usually chemical fertilizers are salts, they will kill most of the microbes such as fungi and bacteria, will repel nematodes and protozoa. killing bacteria and fungi will eliminate the competition in the root rhizosphere which will result the rapid growth of diseases spores (more faster in growth than beneficial organisms)
plant nutrients are available ecologically through nutrient cycling in the soil, without a good balance depending on the culture you are cropping, the plant residues or hormones exudates will attracts bad organisms such as bad bacteria and fungi (agents causing diseases). root nematode will also appear in the rhizosphere. insect will only appear in a later stage when the plant is weakened and lacks protection.
Excessive use of nitrogenous fertilizers leads to an increase in incidence of pests, while the application of phosphate and potassium fertilizers reduces the incidence of pests.
Matching applied nutrient to plant demand, including key timings will reduce stress in the plant - this will reduce the plants sugar production (in basic terminology) which tends to attract insects. Some nutrients will have indirect benefits such as K driving water use efficiency in the heat which again reduces the stress response
Yes, Plant nutrition through fertilizer can negatively affects the crops. Excessive use of nitrogen fertilizer on rice can inhibits the growth of bacterial blight and this can be so devastating if not attended to early enough. Also, some fertilizer tends to kill beneficial microbes in the soil if not properly managed.
The modern day varieties of various crops have been developed are mainly vertical breeding considering yield as the major component, with little attention to the diseases and insects resistance characteristics the land races and local cultivars had. For achieving higher yields, supplementation of nutrients through fertilizer is essential, inviting more of diseases and insects. Hence, need to manage those through out side components including agrochemicals.
Unbalanced use of fertilizers can decrease plant resistance to diseases and pests. The most obvious example is applying high amounts of nitrogen fertilizers.