Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake
Deep lakes play a critical role in global elemental cycling and serve as habitats for diverse microbial communities. However, studies on the effects of lake stratification on microbial composition and functional potential in surface sediments remain limited. Here, we investigated microbial community...
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Frontiers Media S.A.
2025-07-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1614055/full |
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| author | Peixuan Zhang Peixuan Zhang Minglei Ren Yan Xu Jianjun Wang |
| author_facet | Peixuan Zhang Peixuan Zhang Minglei Ren Yan Xu Jianjun Wang |
| author_sort | Peixuan Zhang |
| collection | DOAJ |
| description | Deep lakes play a critical role in global elemental cycling and serve as habitats for diverse microbial communities. However, studies on the effects of lake stratification on microbial composition and functional potential in surface sediments remain limited. Here, we investigated microbial community structure and functional composition using metagenomics of 38 surface sediments across a depth gradient of 0–90 m in Lugu Lake, China. Our results showed that Shannon diversity peaked at the thermocline for microbial communities, while a U-shaped pattern for functional genes. Microbial communities and functional genes in the surface sediments showed higher spatial heterogeneity at the shallow layer, whereas those at deeper layers tended toward more homogenized. Although water depth was the most important driver in explaining 29.9 and 26.5% of variance in microbial and functional gene composition, stochastic processes primarily governed the community assemblages, particularly dispersal limitation with the contribution of 43.7%. We further found the surface layer was enriched in genes mainly involved in aerobic metabolism and methanogenesis. In contrast, genes related to reduction reactions, including dissimilatory nitrate and sulfate reduction were more abundant in the thermocline and deep layer, reflecting lower redox potential in a deeper layer. Overall, our results provide evidence for microbial community stratification and functional partitioning in deep lakes. |
| format | Article |
| id | doaj-art-f9670c8f69384784a46f6bc90c814e32 |
| institution | Kabale University |
| issn | 1664-302X |
| language | English |
| publishDate | 2025-07-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-f9670c8f69384784a46f6bc90c814e322025-08-20T03:56:09ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-07-011610.3389/fmicb.2025.16140551614055Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lakePeixuan Zhang0Peixuan Zhang1Minglei Ren2Yan Xu3Jianjun Wang4Department of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, ChinaState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, ChinaState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, ChinaDepartment of Municipal Engineering, School of Civil Engineering, Southeast University, Nanjing, ChinaState Key Laboratory of Lake and Watershed Science for Water Security, Nanjing Institute of Geography and Limnology, Chinese Academy of Sciences, Nanjing, ChinaDeep lakes play a critical role in global elemental cycling and serve as habitats for diverse microbial communities. However, studies on the effects of lake stratification on microbial composition and functional potential in surface sediments remain limited. Here, we investigated microbial community structure and functional composition using metagenomics of 38 surface sediments across a depth gradient of 0–90 m in Lugu Lake, China. Our results showed that Shannon diversity peaked at the thermocline for microbial communities, while a U-shaped pattern for functional genes. Microbial communities and functional genes in the surface sediments showed higher spatial heterogeneity at the shallow layer, whereas those at deeper layers tended toward more homogenized. Although water depth was the most important driver in explaining 29.9 and 26.5% of variance in microbial and functional gene composition, stochastic processes primarily governed the community assemblages, particularly dispersal limitation with the contribution of 43.7%. We further found the surface layer was enriched in genes mainly involved in aerobic metabolism and methanogenesis. In contrast, genes related to reduction reactions, including dissimilatory nitrate and sulfate reduction were more abundant in the thermocline and deep layer, reflecting lower redox potential in a deeper layer. Overall, our results provide evidence for microbial community stratification and functional partitioning in deep lakes.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1614055/fullmicrobial communityfunctional genemetagenomicwater depthdeep lake |
| spellingShingle | Peixuan Zhang Peixuan Zhang Minglei Ren Yan Xu Jianjun Wang Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake Frontiers in Microbiology microbial community functional gene metagenomic water depth deep lake |
| title | Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake |
| title_full | Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake |
| title_fullStr | Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake |
| title_full_unstemmed | Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake |
| title_short | Metagenomic insights into surface sediment microbial community and functional composition along a water-depth gradient in a subtropic deep lake |
| title_sort | metagenomic insights into surface sediment microbial community and functional composition along a water depth gradient in a subtropic deep lake |
| topic | microbial community functional gene metagenomic water depth deep lake |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1614055/full |
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