The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison
Abstract Different proxies for changes in structure and/or function of microbiomes have been developed, allowing assessing microbiome dynamics at multiple levels. However, the lack and differences in understanding the microbiome dynamics are due to the differences in the choice of proxies in differe...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Oxford University Press
2022-08-01
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| Series: | ISME Communications |
| Online Access: | https://doi.org/10.1038/s43705-022-00164-x |
| _version_ | 1827299213131644928 |
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| author | Haitao Wang Mareike Meister Corinna Jensen Andreas W. Kuss Tim Urich |
| author_facet | Haitao Wang Mareike Meister Corinna Jensen Andreas W. Kuss Tim Urich |
| author_sort | Haitao Wang |
| collection | DOAJ |
| description | Abstract Different proxies for changes in structure and/or function of microbiomes have been developed, allowing assessing microbiome dynamics at multiple levels. However, the lack and differences in understanding the microbiome dynamics are due to the differences in the choice of proxies in different studies and the limitations of proxies themselves. Here, using both amplicon and metatranscriptomic sequencings, we compared four different proxies (16/18S rRNA genes, 16/18S rRNA transcripts, mRNA taxonomy and mRNA function) to reveal the impact of a severe summer drought in 2018 on prokaryotic and eukaryotic microbiome structures and functions in two rewetted fen peatlands in northern Germany. We found that both prokaryotic and eukaryotic microbiome compositions were significantly different between dry and wet months. Interestingly, mRNA proxies showed stronger and more significant impacts of drought for prokaryotes, while 18S rRNA transcript and mRNA taxonomy showed stronger drought impacts for eukaryotes. Accordingly, by comparing the accuracy of microbiome changes in predicting dry and wet months under different proxies, we found that mRNA proxies performed better for prokaryotes, while 18S rRNA transcript and mRNA taxonomy performed better for eukaryotes. In both cases, rRNA gene proxies showed much lower to the lowest accuracy, suggesting the drawback of DNA based approaches. To our knowledge, this is the first study comparing all these proxies to reveal the dynamics of both prokaryotic and eukaryotic microbiomes in soils. This study shows that microbiomes are sensitive to (extreme) weather changes in rewetted fens, and the associated microbial changes might contribute to ecological consequences. |
| first_indexed | 2024-04-24T15:29:02Z |
| format | Article |
| id | doaj.art-a334e6f9c3ec47d2b9ec506c1b98d4ef |
| institution | Directory Open Access Journal |
| issn | 2730-6151 |
| language | English |
| last_indexed | 2024-04-24T15:29:02Z |
| publishDate | 2022-08-01 |
| publisher | Oxford University Press |
| record_format | Article |
| series | ISME Communications |
| spelling | doaj.art-a334e6f9c3ec47d2b9ec506c1b98d4ef2024-04-02T05:14:28ZengOxford University PressISME Communications2730-61512022-08-01211410.1038/s43705-022-00164-xThe impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparisonHaitao Wang0Mareike Meister1Corinna Jensen2Andreas W. Kuss3Tim Urich4Institute of Microbiology, University of GreifswaldDiabetes Competence Centre Karlsburg (KDK), Leibniz Institute for Plasma Science and Technology (INP)Human Molecular Genetics Group, Department of Functional Genomics, University Medicine GreifswaldHuman Molecular Genetics Group, Department of Functional Genomics, University Medicine GreifswaldInstitute of Microbiology, University of GreifswaldAbstract Different proxies for changes in structure and/or function of microbiomes have been developed, allowing assessing microbiome dynamics at multiple levels. However, the lack and differences in understanding the microbiome dynamics are due to the differences in the choice of proxies in different studies and the limitations of proxies themselves. Here, using both amplicon and metatranscriptomic sequencings, we compared four different proxies (16/18S rRNA genes, 16/18S rRNA transcripts, mRNA taxonomy and mRNA function) to reveal the impact of a severe summer drought in 2018 on prokaryotic and eukaryotic microbiome structures and functions in two rewetted fen peatlands in northern Germany. We found that both prokaryotic and eukaryotic microbiome compositions were significantly different between dry and wet months. Interestingly, mRNA proxies showed stronger and more significant impacts of drought for prokaryotes, while 18S rRNA transcript and mRNA taxonomy showed stronger drought impacts for eukaryotes. Accordingly, by comparing the accuracy of microbiome changes in predicting dry and wet months under different proxies, we found that mRNA proxies performed better for prokaryotes, while 18S rRNA transcript and mRNA taxonomy performed better for eukaryotes. In both cases, rRNA gene proxies showed much lower to the lowest accuracy, suggesting the drawback of DNA based approaches. To our knowledge, this is the first study comparing all these proxies to reveal the dynamics of both prokaryotic and eukaryotic microbiomes in soils. This study shows that microbiomes are sensitive to (extreme) weather changes in rewetted fens, and the associated microbial changes might contribute to ecological consequences.https://doi.org/10.1038/s43705-022-00164-x |
| spellingShingle | Haitao Wang Mareike Meister Corinna Jensen Andreas W. Kuss Tim Urich The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison ISME Communications |
| title | The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison |
| title_full | The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison |
| title_fullStr | The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison |
| title_full_unstemmed | The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison |
| title_short | The impact of summer drought on peat soil microbiome structure and function-A multi-proxy-comparison |
| title_sort | impact of summer drought on peat soil microbiome structure and function a multi proxy comparison |
| url | https://doi.org/10.1038/s43705-022-00164-x |
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