First Report of Kosakonia Cowanii Causing Grain Discolouration of Rice ( Oryza sativa L.) in Indonesia

At the end of 2023, rice crop failures were reported in fields across Pagerageung, Tasikmalaya, West Java, Indonesia. Disease symptoms included brownish necrotic lesions on spikelets and panicles, grain discolouration, and unfilled grains, which resemble symptoms reported for bacterial panicle blight (Figure 1). Five diseased rice panicles were collected from each of the two most severely affected plots, surface-disinfected, and macerated in 0.85% saline solution. The resulting suspensions were serially diluted and plated onto S-PG medium (Jungkhun et al. 2022) followed by incubation for 72 h at approximately 30°C. Two isolates (TM14B and TM25B) with characteristics of the Burkholderia genus, i.e., round magenta colonies with a purple reflective centre, were selected for further purification. Upon purification on nutrient agar, isolates TM14B and TM25B had convex round colonies and a yellowish-cream colour similar to Kosakonia species (Han et al. 2023). Both isolates were Gram-negative, positive for KOH (3%), catalase, starch hydrolysis, gelatinase and nitrate reduction tests, but negative for arginine dihydrolase and toxoflavin pigment production. PCR amplification of the 16S rRNA gene was done using universal primers 27F and 1492R. Based on sequence analysis, TM14B (GenBank Accession No. PX061990) shared >99% identity with K. cowanii reference strains (CP022690.1, PQ344130.1 and KY933469.1), whereas TM25B (PX061992) shared >99% identity with K. cowanii reference strains (MK649841.1, MN636687.1 and MN636684.1). Phylogenetic analysis confirmed their placement within the Kosakonia clade. To confirm pathogenicity, isolates were inoculated into rice panicles as described by Uddin et al. (2025). Single panicles on rice plants (10 per isolate) growing in pots in a greenhouse at 30°C–35°C were sprayed at heading stage ten with bacterial suspensions at a concentration of 108 CFU/mL. Control plants were sprayed with sterile distilled water. After inoculation, plants were enclosed in plastic bags for 48 h. Two weeks later, grains developed brown spots similar to those described by Md-Zali et al. (2023) and Uddin et al. (2025), while control plants did not (Figure 2). Bacteria re-isolated from symptomatic grains produced colonies identical to the original isolates and were confirmed as K. cowanii by 16S rRNA gene analysis. To the best of our knowledge, this is the first confirmed occurrence of K. cowanii causing a disease on rice, characterized primarily by grain discolouration and symptoms resembling those reported for panicle blight, commonly attributed to Burkholderia species. Previously classified as Enterobacter cowanii, this bacterium was initially regarded as non-pathogenic or a probable endophyte. However, recent studies have identified K. cowanii as an opportunistic plant pathogen affecting hosts such as soybean and foxtail millet (Han et al. 2023; Krawczyk and Borodynko-Filas 2020). Although reports of K. cowanii associated with rice are limited, Kosakonia spp. DNA has been detected at increased relative abundance in abnormal rice seedlings (Nanfack et al. 2024). Kosakonia cowanii may represent an emerging pathogen of rice, highlighting the need for further studies to support accurate disease diagnosis and effective management strategies. The authors thank the Ministry of Higher Education, Science and Technology for the generous financial support for this research project, through Fundamental Research, grant number 093/C3/DT.05.00/PL/2025, and 1609/ UN6.3.1/PT.00/2025 from Universitas Padjadjaran, awarded to Mia Miranti.