The research interests in the lab are in Microbial Ecology and Environmental Microbiology. Microbes in nature live in consortia and communities interacting in many different ways. These interactions are important for the microbes as well as for the functioning of the ecosystem. Research in the lab focuses on examples of interactions to elucidate if and how these interactions profit and/or harm the microbes and the environment. Profit to the environment is for example the potential for bioremediation and harm to the environment the production of high amounts of nitrate by nitrification.
Ammonia oxidation is the first and rate-limiting step in nitrification - the oxidation of ammonium to nitrate. Nitrate is well known to cause algal blooms and contaminations in the ground water.
Niche differentiation between Ammonia-oxidizing Archaea versus Ammonia-oxidizing Bacteria
We investigate the interactions between Ammonia-oxidizing Archaea (AOA) and Bacteria (AOB), two groups of microbes that belong to two different domains of life but have basically the same metabolism. Because the AOA have been discovered only recently there is a lot of discussion about the question: “Who is responsible for the ammonia oxidation in the environment - AOA, AOB or both?”. We investigate this question using a combination of cultivation dependent (chemostats and in-situ techniques) and cultivation independent methods. Our focus is all kinds of freshwater environments from oligotrophic to hyper-eutrophic lakes.
Sequencing of the Genome of Nitrosomonas sp. Is79
The AOB Nitrosomonas sp. Is79 has been isolated from freshwater sediment in the Netherlands and is adapted to low ammonium concentrations in the environment. Recently the whole genome of this strain became available. Based on the whole genome we will investigate the adaptation of Nitrosomonas sp. Is79 to low ammonium concentrations.
Interactions between Ammonia oxidizers and Heterotrophs
Among scientists working with Ammonia-oxidiziers it is well know that ammonia oxidizing enrichment cultures grow much better than pure cultures. We investigate the identity of the heterotrophs that have positive impacts on ammonia oxidizers. Furthermore we will use proteomic and genomic methods to investigate the impact of heterotrophs on the ammonia oxidizers using the AOB Nitrosomonas sp. Is79 and the enrichment culture G5-7 as models.
Culturing the "unculturables"
Up to now only 1% of all microbes in the environment have been cultivated in the laboratory. We use a combination of in-situ and lab methods to cultivate new microbes from different environments. This technique has been used to cultivate bacteria from freshwater pond sediment, the FRC area in Oak Ridge, TN and the wastewater treatment plant in Hamilton, OH. We will continue using the diffusion chamber to cultivate new bacteria with a focus on bacteria that can degrade cellulose.
Uranium in bacterial consortia
Uranium is a highly toxic heavy metal. Bacteria from uranium contaminated subsurface sediment in Oak Ridge (TN) have been isolated and are investigated for their ability to grow in the presence of heavy metals as pure and mixed cultures. Consortia show much better growth than pure cultures in the presence of heavy metals. The Joint Genome Institute has recently sequenced several of these strains and we will use the information to further investigate the mixed cultures in comparison to the pure cultures using a combination of genomic and proteomic methods to elucidate what makes this interaction work.