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Alkaline phosphatases such as PhoD and PhoX are important in organic phosphorus cycling in soil. We identified the key organisms harboring the phoD and phoX genes in soil and explored the relationships between environmental factors and the phoD- and phoX-harboring community structures across three land uses located in arid to temperate climates on two continents using 454-sequencing. phoD was investigated using recently published primers, and new primers were designed to study phoX in soil. phoD was found in 1 archaeal, 13 bacterial and 2 fungal phyla, and phoX in 1 archaeal and 16 bacterial phyla. Dominant phoD-harboring phyla were Actinobacteria, Cyanobacteria, Deinococcus-Thermus, Firmicutes, Gemmatimonadetes, Planctomycetes and Proteobacteria, while abundant phoX-harboring phyla were Acidobacteria, Actinobacteria, Chloroflexi, Planctomycetes, Proteobacteria and Verrucomicrobia. Climate, soil group, land use and soil nutrient concentrations were the common environmental drivers of both community structures. In addition, the phoX-harboring community structure was affected by pH. Despite differences in environmental factors, the dominant phyla in the phoD-harboring community remained similar in all samples, while the composition of phoX differed substantially between the samples. This study shows that the composition of phoD and phoX is governed by the same environmental drivers but that phoD and phoX occur partly in different phyla.

SoilphoDandphoXalkaline phosphatase gene diversity responds to multiple environmental factors