Microbial communities respond to stressor-driven events, by changing their structure and activity, as shown by multiple rRNA gene-based studies. In this proposal we will focus on how the bacterial and viral microdiversity is affected by degradation under the influence of different stressors, and on how it recovers. A22 is built on the hypothesis that stressors modulate bacterial microdiversity in river sediments, by direct or indirect selection of genomovars with traits favourable for survival under the respective stressor conditions. Viral microdiversity will be driven by the necessity to successfully infect and counteract the anti-viral abilities of the host. While microdiversity can decrease during the degradation phase, at recovery will return to initial levels, but different genomovars will dominate (asymmetry of paths). To test these hypothesises, we will turn to metagenomics, supplemented in some cases with culture-dependent work. We will evaluate the microdiversity based both on single nucleotide variants (SNVs) and on structural variants (SVs). Various stressors will be investigated, either alone or in combination, by relying on data from several highly parallelized mesocosm experiments (the ExStream setup) from Phase I: low or high flow velocity, temperature and salt. In addition, the effects of drought will be investigated in ExStream/SIGMA experiments from Phase II, as well as in field streams, via sampling through the drying period in three consecutive years. All in all, we will explore changes in microbial microdiversity across different stressor types and intensities, both at degradation and recovery.

Hsin-Tung Lai (University of Duisburg-Essen)

Viral (and host) microdiversity reponse to multiple stressors in freshwater ecosystem

Prokaryotic microbes, that is bacteria and archaea, constitute the majority of microorganisms in most ecosystems, including rivers. Due to their wide-ranging metabolic capabilities, prokaryotes serve as key drivers of biogeochemical cycles, influencing all trophic levels from the base upward. Furthermore, interactions between prokaryotic hosts and their viruses play a crucial role in shaping the structure of entire microbial communities. Previous studies leveraging metagenomics and amplicon sequencing, including those from the first phase of RESIST, have shown that prokaryotic and viral diversity in river sediments is influenced by various stressors. However, to date, there are very few studies investigating the effect of stressors on the microdiversity of riverine prokaryotic communities, leaving major gaps in our understanding of how these communities respond to environmental change.

In this PhD project, we aim to uncover how environmental stressors shape the microdiversity of sediment-dwelling prokaryotes and viruses, further linking their genomic variations to the resilience of their populations. To achieve this, we will develop a bioinformatics pipeline for analyzing structural variants and single nucleotide polymorphisms in metagenomic samples. In the first phase, we will apply this pipeline to over 250 metagenomic datasets from ExStream Phase I sediment samples, which were exposed to different stressors (flow velocity, temperature, and salinity), to investigate whether the respective stressors have influenced host and viral microdiversity. In the second phase, this pipeline will be applied to drought-exposed samples from RESIST phase II, collected from ExStream experiments and field streams in the Boye catchment. Moreover, cultivation-based techniques will complement the sequencing approach by revealing additional structural and nucleotide-level microdiversity. Together, this will improve our understanding of how the microbial communities in freshwater sediments respond and adapt to multiple stressors, which is essential for predicting ecosystem resilience under changing environmental conditions.

Contact: hsin.lai@uni-due.de

First Supervisor: Dr. Cristina Moraru (Environmental Metagenomics)
Second Supervisor: Prof. Dr. Alexander Probst (Environmental Metagenomics)