B, the strain has strong ability to decompose organic pollutant A, and the content of organic pollutant A in the culture medium is low, so the microorganism in the culture bottle with the lowest content of substance A should be selected for further inoculation in step ③; B correct.
C, as can be seen from the title map, the purpose of inoculation process ④ is to separate and purify strains that can decompose organic matter A; C is correct.
D. The purpose of repeating the process ⑤ for many times is to expand the culture and obtain more target bacteria, instead of improving the ability of bacteria to decompose organic matter A; D error.
Therefore, choose: d.