Kombucha Microbiome as a Potential Plant Architecture-Supporting Biostimulant: Metabarcoding Characterization of Its Bacterial and Fungal Community Structure

Identifying novel microbial resources for sustainable agriculture requires characterization of community composition and careful definition of functional and biosafety potential. This study characterized bacterial and fungal communities in the dried cellulosic pellicle (KP) and fermentation liquid (KS) fractions of a Kombucha Microbiome previously associated with plant architecture, pigment metabolism, and redox responses in tomato. Three independent fermentations were pooled within each fraction, and composite KP and KS samples were analyzed by 16S rRNA and ITS metabarcoding, with 18S rRNA as a complementary marker. Final analyses yielded 363, 98, and 30 OTUs in the 16S, ITS, and 18S data sets, respectively. The KS bacterial community was dominated by Komagataeibacter (58.81%), whereas KP showed a more heterogeneous profile, with the Burkholderia-Caballeronia-Paraburkholderia complex as the strongest classified signal (16.30%). Fungal communities differed more markedly: KS was dominated by Dekkera (96.80%), while KP contained Fusarium (37.72%), Aspergillus (18.02%), Malassezia (9.26%), Penicillium (8.50%), Filobasidium (5.57%), Clonostachys (4.85%), and Lecanicillium (2.49%). The Brettanomyces signal in KS-18S supported the Dekkera/Brettanomyces axis, and Kraken2-Bracken cross-checking reproduced dominant taxonomic patterns. Because biological sequencing replicates and a sequenced negative control were unavailable, KP-KS differences were interpreted descriptively. Overall, the two fractions were microbiologically distinct. This inventory does not establish a proven plant growth-promoting product, but provides a taxonomic basis for fraction selection, candidate isolation, functional and colonization studies, biosafety assessment, and development of standardized microbial consortia with potential plant architecture-supporting biostimulant activity.