Soil is a precious and complex natural resource that represents a huge reservoir of biodiversity with several billion prokaryotic and eukaryotic microorganisms. These microbes significantly share biomass and ecosystem functions in both natural and managed agricultural soils (Sidorenko et al., 1978). Microbial diversity is directly or indirectly affected by cultivation techniques, management practices, crop rotation, soil tillage, animal grazing, plant species and climatic changes (Acosta-Martínez et al., 2014; Chen et al., 2017; Gangireddygari et al., 2017; Liu et al., 2017; Yao et al., 2017). Variations in soil temperature, precipitation and soil pH also influence soil fungal diversity. Fungi are the dominant eukaryotes among soil microbial communities where they play crucial and key roles in terrestrial ecosystems (Abed et al., 2013; Peay et al., 2013; Acosta-Martínez et al., 2014).

Oman is situated at an arid region in the eastern part of the Arabian Peninsula and in summer, the temperature can rise up to 50°C. Most farms in Oman use traditional methods to promote biodiversity by cultivating several crops in the same field. The majority of farms in the northern part of the country grow date palms, while rest occupies citrus, vegetable crops such as tomatoes and cucumbers and other crops (Kazeeroni and Al-Sadi, 2016). Tomato is the major vegetable crop produced in Oman with the total production of over 70,000 tons in 2014 (FAO, 2015). Most tomato production in Oman is in commercial farms in the main agricultural area, the Batinah region. However, some of the farms that are located in desert areas also produce crops including tomatoes.

Microbial abundance, diversity and activity largely have implications on sustainable productivity of agricultural land and production systems. Information on the microbial communities associated with rhizospheres and their complex interrelationship is essential in the selection of sustainable crop rotations and management practices (Lenc et al., 2015; Chen et al., 2017). Direct culture of microorganisms and molecular methods are widely used to analyze soil microbes (Al-Sadi et al., 2015; Thomson et al., 2015; Kazeeroni and Al-Sadi, 2016). With the advent of next generation sequencing technologies, 454 pyrosequencing is used nowadays for assessing fungal diversity because of its high sensitivity (Esmaeili Taheri et al., 2015; Kazeeroni and Al-Sadi, 2016).

Although several studies addressed tomatoes, the information about the occurrence and the organization of fungal organisms in the tomato rhizosphere is currently limited. Furthermore, studies on fungal diversity in desert farming systems remain rare. Considering the different ways that can change the farming systems underlying soils and soil microbes, it is essential to understand the fungal diversity and their functions in soils under different managements. In this study, we examined soil fungal composition and diversity using pyrosequencing and culture-based techniques in two different tomato-farming systems: commercial vs. desert. Our main objective was to study how the changes of soil fungal communities vary with the different farming techniques. Knowledge in these areas will help predict how fungal communities vary under varying cultivation systems.

Several studies using molecular techniques and cultivation-based methods have described the fungal communities present in different farming systems (Al-Sadi et al., 2015; Van Geel et al., 2015; Kazeeroni and Al-Sadi, 2016). These studies have shown that fungal communities present in each system vary with the soil physiochemical properties and the cropping systems (Huang et al., 2015; Thomson et al., 2015). Our results demonstrate that CM and DE soil are highly diverse in soil microbiota. In general, the fungal diversity in the CM farming system was high compared to the DE system. The presence of relatively high percentage of TOC and TIC in both farming systems may be favorable for the growth of most fungi. In addition, N, P and K levels are relatively high in CM soil and this is probably because of the addition of a certain amount of organic and chemical fertilizers to the soil. Thus, the application of fertilizers by growers could have contributed to creating differences in the available minerals in soils between the two farming systems and soil types (Grüter et al., 2017; Wang et al., 2017). Grantina et al. (2011) reported positive impact of the available potassium in soil on the total number of cultivable filamentous fungi (CFF) and on the fungal diversity. In another investigation, a negative impact of phosphorus was observed on species richness of fungi in soil (Huang et al., 2005). As suggested by Gyaneshwar et al. (2002), this could be due to variations in the number of phosphate solubilizing microorganisms in soil.

Ascomycota is the largest and widespread phylum of fungi and is abundant in soil and composts (Abed et al., 2013; De Gannes et al., 2013; Kazeeroni and Al-Sadi, 2016). They are considered important decomposers and causal agents of several soil-borne diseases. In the present study based on the culture-based technique, Ascomycota was dominant in both farming systems. Eurotiomycetes was identified as the dominant class in both CM and DE, mainly because it contains two of the most common fungal genera viz., Penicillium and Aspergillus in most of the ecosystems (Godinho et al., 2015; Yee et al., 2016). Many saprophytic fungi were detected in DE; whereas plant pathogenic fungi viz., Cladosporium sp., Fusarium spp. and Pythium sp. were detected in CM soil. In the present study, Fusarium that causes wilt disease in tomato was detected in CM soil samples. The prevalence of Fusarium in CM soil might be due to the potential ability of chlamydospores of Fusarium to survive in the soil for many years under harsh environmental conditions. Chellemi et al. (2012) demonstrated that repeated tomato cultivation increased the incidence of Fusarium wilt caused by F. oxysporum f. sp. lycopersici by 20% or more.

The mycoparasite, Chaetomium sp. was detected in the CE soil. However, other fungal biocontrol agents like Trichoderma spp. and Gliocladium virens were not detected in both the farming systems. The existence of these organisms in soil is crucial for suppression of damping off and Fusarial wilt diseases of tomato (Blaya et al., 2013; Guzmán-Valle et al., 2014). Hence, the soil health in both the farming systems has to be improved by incorporation of organic amendments and application of biopesticides. Some of the fungal isolates could not be identified to the species level, possibly because they are new species or they need more genes to be sequenced. Future studies may address the identity of these isolates.

Pyrosequencing revealed that 95% of the taxa in DE soil belonged to the Ascomycota, whereas 60% of the taxa present in CM soil belonged to the phylum Microsporidia (a group of spore-forming unicellular parasites) and the genus Systenostrema. This is in agreement with our previous findings that Microsporidia are one of the dominant phyla in soil of farming systems in Oman (Kazeeroni and Al-Sadi, 2016). Microsporidia are obligate, spore-forming, fungi-related, intracellular parasites that infect many vertebrates and invertebrates. Several species of microsporidia have been described as biocontrol agents and pathogens of several beneficial insects (Bjornson and Oi, 2014). For example, Nosema pyrausta is effective in controlling European corn borer (Ostrinia nubilalis) (Lewis et al., 2009). A formulation of Paranosema locustae is commercially available for biological control of rangeland grasshoppers (Bjornson and Oi, 2014). Several studies reported that Microsporidia are natural intracellular parasites of the nematodes including Caenorhabditis (Kaya et al., 1988; Troemel et al., 2008; Zhang et al., 2016). The Microsporidia, Nematocida parisii was reported as a natural intracellular pathogen of Caenorhabditis elegans (Troemel et al., 2008). Zhang et al. (2016) described six new species in the Nematocida genus that are capable of infecting Caenorhabditis elegans.

In general, fungal species diversity was higher with the pyrosequencing than the culture-based method. These dissimilarities are to be expected and are not surprising since many of the fungi are not cultivable. Some studies showed that approximately 1% of the total microbes could be detected by culture-based methods (Sugiyama et al., 2010). On the contrary, some fungi can easily be cultured even they are present in small quantities. In addition, the high temperature in the Omani desert, which sometimes exceeds 50°C in summer, could have affected fungal diversity in soil by killing or suppressing several fungal species that are heat sensitive (Abed et al., 2013; Classen et al., 2015; Costa et al., 2015). This in turn could have affected the number of fungal species recovered from soil by culture-dependent methods. Also the absence of Chytridiomycota and Basidiomycota in culture-based method could have been because they either need specific media or their presence was limited as evidenced by pyrosequencing analysis (only 3.51% and less than 0.77% of the total soil population, respectively) (Gleason et al., 2007; Yee et al., 2016). Therefore, the detection of the precise diversity of fungi in a habitat using culture-based techniques is still challengeable. Pyrosequencing recovered more species that were not revealed by the culture-based method, implying that this approach will speed up the detection of very rare fungal species (Huang et al., 2015; Liu et al., 2017). However, pyrosequencing still has some limitations in describing fungal diversity. Future studies should investigate if using other media in addition to PDA and also other genes for pyrosequencing could help recover more fungal species and reduce the existing gap between pyrosequencing and culture based techniques.

This study provided evidence that farming systems strongly influence the composition of soil fungal communities. It is surprising to note that a few soil fungi that were detected by direct culturing method could not be detected by pyrosequencing. More research is required by using different soil DNA extraction procedures. Culturing fungi by using multiple nutrient media might result in the isolation of additional fungi from soil. Viability of fungal communities in soil needs to be considered when assessing their diversity in a farming system. One of the major drawbacks in PCR-based methods is their inability to discriminate between nucleic acids from viable and dead cells. The DNA extracted from dead cells can also serve as a template in PCR amplification. To overcome such issues, viability PCR using propidium monoazide (PMA) that differentiate nucleic acids from live and dead cells (Cangelosi and Meschke, 2014) has to be tested.

AA-S, EK, SM, and HA-M planned the experiment. EK and HA-M conducted the experiment, AA-S, EK, SM, and VR analyzed data, EK, AA-S, SM, VR, and HA-M wrote the manuscript. All authors approved the manuscript.

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.