Abstract:[Background] Anaerobic ammonium oxidation (anammox) bacteria, members of the phylum Planctomycetes, which drive effective N-removal of high concentration ammonia from municipal or industrial wastewater, are designated as eco-friendly microorganisms. However, the structural and functional differentiation of Planctomycetes communities across space and the main environmental drivers have not been paid much attention. [Objective] To elucidate the spatial differentiation of Planctomycetes community structure and the main environmental factors driving associated anammox or denitrification. [Methods] 16S rRNA gene high-throughput sequencing was used to detect the spatial distribution changes of Planctomycetes community structure in sandy or silty sediments/soils of river ecosystem from the temperate semi-arid region. Meanwhile, statistical method was used to analyze the effect of physicochemical factors such as silt particles and water content on the structural differentiation of Planctomycetes communities. [Results] OM190_ub_o_o. o1 population was mainly distributed in oligotrophic sandy sediments, only positively driven by sand particles. OM190_o_o_o. o2 and SM1A02. ub5 populations were mainly distributed in mesotrophic silty-sandy soils, positively driven by water content and pH, etc. AKYG587. ub3, Pla4_lineage_o_o_o. o6, Singulisphaera o7, Singulisphaera ub8 and Planctomycetaceae_u. ub9 populations were mainly distributed in copiotrophic silty soils, positively driven by the clay and silt particles, salinity, organic carbon, total nitrogen, total phosphorus and nitrate nitrogen. Although Phycisphaera ub4 population was preferentially distributed in mesotrophic silty-sandy soils, it displayed a tendency from mesotrophs to copiotrophs, negatively driven by nitrate nitrogen. The entire populations were negatively driven by ammonia nitrogen. Variation partitioning analysis showed that silt particles, ammonia nitrogen, water content contributed to the spatial variation of Planctomycetes communities with 52.7%, 10.4%, 10.3%, respectively. [Conclusion] Planctomycetes communities of river ecosystem in temperate semiarid showed obvious spatial differentiation characteristics, mainly driven by soil/sediment silt particles, ammonia nitrogen and water content. Planctomycetes communities in copiotrophic silty soil might be particle-attached heterotrophic denitrifying bacteria, while Planctomycetes communities in oligotrophic silty soils might be free-living autotrophic ammonia oxidizing or denitrifying bacteria with high affinity for ammonia nitrogen and nitrate nitrogen, respectively. This study provides a scientific basis for the efficient application of ammonia oxidizing bacteria and denitrifying bacteria associated with Planctomycetes to biological removal of high concentration ammonia from polluted systems.