why do biofuils have a environmental effect on the atmosphere?

Answer 1

Plants absorb CO2 and release O. When they die (rot away or burn), they re-combine C and O to CO2 and the cycle is looping.
Mineral oil, natural gas and coal is fossil fuel that should have looped its cycle millions of year ago. When we burn it no, we upset today's cycle.
Bio-fuel means simply that we use what we recently produced, what had recently absorbed CO2.

That was in a nutshell. The picture is more complex as to deforestation, etc.

Answer 2

Biofuels are derived from plants which absorb the planet-warming greenhouse gas carbon dioxide as they grow, and so are meant as a climate-friendly substitute for fossil fuels.

But the biofuels actually have destroyed the rain forests to release more greenhouse gases than they save, because of the fertilizer used in modern farming practices.
Destruction of trees has led to very little of CO2 absorption from the atmosphere & replenishing of O2.
The crops grown to produce a "green"alternative transport fuel actually speedup global warming because of industrial farming methods.
This has led to unintended side effects such as rainforest clearance and raised food prices, from competing with forests and food for land.
Using biodiesel derived from rapeseed would produce between 1 and 1.7 times more greenhouse gas than using conventional diesel.
Maize is the main biofuels feedstock used in the United States, and produced between 0.9 and 1.5 times the global warming effect of conventional gasoline.
Biofuels depend on the manufacturing of fertilizers, fuel used
to power equipment, and fuel used to transport crops
Scientists and farmers should focus on crops needing little fertilizer, and harvesting methods that were not energy intensive.