The article linked from the question mentions crepitus (joint popping) as one of the symptoms of arthritis in Lyme disease.
Crepitus is quite a general term, which means "grating, crackling or popping sounds and sensations experienced under the skin and joints or a crackling sensation due to the presence of air in the subcutaneous tissue."
In arthritis, crepitus occurs due to inflamed (and hence rough) surfaces (bone cartilages, synovial membranes) that slide one against another. For crepitus to occur, there doesn't need to be any gas or bacteria present in the joint; in Lyme arthritis, bacteria may or may not be present in the synovial fluid (Medscape).
Crepitus in the joints can also occur in noninfectious arthritides, such as osteoarthritis (UpToDate).