## Materials and Methods  
### Sample Collection  
We set up experiments to evaluate the suitability of FAPROTAX to assign functions of soil bacterial and archaeal OTUs. Soil samples from two major terrestrial ecosystems, agricultural grassland and forest were collected. Furthermore, one published dataset on rhizosphere soil of _Rhizophora stylosa_ was also added in this study [33]. Mangrove ecosystems are considered as the interface between aquatic and terrestrial ecosystems [34]; thus, the mangrove soil samples were used as the borderline between the aquatic and terrestrial ecosystems.  
In the agricultural grassland ecosystem, bulk soil and rhizosphere soil of _Trifolium pratense_ were taken from five experimental plots of extensively used meadow (ambient treatment) at the Global Change Experimental Facility (GCEF), Germany (51\({}^{\circ}\)22\({}^{\prime}\)60\({}^{\prime\prime}\) N, 11\({}^{\circ}\)50\({}^{\prime}\)60\({}^{\prime\prime}\) E) [35; 36]. These experimental plots are managed as described in [PERSON] et al. [35], where grasses and legumes growing in the plot are used to feed livestock. In this study, three healthy _pratense_ plants, which represent three subsamples, were taken from each experimental plot. Bulk soil and rhizosphere soil were collected following the protocol as described by [PERSON] et al. [37]. Briefly, bulk soil attached to the root was first removed by vigorous shaking, then rhizosphere soil was collected by shaking the root in PCR-grade water. Three subsamples of bulk soil and rhizosphere soil collected from the same plot were pooled into one composite sample for each soil fraction. Overall, five composite samples of bulk soil and five composite samples of rhizosphere soil (representing five true replicates) were obtained.  
In the forest ecosystem, soil samples were taken from a bamboo-deciduous forest [38] which was dominated by _Dendrocalanus membranaceous_ and _Bambusa bambos_, in northern Thailand (18\({}^{\circ}\)32\({}^{\prime}\)23\({}^{\prime\prime}\) N, 99\({}^{\circ}\)34\({}^{\prime}\)47\({}^{\prime\prime}\) E). In detail, five replicated plots (5 \(\times\) 5 m\({}^{2}\)) \(>\) 20 m apart were selected. Five soil subsamples were collected to 10 cm depth in each plot using an auger with 10 cm in diameter. The subsamples were then pooled into one composite sample. In this study, all composite soil samples were homogenized and sieved (2 mm) to remove stones, roots, macrofauna, and litter.  
For the mangrove ecosystem, we used the dataset that has previously been published by [PERSON] et al. [33]. In detail, this dataset consisted of 5 replicated samples of rhizosphere soil of _R. stylosa_ located in wetland at Pingtung County, southern Taiwan (22\({}^{\circ}\)26\({}^{\prime}\)17.6\({}^{\prime\prime}\) N, 120\({}^{\circ}\)29\({}^{\prime}\)29.6\({}^{\prime\prime}\) E). Sample collection was described in detail in [PERSON] et al. [33]. Briefly, five healthy, mature _stylosa_ trees were selected, then four subsamples of rhizosphere soil around each selected tree were collected, pooled and sieved to make a composite sample.  
All soil samples, including those from agricultural grassland, deciduous forest and mangrove ecosystems, were kept at \(-\)20 \({}^{\circ}\)C for further analyses.