News

We are happy to announce that our open-source workflow for the processing of HSI-data is now public and can be cited as: Guillaume Witz, & michaelh00. (2025). guiwitz/napari-sediment: v0.4.0 (v0.4.0). Zenodo. https://doi.org/10.5281/zenodo.14932597

Go check out the tool and play around with some included demo-data! We are happy to hear your feedback.

Sediments are sources and sinks of contaminants and play an essential role in mediating pollutants across compartments of ecosystems. Following ContaSed 2021, ContaSed2025 will focus on natural and anthropogenic contaminants, primarily on emerging and already regulated organic pollutants, metallorganics, heavy metals, microplastics and algae toxins. A Session is dedicated to risk assessment, remediation and policy. We invite contributions with empirical or modelling studies to the following Sessions:

Session 1: Analytical procedures and methods for assessing sediment contamination
Session 2: From source to sink: transport and deposition of contaminants in sediments from inland and marine waters
Session 3: Assessing risks of contaminants in sediments: methodologies, ecotoxicological case studies, and risk succession
Session 4: Fate of contaminants in depositional settings
Session 5: Remediation and policy

Venue: 2 – 4 September 2025, University of Bern, Switzerland

Deadlines:

• Abstract submission: 15 April 2025
• Notification for acceptance of papers/form of presentation: 15 May 2025
• Registration and payment (presenters): 15 June 2025
• Deadline for registration: 1 August 2025

All informationen regarding the conference here.

We are happy to announce that the manuscript "Lake anoxia, primary production and algal community shifts in response to rapid climate changes during the Late-Glacial " detailing part of Stan's PhD project is availble for public review on the EGUsphere preprint repository. The paper discusses records from sediment of Lake Amsoldingen in Switzerland for the period of the Late-Glacial, showing that anoxic phases have occurred in cold phases. Additionally, it reveals primary production and algal communities to have responded already to initial relatively weak warming during Heinrich-1 (16.1 ka BP) long before the rapid Bølling warming and synchronously to rapid climatic changes during Late-Glacial times.
The preprint is available at https://egusphere.copernicus.org/preprints/2025/egusphere-2025-440/

Our latest paper demonstrates that hyperspectral imaging can detect and quantify phycocyanin in lake sediments non-destructively, thereby enabling high-resolution reconstructions of past cyanobacterial blooms and opening promising applications for ecosystem-health assessment and environmental change monitoring. 

It is available at https://doi.org/10.1007/s10933-024-00350-y

Human-induced environmental alterations via climate change, land use change, or eutrophication have pushed freshwater ecosystems beyond crucial thresholds, resulting in widespread oxygen depletion – anoxia. The consequences include biodiversity loss, water quality deterioration, and toxic algal blooms. To explore past eutrophication events over the last 12 000 years, we study lake sediments which contain a wealth of information about past environmental conditions. We scan sediment cores using high-resolution hyperspectral imaging (HI) and identify algal or biogenic pigments through their absorbance. Pigments in turn reflect changes in aquatic productivity and anoxia in the lake over time. HI produces large datasets whose analysis requires a complex computational workflow. To replace slow, proprietary software currently used for that task, the Institute of Geography (GIUB) and the Data Science Lab (DSL) have been developing an alternative Python-based software leveraging open-source libraries (dask, scikit-learn, spectral etc.) and data formats (zarr). The entire workflow is implemented as a set of interactive plugins for the fast multi-dimensional visualization software napari. In an effort to promote open-science and foster data exchange, the software is being made available on the data science platform Renku in collaboration with the Swiss Data Science Center. The project was presented at this years Data4Sciences Conference in Bern.

Stan Schouten, PhD in the Paleolimnology group, made it to the final selection with his photo "Permafrost melt and glacial retreat outpacing human expectations." in the final selection of the European Geosciences Union (EGU) photo competition. Please vote here until April 18.
We are keeping our fingers crossed!

Our limnology research on Yellowstone Lake explored the role of silicon in its biogeochemistry, analyzing dissolved Si concentrations, silicon isotope composition, and Ge/Si ratios. Despite past hydrothermal explosions, our findings showed a resilient system, with no notable impact on biogenic silica accumulation or 𝛿30Si signatures. The study emphasized the intricate dynamics of silicon cycling in lacustrine ecosystems, revealing a stable and homogeneous dissolved silicon source throughout the Holocene. The weak correlation between biogenic silica variations and changes in 𝛿30Si fossil diatom records suggested a complex interplay influenced by climate, soil formation, and shifts in weathering and diatom production. Link to Publication

Lake Victoria, East Africa, is a hotspot of young and massive species radiation. In less than 16,000 years, more than 500 species of cichlid fish have evolved. Fossil fish teeth preserved in lake sediments provide detailed insight into the process and timing of the adaptive radiation. Apparently, cichlid fish diversification is closely related to the infilling history of Lake Victoria in the Latest Pleistocene. Lake Voctoria was completely desiccated 17,000 years ago. Link to Publication