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.