The endophytes were separated from Xinjiang carrots using gradient dilution method. There were 59 endophytes obtained by the separation and purification method, including 49 strains of endophytic bacteria, 10 strains of endophytic fungi. These endophytes incorporated 10 strains isolated from the head skin, 18 strains separated from central skin, 13 strains segregated from the tail skin, 9 strains derived from shallow meat, and 9 strains did from deep meat, which of the most number belonged to 30.5% of central skin. Gram staining experiment of endophytic bacteria authenticated 43 strains of gram-positive bacterium and 6 strains of gram-negative bacterium. Through observing the strain of morphological characteristics under a microscope, and identification of physiology and biochemistry as well as molecular biology, some strains were classified, for example 3 strains of Enterobacter cloacae strains, 5 strains of Enterobacter ludwigii strain, 1 strains of Pantoea dispersa strain, 2 strains of Pantoea, 1 strains of Enterobacter, 1 strains of Raoultella, 1 strains of Enterobacteriales bacterium, 4 strains of Enterobacter asburiae strain, 3 strains of Enterobacter aerogenes strain, 2 strains of Pantoea vagans partial, 1 strains of Pantoea agglomerans strain, 1 strains of Kluyvera cryocrescens, 1 strains of Enterobacter asburiae, 1 strains of Enterobacter cloacae subsp, 1 strains of Enterobacter mori strain. 1 strains of Aspergillus niger strain. 1 strains of Ciadosporium. 1 strains of Corynespora torulosa. Among these strains, enterobacterium was the largest, accounting for 17.9% of the total number.

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