• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Flow-through stable isotope probing (Flow-SIP) minimizes cross feeding in complex microbial communities

Stable isotope probing (SIP) is a key tool for identifying the microorganisms catalyzing the turnover of specific substrates in the environment and to quantify their relative contributions to biogeochemical processes. However, SIP based studies are subject to the uncertainties posed by cross-feeding, where microorganisms release isotopically labelled products, which are then used by other microorganisms, instead of incorporating the added tracer directly. Here, we introduce a SIP approach that has the potential to strongly reduce cross-feeding in complex microbial communities. In this approach, the microbial cells are exposed on a membrane filter to a continuous flow of medium containing isotopically labelled substrate. Thereby, metabolites and degradation products are constantly removed, preventing consumption of these secondary substrates. A NanoSIMS-based proof-of-concept experiment using nitrifiers in activated sludge and 13C-bicarbonate as an activity tracer showed that Flow-SIP significantly reduces cross-feeding and thus allows distinguishing primary consumers from other members of microbial food webs.

Kitzinger K, Mooshammer M, Schintlmeister A, Ahmerkamp S, Nielsen J, Nielsen PH, Wagner M
2020 - ISME J, in press

Technology readiness and overcoming barriers to sustainably implement nanotechnology-enabled plant agriculture

Nanotechnology offers potential solutions for sustainable agriculture, including increasing nutrient utilization efficiency, improving the efficacy of pest management, mitigating the impacts of climate change, and reducing adverse environmental impacts of agricultural food production. Many promising nanotechnologies have been proposed and evaluated at different scales, but several barriers to implementation must be addressed for technology to be adopted, including efficient delivery at field scale, regulatory and safety concerns, and consumer acceptance. Here we explore these barriers, and rank technology readiness and potential impacts of a wide range of agricultural applications of nanotechnology. We propose pathways to overcome these barriers and develop effective, safe and acceptable nanotechnologies for agriculture.

Thilo Hofmann, Gregory Victor Lowry, Subhasis Ghoshal, Nathalie Tufenkji, Davide Brambilla, John Robert Dutcher, Leanne M. Gilbertson, Juan Pablo Giraldo, Joseph Matthew Kinsella, Markita Patricia Landry, Wess Lovell, Rafik Naccache, Mathews Paret, Joel Alexander Pedersen, Jason Michael Unrine, Jason Christopher White, Kevin James Wilkinson
2020 - Nature food, 1: 416–425

Exploring the upper pH limits of nitrite oxidation: diversity, ecophysiology, and adaptive traits of haloalkalitolerant Nitrospira

Nitrite-oxidizing bacteria of the genus Nitrospira are key players of the biogeochemical nitrogen cycle. However, little is known about their occurrence and survival strategies in extreme pH environments. Here, we report on the discovery of physiologically versatile, haloalkalitolerant Nitrospira that drive nitrite oxidation at exceptionally high pH. Nitrospiradistribution, diversity, and ecophysiology were studied in hypo- and subsaline (1.3-12.8 g salt/l), highly alkaline (pH 8.9-10.3) lakes by amplicon sequencing, metagenomics, and cultivation-based approaches. Surprisingly, not only were Nitrospira populations detected, but they were also considerably diverse with presence of members of Nitrospira lineages I, II and IV. Furthermore, the ability of Nitrospira enrichment cultures to oxidize nitrite at neutral to highly alkaline pH of 10.5 was demonstrated. Metagenomic analysis of a newly enriched Nitrospira lineage IV species, “Candidatus Nitrospira alkalitolerans”, revealed numerous adaptive features of this organism to its extreme environment. Among them were a sodium-dependent N-type ATPase and NADH:quinone oxidoreductase next to the proton-driven forms usually found in Nitrospira. Other functions aid in pH and cation homeostasis and osmotic stress defense. “Ca. Nitrospira alkalitolerans” also possesses group 2a and 3b [NiFe] hydrogenases, suggesting it can use hydrogen as alternative energy source. These results reveal how Nitrospira cope with strongly fluctuating pH and salinity conditions and expand our knowledge of nitrogen cycling in extreme habitats.

Daebeler A, Kitzinger K, Koch H, Herbold CW, Steinberger M, Schwarz J, Zechmeister T, Karst S, Albertsen M, Nielsen PH, Wagner M, Daims H
2020 - ISME J, in press