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A Gram-stain-negative, rod-shaped, motile bacterium, designated AER10(T), was isolated from the roots of Ammodendron bifolium collected from Takeermohuer desert in Xinjiang Uygur Autonomous Region, northwestern China. Growth was found to occur from 10 to 45 degrees C, at pH 5.0-9.0, and could tolerate up to 10% (w/v) NaCl. 16S rRNA gene sequence result indicated that the strain AER10(T) belongs to the genus Alcaligenes and was closely related to Alcaligenes aquatilis (98.4 %), Alcaligenes faecalis subsp. parafaecalis (98.4 %), Alcaligenes faecalis subsp. faecalis (98.1 %) and Alcaligenes faecalis subsp. phenolicus (97.9 %). However, the DNA-DNA hybridization values between the strain AER10(T) and the above strains were less than the threshold value (below 70 %) for the delineation of genomic species. The DNA G+C content was 53.3 mol%. Ubiquinone-8 (Q-8) was the only quinone system present. The major fatty acids were summed feature 8 (C-18:1 omega 7c, 25 %), C-16:0 (24.2 %), summed feature 3 (C-16:1 omega 7c and/or C-16:1 omega 6c, 19.3 %) and cyclo-C-17:0 (10.5 %). The polar lipid profile of the strain AER10(T) consists of diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylserine, two unidentified aminolipids and five unknown polar lipids. On the basis of the evidence presented in this study, strain AER10(T) is a representative of a novel species in the genus Alcaligenes, for which the name Alcaligenes endophyticus sp. nov. is proposed. The type strain is AER10(T) (=DSM 100498(T)=KCTC 42688(T)).