• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Cultivation and genomic characterization of novel and ubiquitous marine nitrite-oxidizing bacteria from the Nitrospirales

Nitrospirales, including the genus Nitrospira, are environmentally widespread chemolithoautotrophic nitrite-oxidizing bacteria. These mostly uncultured microorganisms gain energy through nitrite oxidation, fix CO2, and thus play vital roles in nitrogen and carbon cycling. Over the last decade, our understanding of their physiology has advanced through several new discoveries, such as alternative energy metabolisms and complete ammonia oxidizers (comammox Nitrospira). These findings mainly resulted from studies of terrestrial species, whereas less attention has been given to marine Nitrospirales. In this study, we cultured three new marine Nitrospirales enrichments and one isolate. Three of these four NOB represent new Nitrospira species while the fourth represents a novel genus. This fourth organism, tentatively named “Ca. Nitronereus thalassa”, represents the first cultured member of a Nitrospirales lineage that encompasses both free-living and sponge-associated nitrite oxidizers, is highly abundant in the environment, and shows distinct habitat distribution patterns compared to the marine Nitrospira species. Partially explaining this, “Ca. Nitronereus thalassa” harbors a unique combination of genes involved in carbon fixation and respiration, suggesting differential adaptations to fluctuating oxygen concentrations. Furthermore, “Ca. Nitronereus thalassa” appears to have a more narrow substrate range compared to many other marine nitrite oxidizers, as it lacks the genomic potential to utilize formate, cyanate, and urea. Lastly, we show that the presumed marine Nitrospirales lineages are not restricted to oceanic and saline environments, as previously assumed.

Mueller AJ, Daebeler A, Herbold CW, Kirkegaard RH, Daims H
2023 - ISME J., in press

Plastics can be used more sustainably in agriculture

Plastics have become an integral component in agricultural production as mulch films, nets, storage bins and in many other applications, but their widespread use has led to the accumulation of large quantities in soils. Rational use and reduction, collection, reuse, and innovative recycling are key measures to curb plastic pollution from agriculture. Plastics that cannot be collected after use must be biodegradable in an environmentally benign manner. Harmful plastic additives must be replaced with safer alternatives to reduce toxicity burdens and included in the ongoing negotiations surrounding the United Nations Plastics Treaty. Although full substitution of plastics is currently not possible without increasing the overall environmental footprint and jeopardizing food security, alternatives with smaller environmental impacts should be used and endorsed within a clear socio-economic framework. Better monitoring and reporting, technical innovation, education and training, and social and economic incentives are imperative to promote more sustainable use of plastics in agriculture.

Thilo Hofmann, Subhasis Ghoshal, Nathalie Tufenkji, Jan Franklin Adamowski, Stéphane Bayen, Qiqing Chen, Philip Demokritou, Markus Flury, Thorsten Hüffer, Natalia P. Ivleva, Rong Ji, Richard L. Leask, Milan Maric, Denise M. Mitrano, Michael Sander, Sabine Pahl, Matthias C. Rillig, Tony R. Walker, Jason C. White, Kevin J. Wilkinson
2023 - Nature Communications Earth & Environment, 4: 332

Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta

Marine sponges are critical components of marine benthic fauna assemblages, where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont, ‘Candidatus Taurinisymbion ianthellae’, residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. ‘Candidatus Taurinisymbion ianthellae’ incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont, ‘Candidatus Nitrosospongia ianthellae’. Metaproteogenomic analyses also suggest that ‘Candidatus Taurinisymbion ianthellae’ imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

Moeller FU, Herbold CW, Schintlmeister A, Mooshammer M, Motti C, Glasl B, Kitzinger K, Behnam F, Watzka M, Schweder T, Albertsen M, Richter A, Webster NS, Wagner M
2023 - The ISME journal, 17: 1208-1223

Lecture series

CeMESS Lecture: "Intercellular interactions in the bee gut microbiome"

Waldan Kwong
Principal Investigator, Instituto Gulbenkian Ciência, Portugal
12:00 h
hybrid, UBB HS 1

DOME Lecture: "Genomes in Rhodnius prolixus symbiotic system"

Eva Nováková
Associate Professor, University of South Bohemia, Czech Republic
12:00 h
hybrid, UBB HS 1

DOME Lecture: "Phage communication: from mechanisms to ecology and evolution"

Avigdor Eldar
Associate Professor, Tel-Aviv University, Israel
12:00 h
hybrid, UBB HS 1