Endophytic bacterial and fungal communities of mustard tuber (Brassica juncea var. tumida Tsen et Lee) and preliminary identification of glucosinolate-degrading strains

The mustard plant ( Brassica juncea ) tubers serve as raw material for zhacai , a traditional pickle product. These tubers host endophytes that may contribute to fermentation and glucosinolate (GSL) degradation. To elucidate the roles of bacterial and fungal endophytes in GSL degradation during zhacai fermentation, a comprehensive range of molecular and chemical approaches was employed to determine biomass, diversity, community structure, and GSL degradation in mustard plant tubers collected from Baisheng, Zhenxi, and Nantuo towns in Fuling, Chongqing. Illumina MiSeq sequencing revealed that Pseudomonas was typically the most abundant bacterial genus, while Aspergillus and Cladosporium were the predominant fungi. Significant differences were observed in bacterial and fungal compositions among tuber samples from the three locations. Using culture methods, 48 tuber endophytes (33 bacteria, 15 fungi) were isolated, of which 11 bacterial strains were identified as GSL degraders. Strain N19 ( Sphingobacterium spiritivorum ) exhibited the highest degradation percentages for sinigrin and gluconasturtiin, reaching 35% and 41%, respectively. Bacillus strains N2 ( Bacillus amyloliquefaciens ) and N1 ( Bacillus velezensis ) also showed notable degrading activities and potential as safe, salt-tolerant candidates for zhacai fermentation. Therefore, these findings demonstrate that mustard tubers harbor active GSL degraders, which could be potentially utilized in zhacai fermentations. • Pseudomonas (bacteria), Aspergillus and Cladosporium (fungi) were the most dominant genus in tuber's endophyte. • Eleven glucosinolate-degrading strains are obtained, among which S. spiritivorum showed the highest activity. • The degrading products of sinigrin include allyl isothiocyanate and allyl thiocyanate. • The degrading products of gluconasturtiin include 3-phenyl-2-propionitrile and 2-phenethyl isothiocyanate.