## 4 Discussion
### Domain Eukaryota  
The taxa that showed higher AB/RA in the bulk soil microbiome include four phyla, e.g., Mucoromycota, Basidiomycota, Zoopagomycota and Blastocladiomycota, and four genera, e.g., _Macrophomina_, _Fusarium_, _Sphaerobolus_, _Spielomyces_, in addition to the genus _Rhizophagus_, compared with those in the rhizosphere microbiome of the _Diptergyium glaucum_ plant. While only three taxa, e.g., the genus _Sordaria_ and its descendent species _Sordaria macrospora_, as well as the species _Pseudogymnouscus destructans_, showed contrary results (Table S20). A possible reason for the higher AB of eukaryotic parasites in the bulk soil includes the inhibition of growth of these parasites in the rhizosphere microbiome by plant root exudates. When these pathogens are nearby plant roots, they might indirectly be beneficial by metabolizing complex molecules to simpler useful ones. Indirect relationships of parasite and plant roots that can be mediated by mycorrhiza avoid direct contact and occurrence of several diseases (e.g., rusts, smuts). Such a type of avoidance resistance of wild plants to these parasites might justify their low AB/RA in the rhizosphere microbiome. More explanation of this type of plant-microbe association is shown below. The question that is required to be answered is how this distant indirect contact is mediated. Members of the phylum Mucoromycota are saprobic Zygospore-forming fungi that live in terrestrial soil or highly polluted water and are historically known to be among the first land colonizers. In addition, Mucoromycota members are considered as powerful factories for biorefinery applications [65]. They act as weak parasites of plants and animals in environments rich in organic matter and are called \"sugar fungi\" because they grow better on simple sugar substrates. Mucoromycota members also have the ability to assimilate complex organic compounds, e.g., carbon sources, and to accumulate several metabolites, including lipids, chitosan, polyphosphates and proteins [66], that are valuable to plants. Members of Blastocladiomycota are aquatic fungi that live in freshwater, mud and soil [67]. Members of Zoopagomycota are terrestrial obligate parasites of soil animals such as nematodes and amoebae, while some are parasites of plants. They are capable of growing on refractory materials, e.g., pollen, cellulose, chitin, etc. [68], and act as parasites of nematodes, midges and crustaceans, as well as plants, e.g., maize, alfalfa and several angiosperms, to cause several diseases (e.g., leaf brown spot). Meanwhile, members of Basidiomycetes include rusts, a well-known devastating pathogen of staple grain crops, and smuts that cause persistent crop losses. In order to recognize the way by which pathogens or parasites and nearby plants interconnect, several reports indicate that the fungal mycbionts Zoopagomycota and Basidiomycetes are both characterized by the previously described indirect plant associations via plant-based ecologies (e.g., mycorrhiza, root endophytes, etc.) [69]. Members of the genus _Macrophomina_ are soil-borne fungi that cause several plant diseases, e.g., stem and root rot, seedling blight, etc. [70]. Pathogenicity of several fungi, including _Macrophomina_, is associated with the fungal ability to produce hydrolytic enzymes to degrade polysaccharides and lignocellulosicoses of the plant cell wall, then penetrate into the host tissue [71]. Again, the low AB of the latter three parasites, Zoopagomycota, Basidiomycetes and _Macrophomina_, in the plant rhizosphere microbiome indicates the possible release of root exudates that inhibit their propagation in the plant rhizosphere [69]. However, there is no prior supporting information to justify differential AB of the genus _Sordaria_ and its descendent species _Sordaria macrospora_ (Table S20), as they seem to present in animal feces, thus their presence in the microbiomes is coincidental.