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

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.

Spheres of Influence: Host Tree Proximity and Soil Chemistry Shape rRNA, but Not DNA, Communities of Symbiotic and Free-Living Soil Fungi in a Mixed Hardwood-Conifer Forest

“…This is likely due, at least in part, to the fact that precursor rRNA represents the metabolically active component of the fungal community (van der Linde and Haller, 2013; Wutkowska et al, 2019), and may therefore more closely mirror local environmental conditions. Supporting this possibility, other studies that have examined both nucleic acids in soils have also found that rRNA-based communities respond to a greater number of deterministic factors than DNAbased communities, or respond to those factors more strongly (Romanowicz et al, 2016;Lüneberg et al, 2018;Lasa et al, 2019;Meyer et al, 2019;Nawaz et al, 2019;Wutkowska et al, 2019). In some cases, like the present study, rRNA communities are the only ones in which deterministic effects on community structure are statistically detectable (Ragot et al, 2016;Gill et al, 2017).…”

Targeting the Active Rhizosphere Microbiome of Trifolium pratense in Grassland Evidences a Stronger-Than-Expected Belowground Biodiversity-Ecosystem Functioning Link

“…The experiment was performed at the Global Change Experimental Facility, a field infrastructure with a realistic scenarios to compare ecosystem effects on biological systems, so the incubation conditions with BrdU was not artificial, no additional substrates (isotopically labeled) were added, and therefore, the results reflect a realistic image of the soil microbial community in an active status. Despite the general assumption that the active soil community represents a subset of the total soil community, reported results showed that these two fractions are quite independent from each other and that the active community is similar in richness as or even more taxonomically diverse than the total community (Baldrian et al, 2012;Romanowicz et al, 2016;Nawaz et al, 2019). In our approach, the active bacterial and fungal community composition could, however, be considered as a subsets of the total microbial community composition, as we detected a low proportion of active bacterial (10.2%) and fungal (6.5%) OTUs unique to the active fraction.…”

“…Comparisons of active and total microbial communities have been done in many ecosystems including terrestrial and aquatic habitats ( Baldrian et al, 2012 ; Romanowicz et al, 2016 ; Cardoso et al, 2017 ; Nawaz et al, 2018 ; Li et al, 2019 ). They revealed significant differences between these two communities, which are shaped partly by similar ( Romanowicz et al, 2016 ; Nawaz et al, 2019 ) but also different ( Rajala et al, 2011 ; Baldrian et al, 2012 ; Zhang et al, 2014 ) environmental factors. Soil physicochemical factors, climate change factors such as warming and altered precipitation patterns are known to modify ecosystem properties and processes and may affect the rhizosphere microbial diversity and community composition ( Wieland et al, 2001 ; Garbeva et al, 2007 ; Drigo et al, 2008 ; Philippot et al, 2013 ; Alkorta et al, 2017 ).…”

Comparing the Influence of Assembly Processes Governing Bacterial Community Succession Based on DNA and RNA Data

“…These discussions are not only relevant for bacterial communities, as fungal communities in groundwater aquifers were also found to have discrepant profiles when based on DNA and RNA approaches. For instance, 30-40% of the total fungal operational taxonomic units (OTUs) were only detected in RNA-based sequencing [43]. Taken together, the copy number of 16S rRNA gene, the metabolic state of a cell and innate ribosome content all can affect the disproportionate recovery of different bacteria based on DNA-and RNA-inferred community profiling.…”