Abstract
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.
Highlights
With a global diversity around 2.2–3.8 million species [1], fungi represent an important group of microbial eukaryotes
Paired-end Illumina sequencing of 40 fungal internal transcribed spacer 2 (ITS2) libraries from 20 groundwater samples representing total and active fungal communities, produced a total of 2,299,575 paired-end reads with correct primer sequences
After clustering the reads at 97% sequence similarities and removal of non-target reads, the DNA-derived community was represented by a total of 20,341 fungal reads, while the RNA-derived community was represented by 19,490 reads
Summary
With a global diversity around 2.2–3.8 million species [1], fungi represent an important group of microbial eukaryotes They play significant ecological roles in environmental processes and ecosystem services as decomposers, pathogens, and symbionts. Out of this huge estimated diversity, fewer than 10% (147,076) of the fungal species are formally described [2]. Since the advent of culture-independent molecular methods and next-generation sequencing (NGS) technologies (which typically do not require cultivation), microbial ecologists have deepened their studies and extended them to previously unexplored habitats This in particular helped in broadening the scope of aquatic mycology [4]. Despite the immense significance of these aquifers to mankind and the vital ecological roles fungi play in aquatic ecosystems, fungal specific studies applying culture-independent high-throughput sequencing (HTS) approaches in natural subsurface aquatic environments are still rare [7]
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