Open Access

Binal Dobariya, Dirk P. Bockmühl

• Apricot kernel shells (AKS) and walnut shells (WS) are byproducts from fruit processing lines and may serve as sustainable alternatives to microplastics in industrial applications due to their high content of natural polymers such as cellulose, hemicellulose, and lignin. Their use necessitates understanding the associated microbial risks to secure the quality of raw materials. This study investigates microbial communities on AKS and WS collected from Kyrgyzstan over a three-year period of harvests (2022-2024), using culture-dependent total viable count (TVC) as well as culture-independent shotgun metagenomic sequencing to explore the taxonomic and functional profile of microorganisms present on the shells. Results indicated higher microbial loads in more recent harvests with a dominance of Proteobacteria on WS comprising Pantonea agglomerans and Xanthomonas arboricola. On AKS, the phylum Firmicutes was prevalent emphasizing on Weissella confusa and Weissella cibaria. Incubation at humid conditions increased the fungal diversity in particular, especially Rhizopus microsporus in WS and Pichia membranifaciens in AKS, highlighting storage humidity as a critical factor which may induce microbial shifts. Functional metagenomic profiling based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway database, highlighted metabolic and relational pathways of microbial community present on AKS and WS. Furthermore, microbial similarities between shell samples and their respective storage environments suggest that handling and storage practices may significantly affect contamination profiles.