Comparison of colonization, diversity, and molecular phylogeny of endophytic fungi in selected traditional and newly improved rice (Oryza sativa L.) varieties in Sri Lanka

Abstract

Rice (On'-fl sativa L.) is the staple diet amongst almost all ethnic groups in Sri Lanka. The use of endophytic microorganisms inhabiting the rice plant is a promising strategy for improving paddy yields. However, little is known about the diversity and the evolutionary relationships among the species of endophytic fungal assemblages associated with different rice varieties in Sri Lanka. Therefore, this study was aimed at the assessment of colonization, diversity, identification, and the phylogenetic relationships of endophytic fungi present in newly improved rice varieties At 362. Bg 352, Bw 367, and a traditional variety, Suwandel. Healthy plant samples of each rice variety were collected during the two main rice-growing seasons, Maha and Yala (2019), from Anuradhapura, Kurunegala, Gampaha, and Kalutara districts in Sri Lanka. Endophytic fungi were isolated from the leaves, stems, and roots of each rice variety using previously developed protocols. All strains were categorized into thirty-nine (39) morphological groups based on colony characteristics and micromorphological features. The Internal Transcribed Spacer (ITS) region of a representative strain of each morphological group was amplified and sequenced. They were identified by phylogenetic analysis based on sequences of ex-types. Thirty-one (31) isolates identified to species level belonged to twenty-two (22) genera within nine (9) orders. Apart from that, four (04) and three (03) isolates were identified up to generic and order levels respectively. One isolate was identified up to the family level. Out of the fungal species, seventeen (17) were novel records for Sri Lanka. Evaluation of the colonization percentages of endophytic fungal assemblages showed that the variety Suwandel collected from Kurunegala during the Maha and Yala seasons respectively had the highest colonization rate (52% and 35%). The study also showed that Aspergillus tereus, Curvularia lunata, Dendryphiella sp.. Fusarium falciforme, Microdochium fisheri, and Penicillium oxalicum were the most dominant species in all rice varieties. Endophytic fungal diversity evaluated by Shannon’s and Simpsons diversity indices showed the highest species diversity in variety Bg 352 collected from Kalutara district during the Yala season.