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Nitrogen (N) is widely distributed in the lithosphere, hydrosphere, atmosphere and biosphere. It is a basic component of every plant cell as well as microorganisms, as a component of proteins, nucleic acids and chlorophyll. It enters soil with organic and mineral fertilizers, plant and animal residues and biological nitrogen fixation. There are various forms of nitrogen in soil, and this element is usually transformed by microorganisms. The transformation of nitrogen compounds (ammonification, nitrification and immobilization) is significantly influenced by climatic conditions and the physicochemical properties of soil. Microbial mineralization of nitrogen organic matter results in the enrichment of soil with this element, which is necessary to generate a yield. The amount of nitrogen entering soil through the mineralization of crop residues ranges from 15 to 45 kg N/ha in cereal residues and from 80 to 144 kg N/ha in winter rape residues. Biological nitrogen fixation can increase the nitrogen content in soil by 30–50 kg/ha/year. In recent decades, the mismanagement of mineral fertilizers has drastically changed the natural balance of the nitrogen cycle. Every year huge amounts of nitrogen compounds enter the aquatic ecosystems and cause their eutrophication. That is why it is important to have adequate knowledge of sustainable fertilization so as to practice integrated crop management.

The article aims to present results of research on anaerobic digestion (AD) of waste wafers (WF-control) and co-substrate system–waste wafers and cheese (WFC-control), combined with digested sewage sludge, as inoculum. The purpose of this paper is to confirm the outcome of adding silica/lignin (S/L; 4:1) material, as a microbial carrier, on the process performance and genetic diversity of microbial communities. The experiment was conducted in a laboratory under mesophilic conditions, in a periodical operation mode of bioreactors. Selected physicochemical parameters of the tested carrier, along with the microstructure and thermal stability, were determined. Substrates, batches and fermenting slurries were subjected to standard parameter analysis. As part of the conducted analysis, samples of fermented food were also tested for total bacterial count, dehydrogenase activity. Additionally, DNA extraction and next-generation sequencing (NGS) were carried out. As a result of the conducted study, an increase in the volume of produced biogas was recorded for samples fermented with S/L carrier: in the case of WF + S/L by 18.18% to a cumulative biogas yield of 833.35 m3 Mg−1 VS, and in the case of WFC + S/L by 17.49% to a yield of 950.64 m3 Mg−1 VS. The largest total bacterial count, during the process of dehydrogenase activity, was maintained in the WFC + S/L system. The largest bacterial biodiversity was recorded in samples fermented with the addition of cheese, both in the case of the control variant and in the variant when the carrier was used. In contrast, three phyla of bacteria Firmicutes, Proteobacteria and Actinobacteria predominated in all experimental facilities.