A Hydroponics-based Agriculture System

[voidbeetles]

Hi!

One of my current writing projects is set in a civilization that has, for thousands of years, lived in a sort of large scifi underground bunker. They have easy access to water, very little access to soil (they're able to compost biomass, add minerals, etc, but that will only get you so far), and no access to sunlight (grow lights will have to suffice) - for these reasons, I imagine that their agriculture system is mostly hydroponics-based. Though I've done a little research on hydroponics, I'm having difficulty extrapolating this information to my worldbuilding, mostly because a lot of the info I've found relates to singular plants without giving a good sense of what fares better/worse compared to others. And also just because I have a hard time wrapping my head around plant cultivation in general, I think. I was wondering if anyone here had any insights! (Or suggestions of topics/resources to look into more!)

The big questions I'm thinking most about are:

• Compared to, say, the modern Western world, would certain foods/food groups be underrepresented or over-represented in this fictional world's cuisine? (for example, I imagine that rice might be the main staple, as flooding rice fields is pretty important to cultivating it... and that potatoes might not be such a good choice, as their "main thing" is growing beneath the soil?)
• What effect would this have on the plant fibers that are most commonly used for making clothes (and other fiber technology like rope)? That is: how would cotton, linen, hemp, etc fare? Would a certain one of these plants be more common? More expensive? Quicker/easier to grow/harvest on large scales? (This question is especially relevant because my protagonist has an interest in textiles.)

Comments

[winterbird]

I will do my best to see if I can explain a bit better!!

I am a little confused on how likely this is to lead to entire groups of plants going extinct, or rather, how this particular setting affects that likelihood.

I mean in the people as well, living in an underground bunker, not just the plants. But anyway, the TL;DR is the reason clones are so susceptible to disease is because they can't evolve into a more resilient form. There's nothing else to cross it with. This is actually an issue for plants if you're basing everything off a single seed (they are self-seeding, that is...basically how we get clones), or a very small amount of seeds (they are cross-pollinating, but eventually through breeding, they will eliminate certain genes and become very similar to one another, until finally that random gene that might help with random new disease no longer exists literally in any of the new plants, and they all get wiped out at once). (To say nothing of the fact that sometimes a very small gene pool just suddenly goes 'oh shit we can't fix nitrogen (or insert other nutrient here) from the soil anymore, whoops, guess we'll all die.') This is where variability in the environment, in nature, and in long-term survival is absolutely vital to that survival, and why diversity in plant life is actually going to be a bit of a fun challenge in a story like this.

Also, take your humans:

In a small and narrowing population, you get inevitable incest and less genetic vigour, in animals and plants. The more plants cross-pollinate within only a tiny number of samples, and the more humans have sex eventually with their own relatives (usually without realising) due to the lack of diversity in the gene pool (depending on how large this underground bunker is), you increase suspectibility to disease over time. Ironically for similar reasons to why clones are so shit at handling disease: You have less and less and less hybrid vigour / genetic vigour, and more and more likelihood that you have no chance to genetically develop resilience to new disease.

Basically the reason why incest in people is bad (it's morally taboo because it kills us with disease and deformity over time due to narrowing our gene pool - literally that's why, because it's biological suicide over time) is the same reason why it's often bad in plants too, especially those that cross-pollinate. In self-seeding plants, you are having plants produce essentially clones of themselves. If that plant has a susceptibility to a disease, what - exactly - in your world is it breeding with to remove that susceptibility? This is often a huge issue in seed banks re: global preservation of plants. And it's something that's been discussed. It would take longer to be an issue in long-growth plants, and definitely if you have geneticists etc. in your bunker that would help a great deal. (To say nothing of how you're going to address pollination, though hand pollination for *some* plants exists. Figs are probably out entirely due to wasp pollination).

Say the first generation of bunker-dwellers is sealed in with a pretty diverse array of crops.

So, hypothetical questions: Are there tens of thousands of humans in this first generation? If not, say its only a few hundred, you are absolutely 100% going to get intense incest-based deformity, disease and genetic bottlenecking here - not in the first or second generations, but by the third and fourth, incest will become largely unavoidable and/or you are dealing with extreme arranged 'you can only mate with X and X and cannot choose your lover' scenarios (which can work out, but given 'everyone is in an underground bunker' - sanity might be thin - especially given the nature of epigenetics around natural disaster + mental illness).

You can handwave this by having like, idk, CRISPR based technology (gene editing), but that introduces its own issues. Sometimes huge ones, if you're messing with autosomal dominant genes. (Idk if you're planning on writing soft or hard science fiction. If it's soft science fiction, this doesn't matter at all. If it's hard science fiction, then this does probably need to be addressed).

As for the plants: Do their diverse crops include hundreds to thousands of seeds from different locations of the same plant? (Not just different crops). If yes, then they're going to do just fine. If no, then you move straight towards the cloning issue we have in bananas. They are seeding the same genetic make-up, if that genetic make-up gets introduced to a new disease, goodbye to that entire species. Obviously it's fiction and you can ignore all of this! But it would be unusual for this not to at least happen to some of your plants. You can even include it as an anecdotal worldbuilding note like 'we're lucky we had a lot of seeds of all of these plants, remember when oranges went extinct because we never had enough seeds and the X blight of X year hit them at once?'

Is it the fact that these conditions are so strict/peculiar that would lead to the lack of genetic diversity?

Partly, but not wholly, it's simply that cross pollination won't be happening as it would in nature. This is a problem on monocrop farms already. I'm not going to get into genetic punnet squares x.x but let's say plant Bob has specific fungal disease resistance (DR for Disease Resistance) but doesn't bear fruit, and doesn't grow fast, and plant Jill (NR for No Resistance) doesn't have disease resistance, but she grows super fast, and bears lots of fruit!

If Jill and Bob cross-pollinate, their genes mix - some genes won't be the same, and will delete other genes along the way. Let's say that disease resistance is *not* a dominant gene, that means in this case the disease resistant gene (DR) gets deleted and replaced with NR in the offspring plant. But maybe the baby plant is a really fast grower! And bears lots of fruit! So those seeds will get saved and preserved among farmers until the next disease blight, in which case everyone finds out all at once 'oh no baby NR has no disease resistance, and it's dead now, and our farms have been destroyed, because we have no more Bobs anymore, because we didn't grow those ones because they didn't grow as well, and we didn't preserve any of those seeds.'

Now, imagine that you need literally hundreds of seeds to actually make sure you preserve say, different elements of - how much water does it need, how well does it grow, how much fruit/veg/whatever does it bear, how much disease resistance does it have to like hundreds of diseases, how susceptible is it to root rot from humidity and damp, how well does it do indoors. All these traits have different genetic markers, and different plants will have different strengths and weaknesses (like idk a DND stat chart), and it's only in constantly mixing them together that we get the vigour we need for species to survive and evolve over time. We can speed it up with selective breeding, but as my example shows above, farmers are going to pick 'grows fast and bears more fruit' over 'survived that disease we forgot about 100 years ago' and that's where we get *big* issues. Even today, in current farming!

This is infinitely more complex in people / humans, but still happens.

And unfortunately some diseases are dominant genes and not recessive, meaning they will delete the healthy gene and replace it with itself (talking from experience here, I have a dominant cancer gene, and it's one of the most hereditary genes in the world, whee). Not only that, but recessive genes do still sometimes win, so recessive genes that might carry more susceptibility to diseases etc. will still sometimes bear out.

If you add onto this a stressed environment - which it would be by default underground for anything that's not supposed to live underground - there is, on top of that, issues that can happen to seeds via not getting enough specific nutrients etc. There's a reason indoor hydroponics to this day isn't favoured over outdoor hydroponics, y'know? Grow lights only do so much.


Would it be possible (in the very long term) to reintroduce genetic diversity by introducing these engineered crops to different environments within the bunker?

Different environments isn't guaranteed to change genetic make up in a predictable or helpful fashion. It can be just as likely to weaken a species over time (evolution isn't intelligent, and sometimes things just die - going extinct is actually more guaranteed than surviving, as a case in point: More animals and plants have gone extinct since life began than have survived, which should give you an idea of how chaotic nature is at sometimes just...not figuring it out sdlakfjsa).

The big question is just how to decide which crops are likely to have these problems.

All of them. Especially the self-seeders that don't need pollination. But pollination is an additional issue to consider. You can hand pollinate cucumbers, for example, but some plants don't do well with hand pollination!

Does it have more to do with how they're propagated? More to do with how hardy they are in this environment? More to do with how genetically diverse they are when reproducing naturally (like, how much you can get away with not cloning/inbreeding/etc)?

It's mostly about the latter. Nature is constantly in an arms race against things like bacteria / viruses / fungi, and they can often evolve much faster than we can. (This is how we unfortunately get things like antibiotic resistant everything, it feels like - but things like MRSA).

One of the reasons 'functionally extinct in the wild' exists as a designation even when there's still 40 wild animals left of a species, is because there's not enough gene diversity to sustain the animal anymore. Eventually incest / gene concentration / lack of vigour will kill the animal off even if it breeds a ton, because there's just no new genes to introduce anymore. (This is also why dog breeders will sometimes import dogs from overseas, to broaden the gene pool, literally, and create more healthy strains of purebreed dog).

This applies to plants too. Sometimes we get lucky and a clone or narrowed gene pool just happens to do well for a long time until it doesn't. But it's unrealistic to expect that would be true across all plant crops, especially underground. Growth environment matters. Seeds take time to develop. If there's a shorter growing season, or the plant doesn't get enough nutrients/sunlight, the seed is often smaller and stunted, it's just weaker, and it creates a weaker plant, and so on and so forth, until one day the seeds just don't grow anymore. So it's definitely a combination of things. Idk if you plan on your people staying underground forever, but you can absolutely generate significant tension and plot by say, characters recognising that they may only have 2-3 generations of people left before they have to figure out a way to rehabilitate the planet, or to get back aboveground. This is something I've seen in science fiction quite a bit before, as a plot point, the lack of genetic diversity in what they're living on to survive starts to ail and weaken (as they are themselves), and they realise that they're basically in a 4,000 year tomb. After all, nature is really good at being like 'ah fuck it, let's just go back to single celled organisms for a while')

Depending on how incredible your scientists are, you might also want to look into them exploiting chemosynthesis (using nutrients/compounds etc. to create life instead of sunlight) to potentially take advantage of underground grown foods like peanuts etc.

At the end of the day you don't have to consider any of this!!! This is just what my brain does, and you do not have to do this to write an amazing science fiction story, trust me. I definitely recommend reading some of the many science fiction novels that all work on a scenario like this one! Because you can see a lot of different ways people choose to solve this issue both in terms of plot, but also in terms of science. :D

[voidbeetles]

Thank you so much again!! This is all incredibly interesting.

The story is indeed very soft scifi, plus, these sorts of details flesh out the background rather than the main content of the plot, but I thought it would be important (and fun!) to get a sense of the details of the science and logistics before I relegate it to that background role… or even bring some of it into the foreground. (If I ultimately decide to solve these problems with scifi BS, I want to know I’m BS’ing it, you know?)

One final question for now… do you have any recommendations for other scifi novels with a similar setting? :D

[hamatebones]

I have one, pretty obscure but a soft-science approach to a completely insular sci-fi situation: Molly Gloss's The Dazzle of Day. It's about Esperanto-speaking Quakers on a generation ship seeking a new homeworld, but "how do the logistics work" is kind of not the point, except the interpersonal logistics I guess.

However, sprinkled through the book are little asides, like the fact that all the cats went extinct at one point due to a new/unknown disease, and they all miss cats. They'd brought cats with them, and kept them for generations, but then they got unlucky. There isn't even an explanation of, you know, probably it was something the cats already had that wasn't that bad, that mutated and became lethal, and the cats all being interbred were in their own genetic bottleneck so might have been genetically weaker... but you can infer that if you're so inclined.

[hamatebones]

I've also been thinking about permaculture lately, and realized that a bunch of the fruit trees/shrubs I'd most like to grow are extremely difficult to keep. Apples? Apple-cedar rust. Peaches? Parasitical worms, leaf blister. I suggested juneberries, and was told, well, maybe not, they're very susceptible to [name I don't remember] fungus.

Why? Because they're domesticated fruit! Because we've been breeding them all out of whack to get something sweeter and bigger and easier to harvest than the wild type, and that automatically brings in a whole host of problems. Domesticated plants are overwhelmingly more susceptible to disease than wild ones, and domesticated fruit trees in particular need a ton of care and prevention to survive right now, in this world, where they have free sun and water and good soil and hardy rootstock!

Backyard gardeners are often willing to commit to that care, but man, it's a commitment. The ornamental, wild-type, non-edible-fruit-bearing version of that tree is always going to be easier to keep alive.