Plants don't just suck up everything randomly, though. Roots are highly evolved organs, serving as the gatekeepers for what gets into the plant's circulation. The anatomy of a root varies depending on its age and the type of plant, but the basic structure of an active root is in rings: an outer fleshy part which is able to absorb whatever's around it, an inner core where the circulatory tissue is, and in between, a ring of cells with an impermeable "mortar" cementing them together. That mortar, called the Casparian strip, is what ensures that anything going into the plant's circulation has to go through one of those guardian cells.
They're picky, too. They only let in a certain amount of water, to keep the interiors of the other cells from getting too diluted. They pay attention to the concentration of ions like iron, magnesium, and potassium, and actively manage their uptake. There are specific gates in the cell membrane for several things, and lots of other molecules get left out.
By the nature of those membranes, some types of molecules can just walk right in, however. Cell membranes are mostly made up of oily compounds called lipids, which glob together to make a fatty bubble, dividing the water inside the cell from the water outside the cell. Molecules which resemble those lipids can sometimes sort of phase right through, like a pedestrian making his way across a line of people. He bumps, and jostles, and comes out the other side. A repeat performance on the other side of the cell, and they're into the part of the root where they can enter circulation.
In some cases, plants will intentionally take up things which they don't actually need, for one reason or another. Many studies have been made of plants which can take up excess minerals, called hyperaccumulators; one such plant managed to accumulate enough nickel to make up a quarter of its sap.1 And food scientists have known for years that rice is very good at accumulating arsenic, to the point that rice from the southeast United States can have significant amounts of it, when grown in old cotton fields where arsenic-related pesticides were once used.2 The reason rice takes up arsenic, even though it's not needed for growth, is that it closely resembles silicon -- and rice uses a lot of silicon, in its common form of sand, to make sturdy stems and leaves. The gates can't tell the difference, so they pull both in.
To take it one step further, bioremediation is the process of using plants to decontaminate soil; beyond taking up simple elements as mentioned above, some plants can accumulate, break down, or attract microbes that eat more complex hazardous materials like PCBs.3 Plants that naturally take up compounds like that are rare, and often have to be specifically engineered for that purpose.
So the quick answer to "Does X make it from the soil into my food?" is... it depends on what X is like. If it's a small ion like those in table salt, it'll only get taken up if the plant wants it. If it's a larger, but still highly water-soluble chemical like white sugar, it's even less likely. The compounds which are most likely to cruise through the gatekeepers and end up in the rest of the plant are slightly oily, smallish molecules that aren't too afraid of water.4,5
There's a lot of those, including ones that are used as pesticides, some antibiotics, and others that are considered hazardous soil contaminants. So it's important to know whether they actually make it into what we're eating. Unfortunately (you saw this coming) it's not simple to figure that out.
Take an antibiotic used in animal feed. In order to end up in your green salad, it has to travel a long way: from the animal feed, through the animal, into the manure, through manure storage and handling, onto (or into) the soil, into the plant root, through the plant's circulatory system, and finally coming to rest in some edible part. There are a lot of ways it can get broken down, diverted, or diluted in all of that. If you want some truly fascinating bedtime reading about the details of animal manure handling, there's at least one good article which summarizes all but the last three links of that chain.6 In short, though results vary widely by the type of antibiotic, a significant amount of drug can make it into animal manure, but washing it into storage ponds or pens and letting it sit there until it's used seems to degrade a lot of residual antibiotics. From there, if it's put on top of the soil, sun can do a real number on some antibiotics, breaking them down fast. Plus, some of them are really water-soluble and get washed out of the root zone pretty quickly.
Some amount often persists. What that amount is depends hugely on the steps up to that point, and what type of soil is involved. If they're present, and studies have documented fields where they are7,8, some antibiotics have been shown to make it into plant roots9, or even whole plants10... but only in the lab, and sometimes with setups as artificial as soybean plants with the green part lopped off. If they do make it into circulation, the plant may break them down. Plant enzymes have been found which resemble the same ones we have to degrade toxins and drugs, leading to what's called the "green liver" effect.11 Finally, the plant might store antibiotics in some part that we don't eat; if we eat its seeds, storage might be in the leaves.
So when it comes to whether our food plants take up small oily molecules, many of which are also easily assimilated by animals (our cell membranes aren't that different), the answer is... we don't know. We know it's possible in theory, but we haven't yet determined whether it happens in real life, or whether it affects us.
Could we do testing of plant-based food to determine antibiotic levels? Sure. But without also collecting data on all the factors up to that point -- remember all the steps between the feed bag and your table? -- it would be of limited use. Was the soil sandy or clay? Was the manure stored before use, and if so, how long? What was the starting concentration of antibiotic in the manure? Until we know all the factors, we don't know enough to figure out what to do to reduce the problem. If it is one. Maybe it's only an issue in clay soils above pH 6, where pig manure was injected into the soil less than five weeks before planting.
This is a classic case of the frustration built into science. It feels like a basic question, but the answer is incomplete and unsatisfying... perhaps now you can see that it's just because the question is so big. To really answer it, we'd have to go through and test each animal antibiotic under all the common situations, for a large sample of the plants we eat. It's equivalent to taking students from a dozen elementary schools all around the country, and forty years later, trying to find out whether they play golf. You could make guesses, based on generalities; those from whiter, wealthier neighborhoods are more likely to play golf. You could ask a bunch of random people, and use those results to estimate what percentage of those people would play golf. But until you track each one down and ask them, you don't know for sure. Repeat that process for each crop plant, with each antibiotic, and it becomes a huge task.
If there's anything to take away from this, it's that some of the research on antibiotics and other contaminants is being done. Enough people feel that it's an issue worth exploring that they have done studies, and those studies have been wrapped into review articles, and those reviews have prompted people to ask more questions. Hopefully you now have a better idea of what questions are worth asking, and what might make a good answer.
Meanwhile, you can put away the sugar container when planting your tomatoes. :)
