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25 protocols using potato dextrose agar (pda)

1

Fungal Isolation from Leaf Lesions

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Leaf samples were processed for the isolation of fungal causal agents. The causal fungi were isolated from lesions using a single conidial isolation on 1.0% water agar containing 0.5 mg/l streptomycin under a stereo microscope according to the method described by Choi et al. [67 ]. The isolated plates were incubated at 25 °C for 24–48 h, and the germinated conidia were transferred onto potato dextrose agar (PDA; Conda, Madrid, Spain) containing 0.5 mg/l streptomycin. Pure fungal isolates were deposited in the Culture Collection of SDBR-CMU Laboratory, as previously mentioned.
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2

Fungal Tolerance to Arsenic and Chromium

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The capacity of the collected fungal strains to grow in the presence of increasing concentrations of As(V) and Cr(VI) was evaluated on solid cultures. Into Petri dishes (12 cm in diameter), we poured potato dextrose agar (PDA; Condalab, Torrejón de Ardoz, Spain) supplemented with 2.5, 5.0, 7.5, 10.0, or 12.5 g of As5+ L−1 from sodium arsenate (Na2HAsO4·7H2O; Thermo Fisher Scientific, Kandel, Germany) and 0.1, 0.5, 1.0, 1.5, and 2.5 g of Cr6+ L−1 from potassium dichromate (K2Cr2O7; Scharlab ExpertQ®, Sentmenat, Spain). Each BF strain was inoculated six times with an inoculation loop on each agar plate containing a defined concentration of As(V) or Cr(VI). The radial growth of each fungal colony was measured by averaging orthogonal diameters, and this value was then averaged again for all six colonies from every single plate. These measurements were repeated after 7, 15, 30, 45, and 60 days of incubation, which was performed at 25 °C under dark conditions. This prolonged timeframe was established to account for the potential long-term adaptation of slow-growing BF strains. Unamended control plates were also included. The tolerance index (TI) was calculated for every strain by dividing the measured growth when exposed to the metal in relation to the control plates.
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3

Isolation of Fungal Pathogens from Strawberry

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Fungal isolations were performed from tissues (stem and crown) of healthy strawberry plants (Fragaria x ananassa) collected in April 2014 from various orchards located in Caserta province, Southern Italy. Tissue fragments (3–4 mm2) were excised with a surgical blade, dipped in 2% (vol/vol) NaClO for 30 s, rinsed twice in sterile distilled water and dried on sterile Whatman filter paper under a laminar flow hood. The samples were placed in 90 mm-diameter Petri dishes containing Potato Dextrose Agar (PDA, Conda, Madrid, Spain), amended with streptomycin sulphate (100 mg/L). The dishes were kept at 24 ± 2 °C in the dark. After 4–5 days of incubation, the fungal colonies emerging on the vegetable fragments were transferred on fresh PDA plates. Single-spore cultures were obtained by spreading 0.2 mL of a suspension containing 1 × 103 conidia/mL, prepared from 7 days-old plates, on 1% water agar plates. Then, the germinated spores were transferred onto PDA dishes. The growing colonies were observed with an optical microscope to allow for a morphological characterization (colony diameter, colony color and degree of sporulation) (Olympus BH-2, Olympus America, Lake Success, NY, USA).
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4

Fungal Strain Characterization Protocol

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Agar plugs (5 mm in diameter) from the edges of each fungal strain were transferred onto plates containing potato dextrose agar (PDA; Condalab, Madrid, Spain), MEA, and oatmeal agar (OA; Difco, Le Pont de Claix, France) and then kept at 25 °C in the dark. After four weeks of incubation, relevant colony features, including aerial mycelium and pigment production, were recorded and the colony diameter was measured. Cardinal growth temperatures were studied on MEA for 4 weeks in the dark at 4, 10, 15, 20, 25, 28, 30, 35, 37, and 40 °C using the method described by de Hoog et al. [3 (link)] with some modifications. A light microscope (Nikon Eclipse Ni-U, Tokyo, Japan) was used to study the micromorphological features of each fungal strain. The anatomical structure related to size data (e.g., hyphae, budding cells, conidia, and chlamydospore) was based on at least 50 measurements of each structure using the Tarosoft (R) Image.
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5

Maintenance of Ascomycete Fungus Strains

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This study was conducted on a KU70Δ mutant [23 (link)] derived from the wild-type strain S. apiospermum IHEM 14462, originally isolated from sputum sample from a CF patient and previously used for whole-genome sequencing [25 (link)]. Strains were maintained at 37 °C by weekly passages on potato-dextrose-agar plus chloramphenicol (PDA from Condalab, containing in g/L: dextrose, 20; infusion extract from potatoes, 4; chloramphenicol, 0.5; and bacteriological agar, 15), supplemented with 20 µg/mL phleomycin or 50 µg/mL hygromycin, for maintenance of the KU70Δ mutant or the double mutant KU70Δ/SODDΔ, respectively. All strains were stored at −80 °C as conidial suspensions in 20% glycerol. Conidia processed into any experiment were collected from 9-day-old cultures grown in PDA or yeast extract-peptone-dextrose (YPD containing in g/L: yeast extract, 10; peptone, 20; glucose, 20; and chloramphenicol, 0.5%) and resuspended in sterile water or saline before to be enumerating by hematocytometer counts.
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6

Metabolomic Exploration of French Guiana Microbiome

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The majority of studied microorganisms are from French Guiana and were studied in previous research projects to explore their metabolome. Briefly, our environmental strain collection includes endophytes, insect-associated microorganisms and entomo- or phytopathogens [33 (link),34 (link),35 (link),36 (link)]. All microorganisms were isolated on Potato Dextrose Agar (PDA, Condalab, Madrid, Spain) medium at 28 °C and stored at −80 °C in a solution of water and glycerol (20:80). Finally, their phenotypes were recorded in the Bank of Natural Substances & Biodiversity (BNSB, ICSN-CNRS, Gif-sur-Yvette, France, https://icsn.cnrs.fr/en/platforms/strain-library (accessed on 1 January 2021). The microorganisms were collected with the following ABS authorizations: ABSCH-IRCC-EN-248781-1; ABSCH-IRCC-EN-248782-1 and ABSCH-IRCC-EN-245916-1 or before 2010.
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7

Phenotypic Characterization of Hortaea werneckii

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The H. werneckii isolate GPS5 used in the present study was plated from a single colony on malt extract agar (MEA, Oxoid, Basingstoke, United Kingdom), potato dextrose agar (PDA; #1022, Condalab, Spain), and Oatmeal Agar (OMA; #2060, Condalab, Spain) and incubated at 25°C for up to 1 month. Colonies’ diameter, color, and structure were recorded after 2 weeks of incubation. The hexadecimal color-coding system (also known as Hex code) was used to describe the color of the colonies using the online tool https://htmlcolorcodes.com/color-picker/.
The microscopic study was performed using light phase contrast microscopy on a glass slide, using 2-week-old culture from the colony center and the colony margin mounted in 60% lactic acid for observation using Leica DMLB Tilting Trinocular Phase Contrast and Dark Field Light Microscope. Micrographs were captured using a Leica DFC500 digital color camera optimized with Micromax Arkon software (V8.12.05).
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8

Isolation and Cultivation of Phosphate-Solubilizing Fungi

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Three phosphate-solubilizing fungi, namely A. chiangmaiensis SDBR-CMUI4, A. pseudopiperis SDBR-CMUI1, and A. pseudotubingensis SDBR-CMUO2, were isolated from the soil in a longan orchard [23 (link)]. All strains of fungi were preserved in the culture collection of the Sustainable Development of Biological Resources, located at the Faculty of Science, Chiang Mai University in Chiang Mai Province, Thailand. The fungi were grown on potato dextrose agar (PDA; Conda, Madrid, Spain) and kept in an incubator set at 25 °C.
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9

Cultivation of Four Fungal Species

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Pure cultures of four fungal species, namely, Lentinus sajor-caju CMU-NK0427, Ganoderma fornicatum CMU-NK0524, Ganoderma williamsianum CMU-NK0540, and Schizophyllum commune CMU-S01, were obtained from the culture collection of the Research Center of Microbial Diversity and Sustainable Utilization, Faculty of Science, Chiang Mai University, Thailand. All fungal strains were cultivated on potato dextrose agar (PDA; Conda, Madrid, Spain) and incubated at 30 °C for 7 days.
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10

Fungal Isolation from Symptomatic Fruits

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All symptomatic fruits were processed to isolate the fungal causal agents by storing them in a plastic container with moistened filter paper to stimulate fungal conidia production. The single conidial isolation technique was used to isolate the causal fungi from rot lesions on 1.0% water agar supplemented with streptomycin (0.5 mg/L) under a stereomicroscope, following the methods established by Choi et al. [84 ]. After 24–48 h of incubation at 25 °C in the dark, individual germ conidia were selected and transferred directly onto PDA (CONDA, Madrid, Spain) including streptomycin (0.5 mg/L). Pure fungal isolates were kept in 20% glycerol and submitted to the culture collection of the SDBR-CMU, Chiang Mai Province, Thailand.
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