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

Abstract

In recent years, metabarcoding has become a key tool to describe microbial communities from natural and artificial environments. Thanks to its high throughput nature, metabarcoding efficiently explores microbial biodiversity under different conditions. It can be performed on environmental (e)DNA to describe so-called total microbial community, or from environmental (e)RNA to describe active microbial community. As opposed to total microbial communities, active ones exclude dead or dormant organisms. For what concerns Fungi, which are mostly filamentous microorganisms, the relationship between DNA-based (total) and RNA-based (active) communities is unclear. In the present study, we evaluated the consequences of performing metabarcoding on both soil and wood-extracted eDNA and eRNA to delineate molecular operational taxonomic units (MOTUs) and differentiate fungal communities according to the environment they originate from. DNA and RNA-based communities differed not only in their taxonomic composition, but also in the relative abundances of several functional guilds. From a taxonomic perspective, we showed that several higher taxa are globally more represented in either “active” or “total” microbial communities. We also observed that delineation of MOTUs based on their co-occurrence among DNA and RNA sequences highlighted differences between the studied habitats that were overlooked when all MOTUs were considered, including those identified exclusively by eDNA sequences. We conclude that metabarcoding on eRNA provides original functional information on the specific roles of several taxonomic or functional groups that would not have been revealed using eDNA alone.

Eukaryotic Biodiversity and Spatial Patterns in the Clarion-Clipperton Zone and Other Abyssal Regions: Insights From Sediment DNA and RNA Metabarcoding

“…Evidence for DNA preservation, notably in the deep-sea sediment (Lejzerowicz et al, 2013a;Corinaldesi et al, 2018), justifies the use of environmental RNA (eRNA). Indeed, eRNA has been proposed as a proxy for active species in various environments (Logares et al, 2012;Adamo et al, 2020;Giner et al, 2020). It yields compositions that differ from eDNA in deep-sea sediments (Guardiola et al, 2016) and may therefore be more useful for interpreting biodiversity and biogeographic patterns.…”

Fungal biodiversity in Arctic paleoecosystems assessed by metabarcoding of lake sedimentary ancient DNA

“…Investigating past fungal biodiversity changes by reconstructing paleoecosystems may generate insights regarding basal structural developments that are to date mostly overlooked in classical palynological approaches due to reliance on microscopic remains (Taylor and Osborn, 1996;Wood and Wilmshurst, 2013;Chepstow-Lusty et al, 2019). While molecular genetic methods are commonly used at present to investigate modern ecosystems (Heeger et al, 2018;Adamo et al, 2020), far fewer studies have been conducted on fungal biodiversity in paleoecosystems. Early studies concentrated on samples from permafrost soils (Lydolph et al, 2005;Bellemain et al, 2013), in which DNA preservation is optimal and which was in general an early target for sedimentary ancient DNA (Willerslev et al, 2003(Willerslev et al, , 2014Haile et al, 2009).…”

Fungal dye-decolorizing peroxidase diversity: roles in either intra- or extracellular processes

“…Grassland and forest soil, as well as deadwood samples from six different contrasted geographic sites in Italy and France, were included in this study (Supplemental Table S2). Four of them had already been described in Adamo et al (2020) and one in Bragalini et al (2014).…”