Mentioning the bacteria is just a side note. The main point is that he has no viable seeds left.
Remember that, earlier in the book, he makes a point of mentioning that the potatoes he used as his initial seed were not frozen for the transfer to Mars -- which is the lucky coincidence that makes them viable in the first place.
Freezing destroys the cell structure. The potato will not sprout, just rot. After the decompression, he has nothing to plant, even if he could somehow make the soil viable again. (Which is why he doesn't really bother checking the soil until later.)