Producing high-quality and safe whole-plant quinoa silage through selecting variety and harvest time

The great potential of whole-plant quinoa (WPQ) as a forage crop has been recognized in recent years. In this study, we investigated the effects of variety and harvest time on the fermentation characteristics, bacterial community, and hygienic quality of WPQ silage. Five varieties (Hongxin, Mengli1, SL577, SL2860, SL923) were grown across five separate experimental fields, with harvest occurring after 90 days (H1), 105 days (H2), or 120 days (H3). The samples were ensiled to evaluate their fermentation characteristics and bacterial composition. Hygienic quality was assessed using the Tax4fun2 and BugBase tools for potential pathogenicity and antimicrobial resistance prediction. The variety significantly influenced (P < 0.05) all fermentation variables (including pH, lactic acid, acetic acid, propionic acid, ethanol, and ammonia nitrogen), while harvest time affected pH and the contents of acetic acid, propionic acid, and NH₃-N (P < 0.05). An interaction between variety and harvest time was detected (P < 0.05) for all fermentation variables. Based on the flieg' score index, silage quality increased for Mengli1 (5.20-54.8), SL577 (36.7-71.5), and SL923 (34.9-77.0) with delayed harvest time, while silage quality decreased for Hongxin (52.1-41.4) and SL2860 (78.4-63.6). Compared to other silages, Hongxin silages exhibited greater differences in bacterial community composition between harvest times (indicated by higher PERMANOVA R²-value). Tax4fun2 and BugBase analyses revealed that delaying harvest time significantly increased (P < 0.05) the relative abundances of pathogenic and antibiotic-resistant KEGG pathways ("Infectious disease: bacterial invasion" and "Drug resistance") and harmful microbes associated with potential pathogenicity and antimicrobial resistance in Hongxin silages. This study highlights the importance of variety and harvest time in producing high-quality, safe WPQ silage, which is beneficial for ensuring the safety in our food supply chain.