Genetically modified crops are often genetically modified to be more resistant to pests as to need fewer pesticides or modified to need a smaller amount of fertilizer. However, GMOs typically require a lot more water and they cause soil erosion much more quickly and harshly than non modified crops. Additionally, there have been some patent issues with GMO seeds floating into neighboring non-GMO farm fields and taking over. Monsanto even sued one of those neighboring farmers in Canada, and won.
From your citation it sounds like the soil erosion and water use issues are issues of any monoculture, genetically modified or otherwise. Apologies if I’ve simply missed the relevant passage.
It depends on which trait the genetically engineered crops carry.
All genetically engineered crops currently on the market benefit the same amount from fertilizer as conventional varieties of the same crops (they’re the same). There are however varieties in development which will use nitrogen more efficiently than conventional crops (first citation).
Crops engineered to contain bt proteins provide control of specific insect pests without the need to spray insecticides, so those genetically engineered crops require less pesticides. Crops that are engineered to survive herbicides (for example roundup ready or liberty link) don’t REQUIRE more herbicides, but the end result is often that more herbicides are sprayed to take full advantage of the trait. Other traits that are involved in controlling weeds or insects have no impact on pesticide use.
Fertilizer: The same, and in the future sometimes less
Pesticide: More, less or the same depending on the kind of GM trait.
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