• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Microbial community composition and hydrochemistry of underexplored geothermal waters in Croatia

In Croatia, a variety of geothermal springs with a wide temperature range and varied hydrochemical conditions exist, and they may harbor different niches for the distribution of microbial communities. In this study, 19 different sites, mainly located in central and eastern Croatia, were selected for primary characterization of spring hydrochemistry and microbial community composition. Using 16S rRNA gene amplicon sequencing, it was found that the bacterial communities that dominated most geothermal waters were related to Proteobacteria and Campylobacteria, while most archaeal sequences were related to Crenarchaeota. At the genus level, the prokaryotic community was highly site-specific and was often dominated by a single genus, including sites dominated by HydrogenophilusSulfuricurvumSulfurovumThiofaba and Nitrospira, while the most abundant archaeal genera were affiliated to the ammonia-oxidizing archaea, Candidatus Nitrosotenuis and Candidatus Nitrososphaera. Whereas the microbial communities were overall highly location-specific, temperature, pH, ammonia, nitrate, total nitrogen, sulfate and hydrogen sulfide, as well as dissolved organic and inorganic carbon, were the abiotic factors that significantly affected microbial community composition. Furthermore, an aquifer-type effect was observed in the community composition, but there was no pronounced seasonal variability for geothermal spring communities (i.e. the community structure was mainly stable during the three seasons sampled). These results surprisingly pointed to stable and geographically unique microbial communities that were adapted to different geothermal water environments throughout Croatia. Knowing which microbial communities are present in these extreme habitats is essential for future research. They will allow us to explore further the microbial metabolisms prevailing at these geothermal sites that have high potential for biotechnological uses, as well as the establishment of the links between microbial community structure and the physicochemical environment of geothermal waters.

Mitrović M, Kostešić E, Marković T, Selak L, Hausmann B, Pjevac P, Orlić S
2022 - Systematic and Applied Microbiology, in press

Impaired mucosal homeostasis in short-term fiber deprivation is due to reduced mucus production rather than overgrowth of mucus-degrading bacteria

The gut mucosal environment is key in host health; protecting against pathogens and providing a niche for beneficial bacteria, thereby facilitating a mutualistic balance between host and microbiome. Lack of dietary fiber results in erosion of the mucosal layer, suggested to be a result of increased mucus-degrading gut bacteria. This study aimed to use quantitative analyses to investigate the diet-induced imbalance of mucosal homeostasis. Seven days of fiber-deficiency affected intestinal anatomy and physiology, seen by reduced intestinal length and loss of the colonic crypt-structure. Moreover, the mucus layer was diminished, muc2 expression decreased, and impaired mucus secretion was detected by stable isotope probing. Quantitative microbiome profiling of the gut microbiota showed a diet-induced reduction in bacterial load and decreased diversity across the intestinal tract, including taxa with fiber-degrading and butyrate-producing capabilities. Most importantly, there was little change in the absolute abundance of known mucus-degrading bacteria, although, due to the general loss of taxa, relative abundance would erroneously indicate an increase in mucus degraders. These findings underscore the importance of using quantitative methods in microbiome research, suggesting erosion of the mucus layer during fiber deprivation is due to diminished mucus production rather than overgrowth of mucus degraders. View Full-Text

Overbeeke A, Lang M, Hausmann B, Watzka M, Nikolov G, Schwarz J, Kohl G, De Paepe K, Eislmayr K, Decker T, Richter A, Berry D
2022 - Nutrients, 14: Article 3802

A high-spatial resolution soil carbon and nitrogen dataset for the northern permafrost region, based on circumpolar land cover upscaling

Soils in the northern high latitudes are a key component in the global carbon cycle; the northern permafrost region covers 22 % of the Northern Hemisphere land surface area and holds almost twice as much carbon as the atmosphere. Permafrost soil organic matter stocks represent an enormous long-term carbon sink which is in risk of switching to a net source in the future. Detailed knowledge about the quantity and the mechanisms controlling organic carbon storage is of utmost importance for our understanding of potential impacts of and feedbacks on climate change. Here we present a geospatial dataset of physical and chemical soil properties calculated from 651 soil pedons encompassing more than 6500 samples from 16 different study areas across the northern permafrost region. The aim of our dataset is to provide a basis to describe spatial patterns in soil properties, including quantifying carbon and nitrogen stocks. There is a particular need for spatially distributed datasets of soil properties, including vertical and horizontal distribution patterns, for modeling at local, regional, or global scales. This paper presents this dataset, describes in detail soil sampling; laboratory analysis, and derived soil geochemical parameters; calculations; and data clustering. Moreover, we use this dataset to estimate soil organic carbon and total nitrogen storage estimates in soils in the northern circumpolar permafrost region (17.9×106 km2) using the European Space Agency's (ESA's) Climate Change Initiative (CCI) global land cover dataset at 300 m pixel resolution. We estimate organic carbon and total nitrogen stocks on a circumpolar scale (excluding Tibet) for the 0–100 and 0–300 cm soil depth to be 380 and 813 Pg for carbon, and 21 and 55 Pg for nitrogen, respectively. Our organic carbon estimates agree with previous studies, with most recent estimates of 1000 Pg (−170 to +186 Pg) to 300 cm depth. Two separate datasets are freely available on the Bolin Centre Database repository (, Palmtag et al., 2022a; and, Palmtag et al., 2002b).

Palmtag J, Obu J, Kuhry P, Richter A, Siewert MB, Weiss N, Westermann S, Hugelius G
2022 - Earth Systems Science Data, 14: 4095–4110

Lecture series

EDGE Lecture: Tracking complex mixtures in the environment and wildlife with in vitro bioassays

Prof. Beate Escher
Helmholtz Zentrum für Umweltforschung, Germany
16:30 h
Eberhard Clar Saal, UZA2

EDGE Lecture: Lead in archeological human bones/teeth reflecting historical changes in lead production

Prof. Yigal Erel
Hebrew University of Jerusalem, Israel
16:45 h
2B201, UZA2

EDGE Lecture: Where microbes meet metals, minerals and magnetism

Dr. James M. Byrne
University of Bristol, UK
16:45 h
2B201, UZA2