There are two different ways to maintain the natural environment for these unculturable bacterias. Either you just incubate in the environment or take back the environment in the lab.

1. In case of water sample: take the water sample from the environment and bring it to the lab and prepare different dilutions of it and add agar into your samples. (this will give the required environment and nutrition to your microbes).
2. In another case, you can just let the bacterium grow in their environment only. One interesting article is there on this type of culturing, where they have used designed an iChip and they have used it grow the bacterium in there environment only. (https://sci-hub.tw/https://www.nature.com/articles/nature14098)
   You can read this article for further reference.