Sediment microbiomes in streams show significant responses to reduced flow velocity as a stressor resulting in altered community composition and altered gene expression. While the molecular mechanisms behind this stress response have been elucidated in A01 of Phase I of RESIST, Phase II will focus on the recovery of sediment microbiomes after severe degradation of the ecosystem, i.e., recovery from drought. We hypothesize that a complex interplay of key and keystone species along with functions stored in mobile genetic elements leads to the recovery of the system; however, we posit that frequently stressed sediments communities recover differently than those that are seldomly stressed. We further hypothesize that these asymmetric end-point communities are at least in part influenced by epigenetic imprints (detected via methylation patterns of bases of DNA in bacteria), and that dispersal plays a minor role in the recovery of the sediment microbiomes. Finally, we will establish a catalogue of protein families across river sediments from datasets available from public resources and gathered within RESIST to identify markers for ecosystems under different stressor levels. To test our hypotheses, we have designed a polyphasic approach that relies on long- and short-read metagenomics, metatranscriptomics and epigenetics. We will make use of ExStream (Z02) with highly parallelized mesocosms, test for drought effects, and sample natural environments of different stressors frequencies. In sum, we aim at generating a mechanistic understanding of how microbial communities recover after drought events by linking cellular to community-wide responses.

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.

Contact: tom.stach@uni-due.de

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)
Mentor:
Dr. Andreas Nocker (Rheinisch-Westfälisches Institut für Wasserforschung gemeinnützige GmbH IWW, Mülheim an der Ruhr)