• Centre for Microbiology and Environmental Systems Science

  • CUBE - Computational Systems Biology

  • DOME - Microbial Ecology

  • EDGE - Environmental Geosciences

  • TER - Terrestrial Ecosystem Research


Latest publications

Tree Species and Epiphyte Taxa Determine the “Metabolomic niche” of Canopy Suspended Soils in a Species-Rich Lowland Tropical Rainforest

Tropical forests are biodiversity hotspots, but it is not well understood how this diversity is structured and maintained. One hypothesis rests on the generation of a range of metabolic niches, with varied composition, supporting a high species diversity. Characterizing soil metabolomes can reveal fine-scale differences in composition and potentially help explain variation across these habitats. In particular, little is known about canopy soils, which are unique habitats that are likely to be sources of additional biodiversity and biogeochemical cycling in tropical forests. We studied the effects of diverse tree species and epiphytes on soil metabolomic profiles of forest floor and canopy suspended soils in a French Guianese rainforest. We found that the metabolomic profiles of canopy suspended soils were distinct from those of forest floor soils, differing between epiphyte-associated and non-epiphyte suspended soils, and the metabolomic profiles of suspended soils varied with host tree species, regardless of association with epiphyte. Thus, tree species is a key driver of rainforest suspended soil metabolomics. We found greater abundance of metabolites in suspended soils, particularly in groups associated with plants, such as phenolic compounds, and with metabolic pathways related to amino acids, nucleotides, and energy metabolism, due to the greater relative proportion of tree and epiphyte organic material derived from litter and root exudates, indicating a strong legacy of parent biological material. Our study provides evidence for the role of tree and epiphyte species in canopy soil metabolomic composition and in maintaining the high levels of soil metabolome diversity in this tropical rainforest. It is likely that a wide array of canopy microsite-level environmental conditions, which reflect interactions between trees and epiphytes, increase the microscale diversity in suspended soil metabolomes.

Gargallo-Garriga A, Sardans J, Alrefaei AF, Klem K, Fuchslueger L, Ramírez-Rojas I, Donald J, Leroy C, Van Langenhove L, Verbruggen E, Janssens IA, Urban O, Peñuelas J
2021 - Metabolites, 11: Article 718

Responses of grassland soil CO2 production and fluxes to drought are shifted in a warmer climate under elevated CO2

As the climate warms, drought events are expected to increase in intensity and frequency, with consequences for the carbon cycleSoil respiration (Rs) accounts for the largest flux of CO2 from terrestrial ecosystems to the atmosphere. While the drought responses of Rs have been well studied, it is uncertain how they will be modified in a future world, when higher temperatures will occur in combination with elevated atmospheric CO2 concentrations. In a global change experiment in a managed temperate grassland, we studied drought and post-drought responses of Rs dynamics under current versus likely future conditions (+3°, +300 ppm CO2). Furthermore, to understand the soil CO2 production (Ps) and transport dynamics underlying Rs fluxes we continuously monitored in-situ soil CO2 concentrations across the soil profile. Our results show that Rs was higher and that drought-induced reductions in Rs were delayed under future compared to current conditions. Peak drought reductions and post-drought pulses of Rs were more pronounced in the future scenario. Annual Rs was reduced by drought only under current but not under future conditions. An in-depth analysis of soil CO2 gradients and fluxes across the soil profile showed that elevated CO2 stimulated Ps primarily in the main rooting horizon and that warming affected Ps also in deeper soil layers. We found that both in the current and the future scenario drought led to the strongest reductions of Ps in the most productive soil layers, which also exhibited the largest depletion of soil moisture. We conclude that a future warmer climate under elevated CO2 amplifies soil CO2 production and efflux and their peak drought and post-drought responses, but delays the onset of the drought responses and thereby eliminates the overall drought effect on annual soil CO2 emissions.

Reinthaler D, Harris E, Richter A, Herndl M, Pötsch E, Wachter H, Bahn M
2021 - Soil Biology and Biochemistry, 163: Article 108436

Successional dynamics and alternative stable states in a saline activated sludge microbial community over 9 years.

Microbial communities in both natural and applied settings reliably carry out myriads of functions, yet how stable these taxonomically diverse assemblages can be and what causes them to transition between states remains poorly understood. We studied monthly activated sludge (AS) samples collected over 9 years from a full-scale wastewater treatment plant to answer how complex AS communities evolve in the long term and how the community functions change when there is a disturbance in operational parameters.
Here, we show that a microbial community in activated sludge (AS) system fluctuated around a stable average for 3 years but was then abruptly pushed into an alternative stable state by a simple transient disturbance (bleaching). While the taxonomic composition rapidly turned into a new state following the disturbance, the metabolic profile of the community and system performance remained remarkably stable. A total of 920 metagenome-assembled genomes (MAGs), representing approximately 70% of the community in the studied AS ecosystem, were recovered from the 97 monthly AS metagenomes. Comparative genomic analysis revealed an increased ability to aggregate in the cohorts of MAGs with correlated dynamics that are dominant after the bleaching event. Fine-scale analysis of dynamics also revealed cohorts that dominated during different periods and showed successional dynamics on seasonal and longer time scales due to temperature fluctuation and gradual changes in mean residence time in the reactor, respectively.
Our work highlights that communities can assume different stable states under highly similar environmental conditions and that a specific disturbance threshold may lead to a rapid shift in community composition. Video Abstract.

Wang Y, Ye J, Ju F, Liu L, Boyd JA, Deng Y, Parks DH, Jiang X, Yin X, Woodcroft BJ, Tyson GW, Hugenholtz P, Polz MF, Zhang T
2021 - Microbiome, 1: 199

Lecture series

CMESS Lecture: "Biogeochemical Fe cycling with a focus on physiology, ecology and environmental consequences of iron-oxidizing bacteria"

Prof. Dr. Andreas Kappler
Professor for Geomicrobiology, University of Tübingen, Germany
12:00 h

EDGE Lecture: "How iron oxidation can direct the fate of organic matter and iron mineral composition in redox dynamic soils"

Prof. Aaron Thompson
Department of Crop & Soil Sciences, University of Georgia, USA
17:00 h