## 3 Results
### General Overview of Bioinformatics and FAPROTAX Assignment of Data Derived from Soil Samples  
A total of 196,366 reads (on average 19,637 \(\pm\) 2355 reads per sample) of bacterial 16S rRNA gene were detected in agricultural bulk soil and rhizosphere soil, after quality filtering and chimeric sequence removal. For forest and mangrove soils, 119,433 reads (on average 23,886 \(\pm\) 1980 reads per sample) and 66,263 reads (on average 19,637 \(\pm\) 2355 reads per sample [33]) were detected, respectively. After rare OTUs were removed, the sequences were normalized to the smallest read numbers per sample, which were 4951, 12,269 and 7086 [33] reads per sample for agricultural soils (bulk soil and rhizosphere soil), forest soil, and mangrove rhizosphere soil, respectively.  
Different bacterial OTUs were obtained from agricultural bulk soil (3329), agricultural rhizosphere soil (3365), forest soil (2177) and mangrove rhizosphere soil of _R. stylosa_ (2497). The proportion of OTUs that were identified to different taxonomic ranks and that of functional assignments were presented in Figure 2. Functional assignment capacities of agricultural soils (bulk soil and rhizosphere soil), forest soil and mangrove rhizosphere soil accounted for 28.24-28.42%, 12.48% and 15.86% (Figure 1) and the number of functions assigned to those samples were 34, 36, 37 and 52 functions, respectively (Figure S1). Predominant functions across all samples belonged to chemoheterotrophy, followed by aerobic chemoheterotrophy (Figure 3). However, when we focused on more specific functions, the result showed differences in dominant functions involved in biogeochemical cycling derived from each ecosystem (Figure 3).  
Figure 2: Taxonomic information across all soil samples and correlation between numbers of identified and functionally assigned OTUs. (**a**) Proportion of OTUs identifying to different taxonomic ranks. (**b**) Bar plot showing FAPROTAX’s functional assignment percentage (TB: agricultural bulk soil, TRh: agricultural rhizosphere soil, SF: forest soil and Rs: mangrove-rhizosphere soil). Linear regression showing [PERSON]'s rank correlation coefficient and \(p\)-value on the relationship between number of FAPROTAX-functional assigned OTUs and number of identified OTUs to different taxonomic ranks which are (**c**) Genus, (**d**) Order and (**e**) Phylum. \"No.\" is an abbreviation of \"Number\".  
Correlation between the Number of Functionally Assigned OTUs and Taxonomically Identified OTUs in Each Taxonomic Rank  
Significant and positive correlations (\(\sigma\) = 0.90-0.95, \(p\) < 0.01, Figure 2c,d) were found between the number of functionally assigned OTUs and number of OTUs assigned at genus and order levels, whereas the correlation between that at phylum level was not statistically significant (\(\sigma\) = 0.11, \(p\) = 0.64, Figure 2e). Although strong correlations between the numbers of functionally assigned OTUs and numbers of OTUs assigned at genus and order levels are detected in this study, we noted that a small set of data (20 samples) was used for the correlation analysis. Thus, these correlation results should be interpreted carefully.