Nitrogen cycling

The Nitrogen Cycle in Aquatic and Terrestrial Environments

This research is primarily the work of Dr. Martina Herrmann and focuses on nitrogen cycling in aquatic and terrestrial environments. (Dr. Herrmann is an independantly funded posdoctoral associate working along with the aquatic geomicrobiology group.) Aerobic and anaerobic nitrogen transformation processes are studied by combining chemical analysis, measurements of microbial activity, and techniques of molecular microbial ecology. The goals of ongoing research projects are (i) to identify key players of selected nitrogen transformation processes and (ii) to understand the environmental factors that determine their abundance, diversity, and activity. We are especially interested in the effect of plants on rhizosphere-associated processes and microbial communities in sediments and semiterrestrial soils.

Current Projects

Archaeal versus bacterial ammonia oxidation in aquatic and semiterrestrial environments – in situ relevance and regulating factors: Our understanding of nitrification has changed substantially in just the last few years. The ubiquity and high abundance of ammonia oxidizing archaea (AOA) suggest that they may be more important for nitrification than ammonia oxidizing bacteria (AOB). However, only little is known about how much AOA really contribute to in situ ammonia oxidation in different environments. In this project, we aim to assess the ecological relevance of archaeal versus bacterial ammonia oxidation, using freshwater sediments and peatland soils as model systems.

- Click here to read about the other research by the Aquatic Geomicrobiology group on Peatlands Geomicrobiology

Nitrification and communities of ammonia-oxidizing prokaryotes in simulated creek ecosystems: In this project, we use experimental flow channels to simulate small creek ecosystems with planktonic and biofilm-associated microbial communities. The goals of this project are (i) to study the influence of ammonium availability and compartment – biofilm versus water column – on the abundance and community composition of ammonia-oxidizing prokaryotes, and (ii) to follow temporal patterns of biofilm-associated nitrification activity as well as ammonia oxidizer community composition and abundance with ongoing incubation of the flow channels.

Effect of freshwater macrophytes on rhizosphere-associated microbial communities of ammonia oxidizers and nitrate reducers: We use freshwater macrophytes such as the isoetid species Littorella uniflora as model species to study interactions between macrophytes and rhizosphere-associated microbial communities in freshwater sediments with a special focus on nitrogen cycling. Littorella uniflora grows in the shallow water of oligotrophic and mesotrophic lakes. It has an extensive root system and influences the chemistry of the sediment by the release of oxygen and organic carbon compounds from the roots. Previous studies showed that L. uniflora stimulates coupled nitrification-denitrification in the rhizosphere and that the abundance of ammonia-oxidizing prokaryotes is higher in the rhizosphere of this plant species compared to unvegetated sediment. Other plant species used as model species in this project are Juncus bulbosus, species of the genus Myriophyllum, and Eriophorum angustifolium (semiterrestrial sites).

Effect of lake trophic status on seasonal and vertical patterns of microbial diversity and abundance in the water column: In this project we compare vertical and seasonal patterns of microbial diversity and abundance in an oligotrophic and a eutrophic lake in the nature reserve “Heiliges Meer” in Northwest Germany. Using fingerprinting techniques, we analyze depth-dependent changes in the community composition of bacteria and archaea and link them to vertical gradients of physico-chemical parameters. In particular, we are interested in the effect of lake trophic status on the abundance and diversity of ammonia-oxidizing bacteria and ammonia-oxidizing archaea.

Nitrogen cycling in aquifers: Microbially mediated processes leading to the formation or removal of nitrate have a strong impact on the chemistry of groundwater especially in areas with high land-use intensity. However, our knowledge of the process rates of nitrogen turnover in aquifers and of the corresponding microbial communities is still limited. We are studying microbial communities involved in nitrogen cycling in aquifers in two different study areas: (i) limestone aquifers in the Hainich area (collaboration with the project AquaDiv@Jena) and (ii) sandy aquifers situated in an area with intense agriculture in Northwest Germany (nature reserve “Heiliges Meer”). We are analyzing depth-dependent changes of water chemistry and microbial communities and activities in order to get insight into nitrification, denitrification, and anammox processes in the different aquifer systems.

Methods/Techniques Overview

Sampling: Sediment cores with or without plants are obtained using plexiglass corers. For sampling water from lake water columns or groundwater, we use a pump. Groundwater samples are obtained from a multilevel-well, which allows the sampling of water from distinct depths.

Chemical analysis: Samples are analyzed for key parameters such as temperature, oxygen, pH, conductivity, inorganic nitrogen compounds (water samples) or water content, pH, C/N, inorganic nitrogen compounds (sediment + peat samples).

Molecular analysis of microbial communities: The community composition and abundance of the microbial groups of interest is analyzed by cultivation-independent approaches using PCR-based techniques. We target functional genes such as the amoA gene encoding ammonia monooxygenase, the key enzyme of aerobic ammonia oxidation, or 16S rRNA-encoding genes. The spectrum of molecular methods includes cloning and sequencing, Denaturing Gradient Gel Electrophoresis, and quantitative PCR. In addition, we study the expression of relevant functional genes by RT-qPCR.