Isolation of Endophytic fungi. Healthy plant samples viz., Allium cepa L., Chenopodium album L., Corchorus olitorius L., Euphorbia hirta L., Haloxylon stocksii (Boiss) Benth. & Hook, Sida ovata Forssk., and Solanum melongena L., growing in the experimental field of Botany Department, Karachi University and agricultural field of Malir, Karachi were collected (along with root, shoot and leaves) and endophytic fungi were isolated within 24 hours. Permission of Chairman, Department of Botany and Campus Office was obtained for collecting the plants from the campus, whereas, plants collected from agricultural filed at Malir with the permission of Owner of the field. Identification of each plant species was confirmed by a taxonomist and herbarium number was assigned (Table 1). All the experiments were performed in accordance with institutional guidelines and regulations.
After washing with tap water, plant samples were cut into small pieces (1 cm long), then sterilized with 1% bleach [Ca(OCl)2] for three minutes, followed by sterilization with 70% alcohol for three minutes and then with sterile water. Sample was crushed in 50 mL sterilized water by using an electric grinder and a dilution was made up to 1:104. From final dilution 0.1mL was spread over Petri plates containing Potato Dextrose Agar (PDA) amended with streptomycin (0.2 g/ L) and Penicillin (100000 units/L). Fungi isolated after incubation at 28oC for 7 days were initially identified on morphological characters according to44,45,46,47,48,49. Identification of endophytic fungi was confirmed by using molecular biological tools.
Molecular identification of endophytic fungi. Fungal mycelium (1.5-2 cm2) was obtained from fresh culture in sterile Eppendorf tubes and the cell was disrupted with glass beads in liquid nitrogen. The DNA extracted by using Biobasic EZ-10 Spin Column, Fungal Genomic DNA Mini-Preps Kit, (CANADA) according to their manufacturer instructions. DNA quality was assessed by using Agarose gel electrophoresis while the purity of DNA was assessed by spectrophotometer (Shimadzu- UV-1800). The primer sets i.e., ITS1 region (5’-TCCGTAGGTGAACCTGCGG-3’) and ITS4 region (3’-TCCTCCGCTTATTGATATGC-5’) used for amplification of rDNA ITS region. For the amplification of targeted region, each PCR reaction mixture comprised of fungal genomic DNA (100ng), 1.0 μL of ITS1 primer (10pmole), 1.0μL of ITS4 (10 pmole), 12.5μL of 2X PCR Master Mix (Thermo Fisher Scientific, MA, USA) up to final volume 25 μL with nuclease free water. PCR amplification was carried out on ABI 2700 thermal cycler (California, USA) using the following conditions: first hold for 5 minutes at 94 °C for DNA denaturation followed by 35 cycles of denaturation at 94 °C for 45 sec, annealing at 55 °C for 45 sec and extension at 72 °C for 1 minute, then second hold for 10 min at 72 °C after that hold at 4 °C. Amplified products evaluated by using 2% Agarose gel electrophoresis at 100 V for 35 min. The amplified products were submitted to BGI Genomic Services (Shenzhen, Guangdong, China) for Sanger sequencing of both ITS1 and ITS4. The consensus sequences were retrieved from both sets of primers and the sequences were edited and aligned manually by using BioEdit software (Version 7.2.6). BLAST analysis carried out for the identification of fungal isolates. Phylogenetic relationships of all isolates constructed using neighbor joining (NJ) method with MEGA-X software (PMID: 29722887). Each Sequence submitted to NCBI Genbank.
Antifungal activity of endophytic fungi. Antifungal activity of endophytic fungi was determined against Rhizoctonia solani, Macrophomina phaseolina, Fusarium solani and F.oxysporum by using Dual culture plate assay. Test isolates were inoculated in Petri dishes having Czapek’s dox agar and on its opposite side pathogenic fungi was placed and incubated at 28oC for 5-7 days. Inhibition zone produced, if any was recorded50.
Antifungal activity of culture filtrates of endophytic fungi. Test fungi grown at (25-30°C) for 15 days in 250mL flasks containing 100mL Czapek’s Dox broth. The broths were filtered over Whatman #1 filter paper in flask and exposed to chloroform vapors under laminar flow hood to kill fungal propagules. Thick sterile discs were impregnated with endophytic fungal culture filtrates at 20, 40 and 60µL/disc and dried. Discs along with control (disc loaded with Czapek’s Dox broth) and +ve control (carbendazim at 20µg/disc) were placed at the periphery of plates. Test fungi (5 mm disc) were inoculated in the center. Zone of inhibition, if any was recorded after 5-7 days of incubation at 30°C27.
Fractionation of culture filtrates of endophytic fungi. The culture filtrates (Chaetomium sp., T. assiutensis, T. trachyspermus) were extracted separately 3 times with n-hexane in a separating funnel. n-hexane insoluble fraction was further extracted with chloroform. Both fractions were dried separately on a rotary vacuum evaporator (Eyela-NE, Japan) and finally gummy mass was obtained51.
Antifungal activity of solvent fractions of endophytic fungal culture filtrates. Each fraction was re-dissolved in their respective solvent at 1.5 mg/mL and 5mm diameter sterile disc of filter papers were loaded at 20µl (30µg/disc), 40µl (60µg/disc) and 60µl (90µg/disc) and dried. Other details are the same as described in antifungal activity of culture filtrates of endophytic fungi.
Gas Chromatography-Mass Spectrometry (GC-MS). The n-hexane soluble portion was oily in nature, which was subjected to GC/MS analysis. GC/MS was conducted on Agilent (6890) Gas Chromatograph linked with Mass Spectrometer: Jeol, JMS: (600H). Operational mode was EI having the ion source at 50oC and their electron energy then maintained at 70 eV. Carrier Gas Volume placed in a range of 1.0-5.0µL. Individual peaks of each compounds were assigned, their mass spectra and retention indices (RI) were matched online with National Institute of Standards and Technology, USA (NIST: Mass Spectrometry Data Center (mainlib) NIST#: 352898 ID#: 113419 DB) and finally compared with Science finder.
Biocontrol potential of endophytic fungi against root rotting fungi. Talaromyces assiutensis and T. trachyspermus isolated in this study were selected for further study as biocontrol agents against root rotting fungi, since other fungal isolates are well known plant pathogens or environmental contaminants. Efficacy of Talaromyces spp., was examined in pots and also in field plots, using sunflower (Helianthus annuus L.) as test crop. Efficacy of Talaromyces spp., was also compared with endophytic Chaetomium sp. (KUCC1359) and Cephalosporium sp. (KUCC1358) obtained from the culture collection center at University of Karachi.
Screen house experiments. The experiment was conducted in February, 2017, in clay pots containing sandy loam soil (15 cm diam.) at 1 Kg/pot and aqueous suspensions of endophytes Talaromyces assiutensis, T. trachyspermus, Chaetomium sp., and Cephalosporium sp., (107 cfu/mL), grown on potato dextrose broth (pH 5.6) at room temperature were applied onto each pot (25 mL/pot). Soil was naturally infested with 3 to 13 % colonization of R.solani, using sorghum seed as bait52, 3000 cfu/g of soil of Fusarium spp., using soil dilution technique53 and 3-9 sclerotia/g of soil of M.phaseolina, by using wet sieving and dilution technique54. Aqueous suspension (25 mL) of endophytes (8 × 107 CFU mL-1) grown in potato dextrose broth (PDB) for 15 days at 28℃ was drenched in each pot after placing the seeds, then covered with soil (about 1.5 cm). Population of endophytes in suspension was determined by dilution plate method on potato dextrose agar using the formula:
Seeds of sunflower (6 seeds per pot) were sown in each pot and randomized with four replicates. Temperature ranged from 25 0C- 350C. Carbendazim (200 ppm in water) at 25mL in each pot used as +ve control; untreated plants were kept as control. In each pot, four seedlings maintained and excess were removed after germination. Observations were recorded after 45 days, plants were uprooted, washed under the tap water, and then blot dried. Root length and shoot length were measured and their fresh weight was recorded on an electronic balance. To determine the incidence of infection of fungi on roots, tap roots were cut into (1 cm) pieces, surface sterilized with 1% bleach. The root pieces were transferred onto PDA plates containing antibiotics, streptomycin and Penicillin as described above. Fungi grown on root pieces after 5 days of incubation at 25oC were identified and infection (%) of each fungus was calculated by using the formula55.
The experiment was repeated in 2018 in similar conditions, in order to confirm the efficacy of endophytic fungi.
Field plot experiments. The experiment was also conducted in field plots (2x2 m) of the Department of Botany in 2017 and repeated in 2018. Aqueous suspension of above mentioned endophytes applied in the planting row at 400 mL-1 2 m. The sandy loam soil (pH 8.0) was infested naturally with root rotting fungi M.phaseolina (6-11 sclerotia / g soil), 7-16 % colonization of R.solani, on seed of sorghum used as a bait , 3300 cfu/g of soil having Fusarium spp. Sunflower seeds (30 per 2m row) were sown and watered after 2-3 days. Complete randomized block design was used in each experiment with 4 replicates. Carbendazim (200 ppm in water) at 400 mL/ 2m row served as +ve control. After 45 and 90 days, 4 plants from each row were uprooted, washed under tap water and data collected from plant growth, suppression of root infecting fungi and plant stress markers were determined.
The experiment was repeated in 2018 in similar conditions to confirm the efficacy of endophytic fungi.
Biochemical parameters. Leaves (1 g) from each plant sample were dried overnight at 70oC in an oven, crushed in 100 mL ethanol (96% v/v) and centrifuged at 504 g for 20 minutes. The supernatant was collected to analyze polyphenol, salicylic acid and antioxidant activity.
Estimation of polyphenols. The Folin-Ciocalteu reagent was used to determine the total phenolic content56, aliquots (100µL) were mixed with 2 mL of Na2CO3 (2% w/v), kept for 2 minutes at room temperature and then Folin-ciocalteu phenol reagent (100µL of 50%) was added, finally kept in dark for 30 minutes. Absorbance (at 720 nm) was recorded and phenolic content was expressed in mg of Gallic acid equivalents (GAE)/g of dried sample.
Estimation of salicylic acid. Sample aliquot (100 µL) was mixed with the freshly prepared (0.1%) solution of ferric chloride, and volume was made up to (3.0 mL). Absorbance was measured on a spectrophotometer at 540nm. The results were expressed as salicylic acid equivalent (mg of SA per gram of dried extract)57.
Determination of antioxidant activity. Antioxidant activity (leaves) was determined by using 2, 2-Di-phenyl-1-picrylhydrazyl (DPPH) as a free radical scavenging activity as described5, where aliquot (0.2mL) was added in (0.8 mL) of 100 mM, Tris-HCl buffer (pH 7.4), mixed with 30µM DPPH (1 mL) and vortex finally. Their absorbance was recorded at 517 nm at 01 minutes, and at 30 minutes after keeping in dark, using 1 mL aqueous ethanol with 01 mL of DPPH served as a control. Following formula used to determine their activity:
Analysis of data. The data was analyzed by using software SPSS, Costat, one-way ANOVA for plant growth and biochemical parameters. Significant value at P < .005 was calculated to compare the means. For fungal infection, two- or three-way ANOVA was used and least significant difference (LSD) was calculated at P < 0.05. and their means were compared at significant level (p<0.05). To highlight the performance of the most effective isolate of endophytic fungi on plant growth, production of resistance markers and antioxidant activity, Principal Component Analysis (PCA) was performed by using software CANOCO Engine Version 5.058.