Yogyakarta, Indonesia is one of the batik centers that is currently growing rapidly. Liquid waste from batik coloring using dyes usually contains heavy metals. Therefore, batik liquid waste treatment using phytoremediation techniques needs to be applied. Thi study aimed to determine the effect of batik liquid waste on the germination and root anatomical structure of marigold (Tagetes erecta L.) and garden Zinnia (Zinnia violacea Cav.), and to determine the concentration of batik liquid waste which most inhibit the germination. Seeds were germinated in cotton treated with batik liquid waste with a concentration of 0%, 25%, 50%, 75%, and 100% for six days. Parameters observed were the number of germinated seeds, shoots, and root length of sprouts and root anatomy. Cross-section of the root was prepared using the paraffin embedding method. The results showed that batik liquid waste inhibited germination, which was characterized by a decrease in the number of germinated seeds, shoots, and root length as well as browning of roots. The higher concentration of batik liquid waste applied, the root become damaged, as shown by damaged cells, with degraded protoplasts and cell walls, and also cells were not further recognized. At control roots from two species, the roots are rounded in shape, cells grow normally and regularly arranged; the epidermal cells are rectangular, the cortex cells are relatively round, and the stele cells are intact. At a concentration of 25%, the root of T. erecta has tetragonal square in shape with damaged epidermal cells and unclear cells shape, square and clear cortical cells. Furthermore, xylem tissue was separated into two parts with degraded cells turn in black and cannot be further recognized. Meanwhile, at the same concentration of 25%, roots of Z. violacea remains intact, except less developed of vascular bundles clearly appeared. At a concentration of 50%, all parts of the T. erecta root tissues were degraded. At a concentration of 75%, T. erecta seeds died on the fourth day, while Z. violacea seeds did not grow. At a concentration of 100%, the seeds of both species did not germinate. The concentration of batik liquid waste, which most inhibits the germination of T. erecta is 100%, while at Z. violacea, the total inhibition started from 75% of liquid waste.

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