## 4 Discussion  
One of the main targets of this study is to use data generated from metagenomic whole genome shotgun sequencing (mWGS) in taxonomic assignment of the _Diptergyium glaucum_ rhizosphere microbiome and surrounding bulk soil microbiome, and shifts due to watering. Although the marker gene sequencing approach, also named the amplicon or metatax-onomic sequencing approach, is faster and less expensive than mWGS (metagenomics), especially when the study includes large numbers of samples, mWGS proved to be more powerful in taxonomic assignment, especially when analyzing complex microbial communities such as those in the open environment [25]. During metagenomic classification, reads or assembled contigs are matched against a database of microbial genomes simply to identify microbiomes through a recent tool called metagenomics classifiers [25].  
In this study, we detected the available patterns of abundance (AB) and relative abundance (RA) of the rhizosphere microbiome of _D. glaucum_ and surrounding bulk soil microbiome for the top 10 highly abundant phyla, genera and species of the four domains, in a trial to understand the natural growth dynamics of microbes responding differently to the soil type and/or watering. Prior metagenomics research has focused mainly on studying relative abundance only, while almost no prior reports give enough emphasis to further studying the abundance of microbes in a given habitat, especially whether the extreme differential abundance of genomes of different domains is feasible. Therefore, we assume that the picture is not complete if relative abundance referring to beta diversity is studied alone. One other reason for this decision is that there are some pairs of microbes that naturally co-exist at a certain abundance level, regardless of their relative abundance level within a microbiome.  
We assume that the growth dynamics of microbes in the present study that showed similar patterns of abundance (AB) and relative abundance (RA), namely AB/RA, e.g., in terms of soil type and/or watering time points, can contribute to all the above-mentioned mechanisms of growth dynamics. An AB/RA pattern refers to a taxon whose AB is higher in a given soil type or watering time point, and also shows a higher RA in the same soil type or watering time point.  
The results in Tables S18-S21 indicate that AB/RA patterns of a given taxon based on soil type do not show the AB/RA pattern in watering time point as well, except in two cases. When analyzing these cases, we found that higher AB/RA of a certain taxon in the rhizosphere microbiome is surprisingly accompanied by lower AB/RA in the watering group B (referring to 24 h watering time point) microbiome, compared with those of other soil types or watering time points (first case). In addition, when a higher AB/RA pattern exists in the bulk soil microbiome, a higher AB/RA pattern in the watering group B microbiome also exists (second case). The first case took place for the two archaeal phyla Euryarchaeota and Crenarchaeota and the bacterial species _Rubellinicrobium mesophilum_, while the second case took place for the eukaryotic genus _Rhizophagus_ and the viral species _Streptomyces phage Mildred21_. We have no explanation for these cases and speculate that they occurred coincidentally.