If they accelerate the burning of fossil fuels, extract and process minerals on land and in the ocean without concern for pollution, replace large areas of the natural world with solar panels, etc., the world could rapidly become hostile for large creatures.
An ocean die out as a result of massive deep sea mining would be particularly devastating. It's very hard to contain pollution in the ocean.
Same for lakes. And without clean water things will get bad everywhere.
Ramping up the frequency of space launches a few orders of magnitude into the solar system for further resources could heavily pollute the atmosphere.
Microbes might be fine, and be able to evolve to changes, for much longer.