FungalTraits vs. FUNGuild: Comparison of Ecological Functional Assignments of Leaf- and Needle-Associated Fungi Across 12 Temperate Tree Species

Abstract

Recently, a new annotation tool “FungalTraits” was created based on the previous FUNGuild and FunFun databases, which has attracted high attention in the scientific community. These databases were widely used to gain more information from fungal sequencing datasets by assigning fungal functional traits. More than 1500 publications so far employed FUNGuild and the aim of this study is to compare this successful database with the recent FungalTraits database. Quality and quantity of the assignment by FUNGuild and FungalTraits to a fungal internal transcribed spacer (ITS)–based amplicon sequencing dataset on amplicon sequence variants (ASVs) were addressed. Sequencing dataset was derived from leaves and needles of 12 temperate broadleaved and coniferous tree species. We found that FungalTraits assigned more functional traits than FUNGuild, and especially the coverage of saprotrophs, plant pathogens, and endophytes was higher while lichenized fungi revealed similar findings. Moreover, ASVs derived from leaves and needles of each tree species were better assigned to all available fungal traits as well as to saprotrophs by FungalTraits compared to FUNGuild in particular for broadleaved tree species. Assigned ASV richness as well as fungal functional community composition was higher and more diverse after analyses with FungalTraits compared to FUNGuild. Moreover, datasets of both databases showed similar effect of environmental factors for saprotrophs but for endophytes, unidentical patterns of significant corresponding factors were obtained. As a conclusion, FungalTraits is superior to FUNGuild in assigning a higher quantity and quality of ASVs as well as a higher frequency of significant correlations with environmental factors.

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“…The FungalTraits database was used to determine the dominant fungal taxa’s ecological information and functional assignment [ 36 , 37 ]. This database categorizes the functional assignment into various “traits”, such as primary and secondary lifestyles, endophytic interaction capacity, aquatic habitat, and many others.…”

More than you can see: Unraveling the ecology and biodiversity of lichenized fungi associated with leaves and needles of 12 temperate tree species using high-throughput sequencing

“…DNA extraction and Illumina sequencing were done according to Tanunchai et al (2022). In our previous study (Tanunchai et al, 2022), we compared FUNGuild and FungalTraits to assign fungal ASVs to lichenized fungi; however; we did not tackle the ecological aspect of those datasets.…”

“…DNA extraction and Illumina sequencing were done according to Tanunchai et al (2022). In our previous study (Tanunchai et al, 2022), we compared FUNGuild and FungalTraits to assign fungal ASVs to lichenized fungi; however; we did not tackle the ecological aspect of those datasets. Briefly, for the preparation for the DNA extraction, up to 10 healthy-looking leaves and needles were carefully selected from five branches per tree individual to avoid contamination from the fungi living on branches.…”

“…Negative control was sequenced along with the samples. Paired-end sequencing (2 × 300 bp) was performed on the pooled PCR products (three technical replicates, ∼45 µL reaction volumes) using a MiSeq Reagent kit v3 on an Illumina MiSeq system (Illumina Inc., San Diego, CA, United States) at the Department of Soil Ecology, Helmholtz Centre for Environmental Research, Germany as outlined earlier (Tanunchai et al, 2022).…”

“…Bioinformatics analysis was conducted according to Tanunchai et al (2022). Briefly, the ITS rRNA gene paired-end sequences were quality-trimmed from the demultiplexed raw reads using cutadapt (Martin, 2011), filtered for chimeras, and merged using the DADA2 package (Callahan et al, 2016) through the pipeline dadasnake (Weißbecker et al, 2020).…”