Project A01

Direct and indirect effects of multiple stressors in freshwater ecosystems on microbial parasites and scavengers

Hypothesis 1 ARC 2 AquaFlow ExStream Viruses Bacteria

Project Summary

Freshwater ecosystems can be exposed to multiple stressors over time, some of them being imposed due to natural (e.g. seasonal) fluctuations, others due to human activity. While the effects of stressors on microbial community composition has been investigated for several freshwater ecosystems, the resulting impacts on microbial interactions including virus-host dynamics remains unexplored. Here, we propose to investigate the dynamics and interactions of microbial parasites, including viruses and microbial scavengers, and their potential hosts when exposed to multiple stressors in freshwater systems.

We will be part of the CRC’s central experiments in the AquaFlow and ExStream systems that are both populated by a variety of different forms of life. Three major stressors, temperature, salinity and hydrology, and their combinations will be used at different intensities to test the two following specific hypotheses: (SH A01-1) Eukaryotic viruses are heavily but indirectly affected by stressor increase and decrease, i.e. through the modification and abundance of their hosts, while (SH A01-2) Prokaryotic viruses (phages), microbial scavengers will strongly rely on biotic interactions with their hosts but their composite relative abundance in the ecosystem is stable throughout stressor increase and release.

To test for these hypotheses, we will leverage state-of-the-art genome-resolved metagenomics coupled to transcriptomics over time, stressor intensities and stressor combinations, whose respective experiments are carried out within project Z02. These data will be accompanied by quantitative PCR of specific 16S rRNA genes to determine accurate fluctuations of populations arising from stressors. The anticipated results create a generic understanding of the effect of multiple stressors on microbial parasites and scavengers.

PhD topic(s)

Tom Lennard Stach (University of Duisburg-Essen)

Thesis: Response of aquatic microbiomes and viromes to multiple stressors

Prokaryotes and viruses represent a major part of biodiversity in stream ecosystems and are essential for food webs impacting all trophic levels. However, little is known about multiple stressor effects on microbial interactions, including microbial parasites and virus-host dynamics.

This PhD project focuses on the dynamics of microbial parasites and scavengers under influence of multiple stressors in freshwater stream ecosystems. Targeted biological entities are eukaryotic and prokaryotic viruses and bacteria belonging to the Candidate Phyla Radiation (CPR). The latter are known for their parasitic, symbiotic and scavenging lifestyle lacking necessary metabolic pathways encoded in their small genomes. DNA and RNA of over 450 sediment samples from AquaFlow and ExStream systems will be sequenced covering various stressor combinations. These samples will be analyzed using genome-resolved metagenomic and transcriptomic approaches to decipher the community dynamics and interactions with host organisms. Relative abundance statistics of CPR bacteria will be normalized using qPCR measurements. Anticipated results of this project will give important insight into a substantial fraction of the biodiversity of stream ecosystems under influence of multiple stressors.


First Supervisor:
Prof. Dr. Alexander Probst (University of Duisburg-Essen, Group for Aquatic Microbial Ecology (GAME))
Second Supervisor:
Prof. Dr. Florian Leese (University of Duisburg-Essen, Aquatic Ecosystem Research)
Dr. Andreas Nocker (Rheinisch-Westfälisches Institut für Wasserforschung gemeinnützige GmbH IWW, Mülheim an der Ruhr)

Overview of all doctoral researchers