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Research Feature: A comparison of nitrite producing soil bacteria
Posted: January 11, 2007
Like many of the Subsurface Biosphere IGERT students, Anne Taylor is enthusiastic about combining different scientific disciplines. She is now working on her PhD in environmental engineering, but had previously earned an MS in soil science and worked as a research assistant in the OSU microbiology department. In April 2006, Anne and her MS advisor, Peter Bottomley, published a comparison study on nitrite producing soil bacteria. In this short web interview, Anne describes the project and some of the lessons it taught her about conducting research in the subsurface biosphere.
What was your research project about?
Our project focused on two genera of bacteria that convert ammonia into nitrite. Most of what we know about this step in the nitrogen cycle, called ammonia oxidation, comes from one species of bacteria, called Nitrosomonas europaea. It is kind of a lab weed; it grows fast and can be cultured readily so it is used in a lot of laboratory experiments. But the genus Nitrosomonas is not that common in the environment. Instead, a different genus of ammonium oxidizing bacteria, one that is less efficient in the lab, dominates in natural soils. It is called Nitrosospira. So, the main goal of this project was to run a comparison of the two types of bacteria when they are grown in whole soil. A secondary goal was to develop procedures for working with the bacteria in whole soil. Most lab experiments are conducted in solution or soil slurry – we wanted to work with the bacteria in conditions that were more similar to the field and were moist rather than wet slurry.
Why is it important to understand this step of the nitrogen cycle?
Ammonia oxidizing bacteria are important in natural and engineered systems. In waste water treatment they begin the process of converting the nitrogen in the waste water stream to N2 gas which is vented back into the atmosphere. In agricultural systems ammonia oxidizing bacteria compete with crops for ammonia, an important plant nutrient. Ammonia oxidizing bacteria oxidize ammonia to nitrite and then nitrite oxidizing bacteria further oxidize nitrite to nitrate. Nitrate is readily leached from soils and into aquifers or surface waters where such an influx of nitrogen can cause an algal bloom and fouling of the water.
How did the project fit into your studies?
I worked on this project when I was a research assistant in the OSU microbiology department. It was a transition for me between finishing my master's degree in soil science and starting on my PhD in environmental engineering through the IGERT program.
This project makes me think about the importance of learning about different processes – I started in soils and am now working on biodegradation. The systems are different but there are many commonalities. I’m hoping that my experiences in different disciplines will make me more well rounded – it’s helpful to have worked in more than one system.
How were your experiments set up?
We ran our experiments in three different soils that we collected from around Corvallis. The samples were gamma-irradiated to sterilize them and kill off all the native bacteria that we were not studying. Then we ran a series of experiments with moist soil samples where we introduced Nitrosomonas europaea or Nitrosospira sp.AVand various concentrations of ammonium. Then we measured the removal of ammonium and the production of nitrite over time.
What did your experiments determine?
One thing we learned was that by working in whole soil, we could sustain reactions with the introduction of very limited substrate – an amount that would have been used up in minutes, had we run the experiment in solution rather than whole soil. That’s because the clay fraction in soils binds cations such as ammonium and releases them slowly and the bacteria can only access what’s in solution.
We also found that the Nitrosospira species had a higher affinity for ammonia. In a really limiting environment, where concentrations of ammonium were very low, Nitrosospira could still utilize the substrate. In contrast, if we increased ammonium levels, then Nitrosomonas europaea would take off. So these bacteria are sitting there and as soon as they have an advantage, they take off.
One of the implications of our study is that pure culture experiments in the lab aren’t always a good model for what’s going on in the environment – they don’t reflect the diversity of microbes that are out there and the ability of different organisms to thrive under different conditions.
What were some of the other lessons of this project?
We learned a lot of interesting things that didn’t relate to the initial goals of the project. First, we tried the experiments in several soils and, to our surprise, we couldn’t measure nitrite accumulation in some of them. For some reason nitrite was unstable in those soils, possibly reacting with organic matter that was released during the irradiation process. Also, ammonium continued to be released in the sterilized soils even though the soils had been irradiated and there were no living cells. We think this may be because there was still some residual enzymatic activity releasing nitrogen from organic material. We also had to develop some new techniques, for example we had to develop a way to measure ammonium in the soil water phase as opposed to extracting ammonium that was bound to the soil.
There are always a lot of surprises. We started out our experiments with whole soils and that caused us to run into some interesting challenges. That’s the way science is, where you end up is not where you thought, but it’s interesting all the same.
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