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Richter, S., I. Fetzer, M. Thullner, F. Centler, P. Dittrich. 2015. Towards rule-based metabolic databases: A requirement analysis based on KEGG. International Journal of Data Mining and Bioinformatics 13: 289–319.
Knowledge of metabolic processes is collected in easily accessible online databases which are increasing rapidly in content and detail. Using these databases for the automatic construction of metabolic network models requires high accuracy and consistency. In this bipartite study we evaluate current accuracy and consistency problems using the KEGG database as a prominent example and propose design principles for dealing with s...
Steffen, W., K. Richardson, J. Rockström, S.E. Cornell, I. Fetzer, E.M. Bennett, R. Biggs, S.R. Carpenter, W. De Vries, C.A. De Wit, C. Folke, D. Gerten, J. Heinke, G.M. Mace, L.M. Persson, V. Ramanathan, B. Reyers, S. Sörlin. 2015. Planetary boundaries: Guiding human development on a changing planet. Science 347: 736, 1259855
The planetary boundaries framework defines a safe operating space for humanity based on the intrinsic biophysical processes that regulate the stability of the Earth system. Here, we revise and update the planetary boundary framework, with a focus on the underpinning biophysical science, based on targeted input from expert research communities and on more general scientific advances over the past 5 years. Several of the boundar...
Lucas, R., A. Kuchenbuch, I. Fetzer, H. Harms, S. Kleinsteuber. 2015. Long-term monitoring reveals stable and remarkably similar microbial communities in parallel full-scale biogas reactors digesting energy crops. FEMS Microbiology Ecology 91(3) DOI: 10.1093/femsec/fiv004
Biogas is an important renewable energy carrier. It is a product of stepwise anaerobic degradation of organic materials by highly diverse microbial communities forming complex interlinking metabolic networks. Knowledge about the microbial background of long-term stable process performance in full-scale reactors is crucial for rationally improving the efficiency and reliability of biogas plants. To generate such knowledge, in...
Glaser, K., A. Kuppardt, J. Boenigk, H. Harms, I. Fetzer, A. Chatzinotas. 2015. The influence of environmental factors on protistan microorganisms in grassland soils along a land-use gradient. Science of the Total Environment 537: 33–42
In this study, we investigated the effect of land use intensity, soil parameters and vegetation on protistan communities in grassland soils. We performed qualitative (T-RFLP) and quantitative (qPCR) analyses using primers specifically targeting the 18S rRNA gene for all Eukarya and for two common flagellate groups, i.e. the Chrysophyceae and the Kinetoplastea. Both approaches were applied to extracted soil DNA and RNA, in or...
Fetzer, I., K. Johst, R. Schawea, T. Banitz, H. Harms, A. Chatzinotas. 2015. The extent of functional redundancy changes as species’ roles shift in different environments. Proceedings of the National Academy of Sciences, USA 112: 14888–14893
Assessing the ecological impacts of environmental change requires knowledge of the relationship between biodiversity and ecosystem functioning. The exact nature of this relationship can differ considerably between ecosystems, with consequences for the efficacy of species diversity as a buffer against environmental change. Using a microbial model system, we show that the relationship can vary depending on environmental conditio...
Journal / article
Krohn, S., S. Boehm, C. Engelmann, J. Hartmann, A. Brodzinski, A. Chatzinotas, K. Zeller, D. Prywerek, I. Fetzer, T. Berg. 2014. Application of qualitative and quantitative real-time PCR, direct sequencing, and terminal restriction fragment length polymorphism analysis for detection and identification of polymicrobial 16S rRNA genes in ascites. Journal of Clinical Microbiology 52(5): 1754-1757.
Qualitative and quantitative 16S rRNA gene-based real-time PCR and direct sequencing were applied for rapid detection and identification of bacterial DNA (bactDNA) in 356 ascites samples. bactDNA was detected in 35% of samples, with a mean of 3.24 log copies ml(-1). Direct sequencing of PCR products revealed 62% mixed chromatograms predominantly belonging to Gram-positive bacteria. Terminal restriction fragment length polymor...
Gharasoo, M., F. Centler, I. Fetzer, M. Thullner. 2014. How the chemotactic characteristics of bacteria can determine their population patterns. Soil Biology and Biochemistry 69: 346-358.
Spatial distribution of soil microorganisms is relevant for the functioning and performance of many ecosystem processes such as nutrient cycling or biodegradation of organic matters and contaminants. Beside the multitude of abiotic environmental factors controlling the distribution of microorganisms in soil systems, many microbial species exhibit chemotactic behavior by directing their movement along concentration gradients of...
Buehligen, F., P. Lindner, I. Fetzer, F. Stahl, T. Scheper, H. Harms, S. Mueller. 2014. Analysis of aging in lager brewing yeast during serial repitching. Journal of Biotechnology 187:60-70.
Serial repitching of brewing yeast inoculates is an important economic factor in the brewing industry, as their propagation is time and resource intensive. Here, we investigated whether replicative aging and/or the population distribution status changed during serial repitching in three different breweries with the same brewing yeast strain but different abiotic backgrounds and repitching regimes with varying numbers of reuses...
Journal / article
Bühligen, F., P. Rüdinger, I. Fetzer, F. Stahl, T. Scheper, H. Harms, S. Müller. 2013. Sustainability of industrial yeast serial repitching practice studied by gene expression and correlation analysis, Journal of Biotechnology 168:718-728, doi:10.1016/j.jbiotec.2013.09.008
Bottom-fermenting Saccharomyces pastorianus strains driving brewing fermentation processes are usually reused several times. It is still unclear, whether the number of successions may have an impact on cell physiology prompting consequences for brewing quality. In this study, fermentation performance of up to twenty consecutive runs in a brewery was investigated. For each run mRNA expression levels of cellular marker molecu...
Koch C., I. Fetzer, T. Schmidt, H. Harms, S. Müller. 2013. Monitoring Functions in Managed Microbial Systems by Cytometric Bar Coding, Environmental Science & Technology :130108105239000, doi:10.1021/es3041048
Cytometric monitoring of microbial community dynamics can be used to estimate stability of technical microbial processes like biogas production by analysis of segregated cell abundance changes. In this study, structure variations of a biogas community were cytometrically recorded over 9 months and found to be of diagnostic value for process details. The reactor regime was intentionally disturbed with regard to substrate overlo...
Stockholm Resilience Centre is a collaboration between Stockholm University and the Beijer Institute of Ecological Economics at the Royal Swedish Academy of Sciences
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