this protocol I used and it work for 16S rRNA gene PCR..you can try it

You can use the following protocol:

Chromosomal DNA was extracted by using the following protocol: 1.5 mL aliquots from the 10 mL culture were centrifuged at 13,000 rpm for 3 minutes. The supernatant was poured off and 200 µL of lysis buffer (40 mM Trizma base, 20 mM sodium acetate, 1 mM EDTA, 1 % SDS, pH 7.8 adjusted with acetic acid) was added to the pellet and mixed thoroughly. Then 66 µL of 5 M NaCl was added and after thorough mixing centrifuged at 13,000 rpm for 10 minutes. Supernatant was transferred to a new tube and 1 µL of RNase A (10 mg/mL) was added and mixed. Tube was incubated at 37˚C in a water-bath for 30 minutes. An equal volume of chloroform/isoamyl alcohol (24:1) was added and mixed gently by inverting tube and centrifuged at 13,000 rpm for 6 minutes. The upper aqueous phase was carefully transferred with a micropipette to a clean tube. 2.5-3-fold volume of cold ethanol (95%) was added and mixed well. Then tubes were kept in a freezer (-20˚C) for 30 minutes to 1 hour and centrifuged at 13,000 rpm for 6 minutes. Ethanol was gently poured off to avoid the removal of DNA pellet and the pellet was washed with 2-fold volume of 70% ethanol and centrifuged at 13,000 rpm for 10 minutes. The ethanol was gently poured off to avoid the removal of DNA pellet. The pellet was dried by using speed vacuum for 5 minutes. 50 µL of 1x TE buffer (10mMTrizma base, 1mM EDTA) was added to pellet and left at 4˚C for one night. Then DNA was stored at -20˚C.

http://D:\Zeeshan Hyder 05-07-2012\Protocoles\Bacterial Chromosomal and Plasmid DNA extraction.docx