Urine crystals suggest a predisposition to form renal stones . This predisposition can be subverted by modifying urine pH. Acidic urine is associated with xanthine, cystine, uric acid and calcium oxalate stones. Alkaline urine is associated with calcium carbonate, calcium phosphate , and magnesium phosphate stones. This mathematical manipulation allows us to measure acidity on a convenient scale of 0 to 14. Only in severe diseases does the pH get slightly below 7.0 or close to 8.0.
More dramatic variation is incompatible with life.
HCO3- is controlled by the kidneys and CO2 is controlled by the lungs. If there is a problem with the kidneys, the lungs will try to compensate and visa versa. Standing in an uncovered container allows CO2 to escape. Bacteria usually increases the pH because they contain enzymes which can break down urea to ammonia , which then combines with hydrogen ions. Drugs that can decrease urine pH include ammonium chloride, chlorothiazide diuretics, and methenamine mandelate.