Hello, I think you should previously isolate the species you want to sequence and then extract the DNA from the pure culture. This should be less chaotic and more precise. Then you should apply the protocl that your laboratory usually use, it depends on your economic resources.

If you have a water sample you have to consider that you'll probably find a vast population includin not only bacteria. To me would be better to isolate all the bacteria before proceeding, use some generic and nutrient media (like MH) to have the colony growth so you can isolate them properly. Filter the water using 0.5-0.2micron dimensions pores philtres, and then sow this philtres directly on the agar media or re-suspend the philter in 1ml of pure aseptic water and sow 100microliter of this on the agar-plates. Incubate your culture over night at 30°C and when you have a growth isolate and identify all the different type of colonies you have. From this perform a DNA extraction usin the lab protocol you have. We usually use an external sequencing service, we give them our DNA extract from the culture already isolated and numbered, so we have a precise identification.

Anyway, I'd like to read some other answers, maybe from whome has already done it.

Good luck.

Thank you very much.....but what method would you advise me to use in the extraction of bacterial DNA following cultures and preparation of pure colonies? Of late, I have been learning about DNA extraction methods but they are mostly oriented at plant and animal DNAs....I wonder what method would work for my bacterial isolates...

You can perform DNA extraction simply with sonication or boiling procedure just to brake the cell walls, then with centrifugation you can separate the DNA from the "dirt". Or you can use an authomatic extractor if you have it.

Thanks a lot Ramona for your in put. Since I am doing my proposal and is seeking funds for this work, what specific  automatic extractor can I go for?

It depend on your area. What biotechnology industry there are near you and how much money you can spend. Try to take a look at links below. Or try to contact some industry you might already know and ask if they have some cheap extractor you can use.

If you have money problem the best solution is to apply an home-made protocol (take a look at the file below).

Let me know if you need something else.

Greetings.

http://www.biocompare.com/Nucleic-Acid-Purification/9977-Automated-DNA-Extraction-Systems/

https://www.qiagen.com/it/products/catalog/automated-solutions/

https://www.beckmancoulter.com/wsrportal/wsr/research-and-discovery/products-and-services/nucleic-acid-sample-preparation/spri-te-nucleic-acid-extractor/index.htm

http://www.autogen.com/automated-solutions/

Thanks Ramona..I will look into these.

Regards