Many people associate the term ‘microbiome’ with the human body. However, rivers and streams, too, host complex microbial communities that are essential for stable ecosystems. “In the sediment, where groundwater and river water intermix, countless microbes ensure that nitrogen and sulphur cycles function properly,” explains Alexander Probst, Professor for Environmental Metagenomics at the University of Duisburg-Essen (UDE) and Research Professor at the Research Centre One Health Ruhr of the University Alliance Ruhr.

To better understand these communities, his team examined water samples and the uppermost sediment layers from 20 North American rivers. As part of a large-scale citizen science project at Colorado State University, they generated extensive datasets from 363 samples. Using a combination of metagenomics, which reveals a community's genetic potential, and mRNA analyses, which show which genes are actually active, the researchers were able to capture the functional spectrum of the microbes in great detail.

The results revealed a striking difference: although microbes in water and sediment have similar genetic traits and perform similar metabolic functions, sediment communities are under constant stress. “They are heavily engaged in transforming sulphur and nitrogen compounds, and while doing so activate an unusually high number of stress genes – including those needed to produce heat-shock proteins,” says Dr Lennard Stach, the study’s lead author and a former doctoral student at the Research Centre One Health Ruhr. “Of course, microbes regularly respond to temperature fluctuations. However, we observe a consistent stress response across North America, regardless of location.”

“River microbiomes are highly adaptable,” concludes Probst. “However, as temperatures rise and extreme events become more frequent due to climate change, this adaptive pressure will intensify, potentially affecting the stability of entire ecosystems.”

In order to integrate rivers from other continents into the Collaborative Research Centre RESIST (CRC 1439), which is based at UDE, Dr Lennard Stach performed a research stay at Colorado State University. This collaboration revealed that the patterns observed in North American rivers are consistent with those in Germany. Here, UDE water researchers had studied stress factors such as heat and salinity in artificial mini-river ecosystems, observing similar responses in microbes.