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Abstract Background During alfalfa harvesting and preservation, it is important to minimize losses and preserve dry matter and nutrients. Soil contamination of alfalfa forage is a common issue that occurs during the ensiling process. Soil contamination can adversely influence the quality of silage, potentially altering the fermentation process, microbial composition, and iron content. Results In this study, different levels of soil (0, 1.5% or 7.5% contamination on a wet basis; silt loam soil) and two types of additives (LP, Lactobacillus plantarum inoculant alone; MLP, combination addition of molasses and Lactobacillus plantarum) were added to alfalfa and subjected to anaerobic fermentation for 45 days to evaluate the iron content as well as the alpha diversity and relative abundance of bacterial and fungal communities. Soil-contaminated alfalfa contained lower levels of LA (14.2–41.8 g kg−1 DM) and higher levels of AN (50.0–156.4 g kg−1 DM) compared to uncontaminated alfalfa. Soil contamination of alfalfa forage increased the abundance of Clostridia, Actinobacteria, and Alphaproteobacteria in silage. The application of LP or MLP in soil-contaminated silage increased the abundance of Lactobacillus and inhibited the growth of Enterococcus faecium, Pediococcus pentosaceus, unclassified_f_Enterobacteriaceae, and Weissella cibaria. In addition, as the level of soil contamination increased, both the total and bioaccessible iron contents in alfalfa silage increased. The dominant bacteria Lactobacillus plantarum exhibited a positive relationship with LA and bioaccessible iron contents and a negative relationship with pH, AN and BA. The dominant fungi Neocosmospora rubicola showed a positive relationship with total iron, BA, AN and pH. Conclusions Soil contamination of alfalfa increased the abundance of Clostridia, Actinobacteria, and Alphaproteobacteria and it also increased the total and bioaccessible iron content in silage. The addition of LP and MLP improved the fermentation quality of soil-contaminated silage by increasing LA production and reducing the relative abundance of Enterococcus faecium, Pediococcus pentosaceus, unclassified_f_Enterobacteriaceae, and Weissella cibaria. Graphical Abstract |
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