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Open AccessArticle

DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors

by Ali Nawaz 1,2,3,*, Witoon Purahong 1, Martina Herrmann 4,5, Kirsten Küsel 4,5, François Buscot 1,5,† and Tesfaye Wubet 1,2,5,*,†
1
Helmholtz Centre for Environmental Research–UFZ, Department of Soil Ecology, 06120 Halle (Saale), Germany
2
Helmholtz Centre for Environmental Research–UFZ, Department of Community Ecology, 06120 Halle (Saale), Germany
3
Institute of Biology, University of Leipzig, 04103 Leipzig, Germany
4
Institute of Biodiversity, Friedrich Schiller University Jena, Dornburger Straße 159, 07743 Jena, Germany
5
German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Deutscher Platz 5e, 04103 Leipzig, Germany
*
Authors to whom correspondence should be addressed.
Senior Authors.
Microorganisms 2019, 7(9), 341; https://doi.org/10.3390/microorganisms7090341
Received: 19 August 2019 / Revised: 8 September 2019 / Accepted: 9 September 2019 / Published: 11 September 2019
(This article belongs to the Section Environmental Microbiology)
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. View Full-Text
Keywords: total fungi; active fungi; aquatic fungi; aquifers; ITS; illumina sequencing; subsurface biosphere total fungi; active fungi; aquatic fungi; aquifers; ITS; illumina sequencing; subsurface biosphere
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Nawaz, A.; Purahong, W.; Herrmann, M.; Küsel, K.; Buscot, F.; Wubet, T. DNA- and RNA- Derived Fungal Communities in Subsurface Aquifers Only Partly Overlap but React Similarly to Environmental Factors. Microorganisms 2019, 7, 341.

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