Additional file 1 of Effects of fungicides on aquatic fungi and bacteria: a comparison of morphological and molecular approaches from a microcosm experiment
Creators: name: Salis, Romana K.
name: Schreiner, Verena C.
name: Rozenberg, Andrey
name: Ohler, Katharina
name: Baudy-Groh, Patrick
name: Schäfer, Ralf B.
name: Leese, Florian
Publisher: name: figshare
Year: 2024
Subjects: subject: Microbiology
subject: FOS: Biological sciences
subject: Ecology

description: Additional file 1: Figure S1. Workflow resulting in the five community composition data sets. The uppermost box showing a schematic illustration of the experimental design was previously published in Schreiner et al. [41]. ASV: amplicon sequence variant. Table S1. Fungal strains sequenced via long-read PacBio sequencing. The coverage refers to the subsection of the long-read sequence, which can be matched to the ITS barcode. Table S2. Number of fungal amplicon sequence variants (ASVs) assigned to the different taxonomic ranks using the three methods of taxonomic assignment. Figure S2. Phylogenetic tree of the order Helotiales (fungi), constructed from sequences from the UNITE database [33], long read sequences of fungal cultures (indicated as orange bars) and ITS metabarcoding sequences from the experimental samples (indicated as purple dots). The outer colour strip indicates the families the sequences are assigned to (see legend on left-hand site). Figure S3. Phylogenetic tree of the order Pleosporales (fungi), constructed from sequences from the UNITE database [33], long read sequences of fungal cultures (indicated as orange bars) and ITS metabarcoding sequences from the experimental samples (indicated as purple dots). The outer colour strip indicates the families the sequences are assigned to (see legend on left-hand site). Figure S4. Phylogenetic tree of the order Hypocreales (fungi), constructed from sequences from the UNITE database [33], long read sequences of fungal cultures (indicated as orange bars) and ITS metabarcoding sequences from the experimental samples (indicated as purple dots). The outer colour strip indicates the families the sequences are assigned to (see legend on left-hand site). Figure S5. Phylogenetic tree of the order Tremellales (fungi), constructed from sequences from the UNITE database [33] and ITS metabarcoding sequences from the experimental samples (indicated as purple dots). The outer colour strip indicates the families the sequences are assigned to (see legend on left-hand site). Figure S6. Phylogenetic tree of the family Psathyrellaceae (fungi), constructed from sequences from the UNITE database [33] and ITS metabarcoding sequences from the experimental samples (indicated as purple dots). The outer colour strip indicates the families the sequences are assigned to (see legend on left-hand site). Table S3. Results of the generalised linear models (GLM) testing the influence of explanatory variables on responses observed via the two identification methods and the five data sets generated. Bold p values indicate statistical significance. Data was missing for the morphologically identified hyphomycete community from cycle 1. LRT: likelihood-ratio test. Table S4. Explained variance and p values of the Redundancy Discriminant Analysis (RDA) variables with Hellinger transformed data, tested by type III ANOVAs. Bold p values indicate statistical significance. Data was missing for the morphologically identified hyphomycete community from cycle 1. Table S5. ANOVA (type II) results testing the Influence of explanatory variables on the aquatic hyphomycete taxa richness observed via both identification methods, morphological and molecular. Figure S7. Comparison between the aquatic hyphomycete community composition (over all cycles) identified morphologically based on morphologically and using ITS sequencing. Colour intensity indicates the relative sporulation rate (in conidia per g leaf dry mass) and relative read abundance, respectively (see legend). Numbers in parentheses (right of ITS read abundance) indicate the number of ASVs assigned to the species. *Articulospora tetracladia (anamorph) recorded in the UNITE database as Hymenoscyphus tetracladius (teleomorph). $ indicates species identified morphologically for which there was no reference sequence in the database. Figure S8. Responses of four common aquatic hyphomycete taxa (that were identified via both morphological identification and metabarcoding and showed at least one significant response) to the different cycles (numbers on top) and treatments (circle: control; triangle: fungicide treatment). Mean relative abundance measured via sequencing is shown in the four upper plots and mean sporulation (morphological identification, in conidia per g leaf dry mass) is shown in the four lower plots. Error bars represent 95% confidence intervals. P values are provided for significant results based on the two-way ANOVAs (type II). Data was missing for the morphologically identified hyphomycete community from cycle 1. Table S6. Differential analysis of fungal and bacterial amplicon sequence variants (ASVs) using DESeq2 [66]. Showing the log-fold change values of ASVs significantly different in treatment and controls for cycles 1, 2 and 3. Positive log fold change values means that ASV normalised read abundance increased in treatment compared to control, and negative log fold change value that ASVs read abundance decreased. Fungi marked with * are saprotrophs, with † are pathotrophs and with § are mixed (exhibit both trophic modes). Figure S9. Percentage of the different fungal groups (aquatic hyphomycetes and chytrids) and trophic modes (pathotrophs, saprotrophs, symbiotrophs and other unclassified fungi) in the different cycles and treatments. P values are provided for significant results based on the two-way ANOVAs (type II). Figure S10. Bubble plot showing the most common bacterial ecological functional groups. The size of the bubbles is referring to the mean read numbers per treatment and cycle, while the colour of the bubbles is referring to the treatment (control = blue, fungicide = yellow). Text S1. Differences field and lab conditions. Figure S11. Experimental setup of the microcosm experiment. Flow was created using magnetic stirrers. The magnetic stirrer bar was separated from the leaf bags using a stainless-steel mesh. Photo by Verena C. Schreiner. Text S2. Response on the ASV level.