In my experience, thermophilic bacteria are sensitive to low temperatures. So at first time it is recommended to find minimum temperature which can grow. I mean if min temp of your strain is near 45 degree Celsius you can not preserve it in a refrigerator as a short-term preservation but interestingly you can use long-term cryopreservation method and maintain them in a nitrogen tank or ultra-freezer. It is more suitable than freeze drying in my experience.