Different organisms in the biological world have different morphological structures, which can be divided into viruses, prokaryotes and eukaryotes. The following biological characteristics are described. A, ① Yeast belongs to eukaryote; ⑥ Tobacco mosaic virus is neither eukaryote nor prokaryote, a mistake;

B, ③ Nitrifying bacteria can be chemically synthesized and belong to autotrophs. B is wrong;

C, 3 nitrifying bacteria can be chemically synthesized and belong to autotrophs, and C is wrong;

D, ③ ④ ⑤ all have cell structure and cell wall. D is correct.

Therefore, choose: d.