• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Single cell analyses reveal contrasting life strategies of the two main nitrifiers in the ocean

Nitrification, the oxidation of ammonia via nitrite to nitrate, is a key process in marine nitrogen (N) cycling. Although oceanic ammonia and nitrite oxidation are balanced, ammonia-oxidizing archaea (AOA) vastly outnumber the main nitrite oxidizers, the bacterial Nitrospinae. The ecophysiological reasons for this discrepancy in abundance are unclear. Here, we compare substrate utilization and growth of Nitrospinae to AOA in the Gulf of Mexico. Based on our results, more than half of the Nitrospinae cellular N-demand is met by the organic-N compounds urea and cyanate, while AOA mainly assimilate ammonium. Nitrospinae have, under in situ conditions, around four-times higher biomass yield and five-times higher growth rates than AOA, despite their ten-fold lower abundance. Our combined results indicate that differences in mortality between Nitrospinae and AOA, rather than thermodynamics, biomass yield and cell size, determine the abundances of these main marine nitrifiers. Furthermore, there is no need to invoke yet undiscovered, abundant nitrite oxidizers to explain nitrification rates in the ocean.

Kitzinger K, Marchant H, Bristow L, Herbold C, Padilla C, Kidane A, Littmann S, Daims H, Pjevac P, Stewart F, Wagner M, Kuypers M
2020 - Nat. Commun., in press

A systemic overreaction to years versus decades of warming in a subarctic grassland ecosystem

Temperature governs most biotic processes, yet we know little about how warming affects whole ecosystems. Here we examined the responses of 128 components of a subarctic grassland to either 5–8 or >50 years of soil warming. Warming of >50 years drove the ecosystem to a new steady state possessing a distinct biotic composition and reduced species richness, biomass and soil organic matter. However, the warmed state was preceded by an overreaction to warming, which was related to organism physiology and was evident after 5–8 years. Ignoring this overreaction yielded errors of >100% for 83 variables when predicting their responses to a realistic warming scenario of 1 °C over 50 years, although some, including soil carbon content, remained stable after 5–8 years. This study challenges long-term ecosystem predictions made from short-term observations, and provides a framework for characterization of ecosystem responses to sustained climate change.

Walker TWN, Janssens IA, Weedon JT, Sigurdsson BD, Richter A, Peñuelas J, Leblans NI Bahn M, Bartrons M, De Jonge C, Fuchslueger L, Gargallo-Garriga A, Gunnarsdóttir GE, Marañon-Jimenez S, Oddsdóttir ES, Ostonen I, Poeplau C, Prommer J, Radujković D, Sardans J, Sigurðsson P, Soong JL, Vicca S, Wallander H, Ilieva-Makulec K, Verbruggen E
2020 - Nature Ecology & Evolution, 4: 101-108

A Bioinformatics Guide to Plant Microbiome Analysis.

Recent evidence for intimate relationship of plants with their microbiota shows that plants host individual and diverse microbial communities that are essential for their survival. Understanding their relatedness using genome-based and high-throughput techniques remains a hot topic in microbiome research. Molecular analysis of the plant holobiont necessitates the application of specific sampling and preparatory steps that also consider sources of unwanted information, such as soil, co-amplified plant organelles, human DNA, and other contaminations. Here, we review state-of-the-art and present practical guidelines regarding experimental and computational aspects to be considered in molecular plant-microbiome studies. We discuss sequencing and "omics" techniques with a focus on the requirements needed to adapt these methods to individual research approaches. The choice of primers and sequence databases is of utmost importance for amplicon sequencing, while the assembly and binning of shotgun metagenomic sequences is crucial to obtain quality data. We discuss specific bioinformatic workflows to overcome the limitation of genome database resources and for covering large eukaryotic genomes such as fungi. In transcriptomics, it is necessary to account for the separation of host mRNA or dual-RNAseq data. Metaproteomics approaches provide a snapshot of the protein abundances within a plant tissue which requires the knowledge of complete and well-annotated plant genomes, as well as microbial genomes. Metabolomics offers a powerful tool to detect and quantify small molecules and molecular changes at the plant-bacteria interface if the necessary requirements with regard to (secondary) metabolite databases are considered. We highlight data integration and complementarity which should help to widen our understanding of the interactions among individual players of the plant holobiont in the future.

Lucaciu R, Pelikan C, Gerner SM, Zioutis C, Köstlbacher S, Marx H, Herbold CW, Schmidt H, Rattei T
2019 - Front Plant Sci, 1313

Lecture series

The environment as training ground: evolution and biology of intracellular microbes

Prof. Dr Matthias Horn
Department of Microbiology and Ecosystem Science, University of Vienna, Austria
16:30 h
Eberhard Clar-Saal (2B 204), Althanstrasse 14 UZA II, 1090 Vienna

Metals and microbial respiration: the molecular basis of bioelectricity production and greenhouse gas destruction

David Richardson
University of East Anglia, Norwich Research Park, Norwich, UK
12:00 h
Lecture Hall HS2, UZA1, Althanstrasse 14, 1090 Wien

ESR as a tool to investigate environmentally persistent and short-lived radicals

Prof. Dr Marc Pignitter
Department of Physiological Chemistry, University of Vienna, Austria
16:30 h
Eberhard Clar-Saal (2B 204), Althanstrasse 14 UZA II, 1090 Vienna