A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils
Root exudates in a plant’s rhizosphere alters microbial community membership and activity, which can in turn alter a plant’s health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-tran...
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Frontiers Media S.A.
2025-06-01
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| Series: | Frontiers in Microbiology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1608399/full |
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| author | Alessandra Ceretto Alessandra Ceretto Cynthia Weinig Cynthia Weinig Cynthia Weinig |
| author_facet | Alessandra Ceretto Alessandra Ceretto Cynthia Weinig Cynthia Weinig Cynthia Weinig |
| author_sort | Alessandra Ceretto |
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| description | Root exudates in a plant’s rhizosphere alters microbial community membership and activity, which can in turn alter a plant’s health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-transcripts (RNA) to define protein synthesis potential (PSP) as a proxy of microbial activity in both rhizosphere and bulk soils of a Wyoming native plant Boechera stricta. Using PSP rather than total microbial membership reveals fine-scale differences in genera between the rhizosphere and control soil communities. This study found DNA community analysis alone disproportionately increased the importance of Saccharibacteria and Gemmatimonadetes phyla in the overall soil community profile, and underestimated the importance of several known root associates (Comamonadaceae, Rhizobacter, and Variovorax), which had elevated PSP in the rhizosphere soil. Thus, the use of DNA-vs. RNA-based community characterization reveals that community composition (DNA) may not completely capture community activity (RNA). Analysis of the PSP community profile also indicated elevated levels of proteins associated with carbohydrate and amino acid metabolism in the rhizosphere-associated bacteria, which may shed light on potential mechanisms by which root exudates shape the rhizosphere soil community. |
| format | Article |
| id | doaj-art-a89a28b8d9374e8a933d8d45c717a21d |
| institution | OA Journals |
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| language | English |
| publishDate | 2025-06-01 |
| publisher | Frontiers Media S.A. |
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| series | Frontiers in Microbiology |
| spelling | doaj-art-a89a28b8d9374e8a933d8d45c717a21d2025-08-20T02:21:34ZengFrontiers Media S.A.Frontiers in Microbiology1664-302X2025-06-011610.3389/fmicb.2025.16083991608399A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soilsAlessandra Ceretto0Alessandra Ceretto1Cynthia Weinig2Cynthia Weinig3Cynthia Weinig4Department of Botany, University of Wyoming, Laramie, WY, United StatesProgram in Ecology, University of Wyoming, Laramie, WY, United StatesDepartment of Botany, University of Wyoming, Laramie, WY, United StatesProgram in Ecology, University of Wyoming, Laramie, WY, United StatesDepartment of Molecular Biology, University of Wyoming, Laramie, WY, United StatesRoot exudates in a plant’s rhizosphere alters microbial community membership and activity, which can in turn alter a plant’s health and fitness. In this study we characterized bacterial community composition, using 16S rRNA-gene (DNA) sequencing to define total community membership and 16S rRNA-transcripts (RNA) to define protein synthesis potential (PSP) as a proxy of microbial activity in both rhizosphere and bulk soils of a Wyoming native plant Boechera stricta. Using PSP rather than total microbial membership reveals fine-scale differences in genera between the rhizosphere and control soil communities. This study found DNA community analysis alone disproportionately increased the importance of Saccharibacteria and Gemmatimonadetes phyla in the overall soil community profile, and underestimated the importance of several known root associates (Comamonadaceae, Rhizobacter, and Variovorax), which had elevated PSP in the rhizosphere soil. Thus, the use of DNA-vs. RNA-based community characterization reveals that community composition (DNA) may not completely capture community activity (RNA). Analysis of the PSP community profile also indicated elevated levels of proteins associated with carbohydrate and amino acid metabolism in the rhizosphere-associated bacteria, which may shed light on potential mechanisms by which root exudates shape the rhizosphere soil community.https://www.frontiersin.org/articles/10.3389/fmicb.2025.1608399/fullprotein synthesis potentialDNA ribosomal sequencesRNA ribosomal 16Ssoil microbial ecologyRNA DNA ratio |
| spellingShingle | Alessandra Ceretto Alessandra Ceretto Cynthia Weinig Cynthia Weinig Cynthia Weinig A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils Frontiers in Microbiology protein synthesis potential DNA ribosomal sequences RNA ribosomal 16S soil microbial ecology RNA DNA ratio |
| title | A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils |
| title_full | A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils |
| title_fullStr | A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils |
| title_full_unstemmed | A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils |
| title_short | A comparison of 16S rRNA-gene and 16S rRNA-transcript derived microbial communities in bulk and rhizosphere soils |
| title_sort | comparison of 16s rrna gene and 16s rrna transcript derived microbial communities in bulk and rhizosphere soils |
| topic | protein synthesis potential DNA ribosomal sequences RNA ribosomal 16S soil microbial ecology RNA DNA ratio |
| url | https://www.frontiersin.org/articles/10.3389/fmicb.2025.1608399/full |
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