Annual Conference 2025 of the Association for General and Applied Microbiology - Jahrestagung 2025 der Vereinigung für Allgemeine und Angewandte Mikrobiologie

Chair

Prof.

Prof. Dr.

Cellular and Molecular Mechanisms of Stress Response in the Thermoacidophilic Archaeon Sulfolobus acidocaldarius

SFB session / Research center session Ruhr

The thermoacidophilic archaeon Sulfolobus acidocaldarius employs diverse strategies to thrive in extreme environments. At the cellular level, stress responses include increased motility and DNA uptake upon UV irradiation 1, enhanced biofilm formation under organic solvent exposure 2, and specific responses to nutrient starvation 3, showcasing its adaptability to various challenges.At the molecular level, trehalose and polyphosphate (polyP) metabolism play critical roles in stress resilience. Trehalose acts as a compatible solute stabilizing macromolecules and membranes, synthesized via three distinct pathways 4. A triple mutant lacking all pathways failed to grow under salt stress, while wild-type cells showed increased trehalose levels under salt stress, emphasizing its role in osmotic stress protection.PolyP functions as an energy and phosphate reserve, contributing to homeostasis under stress. We identified a novel archaeal polyphosphate kinase, SaPPK3, with reversible activity that drives ATP formation under low energy charge 5. With a combined experimental modelling approach using quantitative 31P NMR, we demonstrated that SaPPK3 buffers energy under stress, synthesizing polyP only when ATP/ADP ratios are high. Phylogenetic analyses place SaPPK3 in a new PPK3 family, patchily distributed across Archaea and Bacteria.Together, these findings provide a deeper understanding of the molecular strategies employed by S. acidocaldarius to cope with extreme conditions, contributing to our broader knowledge of archaeal stress physiology and offering potential applications in biotechnology and industrial microbiology.1 Schult, F. et al. Nucleic Acids Res (2018). https://doi.org/10.1093/nar/gky5272 Benninghoff, J. C. et al. Applied and environmental microbiology 87 (2021). https://doi.org/10.1128/aem.02988-203 Bischof, L. F. et al. Frontiers in microbiology 9, 3201 (2018). https://doi.org/10.3389/fmicb.2018.032014 Stracke, C. et al. Applied and environmental microbiology 86 (2020). https://doi.org/10.1128/aem.01565-205 Höfmann, S. et al. bioRxiv (2024). https://doi.org/10.1101/2024.08.28.610084

Invited lecture

A tale of two habitats: Diverging microbial stress-responses in water and sediment

Aquatic environments are increasingly impacted by a variety of stressors, such as temperature fluctuations and rising salinity, often driven by climate change, human activities, and land-use changes. These stressors can influence microbial communities in different ways across water and sediment habitats. Alterations in microbial community composition can disrupt nutrient cycling, food web dynamics, and overall ecosystem functioning, with potential consequences for biodiversity and water quality. Understanding how microbial communities in both habitats respond to these stressors is crucial for assessing ecosystem resilience and the broader impacts of environmental stressors on aquatic ecosystems. This study investigates the effects of salt and temperature stress, both individually and in combination, on microbial communities in freshwater environments. We focused on assessing differences between water and sediment communities using 16S and 18S rRNA gene sequencing. A controlled mesocosm experiment was conducted using water and sediment samples exposed to four treatments: control, salt stress, temperature stress, and combined salt-temperature stress. Samples were taken following a 10-day acclimatization phase over a 10-day period, with stressors applied on day 2 and removed on day 6. Microbial community composition was analyzed using amplicon sequencing (16S for prokaryotes, 18S for eukaryotes). Our results demonstrated that microbial communities in water and sediment remained largely distinct, reflecting strong habitat specificity. Water communities were significantly impacted by salt and combined treatments, whereas temperature stress had negligible effects. A significant, yet much weaker, effect of the various stressors on community composition was observed in the sediment samples, compared to the more pronounced changes in the water samples. Eukaryotic communities (18S) were more sensitive to stressors than prokaryotic communities (16S), highlighting differential responses to environmental changes. This study demonstrates that microbial communities in freshwater ecosystems exhibit distinct responses to environmental stressors, with water habitats being more vulnerable to salt. The heightened sensitivity of eukaryotes suggests they may serve as early indicators of ecosystem perturbation. These insights are crucial for developing targeted conservation strategies to mitigate the impacts of stressors on aquatic biodiversity.

Short lecture

Unraveling microbial roles in stream ecosystem functioning: Insights into stressor impacts and community interactions through metatranscriptomics and metabarcoding

Streams are subjected to multiple stressors that interact in complex ways, significantly impacting biodiversity and ecosystem functions. These interactions make it challenging to predict changes in these systems. A comprehensive mechanistic understanding of ecosystem degradation and recovery is still lacking, which hinders our ability to predict stressor impacts on biodiversity and ecosystem functioning and to manage the restoration of degraded freshwater systems.In our recent work, we have investigated diverse stressor effects, including changes in temperature, salinity, hydrology, inundations, and treated wastewater discharge, on prokaryotic and eukaryotic microbes. Further, we are currently investigating a key ecosystem function: leaf litter degradation in streams, mediated by bacterial and fungal heterotrophs. The specific taxa involved, their interactions within microbial decomposer communities, and the enzymatic and metabolic pathways driving these processes remain largely unexplored and are not yet well understood, potentially varying with environmental conditions. This project aims to elucidate the roles of different fungal and bacterial groups in the enzymatic decomposition of coarse particulate organic matter (CPOM) under single and multiple stressor scenarios. By employing metatranscriptomics, metabarcoding, and DNA-SIP, we seek to uncover the contributions and interactions of these microbial groups. Specifically, we investigate functional redundancy and interrelationships between taxonomic groups to better understand ecosystem resilience and functionality.

Degradation and recovery of microbial ecosystem functions in rivers exposed to multiple stressors

Microorganisms in sediments are key players for the functioning of rivers, yet, we do not understand how they respond to and recover from multiple anthropogenic stressors, which are increasingly threatening river ecosystems worldwide. We therefore investigated the effects of two globally relevant stressors, temperature increase and salinization, on two microbe-driven ecosystem processes, which are degradation of dissolved organic carbon (DOC) and degradation of bacterial dead biomass (necromass). Using controlled lab experiments with isolated sediment microbial communities, we found that temperature increase had clear positive and salinization clear negative effects on the degradation of DOC and necromass, even at rather low stressor levels. Using outdoor mesocosm experiments where sediment microbial communities are integrated into the riverine food web, we found that the same low stressor levels had no effect on DOC degradation but on necromass degradation, whereas stressor release increased DOC degradation but not necromass degradation. The results indicate that the effects of multiple stressor increase and release on sediment microbial processes depend on the concentration and the bioavailability of the carbon source, and that changes in energy availability may mask multiple stressor effects.

Flow Velocity and Anthropogenic Stressors Drive Microbial Community Dynamics in Riverine Ecosystems

Microbial communities in riverine ecosystems are essential drivers of biogeochemical cycling, mediating nutrient transformation and energy flow. However, they are substantially affected by anthropogenic stressors such as pollution, alteration in flow regime and land-use change and, which can alter their composition and functionality, leading to ecosystem degradation. Here, we performed metagenomic analyses of sediment samples from four different flow-through stream mesocosm setups in Germany, Ireland and New Zealand encompassing a total of 254 mesocosms. Our results revealed differential responses of microbial communities to altered flow velocity, an important stressor identified in previous research. Microbial communities from two riverine ecosystems showed significant compositional shifts at slower flow in the mesocosms, whereas the other two showed only minor changes, suggesting a resilience that we infer to be linked to higher microbial diversity. We also identified significant differences in encoded metabolic gene profiles between the microbial communities of the European and New Zealand experiments, particularly in genes associated with nitrogen, methane and sulfur cycling. To further investigate this difference, we selected one stream ecosystem substantially affected by reduced flow velocity and performed in-depth metatranscriptomic analyses revealing up-regulation of, e.g., heat-shock proteins across multiple community members. Notably, a combination of elevated water temperature and flow velocity reduction showed an antagonistic effect at transcription level, highlighting the complexity of stressor interactions associated with river ecosystems. This study stresses the importance of understanding anthropogenic impacts on river microbial communities to mitigate the consequences of these stressors.

SFB session
Research center session Ruhr

Appointment

Chair

Programme

SFB sessionResearch center session Ruhr

Appointment

Chair

Programme

SFB session
Research center session Ruhr