## 4 Discussion
Although FAPROTAX is unable to reveal functional phenotypes of all taxa in the community, previous studies have shown that it was a helpful tool to highlight functions related to biogeochemical dynamics, especially on N and C cycle in non-aquatic samples and to compare functional profiles among treatments. Our results also showed that sample source was not a primary factor that limited the application of FAPROTAX, especially in soil samples. A strong positive and significant correlation between the number of functional assigned OTUs and the number of OTUs identified to the order and genus levels, but not with those assigned to phylum level implies that poor taxonomic identification was an important factor that limited FAPROTAX functional assignment in soil samples. Since certain functions are conserved at low taxonomic levels (species, genus or order), OTUs identified only at a phylum level usually cannot be assigned to any function. The study cases on agricultural and forest soil samples reported that more than 97% of functionally assigned OTUs have previously been reported to exist (previously reported on both appearance and functional performance) in soil samples (Tables S2.1-S2.3). We found several studies that confirmed the presence of functionally assigned taxa in soil bacterial communities. For example, taxa related to C-cycle such as _Nocardioides_, which was previously isolated from soil, was assigned to aromatic compound degradation and confirmed the ability to degrade hexachlorobenzene [61]. _Rhodococcus_ species was also assigned to hydrocarbons degradation and was found to have the ability to utilize various hydrocarbons groups in soil [62]. Similarly, taxa involved in nitrogen cycles, such as _Rhizobium gallicum_ (nitrogen fixation) and _Micromanospora aurantiaca_ (nitrate reduction and cellulolysis), were also found in soil [63,64] (see Tables S2.1-S2.3 for more information). These lines of evidence confirmed that some taxa available in the FAPROTAX database are generally dispersed across different ecosystems, including soil, even though they were originally generated from aquatic samples. Moreover, we showed that bacterial taxa and functional prediction presented in the FAPROTAX database were not only derived from aquatic samples but also from soil, plants and animals (Table S4). These results support our hypothesis that FAPROTAX was compatible with terrestrial ecosystems. On the other hand, lower portion of soil-detected taxa but high portion of marine-detected taxa in mangrove rhizosphere soil was not surprising results because mangrove land is located at the boundary between terrestrial and aquatic ecosystems. Therefore, it is possible to detect both marine and soil bacterial taxa in the area [65]. More importantly, we confirmed that a number of bacterial taxa found in mangrove rhizosphere soil were also found in soil system. Furthermore, we demonstrated that the addition of references on bacterial taxa capable of a particular function could significantly increase the efficiency of the functional assignment. This study showed that adding more references to nitrogen fixation function can increase the number of OTUs assigned to the function by 2-3 times, accounting for a 2% increase in total functional assignment percentage. The absence of the nitrogen fixation function may be due to FAPROTAX being created based on aquatic samples [9]; thus, some terrestrial specialized taxa were neglected from the database. Furthermore, bulk and rhizosphere soils of red clover (_Trifolium pratense_) are known to colonize by diverse N-fixing bacteria [66]. Consequently, using relevant and up-to-date references of current status of N-fixing bacterial legume symbiosis can strongly increase the number of functional assigned bacterial taxa. Specifically, many important N-fixing bacterial genera, for examples _Ensifer_, _Bradyrhizobium_, _Microviga_, _Mesorhizobium_, _Devosin_, etc., are not included in FAPROTAX as N-fixing bacteria.