In the acid-fast or Ziehl-Neelsen stain, following the referred washing, the slide should be covered in 1%-3% acid alcohol to decolourise until the smear turns into light pink. After that, wash well with clean water to stop the decolourisation.
If you mean the change in water Temperature then they simply just go on in life, they are very adaptable creatures.
The mitochondria carry out cellular respiration.
Movement of lithospheric plates created isolation between populations and with isolation comes different mutations and lineages which is how evolution occurs. (This is called allopatric speciation!).