Research on the biological diversity of soil microorganisms is concentrated on three aspects of diversity: species, genetic and functional (Bundy et al., 2009; Bowles et al., 2014). In biodiversity analysis, it is important to evaluate the microbiome as a whole, not only its individual components (Daghino et al., 2012). Research on microbial activity in different environments is essential to increase knowledge about the ecology of their biocenosis and should be analyzed in connection with the existing environmental conditions, considering both biotic and abiotic factors (Bowles et al., 2014). Undoubtedly, an important aspect of such research is the selection and development of appropriate indicators and methods for assessing soil biodiversity and the activity of soil microorganisms, so that they can give the most reliable and reproducible results (Brussaard et al., 2007; Ghimire et al., 2014).

Investigation of soil biological activity as one of the indicators in the evaluation of tillage systems for the needs of sustainable agriculture was undertaken. It has been assumed that through the elaboration of the correct cropping technique, it will be possible to significantly increase the degree of fungal and bacterial diversity and reducing loss soil biodiversity (Danielsen et al., 2012).

Additionally, the introduction of such a cropping system should result in the reduction of energy consumption and labor-intensive tillage (Brussaard et al., 2007). The cultivation of plants in monoculture may be such a system. Tillage practices and cultivation techniques as well as residue management have an important effect on biological activities and the functional diversity of microorganisms (Lupwayi et al., 1998). Monoculture of plants can induce important changes in the soil environment and biological activity related to the reduction of fungal diversity (Liang et al., 2011). Many authors have suggested that long-term cropping of plants in monoculture induces degradation processes in the soil that can lead to a reduction in the a number of fungal species and a decline in organic matter (Brussaard et al., 2007; Liang et al., 2011; Han et al., 2017). Maize cultivation in monoculture is practiced in many countries. The cultivation of maize in direct sowing (zero-tillage) in Polish conditions is a good alternative but requires further systematic research on interactions between system factors: biotic and abiotic factors, soil environment, plants and fungi (Gałązka et al., 2017a,b). Maize (Zea mays L.) is one of the most important crops and is widely used in agriculture and industry, but its cultivation is very energy-intensive, hence agricultural practice is looking for a simpler solution (Liang et al., 2011; Gałązka et al., 2017c). The cultivation of some plants such as maize in a zero-tillage system is the most attractive and gives the biggest economic profits. Maize is grown increasingly in direct sowing and in this system leaves many crop residues are left on the surface of the field (Zhang et al., 2012).

The effects of long-term monoculture on soil quality, especially fungal genetic diversity, are not widely recognized for cultivation. Research on the effects of long-term cultivation of maize in monoculture on changes in soil quality, vegetation and yield of maize has been conducted at IUNG (Institute of Soil Science and Plant Cultivation, State Research Institute, Pulawy, Poland) for many years (Gałązka et al., 2017a,c). Long-term monoculture has a strong influence on soil parameters, especially on soil microorganisms and enzymes.

However, it is not known how the use of different techniques for cultivating maize growth may influence the composition of the fungal community. Biochemical and microbial properties of soil respond very rapidly to even small changes in environmental factors, such as temperature, moisture, tillage or cultivation techniques, and may have a strong impact on the core microbiome of fungi (Liang et al., 2011; Zhang et al., 2012). The term “core microbiome of fungi” can be understood as the group of fungi comprised of the members common to two or more fungal assemblages associated with a habitat (Shade and Handelsman, 2011). Evaluating the core fungal species is essential to unraveling the ecology of fungi consortia. Hence, bacterial and fungal communities are very often used as early indicators of soil alteration induced by agricultural management (Nannipieri, 2011).

Fungi constitute the biodiversity group agricultural soil and perform numerous important ecosystem functions such as influencing plant health (Wang et al., 2017). Fungal biodiversity in soil has been increasingly recognized as being beneficial for soil health (Fisher et al., 2012; Duniere et al., 2017). In current research on fungal biodiversity, a very important issue is not only the identification and distribution of this group, but also the definition of their important roles in ecosystems (Fisher et al., 2012). Comparison of the functional diversity of soil and the genetic diversity of fungi may enable a better understanding of their fundamental and ecological role and impact on plant health. Several environmental factors, including the physicochemical properties of soil, biological activities, soil moisture, biomass carbon and nitrogen, organic matter content, climate, season and also tillage systems, may significantly impact the diversity of the fungal genetic community in the soil environment (Liang et al., 2011).

The functional and structural diversity of soil fungi have been evaluated using several parameters, such as microbial biomass, respiration and enzymatic activities, as well as molecular methods, including next-generation sequencing (Lim et al., 2010; Xu, 2010; Zhang et al., 2012; Welc et al., 2014; Wang et al., 2017). Next-generation sequencing (NGS) of the hyper -alternating regions (16S rDNA for bacteria and ITS for fungi) enables definition of the genetic diversity of microorganisms without cell culture cultivation (Kozich et al., 2013; Orgiazzi et al., 2013). It relies on the isolation of total DNA from soil samples and preliminary amplification of hyper-alternating regions with the use of specific starters. In the next stage, correct adaptors and indexes are attached to amplicons (Ranjard et al., 2003; O'Brien et al., 2005; Schoch et al., 2012; Orgiazzi et al., 2013). The concentrations of samples are normalized and then all samples are combined into one cumulative sample that is designated for sequencing. The use of adequate indexes allows individual amplicons to be assigned to appropriate samples (Bartram et al., 2011; Kozich et al., 2013; Zoll et al., 2016).

In current paper, we propose that more insight should be gained into the determination of fungal structural diversity and community level and physiological profiling of microorganisms in the soil under long-term maize monoculture. The other objective of this work was to identify which groups of soil fungi are most sensitive to these techniques. Application of both genetic and functional methods will allow investigation of the composition of the fungal community and functionality of soil microorganisms directly in the soil. It will also allow explanation of the possible relationships between fungi and microbial community with using cultivation techniques.

In our study, the soils taken before the sowing of maize were characterized by statistically lower indexes of biological activity of substrate utilization than the soil collected at the flowering stage of maize. The highest Shannon—Weaver index was found in the soil from full tillage in both sampling times: before the sowing and flowering stages of maize growth, but in contrast, the lowest diversity was recorded for the soil collected before sowing from direct sowing. Other authors suggest that the microbial community, especially enzymatic activities is comparatively active in the flowering stage, while before sowing, in spring there is a decrease in their activity (Nannipieri et al., 2003; Brussaard et al., 2007; Bowles et al., 2014; Gajda et al., 2016). This hypothesis was probably connected with the quantitative composition of different root exudates of plants (Fisher et al., 2012; Baetz and Martinoia, 2014). The plant root exudates are very rich in various substances such as aminoacids, hydrocarbons, vitamins, organic acids and enzymes (Liang et al., 2011; Razavi et al., 2016). These substances may inhibit or stimulate the growth and development of fungi. On the other hand, changes in the availability of different nutrient compositions coming from different sources such as dead plant cells, root exudates and plants metabolites may have a significant effect on the selection of main fungal species and change their function (Spedding et al., 2004). In our study, the highest Average Well-Color Development (AWCD) index was observed in the soils obtained in the flowering stage of maize growth cultivated using different sowing techniques. The soil community level physiological profiling is not only connected with the plant species but also depends on the amount of plant remains from the root system (Zhang et al., 2012; Gałązka et al., 2017a). Biolog EcoPlate is the very sensitive method used by many authors for indicating even small changes in microbial structure in the soil under the influence of different abiotic and biotic factors (Frac et al., 2012; Wang et al., 2017).

The current paper focuses on the evaluation of the genetic diversity of fungi against the background of the general functional diversity in soil. The authors have choosen the Biolog EcoPlates for research, instead of specialty plates, dedicated to fungi identification (FF or SF). The Biolog EcoPlates indicate even slight changes in microbial structure in the soil under the influence of different abiotic and biotic factors. Many authors confirm that the results of functional diversity obtained from comparison of functional activity in soil with the use of the Biolog EcoPlates, FF-Plates and SF-Plates may be significantly different (Preston-Mafham et al., 2002; Klimek and Niklinska, 2007). In opinion of other authors the Biolog SF-N plates help to avoid the toxicity of TTC dye (present in the EcoPlates) to fungi (Deacon et al., 2006). In current paper, the intention of the authors was to assess only the genetic diversity of fungi against the background of functional diversity of microbial communities in soils under long-term monoculture of maize using different cultivation techniques. That's way community-level physiological profiling (CLPP) method with Biolog multiwell plates was chosen to evaluation functional diversity of microbial communities.

The post-harvest residues in direct sowing positively affect soil properties (Zhang et al., 2012; Wang et al., 2017). Also, a plant cultivation technique is a very important factor that can influence the biochemical activity of soil, and fungal diversity. In the opinion of many authors, plant cultivation in a long-term monoculture and intensive cultivation have a negative impact on the soil quality and can cause changes in the structure of the bacterial and fungal communities (Rice and Gowda, 2011; Wang et al., 2017). Plant cultivation in permanent monoculture is accompanied by a one-sided exhaustion of nutritive components, as well as by changes in the functional and genetic structure of soil microorganisms (Wang et al., 2009).

The results of our study indicate that the main group of fungi accounted for three phyla: Zygomycota, Basidiomycota and Ascomycota, while six dominant fungal classes identified as: Dothideomycetes, Eurotiomycetes, Leotiomycetes, Pezizomycetes, Tremellomycetes, and Mortierellomycotina. Ascomycota was the dominant phylum identified in all the analyzed soil samples. Our results are consistent with the results of other authors (Ma et al., 2013). The soils collected from full tillage in summer at the flowering stage of maize were characterized by the highest diversity in the genetic structure of the fungal community.

Klaubauf et al. (2010) investigated fungal diversity in four arable soils and one grassland in Lower Austria. According to the results of their research all soils were dominated by the ascomycetous orders Sordariales, Hypocreales, and Helotiales, taxa that are known from conventional cultivation approaches occurring in agricultural soils (Klaubauf et al., 2010). Our results also confirm these relationships.

On the other hand, a higher fungal genetic diversity in the soil collected from full tillage indicates that the maize is a very good plant to be grown in monoculture due to the large amount of root exudates into the soil (Baetz and Martinoia, 2014). Han et al. (2017) have proven how biotic and abiotic factors affected fungal diversity in the soil. This study raises questions about the important roles and ecological implications of fungal diversity associated with plant and environmental factors. According to these results compared with edaphic properties controlling soil fungal community patterns, the plant growth stage was the dominant factor in determining their dynamics and development.

The differences in fungal genetic communities in soils under long-term monoculture using different cultivation techniques were significant and caused characteristic changes in the structure of the fungal population (Lupwayi et al., 1998; Brussaard et al., 2007; Bowles et al., 2014; Ghimire et al., 2014). In our study, there was a negative impact observed on community level physiological profiling and fungal genetic structure in the soil under maize cultivated in long-term monoculture and full tillage. But, on the other hand, maize cultivated in direct sowing did not cause negative changes in the fungal structure making it more stable even during seasonal changes.

Direct sowing and reduced tillage are very good cultivation techniques for the development of the some group of fungi, especially mycorrhizal fungi. The large amount of crop residues left on the soil surface and slight interference with the soil structure may beneficially affect the stability of hyphae in the soil. In full tillage, the fungal hyphae are torn off, which significantly reduces their strangeness in the soil (Gianinazzi et al., 2010). In our study, the order Glomerales (belonging to mycorrhizal fungi) was identified in soils collected from direct sowing and reduced tillage. The order Glomerales, which includes the family Glomeraceae with genus the Glomus, is the very important group of arbuscular mycorrhizal fungi (AM) (Ngosong et al., 2010; Gałązka et al., 2017b). AM fungi participate in the bilateral exchange of carbon, phosphorus and other physiologically significant particles. These fungi also have the ability to produce and store in fungal filaments, the special fungal glycoproteins (glomalins) (Rillig, 2004). The carbon present in the glomalins has a large share of the organic carbon in the structure (Gianinazzi et al., 2010). In the natural environment, there is a large diversity of AM fungi (Ngosong et al., 2010). No other fungi, except for Glomeromycota, produce glomalins in a significant quantity.

Other genera that are very common in the soils collected from direct sowing and reduced tillage are Fusarium and Penicillium. Species of Penicillium are ubiquitous soil fungi preferring a moderate climate, commonly present wherever organic material is available (Duniere et al., 2017). Fusarium is commonly found in the soil and on underground and above - ground parts of plants, including seeds, plant residues and other organic substrates (Leslie and Summerell, 2013). Fusarium is common in temperate and tropical climate zones. This genus includes saprotrophic species and economically important species that are pathogenic for plants, causing significant economic losses in cereals (McMullen et al., 2012; Salgado et al., 2015). Of particular importance is the ability of Fusarium to produce a variety of toxins, very harmful to humans and animals, which contaminate plant foods with feed and food. Fusarium also produces phytotoxins that inhibit the growth of infected plants or cause their wilt, mainly seedlings (Salgado et al., 2015). They can also alter the metabolism of plants in an unfavorable way and act as virulence factors.

The main research objective presented in this paper involved examination of fungal structural diversity in the soil. The results of this study have contributed to a better understanding of genetic diversity and the composition of the population of fungi in the soil environment under the influence of the changes that take place in the soil under long-term maize cultivation. The cultivation techniques can modify the fungal community in the soil under long-term monoculture of maize. Maize cultivated in direct sowing did not cause negative changes in the fungal structure, making it more stable even during seasonal changes. The biggest changes in the fungal community were observed in full tillage of maize cultivation. In this study, soil under direct sowing and reduced tillage treatment had a higher biological activity, based on community level physiological profiling (especially in the soil samples collected from the flowering stage of maize growth), than that under full tillage and crop rotation treatment. The fungal genetic structure was significantly correlated with agricultural practices and seasons. Agricultural practices and seasons were two important factors affecting the fungal community. Further research is needed to determine the function of the main genera and species dominant in soil under monoculture of maize and to identify key organisms and their dynamics under maize growth using different agricultural management practices. Also, further studies need to quantify the fungal effects on soil biochemical cycling of nutrients and maize production. It is also necessary to conduct further studies on the bacterial identification and comparison of the bacterial and fungal relationship in the soil from long-term monoculture of maize.

AG: Contributions to the conception of the experiment; AG: Contributions to the design of the experiment; AG, JG: The acquisition and analysis of the data; AG, JG: The interpretation of data for the work; AG, JG: Drafting and writing the work; AG, JG: Revising the manuscript; AG, JG: Final approval of the manuscript and agreement to be accountable for all aspects of the work.