Microbial communities make up a significant portion of the soil, and their activity is crucial to the soil's ability to function. In this study, we aim to evaluate the influence of animal waste-based digestate as N source on soil microbial activity and crop productivity over a three-year period in a crop rotation system. Two experimental field trials using the same design were performed in the year 2018–2020 and 2019–2021, respectively. Four different fertilization treatments, namely Synthetic Nitrogen, Chicken manure digestate, Cow manure digestate, and Pig manure digestate split fertilized (90 kg ha−1 N and 80 kg ha−1 N), and unfertilized treatment (control) were studied while growing different annual crops (spring wheat, triticale, and barley). There was a more significant positive effect on the soil microbial biomass carbon noticeably observed after the first year of digestate application, with an increase of 20.2–75% when compared to the unamended soil. Soil dehydrogenase activity was a less sensitive indicator for the effect of fertilization on soil biochemical activity, but the average data from both experiments showed an increase in fertilized soils from 6.6 to 8.5% in fertilized soils. The soil moisture did not significantly influence the microbial biomass and the enzymatic activity. However, crop productivity consistently rose each successive year, a positive effect of digestate use. We deduced that the long-term application of animal manure digestate under natural conditions coupled with other variable factors such as seasonal conditions and agricultural management techniques significantly influenced the microbial biomass contents – a critical component of the biological state of the soil. Our findings will help identify how and what could make soil microbial communities and crop productivity vulnerable to seasonal changes in relation to the consistent application of animal manure digestate to agricultural soils and the agricultural techniques employed.
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