Carisse, O. | bioRxiv Science

bioRxiv2025

Exploring the mycovirome: novel and diverse mycoviruses in Botrytis cinerea

Botrytis cinerea is a necrotrophic fungal pathogen that causes significant economic losses to many crops, including vegetables, fruits, and ornamental plants. The management of B. cinerea is difficult due to a rise in fungicide resistance. Harnessing mycoviruses that cause reduced virulence (hypovirulence) in B. cinerea is a promising alternative. Over 100 mycoviruses have been identified in Botrytis spp. to date, including several hypovirulence-inducing mycoviruses. This research aimed to further explore, for the first time in Canada, the mycovirome of B. cinerea and identify potential hypovirulence-inducing mycoviruses. Isolates of B. cinerea were collected from fruits and vegetables in the province of Quebec. Fitness and pathogenicity criteria, including sclerotia production, colony morphotype, and lesion size were evaluated. A double-stranded RNA (dsRNA) extraction protocol tailored to the detection of mycoviruses was used to sequence dsRNA from 45 isolates with low fitness/pathogenicity, and an in-house bioinformatics workflow was used to profile the mycovirome. Mycoviruses were identified in 44/45 isolates. Most of these had positive single-stranded RNA or dsRNA genomes, and a small number had negative single-stranded RNA, single-stranded DNA, or reverse transcriptase RNA genomes. Following deep analysis of RNA-dependent RNA polymerase and replication initiation proteins, a total of 62 unique contigs were identified belonging to new strains of mycovirus species. Furthermore, four putative novel mycovirus species belonging to Endornaviridae, Botybirnaviridae, Peribunyaviridae, and Bunyavirales taxa were identified. Several mycovirus species positively and/or negatively co-occurred with B. cinerea isolates collected from strawberry or raspberry. This study revealed a high degree of diversity in the mycovirome of B. cinerea. Species accumulation curve analysis indicated that, with the number of isolates characterized, we were unable to capture the full extent of expected diversity. Nevertheless, we identified potential hypovirulence-inducing mycoviruses, including Botrytis cinerea mitovirus 1, Botrytis cinerea hypovirus 1, and Botrytis porri botybirnavirus 1. Some of these novel mycoviruses belonged to taxa known to produce viral particles, which can be an interesting feature for their use as biocontrol agents (BCA). ImportanceThis study provides the first comprehensive profiling of mycoviruses infecting Botrytis cinerea in Canada, a significant step in understanding how these viruses can naturally limit crop disease. Due to growing resistance against conventional fungicides, new biological methods to control B. cinerea are crucial. By profiling mycoviruses in fungal samples collected in Quebec, we identified several novel viruses that appear to reduce the pathogenicity of B. cinerea. These viruses, known as hypovirulence-inducing mycoviruses, could be used to develop biocontrol agents (BCA), offering a more sustainable disease management alternative. Notably, we found virus families with extracellular potential, which may enable easier application as BCAs in agriculture. This research not only broadens the understanding of fungal virology but also holds promise for innovative, eco-friendly approaches to managing Botrytis cinerea in Canada.

genomics↗

bioRxiv2024

Experimental field trials model how the climate crisis will alter the phyllosphere and carposphere fungal communities of Vitis sp. L'Acadie Blanc

The climate crisis is changing temperature regimes worldwide, threatening global viticulture and wine production, as temperature is a primary driver of grape development. In Atlantic Canada, temperatures are projected to increase, inducing premature grape ripening, which can impact their biochemical profiles and, consequently, the quality of the vines and wines produced. Temperature is also a key factor in determining the composition and structure of resident fungal communities on the leaves (phyllosphere) and fruits (carposphere) of grape vines. Therefore, to better understand how these communities might change under potential future temperature regimes, we experimentally manipulated grapevines (Vitis sp. cv. LAcadie blanc) in the field. We used on-the-row mini-greenhouses to increase the temperature at different developmental, or phenological, stages of the fruits, and across the whole season. Phyllosphere and carposphere were sampled at four developmental stages, their DNA was extracted, and the fungal communities were identified via ITS metabarcoding. We found that phyllosphere and carposphere had significantly different community composition, which remained relatively stable throughout plant development. Increased temperature treatments had the most significant effect on fungal phyllosphere communities; we observed that phyllosphere samples exposed to higher temperatures before the onset of ripening maintained more diverse fungal communities throughout development. Our analysis showed that the increase in fungal diversity among phyllopshere communities corresponds to enrichments in potential phytopathogenic fungal taxa. However, this increase in phyllosphere fungal diversity was not conserved at other growth stages when the leaves developed at higher temperatures for the whole season. The results of this study will contribute to better understanding the impact of the climate crisis on grapevine phyllosphere and carposphere fungal community composition and assembly. This will allow producers to better adapt to climate variability and to better understand the role that these communities could play on grapevine health.

microbiology↗