## 4 Discussion
### Domain Viruses  
At the virome level, as a part of the rhizosphere microbiome of _Diptergium glaucum_, none of the genera showed AB/RA in either soil type or watering time points (Table S21). Rather, three species, e.g., _Oclroachtrum phage POA1180, Mycobacterium phage Edugator_ and _Mycobacterium phage Kratio_, showed higher AB/RA in the rhizosphere microbiome than in the bulk soil, while two species, _Streptomyces phage Mildred21_ and _Citrus endogenous pararetrovirus_, showed contrary results (Table S21). The prophages of _Ochroachtrum_ naturally release phage particles, e.g., phage POA1180 (41,655 bp) with bacterial species \(O\). _intermedium_ as the most known host. However, this action is increased when the prophages are induced by various stress factors. The viral  
Figure 9: Non-redundant gene abundance of the genera _Burkholderia_, _Trichoderma_ and _Fusarium_ of the rhizosphere microbiome (R) of _Diptergium glaucum_ and the surrounding bulk soil microbiome (S) across watering time points. genome contains genes for DNA packaging and virion assembly, and other encoding terminase, transposase, methyltransferases, capsid protein, ATPase, transcriptional regulators and several tail proteins [81]. Moreover, the genome contains two genes that allow the bacteria to resist chromium [82]. In the soil, this phage is beneficial for its bacterial host [82]. For example, it confers resistance against chromate to _Ochroductrum_[83] and improves the supply of the host with sulfate [84], characteristics that give _Ochroductrum_ a selective advantage in its environment. _Ochroductrum_ further promotes plant growth and an important action among bacteria, quorum sensing [85]. As the phage can either be integrated into the bacterial chromosome or exists as an extrachromosomal entity, it is expected that the AB of the bacteria and of the virus shows the same AB pattern (Figure 10 and Tables S12, S13, S19 and S21). Then, the bacteria have symbiotic activities with the plant, on the one hand, and with the integrated phage, on the other hand, to form a complex symbiotic relationship (Figure 11). After infection, segments of several endogenous pararetroviruses (EPRVs) are integrated in several plant genomes, including citrus (CitPRV), and their biological effects were studied [86]. Many of these segments were identified in Citrinae genomes and proved to be involved in the occurrence of citrus sudden death (CSD) [86]. This virus is more highly abundant in the bulk soil microbiome than in the rhizosphere microbiome of _Diptergium glaucum_ (Table S21). Based on the AB level in the rhizosphere microbiome, it is possible that the wild plant possesses a mechanism to prevent integration of this virus in its genome, thus lessening its propagation. However, the existence of the virus in the bulk soil is hard to justify, as it is not propagated in a bacterial host. More research might be required in order to detect the intensity of viral segments integrated in this wild plant genome and to decipher this relationship at the physiological and molecular levels. Figure 11: Complex symbiotic associations among the plant root, bacteria (_Ochroductrum_) and phage (_Ochroductrum phage POA1180_). Figure 10: Non-redundant gene abundance of the genus _Ochroductrum_ and its integrated virus _Ochroductrum phage POA1180_ of the rhizosphere microbiome (R) of _Diptergium glaucum_ and the surrounding bulk soil microbiome (S) across watering time points. The AB/RA of _Streptomyces phage Mildred21_ aligned with that of the bacterial host _Streptomyces_, as both taxa showed higher performance in the bulk soil (Tables S19 and S21). The phage also showed higher AB/RA after watering. This phage was highly dynamic in terms of its AB/RA in the soil or due to watering, and we justify its performance in the bulk soil by that of the bacteria that hosts it. In addition, very little is known about both phages of _Mycobacterium_, i.e., _Edugator_ and _Kratio_, in terms of their influence on the host range.