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Stratification-driven divergence between taxonomic and functional diversity in a deep lake microbiome
Jianing Ding1,2, Chunyan Yu1,3, Jiawei Gao1,3
1Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing 211135, China.
FEMS Microbiology Ecology
|December 24, 2025
Summary
Deep lake microbes show distinct adaptations to stratified waters. The hypolimnion has higher bacterial richness, while the epilimnion boasts greater metabolic flexibility, driven by oxygen and nutrients.
Area of Science:
- Aquatic Microbiology
- Limnology
- Molecular Ecology
Background:
- Deep lakes exhibit thermal stratification, influencing microbial community structure.
- Comparative studies of epilimnetic (surface) and hypolimnetic (deep) microbiomes are limited.
- Understanding these dynamics is crucial for biogeochemical cycling in stratified aquatic ecosystems.
Purpose of the Study:
- To investigate stratification-induced shifts in microbial community composition and functional potential in a deep monomictic lake.
- To compare taxonomic and functional diversity between epilimnetic and hypolimnetic water layers.
- To identify key environmental drivers of microbial stratification.
Main Methods:
- 16S rRNA gene sequencing for taxonomic analysis.
- Functional microarray (GeoChip 5.0) for assessing functional gene potential.
- Molecular ecological network analysis to explore community interactions.
- Multivariate statistical analyses to link environmental factors and microbial communities.
Main Results:
- Partial decoupling of taxonomic and functional diversity across water layers.
- Hypolimnion showed higher bacterial richness with distinct taxa (Nitrospirae, Parcubacteria, Thaumarchaeota).
- Epilimnion displayed greater functional gene richness and metabolic flexibility.
- Dissolved oxygen and nutrient availability were identified as key drivers of stratification.
Conclusions:
- Microbial communities in deep lakes exhibit distinct adaptations to stratified conditions.
- Epilimnetic and hypolimnetic communities play unique roles in lake biogeochemical cycling.
- Findings provide insights into microbial responses to climate-mediated thermal regime shifts in deep lakes.
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