The genus Fusarium includes many pathogenic species causing a wide range of plant diseases that lead to high economic losses. In this review, we describe how the Fusarium taxonomy has changed with the development of microbiological methods. We specify the ecological traits of this genus and the methods of its identification in soils, particularly the detection of phytopathogenic representatives of Fusarium and the mycotoxins produced by them. The negative effects of soil-borne phytopathogenic Fusarium on agricultural plants and current methods for its control are discussed. Due to the high complexity and polymorphism of Fusarium species, integrated approaches for the risk assessment of Fusarium diseases are necessary.

Polymeric and supramolecular models of humic substances (HSs) are considered. It has been noted that the HSs in natural objects can simultaneously occur in the forms of macromolecular polymers and supramolecularly organized monomers; macromolecular polymers of HSs can have some properties of suprastructures or be associated into aggregates, and covalent bonds can be formed between the monomers of supramolecules. Mineral particles of soil act as catalysts in chemical reactions between individual compounds, sorbents of biomolecules, and a surface for self-assembling HSs. It is supposed that the combination of such physicochemical processes and phenomena in soil as cementation, charring, incrustation, occlusion, sedimentation, sorption, coagulation, flocculation, encapsulation, complexation, and intercalation, as well as the entrapment of macroorganic, particulate, and soluble organic substances in micropores, can be as important for the stabilization of organic matter as the interactions between biomolecules with the formation of HSs.

Modern progress in soil biology is associated with the use of new molecular biology methods based on the isolation of total DNA from soil and its further analysis. The two main approaches to the study of soil microbial DNA are metabarcoding, the identification of the community composition via analysis of the sequences of barcode marker genes, and metagenomics, the analysis of the collective genomes of the community. These two methods provide direct access to the enormous genetic diversity of the “uncultivated majority” of soil microorganisms and have become an essential part of many soil biology studies. The review considers the application of these research methods to the study of the ecology and diversity of soil microorganisms. The methodological limitations of molecular genetics methods due to soil specificity as an object of research are discussed. The achievements, challenges, and prospects of metabarcoding and metagenomics in soil ecology research, as well as their combination with other research approaches, are considered.