the right things, we need field studies (validation studies) and in order to know what to put in to the models in the first place, we need field studies (parameterisation studies). Models only tell us what they know about, which is what we input into them. A complex computer model can give us far more detail on complex processes than we would ever be able to get without them, but without field measurements to provide references and comparisons, we will never know if we’re going wrong.

In the next blog article, I’ll return to the technical articles and write a little more about city environments and their influence on the lower atmosphere. In the next insight article I will write about the importance of literature in a scientist’s life and the perils that are associated with under and over exposure to the enormous piles of reading that accumulate in the scientist’s in-tray.