• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Atypical enteropathogenic are associated with disease activity in ulcerative colitis.

With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic (aEPEC) with IBD disease activity. The presence of diarrheagenic was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins and distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.

Baumgartner M, Zirnbauer R, Schlager S, Mertens D, Gasche N, Sladek B, Herbold C, Bochkareva O, Emelianenko V, Vogelsang H, Lang M, Klotz A, Moik B, Makristathis A, Berry D, Dabsch S, Khare V, Gasche C
2022 - Gut Microbes, 1: 2143218

Generation of Reproducible Model Freshwater Particulate Matter Analogues to Study the Interaction with Particulate Contaminants.

Aquatic fate models and risk assessment require experimental information on the potential of contaminants to interact with riverine suspended particulate matter (SPM). While for dissolved contaminants partition or sorption coefficients are used, the underlying assumption of chemical equilibrium is invalid for particulate contaminants, such as engineered nanomaterials, incidental nanoparticles, micro- or nanoplastics. Their interactions with SPM are governed by physicochemical forces between contaminant-particle and SPM surfaces. The availability of a standard SPM material is thus highly relevant for the development of reproducible test systems to evaluate the fate of particulate contaminants in aquatic systems. Finding suitable SPM analogues, however, is challenging considering the complex composition of natural SPM, which features floc-like structures comprising minerals and organic components from the molecular to the microorganism level. Complex composition comes with a heterogeneity in physicochemical surface properties, that cannot be neglected. We developed a procedure to generate SPM analogue flocs from components selected to represent the most abundant and crucial constituents of natural riverine SPM, and the process-relevant SPM surface characteristics regarding interactions with particulate contaminants. Four components, i.e., illite, hematite, quartz and tryptophan, combined at environmentally realistic mass-ratios, were associated to complex flocs. Flocculation was reproducible regarding floc size and fractal dimension, and multiple tests on floc resilience towards physical impacts (agitation, sedimentation-storage-resuspension, dilution) and hydrochemical changes (pH, electrolytes, dissolved organic matter concentration) confirmed their robustness. These reproducible, ready-to-use SPM analogue flocs will strongly support future research on emerging particulate contaminants.

Helene Walch, Antonia Praetorius, Frank von der Kammer, Thilo Hofmann
2022 - Water Research, in press

Effect of Polymer Properties on the Biodegradation of Polyurethane Microplastics

The release of fragments from plastic products, that is, secondary microplastics, is a major concern in the context of the global plastic pollution. Currently available (thermoplastic) polyurethanes [(T)PU] are not biodegradable and therefore should be recycled. However, the ester bond in (T)PUs might be sufficiently hydrolysable to enable at least partial biodegradation of polyurethane particles. Here, we investigated biodegradation in compost of different types of (T)PU to gain insights into their fragmentation and biodegradation mechanisms. The studied (T)PUs varied regarding the chemistry of their polymer backbone (aromatic/aliphatic), hard phase content, cross-linking degree, and presence of a hydrolysis-stabilizing additive. We developed and validated an efficient and non-destructive polymer particle extraction process for partially biodegraded (T)PUs based on ultrasonication and density separation. Our results showed that biodegradation rates and extents decreased with increasing cross-linking density and hard-segment content. We found that the presence of a hydrolysis stabilizer reduced (T)PU fragmentation while not affecting the conversion of (T)PU carbon into CO2. We propose a biodegradation mechanism for (T)PUs that includes both mother particle shrinkage by surface erosion and fragmentation. The presented results help to understand structure–degradation relationships of (T)PUs and support recycling strategies.

Patrizia Pfohl, Daniel Bahl, Markus Rückel, Marion Wagner, Lars Meyer, Patrick Bolduan, Glauco Battagliarin, Thorsten Hüffer, Michael Zumstein, Thilo Hofmann, Wendel Wohlleben
2022 - Environ. Sci. Technol., in press

Lecture series

EDGE Lecture: Clustering Methods with Potential Applications in Geosciences

Prof. Claudia Plant
University of Vienna
16:45 h
2B201, UZA2

EDGE Lecture: The untapped potential of fungi for contaminant biodegradation

Dr. Lukas Wick
Helmholtz Centre for Environmental Research
12:00 h
HS 1, UBB University Biology Building

CMESS Lecture: "Role of pelagic fungi in the oceanic water column"

Federico Baltar
Associate Professor, Department of Functional and Evolutionary Ecology, University of Vienna
12:00 h
hybrid, UBB HS 1