Soil depletion: http://news.berkeley.edu/2015/05/07/soil-depletion-human-sec...

Groundwater depletion: https://water.usgs.gov/edu/gwdepletion.html

Antibiotic resistance: https://www.newscientist.com/article/mg23231044-000-antibiot...

Shall I go on?

Yes, please! Because the only response I can think of to the list you've posted is "so what?"

Humanity faced a lot of problems in the past. Let me remind you just a few:

* multiple plagues decimating European population

* wheat rust (and unpredictable famines ensuing)

* guano depletion

However, we engineered our way out of them. I can't see why the problems you've listed are any different.

Yes, we engineered our way out of them providing better conditions for future generations. We are not engineering our way out of the problems I listed, but rather making them worse and worse and creating worse conditions for future generations.

Plagues could still happen again. We know more about how they occur and how to contain them, but we don't have any magic bullet against all future plagues that will occur.

Rust is still a problem. I'm not sure why you think it isn't. We have more resistant lines and fungicides but the rust is adapting rapidly.

The difference is, apart from maybe the guano depletion, none of the problems you list of the past were due to human actively making things worse. All of the problems I listed are due to action right now that will cause major problems in the future.