Dead or Alive; or Does It Really Matter? Level of Congruency Between Trophic Modes in Total and Active Fungal Communities in High Arctic Soil

Abstract

Describing dynamics of belowground organisms, such as fungi, can be challenging. Results of studies based on environmental DNA (eDNA) may be biased as the template does not discriminate between metabolically active cells and dead biomass. We analyzed ribosomal DNA (rDNA) and ribosomal RNA (rRNA) coextracted from 48 soil samples collected from a manipulated snow depth experiment in two distinct vegetation types in Svalbard, in the High Arctic. Our main goal was to compare if the rDNA and rRNA metabarcoding templates produced congruent results that would lead to consistent ecological interpretation. Data derived from both rDNA and rRNA clustered according to vegetation types. Different sets of environmental variables explained the community composition based on the metabarcoding template. rDNA and rRNA-derived community composition of symbiotrophs and saprotrophs, unlike pathotrophs, clustered together in a similar way as when the community composition was analyzed using all OTUs in the study. Mean OTU richness was higher for rRNA, especially in symbiotrophs. The metabarcoding template was more important than vegetation type in explaining differences in richness. The proportion of symbiotrophic, saprotrophic and functionally unassigned reads differed between rDNA and rRNA, but showed similar trends. There was no evidence for increased snow depth influence on fungal community composition or richness. Our findings suggest that template choice may be especially important for estimating biodiversity, such as richness and relative abundances, especially in Helotiales and Agaricales, but not for inferring community composition. Differences in study results originating from rDNA or rRNA may directly impact the ecological conclusions of one’s study, which could potentially lead to false conclusions on the dynamics of microbial communities in a rapidly changing Arctic.

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

“…This approach can even be used for targeting the universal DNA barcode region for fungi, the nuclear ribosomal internal transcribed spacer region (ITS) [15], and the few available studies showed that rRNA derived fungal communities differ from those derived from rDNA at the levels of richness, abundance of certain taxa and overall community composition [14,16,17,18,19]. However, such studies comparing total and active fungal communities have mostly been carried out either in surface soils from different biomes [14,16,17,20], or in communities associated with different plant species [19,21], but equivalent studies in subsurface aquatic ecosystems are largely missing.…”

Metabarcoding on both environmental DNA and RNA highlights differences between fungal communities sampled in different habitats

“…In addition to soil samples we observed a similar trend in decaying wood samples. Concerning Agaricomycetes there is a notable difference in RNA:DNA ratio, that is higher in wood, dominated by saprotrophs [89][90][91], than in soils where mycorrhizal symbionts thrive [31,89,[92][93][94].…”

“…Reports of microbial, either prokaryotic or eukaryotic, community metabarcoding on both eDNA and eRNA highlighted either a strong correlation between "active" (RNA-based) and "total" (DNA-based) microbial communities [25][26][27][28][29], or on the contrary identified significant differences between the different datasets [28,30,31]. For example, a greater taxonomic alpha diversity was often, but not always (see [31]), deduced from DNA compared to RNA datasets [30][31][32][33]. This could be a consequence of the presence of DNA from dead or resting organisms (legacy DNA) that do not, or no longer, participate to ecosystem processes [34].…”

“…This could be a consequence of the presence of DNA from dead or resting organisms (legacy DNA) that do not, or no longer, participate to ecosystem processes [34]. At the same time, several studies [30,31,[35][36][37] also revealed the unexpected presence of RNA-specific taxa. As regards fungi, almost all metabarcoding studies made use of eDNA, directly extracted from environmental matrices, to characterize fungal communities after amplification and sequencing of a fungal-specific barcode sequence.…”

“…As regards fungi, almost all metabarcoding studies made use of eDNA, directly extracted from environmental matrices, to characterize fungal communities after amplification and sequencing of a fungal-specific barcode sequence. Few studies reported the use of eRNA or both eDNA and eRNA to assess fungal diversity [25,31,[37][38][39][40][41][42][43].…”