Hi, Bacillus as know as thermophlic bacteria, because it formulate spores, so just heat treated the sample to 70-80 C for 30-1 h and grow it on NA,

The Bacillus species are endosporic and have remarkable resistance to heat treatment. It has a very wide ability to grow on may Carbon and Nitrogen sources. Among its properties is a tolerance to elevated salt compared to many other bacteria. I would suggest a Potato dextrose agar (PDA) with 3% sodium chloride we used and then single colonies from dilutions will be easier to pick up and purify. The protocol of Oadi Matny would be coupled with isolation media.  After isolation I would just use no salt PDA.

Hope this information is useful.

To isolate bacilli can be used many means of cultivation , as others have said before this intervention , however , when in tissue is recommended that let them dry for nonsporulating to die and after heat treatment recommended 80 degree Celsius for 10 min and then ice moment shows another 10 minutes. then make agar dilution and seeding. you recover only spore forming bacteria.

I think, to target novel endophytic Bacillus, one should design different formulation that is different from conventional culture media.

One can try out with a nutritionally poor medium such as (50 times diluted Tryptic soy broth, supplemented with manganese salt and filter sterilized extract of plant from which such trial has been attempted). The filter sterilized extract must be added to autoclaved, well cooled basal medium. I think choice of a range of incubation temperature (between 30 to 60 degree C, with 10 degree interval) may be useful. For first enrichment cycle, broth medium may be preferred with a subsequent transfer followed by dilution plating on respective agar plate having composition as described above (with 1.5% Difco agar or extra pure agar from HiMedia, India). 

Most of the conventional media do not support isolation of autochthonous micro-flora simply for the reason that they are nutritionally too rich and the metabolic potential of major endophytic bacteria might not have been designed over million years of association with the respective plant sp.. The plant extract will provide selective nutritional supplements (mostly unknown) for growth of such endophytic micro-flora. 

Another factor may also be looked for, that is supplementing above formulation with Homo serine lactone or similar quorum sensing chemicals.

My experience with isolation and cultivation of oligotrophic bacteria has taught me these lesson.

This idea may be incorporated for isolation of Bacillus. I am sure one will definitely get more novel bacteria other than Bacillus from such niches.  

yes. some endophytes can be isolated from plant tissue. Exogenous presence of bacillus on soft plant tissue like lactobacillus planterum, bacillus subtilis etc.