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.

Rena Sophie Andräs (University of Duisburg-Essen)

Thesis: Microbial key processes and key species during drought and re-wetting of river sediments

Microbes in river sediments support ecosystem resilience, nutrient turnover, and the metabolic functioning of river ecosystems. Ongoing climate change alters natural hydrological fluctuations, resulting in more frequent and severe hydrological droughts. As water is essential for microbial processes as it facilitates transport and solubility of molecules, water scarcity can severely impact microbial composition, function, and activity. However, the effects of severe drought and subsequent rewetting on microbial communities and associated functions, remain major gaps in the current body of literature. This PhD project is set out with the aim of deciphering the response of sediment microbiomes to drought in riverine ecosystems during both, degradation and recovery. Sediment samples for metagenomics and metatranscriptomics will be taken from field sites and ExStream. Investigating these field sites will help constraining microbial recovery trajectories based on different stressor histories of the rivers. These histories refer to rivers that will have undergone frequent, intermitted or seldom drying of the riverbeds. By contrast, ExStream will focus on different drought durations which will be simulated in individual mesocosms. Metagenomic analyses will be done using a hybrid approach, combining the high accuracy and coverage of short reads with the extended sequence contiguity of long reads to assemble high quality metagenomes despite the complexity of the microbiome. Together with findings transcriptomic analyses, key species (highly active and highly abundant) and keystone species (highly active and low abundant) will be identified. Ultimately, the generated dataset will help to decipher both, key taxa and key functions, during and after drought and provide insight into stressor and recovery processes of severely degraded river sediment microbiomes.

Contact: rena.andraes@uni-due.de

First Supervisor:
Prof. Dr. Alexander Probst (University of Duisburg-Essen, Group for Aquatic Microbial Ecology (GAME))

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)