Our main scientific goal is to assess the role of the cost of nutrient acquisition from the environment on adaptive mechanisms that have shaped the genetic material of organisms in natural communities. Our research is centered on how the evolution of genes and proteins may be affected by the availability of elements, such as nitrogen and phosphorus, that are typically limiting in natural ecosystems and are fundamental components of nucleotides and amino acids. Previous work has indicated a pivotal role of nitrogen limitation in driving genome composition within and among species in eukaryotic lab model organisms. However, these studies, while profiting from the large sets of sequences, and accurate phylogenies, have left the question of the relevance of adaptation to nutrient availability in natural environments only partially addressed. Furthermore, despite the fundamental role of nitrogen in shaping the interdependence between ecological and evolutionary dynamics, a clear understanding of the strength of natural selection and of the type of processes involved is still lacking.
With the possibility to establish my own working group in Münster, I have focused on the relevance of the material costs of evolutionary change in natural environments and on the molecular mechanisms behind it. I am tackling these questions with a combination of several approaches, integrating my background in computational comparative genomics with experimental molecular biology on micro-organisms grown under controlled conditions in the lab, as well as on environmental samples from natural ecosystems. These are the main lines of the research I have established in our group.
Research
I) Metatranscriptomics in a biogeochemistry context
Recent advances in metagenomics and metatranscriptomics allow us to extend our understanding of the genetic basis of adaptation to environmental challenges in natural communities. The tremendous potential of this approach primarily relies on the possibility to identify pools of functional genes involved in key biogeochemical reactions directly in natural ecosystems, inferring a molecular picture of the microbial community composition and biological activity in the environment. To further test the relevance of the hypothesis that environmental Nitrogen availability is one of the drivers of genome composition, we have started exploratory work on publicly available datasets, and then designed our own experiment combining biogeochemistry with metatranscriptomics in collaboration with Prof. Dr. Harald Strauss (WWU, Münster) and with Prof. Dr. Rolf Daniel (University of Göttingen).
II) A systems biology approach to nitrogen starvation: from short term responses to experimental evolution
The use of data from natural communities has the advantage to offer a realistic picture of the dynamics affecting natural environments, however it might be difficult to interpret, due to the large number of factors that shape ecosystem evolution. In order to gain further insights, parallel to the analysis of environmental samples, we are also studying the response to nitrogen starvation under controlled laboratory conditions. We have established a continuous chemostat culture of Escherichia coli in which nitrogen availability is directly controlled over an evolutionarily relevant timescale (about 1000 generations, and over one year of running time) to study evolution in action of two clonal populations of E. coli cultivated under identical conditions, except for the different availability of inorganic nitrogen provided in the medium. For this, we collaboration with Prof. Dr. Ulrich Dobrindt, WWU Münster. Based on the genomic changes detectable during the experiment via an integrated genomics and transcriptomics approach, it will be possible to directly evaluate selection for nitrogen conservation acting in response to the different levels of nitrogen limitation.
III) Stoichiometric variation between species and within natural populations
In our previous work, we have detected a signature of environmental nitrogen availability in the interspecific divergence between plants and animals, using animals as a reference point for the comparison with autotrophs. This assumption is strongly rooted in the drastic differences in the physiology of nitrogen uptake between plants and animals: plants take up nitrogen and carbon independently from each other (inorganic nitrogen, and carbon dioxide) and build nucleotides and amino acids, while animals feed on pre-formed amino acids acquired from the diet.