I quickly came up with many topics relating to the problems associated with Industrial Agriculture and only afterwards did I realize that I had neglected any suggestions relating to Sustainable Agriculture. I added those at the end. Looks like I need to focus on the positive a little more. Here is the text of the response to her request.
There are so many issues with industrial agriculture. Here's some off the top of my head;
If you want to deal with the nitrogen cycle and overfertilization you can look at it's contribution to climate change as nitrous oxide is 300X more potent as a greenhouse gas. Or you could look at the dead zones in the Gulf of Mexico and other river mouth oceanic areas around the world largely attributed to excess nitrogen runoff, again from overfertilization. There is also the issue that the nitrogen in chemical fertilizers break down and dissipate into the water table, atmosphere, rivers, far faster than organic fertilizers such as manure and compost.
A related issue is factory farming of livestock and it's link to the development of superbugs and the decreased effectiveness of antibiotics, not to mention the issues of cruelty.
Of course there is the well trodden issue of food miles with it's related issues of chemical use to keep food from ripening, thus drastically reducing nutritive content and exposing the populace to the excess pesticides used. Clearly Food miles also has implications to climate change and peak oil as it so heavily reliant on fossil fuels.
Another heavily debated issue is the energy balance in corn ethanol and the the effect this industry is having on food prices as it furthers the damaging effects of the commodification of food (an issue in and of itself).
There are social justice issues having to do with the treatment of migrant labor, the destruction of the family farm, and of course the effects of climate change which impacts the poor disproportionately. A little known fact is that Industrial agriculture is one of the largest contributors to climate change on the planet when you factor in the deforestation involved with palm oil plantations and cattle ranches. Even without that it is one of the highest emitters in North America.
You could look at the estrogenic effects of the plastics used in food packaging, both on humans; girls reaching puberty much earlier, and on the feminization of various aquatic species. Other issues include;
Pesticides in the water table, specifically atrazine.
Corporate control of government regarding agriculture
(the subsidization of agribusiness via the farm bill)
Damage done to biodiversity via habitat loss and chemical usage.
The epidemic of obesity and diabetes since the widescale promotion of High Fructose corn syrup and it's leptin suppressing qualities.
The reduction in depth and quality of soils worldwide.
Farmer suicides worldwide, worst in India.
I can recommend you check out Rodale and the Organic Consumers Association for research and links to take you the other direction in investigation of positive alternatives, of which there are many.
Advantages of Organic Agriculture include;
carbon sequestration, superior nutrition, enhanced biodiversity, reduced food miles (if done that way), increased local resiliency (again if kept local), less reliance on fossil fuels, reduced reliance on medical infrastructure due to better nutrition and reduced farm related poisoning, protection of the water table, builds soil rather than destroys it, ....
You could also explore alternative agricultural technologies; foot powered water pumps, keyline design, permaculture, biogas production, composting, rainwater harvesting and storage, bio dynamics, biointensive, ....
Check out Appropedia and Agroinnovations sites.