Thermo Fisher Scientific Inc. president and CEO Marijn Dekkers is stepping down to take the top job at German pharma giant Bayer AG.

The Waltham, Mass.-based lab instruments maker said it’s promoting executive vice president and COO Marc Casper to the corner office, effective immediately.

Dekkers, who spent nine years at Thermo Fisher, will succeed Bayer CEO Werner Wenning when he retires Oct. 1, the Wall Street Journal (paid) reported.

Casper has been COO since May of last year, after a stint as president of the company’s analytical technologies businesses after Thermo Electron and Fisher Scientific merged in 2006. He’s been with the company since December of 2001, when he was hired to be president of the life and lab sciences division.

Thermo Fisher also confirmed its outlook for the rest of 2009, saying it expects sales of up to $10.1 billion and adjusted earnings per share of up to $3.10 for the full year.

The company posted net income of $207 million during the second quarter on about $2.5 billion in sales, compared to $246 million on $2.7 billion in sales during the same period last year.