Effects of Plant Extracts and Pesticides on Rice Seed Microbial Communities in Burkina Faso

Context: As the first link in the plant production chain, seeds play a crucial role in establishing healthy, resilient crops. Contamination at this stage can reduce yields. Objective: This study aimed to evaluate the efficacy of two plant extracts compared to two chemical fungicides in promoting the health of three rice varieties grown in Burkina Faso, in terms of both fungi and bacteria. Methodology: The grains of three rice varieties were treated. Before and after treatment, the microbial community and germination rates on their seeds were assessed. Results: Although some varieties showed a significant reduction after treatment, the seeds retained an overall good germination capacity (>80%). Mycological analysis of the untreated seeds revealed 16 fungal species belonging to 14 genera, eight of which were rice pathogens. Fusarium moniliforme was the most prevalent species, particularly in the FKR 62 N variety. The plant extracts exhibited significant antifungal activity, achieving reduction rates of over 75% in more than 75% of cases. This result was often equivalent to or better than that of the fungicides. However, copper hydroxide sometimes stimulated the growth of undesirable fungi, such as Aspergillus flavus and A. niger. Analysis of bacterial diversity revealed 23 isolates in 10 genera, including Enterobacter, Kosakonia, Klebsiella, Pseudomonas, Bacillus and Methylobacterium. The FKR 64 variety exhibited the greatest bacterial richness, with Bacillus and Kosakonia present throughout, even after treatment. Herbal treatments generally preserved greater microbial diversity than fungicides. However, mancozeb exhibited greater activity, albeit with a variable impact on bacterial communities. Conclusion: These results highlight the potential of L. multiflora and E. alba extracts as natural alternatives to chemical fungicides for improving the sanitary quality of rice seeds while preserving their beneficial microbiome.