Monitoring and Surveillance of Aerial Mycobiota of Rice Paddy through DNA Metabarcoding and qPCR

• Main Authors: Sara Franco Ortega, Ilario Ferrocino, Ian Adams, Simone Silvestri, Davide Spadaro, Maria Lodovica Gullino, Neil Boonham
• Format: Article
• Language: English
• Published: MDPI AG 2020-12-01
• Series: Journal of Fungi
• Subjects: airborne; spore trap; DNA metabarcoding; rice; <i>Pyricularia</i>; <i>Bipolaris</i>
• Online Access: https://www.mdpi.com/2309-608X/6/4/372

The airborne mycobiota has been understudied in comparison with the mycobiota present in other agricultural environments. Traditional, culture-based methods allow the study of a small fraction of the organisms present in the atmosphere, thus missing important information. In this study, the aerial mycobiota in a rice paddy has been examined during the cropping season (from June to September 2016) using qPCRs for two important rice pathogens (<i>Pyricularia oryzae</i> and <i>Bipolaris oryzae</i>) and by using DNA metabarcoding of the fungal ITS region. The metabarcoding results demonstrated a higher alpha diversity (Shannon–Wiener diversity index H′ and total number of observed species) at the beginning of the trial (June), suggesting a higher level of community complexity, compared with the end of the season. The main taxa identified by HTS analysis showed a shift in their relative abundance that drove the cluster separation as a function of time and temperature. The most abundant OTUs corresponded to genera such as <i>Cladosporium</i>, <i>Alternaria, Myrothecium</i>, or <i>Pyricularia</i>. Changes in the mycobiota composition were clearly dependent on the average air temperature with a potential impact on disease development in rice. In parallel, oligotyping analysis was performed to obtain a sub-OTU identification which revealed the presence of several oligotypes of <i>Pyricularia</i> and <i>Bipolaris</i> with relative abundance changing during monitoring.