DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors
Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different ter...
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| Format: | Article |
| Language: | English |
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MDPI AG
2019-09-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/7/9/341 |
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| author | Ali Nawaz Witoon Purahong Martina Herrmann Kirsten Küsel François Buscot Tesfaye Wubet |
| author_facet | Ali Nawaz Witoon Purahong Martina Herrmann Kirsten Küsel François Buscot Tesfaye Wubet |
| author_sort | Ali Nawaz |
| collection | DOAJ |
| description | Recent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%−40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems. |
| first_indexed | 2024-12-10T05:01:38Z |
| format | Article |
| id | doaj.art-4e80fa5eb3854a9c8a7047bd77d469a0 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-12-10T05:01:38Z |
| publishDate | 2019-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-4e80fa5eb3854a9c8a7047bd77d469a02022-12-22T02:01:22ZengMDPI AGMicroorganisms2076-26072019-09-017934110.3390/microorganisms7090341microorganisms7090341DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental FactorsAli Nawaz0Witoon Purahong1Martina Herrmann2Kirsten Küsel3François Buscot4Tesfaye Wubet5Helmholtz Centre for Environmental Research–UFZ, Department of Soil Ecology, 06120 Halle (Saale), GermanyHelmholtz Centre for Environmental Research–UFZ, Department of Soil Ecology, 06120 Halle (Saale), GermanyInstitute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, GermanyInstitute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, GermanyHelmholtz Centre for Environmental Research–UFZ, Department of Soil Ecology, 06120 Halle (Saale), GermanyHelmholtz Centre for Environmental Research–UFZ, Department of Soil Ecology, 06120 Halle (Saale), GermanyRecent advances in high-throughput sequencing (HTS) technologies have revolutionized our understanding of microbial diversity and composition in relation to their environment. HTS-based characterization of metabolically active (RNA-derived) and total (DNA-derived) fungal communities in different terrestrial habitats has revealed profound differences in both richness and community compositions. However, such DNA- and RNA-based HTS comparisons are widely missing for fungal communities of groundwater aquifers in the terrestrial biogeosphere. Therefore, in this study, we extracted DNA and RNA from groundwater samples of two pristine aquifers in the Hainich CZE and employed paired-end Illumina sequencing of the fungal nuclear ribosomal internal transcribed spacer 2 (ITS2) region to comprehensively test difference/similarities in the “total” and “active” fungal communities. We found no significant differences in the species richness between the DNA- and RNA-derived fungal communities, but the relative abundances of various fungal operational taxonomic units (OTUs) appeared to differ. We also found the same set of environmental parameters to shape the “total” and “active” fungal communities in the targeted aquifers. Furthermore, our comparison also underlined that about 30%−40% of the fungal OTUs were only detected in RNA-derived communities. This implies that the active fungal communities analyzed by HTS methods in the subsurface aquifers are actually not a subset of supposedly total fungal communities. In general, our study highlights the importance of differentiating the potential (DNA-derived) and expressed (RNA-derived) members of the fungal communities in aquatic ecosystems.https://www.mdpi.com/2076-2607/7/9/341total fungiactive fungiaquatic fungiaquifersITSillumina sequencingsubsurface biosphere |
| spellingShingle | Ali Nawaz Witoon Purahong Martina Herrmann Kirsten Küsel François Buscot Tesfaye Wubet DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors Microorganisms total fungi active fungi aquatic fungi aquifers ITS illumina sequencing subsurface biosphere |
| title | DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors |
| title_full | DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors |
| title_fullStr | DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors |
| title_full_unstemmed | DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors |
| title_short | DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors |
| title_sort | dna and rna derived fungal communities in subsurface aquifers only partly overlap but react similarly to environmental factors |
| topic | total fungi active fungi aquatic fungi aquifers ITS illumina sequencing subsurface biosphere |
| url | https://www.mdpi.com/2076-2607/7/9/341 |
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