I want to create a world were soil mining is a major industry. Imagine a vaguely Earth sized world where almost the entire surface of the planet is under, ocean, ice caps or is a hot or cold desert with nonexistent or very poor soils.
Soil or soil like organic matter does exist, but only quite deep underground and the inhabitants are forced to dig soil mines so that they can bring it to the surface for use in growing crops. How could such a strange state of affairs come about?
Glaciers cover the old landscape.
Preservation of a Preglacial Landscape Under the Center of the Greenland Ice Sheet
Continental ice sheets typically sculpt landscapes via erosion; under certain conditions, ancient landscapes can be preserved beneath ice and can survive extensive and repeated glaciation. We used concentrations of atmospherically produced cosmogenic beryllium-10, carbon, and nitrogen to show that ancient soil has been preserved in basal ice for millions of years at the center of the ice sheet at Summit, Greenland. This finding suggests ice sheet stability through the Pleistocene (i.e., the past 2.7 million years). The preservation of this soil implies that the ice has been nonerosive and frozen to the bed for much of that time, that there was no substantial exposure of central Greenland once the ice sheet became fully established, and that preglacial landscapes can remain preserved for long periods under continental ice sheets.
In your world, glaciers cover what used to be fertile fields. Your people tunnel down through the glacier to access those fields and their soil. Under the ice, they may find other remnants of the world that once was.
The asteroid that killed dinosaurs did not kill all of them by direct kinetic strike. Most of the world was affected in two ways:
If the world has been hit by an asteroid like that in recent eras, it may take a million years or more for land to recover naturally. If mankind was just getting off bunkers months after the asteroid hit and the dust has settled, they'll have to dig for Earth that has good nutrients, and will have to treat that soil in order to make it arable.
In lieu of an asteroid, a global nuclear winter would do. You have to dig through all that radioactive ash in order to get good soil. This may also happen due to global warning (not a typo).
Soil is primarily made up of the decomposed remains of other life, so a planet where plant life never made it to solid ground will have all of it's soil in water and around its bodies of water, but the vast majority of dry land will just be exposed bedrock, sand, and volcanic ash.
Furthermore, most plants do not have roots capable of penetrating solid rock; so, even in places where the ground may contain the nutrients they need, they still rely on pioneer species break up the ground enough to create arable soil, and prevent erosion. Without this, any soil that might try to build up from the remains of microbial life will just be washed away or compress into sedimentary rock.
Is this possible?
Absolutely. Plant life only moved to solid ground on Earth about 475 million years ago, but Earth has had aquatic life for billions of years. So, if you were to just find an Earth like world that is 500 million years or so behind us on its evolutionary path, then you will not find usable soil on most of the dry land, but you will find soil in bodies of water where the remains of microbes have gathered, and been kept soft from constant exposure to water.
Using pioneer plants, you could begin terraforming this world's dry land into soil, but this process takes a few thousand years, and most pioneer plant species are not agriculturally useful. So, in the meantime, your colonists would need to rely on dredging up soil from rivers and lakes to create artificial topsoil.
If your planet has only very little of natural land and the rest would be covered with water, then as soon as the inhabitants reach a certain number, the would have to get creative for food production, as there is only so and so much space for farming.
The first thing to do would probably be to move all housing and industry on platforms in the sea, but once that is done and all available natural land is filled up with farms, the only way to increase space for farming would be, to put soil on the platforms and farm there.
That of course means that the soil has to come from somewhere and as you don't want to destroy more fo the farming land you already have than is absolutely necessary, digging deep comes to mind.
Now bare in mind that soil is not dirt and it takes more than to mix the right amounts of nutrients and micronutrients with sand. The little critters living in the soil are just as important as all the nutrients, because they make them available for the plants.
That is why I would start the world with a bit of good soil, so the critters can be transplanted to the artificial soil.
A world like that would have to be very focussed on recycling all the organic material that is available. As it becomes valuable soil.
So this world would not actually be mining soil, there simply is no soil underground, just rocks, gravel and minerals. They would be mining the ingredients for soil and then make it.
That is not too far from what we do now to make our crops grow, since soil depletes quickly as you grow crops. "Crops perform better when they have nutrient-rich soil. Healthy soils contain a balance of nitrogen (N), phosphorus (P) and potassium (K). These three nutrients help plants grow in different, yet each important, ways:
Nitrogen helps a plant’s leaves grow; Phosphorus supports a plant’s root growth and flower and fruit development; and Potassium is a nutrient that improves the plant’s overall health."
Google Potash mines images and you will get some great ideas for what an underground "soil" mine would look like. Potash is made of potassium.
Then you'd need Nitrogen--"Nitrogen fertilizers are made from ammonia (NH3), which is sometimes injected into the soil directly. The ammonia is produced by the Haber-Bosch process. In this energy-intensive process, natural gas (CH4) usually supplies the hydrogen, and the nitrogen (N2) is derived from the air." So rather than mining Nitrogen you would be manufacturing it. No doubt human waste could help in the processing...
Lastly you need phosphorus- "Most of the phosphorus used in fertilizer comes from phosphate rock, a finite resource formed over millions of years in the earth's crust. Ninety percent of the world's mined phosphate rock is used in agriculture and food production, mostly as fertilizer, less as animal feed and food additives."
Google phosphate mining and it appears that form of mining is usually strip mining on the surface. But... creative license..
So over all you need not come up with too fantastical of an idea which the world would have to mine soil. Since we already do. Any of your ideas, Global freeze, Global flood. Global disaster...
If you look at human evolution, and movement to cities, you could take the angle of megastructure civilizations. These massive societies all contained in a few buildings around the world would still need to grow plants to feed people and to develop things like medicines. The thing with moving everyone inside though is that the population will still increase, requiring the need for more and more soil to produce food.
To make the "outside world" uninhabitable, you could pick from almost any list, authoritarian government mandate, nuclear war, supervolcanic eruptions, the return of the glaciers, or even an atmosphere that is in heavy deterioration which leads to heavy radiation of organic topsoil.
