Soil represents a complex system arising from interactions between a highly variable physicochemical matrix and diverse assemblages of organisms and nutrients. Natural processes can disrupt this intricate balance, leading to the degradation of soil properties and its ability to support biomass production. Effective management of soil nutrients hinges on understanding the soil-microbial community-plant system. This can be achieved by quantifying the soil proprieties and microbial densities, allowing for the establishment of a balanced relationship between these components for optimal ecosystem function (Rhouma et al., 2019; Rhouma et al., 2021; Iqbal et al., 2023).
The study likely investigated the relationship between different vegetable crops and the fungal communities in the soil, particularly Trichoderma spp. The findings suggest that the composition and abundance of fungi in the soil varied depending on the vegetable crop planted. Interestingly, the pomegranate cultivar Gabsi was observed to have the highest abundance of fungi, while tomato varieties Firenze and Dorra showed the least. This indicates that different vegetable crops might influence the type and amount of fungi present in the surrounding soil. In simpler terms, the type of vegetables you plant might affect the types of fungi living in the soil around them (Rhouma et al., 2019; Rhouma et al., 2021; Janowski & Leski, 2022).
Plant communities play a key role in shaping the composition and diversity of soil fungal communities through both direct and indirect interactions (Burke et al., 2009; Rousk and Bååth, 2011; Tedersoo et al., 2020). Plants directly interact with specific fungal groups, such as mycorrhizal and pathogenic fungi. Additionally, they indirectly modify the local soil environment by releasing carbohydrates through their roots (Moll et al., 2016; Janowski & Leski, 2022). Plant litter deposition also influences soil acidity and nutrient content (Aponte et al., 2010), while dead wood and organic matter contribute further organic material (Mäkipää et al., 2017). The varying degrees of plant interaction among different soil fungal trophic guilds leads to differential distribution patterns within the soil community (Tedersoo et al., 2020). Furthermore, the leaf litter can decrease local soil pH, hindering the activity of many fungal taxa (Tedersoo et al., 2020; Janowski & Leski, 2022).
Plant-microbe interactions and niche adaptations significantly influence fungal community composition across the rhizosphere. Plant root exudates containing signaling molecules (flavonoids, strigolactones) and various organic compounds (organic acids, amino acids, proteins, fatty acids) shape these interactions (Sundin & Jacobs, 1999; Zhalnina et al., 2018). Additionally, factors like temperature, oxygen levels, and UV light play a role, and these factors vary considerably across locations, plant root structures, and plant types themselves (Põlme et al., 2018; Chen et al., 2020; Zhang et al., 2020).
The rhizoplane, the root surface zone directly influenced by root exudates, exhibits lower fungal diversity and richness compared to the surrounding rhizosphere soil. This suggests selective pressure from plant roots limits the number of colonizing species (Lee et al., 2019). Consequently, the fungal communities within each rhizo-compartment (rhizoplane vs. rhizosphere) are distinct and susceptible to further manipulation by host-controlled processes (Gottel et al., 2011; Janowski & Leski, 2022). Potential variations in communication and mutualistic relationships between plants and fungi might also exist between these compartments. For example, mycorrhizal fungi interacting with root cortical cells may influence the colonization of other fungal species within the rhizosphere (Parniske, 2008; Iqbal et al., 2023). The interplay of plant immunity and microbial competition likely exerts different selective pressures on the root surface compared to the bulk soil. This phenomenon could ultimately lead to the development of unique fungal communities adapted specifically to the rhizoplane environment (Parniske, 2008; Zamioudis et al., 2014; Stringlis et al., 2018; Iqbal et al., 2023).
Despite their crucial role as plant symbionts, fungal endophytes (Trichoderma spp.) remain a relatively unexplored component of the soil fungal community. Due to their recent rise in scientific interest, limited research exists on the factors shaping their distribution patterns. While most fungal endophytes exhibit generalist tendencies, colonizing a wide range of plant taxa (Suryanarayanan et al., 2018; Janowski & Leski, 2022). U’Ren et al. (2019) suggested that plant host identity at the clade level might influence their soil distribution.
Our findings demonstrate a significant influence of tomato variety on the associated fungal community. Our finding is in concordance with previous studies in maize (Zea mays) where variety did not significantly impact alpha diversity (species richness within a site) but did influence beta diversity (species composition differences between sites) to some extent (Kong et al., 2020). Similar to our results, potato (Solanum tuberosum) variety has been shown to significantly affect fungal community composition (Hannula et al., 2010; Kong et al., 2020; Guo et al., 2023). Plant root secretions provide carbon substrates, including primary and secondary metabolites, utilized by fungi (Jones et al., 2004; Broeckling et al., 2008; Guo et al., 2023). This suggests that different plant varieties may influence the resident soil fungal community through variations in their root exudate composition. This aligns with prior research demonstrating the ability of diverse plant species to shape fungal communities via root secretions. The observed differences in fungal communities associated with different tomato varieties potentially stem from this mechanism (Jones et al., 2004; Broeckling et al., 2008; Guo et al., 2023).
Studies have shown a strong correlation between changes in soil environmental factors and soil microbial biomass (Zhao et al., 2009). Particularly, research suggests that improvements in soil porosity and moisture content are key drivers of increased microbial biomass and activity (Hu et al., 2016). Enhanced porosity is believed to improve soil aeration, creating a more optimal environment for soil microorganisms by facilitating gas exchange and potentially mitigating limitations caused by low oxygen availability (Zhao et al., 2022). Soil compaction, often caused by heavy machinery or unsustainable cropping practices, negatively impacts soil physical properties, potentially hindering microbial activity and essential biochemical processes crucial for nutrient availability. Research demonstrates a linear decline in microbial populations with increasing soil bulk density (Li et al., 2002). Li et al. (2002) observed a 26–39% decrease in microbial communities when soil bulk density increased from 1.00 to 1.60 mg m-3. These findings align with studies by Landina and Klevenskaya (1985) and Smeltzer et al. (1986) showing a reduction in microbial biomass carbon with compaction, which strongly correlates with microbial numbers. While plate counting methods used only capture a fraction of the total soil microbial community, the significant decrease in measured populations underscores the detrimental effect of soil compaction on microbial activity (Torsvik et al., 1996).
Soil texture, defined by the relative proportions of sand, silt, and clay, is a well-established factor influencing soil microbial communities (Fierer, 2017). Finer textured soils, with higher clay content, tend to have a greater surface area and water-holding capacity (Mathieu & Pieltain, 2003; Lucas et al., 2014). This creates more favorable conditions for a wider variety and abundance of microbes. Conversely, coarse-textured soils with high sand content offer less surface area and limited water retention, potentially limiting microbial diversity and favoring microbes adapted to drier environments. Ultimately, soil texture influences the physical environment that soil microbes inhabit, impacting factors like oxygen availability, nutrient absorption, and water accessibility, all of which play a crucial role in determining the types and overall activity of the soil microbial community (Grandy et al., 2009; Lucas et al., 2014; Diao et al., 2021).
Soil pH acts as a key environmental factor influencing the composition and function of microbial communities. It can directly impact microbial activity by altering the efficiency and functionality of enzymes critical for various metabolic processes. Additionally, pH indirectly affects microbial communities by influencing the solubility and availability of essential nutrients such as phosphorus and potassium. This altered nutrient profile can then selectively favor specific microbial taxa with adaptations to grow under those conditions. Studies by Bodenhausen et al. (2023) support this notion, demonstrating a significant influence of potassium and phosphorus on fungal community structure in arable soils. Similarly, research by Fierer & Jackson (2006) has established the well-known role of nitrogen and phosphorus availability in shaping the composition of microbial communities.
Soil characteristics including pH, nitrate nitrogen content, organic carbon level, and clay content have been identified as key factors shaping fungal community composition (Huang et al., 2020). This aligns with previous research highlighting the prominent roles of pH and organic carbon in structuring overall soil fungal communities (Grandy et al., 2009; Ma et al., 2019). Organic matter amendments, by optimizing soil structure, demonstrably promote fungal abundance (Lucas et al., 2014; Huang et al., 2020). Additionally, factors like soil salinity and land-use type exert significant influence on the composition and structure of fungal communities (Rath et al., 2019). Land-use type or past land management practices have also been shown to play a part in shaping fungal community structure (Ma et al., 2019). This collective evidence underscores the multifaceted nature of factors influencing fungal communities in soil ecosystems (Huang et al., 2020).
Aciego Pietri et al. (2008) and Deng et al. (2017) observed an inverse relationship between soil pH, total nitrogen content, and the composition of microbial communities, which aligns with previous research. This suggests that lower pH and higher total nitrogen levels influence microbial community structure (Li et al., 2023). organic matter emerges as a key factor shaping fungal communities, as evidenced by its positive correlation with numerous fungal species (Wei et al., 2022). Furthermore, findings by Sun et al. (2021) on total nitrogen, organic carbon, and organic matter mirrored the present study's observations. Network analysis revealed positive correlations between total nitrogen and 30 fungal species, while organic matter showed a similar positive association with 27 species, many of which overlapped with those linked to total nitrogen. In contrast, available phosphorus only correlated positively with 12 fungal species (Billah et al., 2019). These findings, along with those of Ma et al. (2024), suggest that environmental factors like organic matter, total nitrogen, and available phosphorus promote the growth and reproduction of diverse fungal communities, whereas pH acts as a potential inhibitor for many microbial taxa. Notably, variations in nitrogen, phosphorus, and potassium availability are crucial for microbial development and reproduction (Billah et al., 2019). In conclusion, the interplay between environmental factors and microbial communities is complex. These factors can directly and indirectly influence the composition and development of microbial communities, impacting nutrient cycling and overall soil quality (Ma et al., 2024).
Our study confirms previous findings (Cline et al., 2018; Canini et al., 2019; Guo et al., 2020) that both soil properties and plant communities are key factors shaping fungal community composition in the soil. Soil properties directly influence fungal communities by providing essential nutrients, with variations in these properties leading to shifts in fungal composition (Yu et al., 2019; Zhang et al., 2020). Plant communities likely play a similar role due to their complex interactions with soil fungi. For instance, plant pathogens rely heavily on specific plant hosts (Nanjundappa et al., 2019). Furthermore, interactions occur among the different fungal groups themselves. Symbiotic fungi and plant pathogens often exhibit mutual inhibition (Li et al., 2021), ultimately influencing the overall fungal community composition. Consequently, both soil properties and plant communities significantly impact not just the total fungal composition but also the functional roles played by different fungal ecological groups within the soil (Rodriguez-Ramos et al., 2021). Given these intricate interactions, further research is warranted to explore the potential triangular relationship between plant communities, soil fungal diversity, and abiotic factors.