So, you're going to have a few things to consider:
* Thousands of years means a genetic bottlenecking, most likely, were there any extinctions of entire groups of plants? Similar to the Gros Michel banana? (The Gros Michel still exists but is no longer a commercial variety, and our current Cavendish is at risk of mass extinction due to genetic bottlenecking).
* Hydroponics also means potential susceptibility to mass infection at once. If a fungal infection gets into a crop, or is in say, a badly stored seed, the spores in the enclosed space can wreak massive havoc, and are likely to grow quickly due to like, the humidity that hydroponics creates unfortunately.
* If they're composting biomass (say, faeces, dead people, dead animal companions if there are any) as well as all vegetable scraps, and paper/cardboard (though this is probably in diminishing supply) and possibly hay, this will actually get you VERY far. Plants like pigeon pea, for example, grow very quickly on very little, are nitrogen fixing (meaning they can be very useful chop/drop mulch for future plants who need nitrogen - which is most edible plants), and will great a lot of 'bulk' that makes a great mulch, compost. It's actually *far* more realistic to have a dual 'soil + hydroponics' system where certain plants are grown in soil - potentially in pot environments (which would allow for trees, fruit crops etc.) - and hydroponics. This also means all dead / dying / pruned hydroponics plants further are useful as a mulch / compost. (Provided there's no spores in the mix).
People produce a lot of waste through living and eating. And while we can eat much more of many plants than we actually do, the reality is that you will have a surprising amount of biomass. It's actually a common problem for people who live in a two-person home, for example, to start composting and realise *very quickly* that they are making far far more compost than they could ever need or use, certainly enough to support a lot of food for more than two people over time. (Although you do need dry matter for compost to work, but grow lights or ovens used to dry out leaves and branches would help with this).
TL;DR do not rule out soil, because biomass really doesn't 'only go so far.' Biomass is going to overwhelm your underground bunker if they don't find a way to recycle literally all their food waste / faeces / etc. In fact most science fiction stories I've read that feature underground bunkers that have been sustaining themselves for a long time will both mention a) genetic bottlenecks making plants more susceptible to disease and b) be using soil from their own waste + plants + food not eaten etc. Hydroponics isn't as common as you'd think in these scenarios! This is largely because clean and fresh water is usually not as abundant as...well...biowaste / plant waste / bodily waste. So you may want to look at a split approach.
*
As for plant fibres, you're probably going to be relying on hemp an awful lot from everything from paper, to clothing, to rope etc. (Hemp does pretty well hydroponically). Cotton can also grow very well hydroponically though it usually has to be developed specifically for the process. But it often has higher yields and needs less water proportionately.
Linen (flax) is less viable.
A big thing to consider overall is that long-season crops invariably do not do great in indoor hydroponics, so you need to look at short season crops - herbs, leafy greens like lettuce, sometimes beans etc. Anything that's longer season will struggle indoors. This is a huge consideration, there's a reason so much of successful hydroponics is done outside, grow lights can only do so much.
As an example, if I were contemplating something like this, I'd grow all green short season crops in hydroponics, and everything else indoors in recycled/composted soil, with an interest in using textiles for both the hydroponics (it helps), and also as dry matter in the compost (it helps), which would open me up to more options and introduce interesting dynamics like...experiments in what grows better in hydro or soil, or arguments over what 'deserves' soil more if it's in smaller quantities or alternative what 'deserves' hydroponics more.
Make sure when you're searching that you're restricting your searches to 'what grows best in indoor hydroponics' and not just 'hydroponics.' Because the word "indoor" takes so many plants out of the equation. Presumably some science developments would help with some things, but disease vectors are rough.
Anyway it's a huge subject! With many different theories etc. there's no single 'this is definitely what always grows best in hydroponics' (like, do you have hard or soft water, can they chemically treat the water, does it have an excess of calcium or lime, how are they dealing with build up, etc.) Water from different places in the same country can impact hydroponics systems very differently!! And obviously some water with some minerals is going to be better for some plants and worse for others (plants usually like a very specific Ph to grow in, and not all plants share that same Ph).
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branchandroot
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Date: 2025-03-09 01:56 pm (UTC)* Thousands of years means a genetic bottlenecking, most likely, were there any extinctions of entire groups of plants? Similar to the Gros Michel banana? (The Gros Michel still exists but is no longer a commercial variety, and our current Cavendish is at risk of mass extinction due to genetic bottlenecking).
* Hydroponics also means potential susceptibility to mass infection at once. If a fungal infection gets into a crop, or is in say, a badly stored seed, the spores in the enclosed space can wreak massive havoc, and are likely to grow quickly due to like, the humidity that hydroponics creates unfortunately.
* If they're composting biomass (say, faeces, dead people, dead animal companions if there are any) as well as all vegetable scraps, and paper/cardboard (though this is probably in diminishing supply) and possibly hay, this will actually get you VERY far. Plants like pigeon pea, for example, grow very quickly on very little, are nitrogen fixing (meaning they can be very useful chop/drop mulch for future plants who need nitrogen - which is most edible plants), and will great a lot of 'bulk' that makes a great mulch, compost. It's actually *far* more realistic to have a dual 'soil + hydroponics' system where certain plants are grown in soil - potentially in pot environments (which would allow for trees, fruit crops etc.) - and hydroponics. This also means all dead / dying / pruned hydroponics plants further are useful as a mulch / compost. (Provided there's no spores in the mix).
People produce a lot of waste through living and eating. And while we can eat much more of many plants than we actually do, the reality is that you will have a surprising amount of biomass. It's actually a common problem for people who live in a two-person home, for example, to start composting and realise *very quickly* that they are making far far more compost than they could ever need or use, certainly enough to support a lot of food for more than two people over time. (Although you do need dry matter for compost to work, but grow lights or ovens used to dry out leaves and branches would help with this).
TL;DR do not rule out soil, because biomass really doesn't 'only go so far.' Biomass is going to overwhelm your underground bunker if they don't find a way to recycle literally all their food waste / faeces / etc. In fact most science fiction stories I've read that feature underground bunkers that have been sustaining themselves for a long time will both mention a) genetic bottlenecks making plants more susceptible to disease and b) be using soil from their own waste + plants + food not eaten etc. Hydroponics isn't as common as you'd think in these scenarios! This is largely because clean and fresh water is usually not as abundant as...well...biowaste / plant waste / bodily waste. So you may want to look at a split approach.
*
As for plant fibres, you're probably going to be relying on hemp an awful lot from everything from paper, to clothing, to rope etc. (Hemp does pretty well hydroponically). Cotton can also grow very well hydroponically though it usually has to be developed specifically for the process. But it often has higher yields and needs less water proportionately.
Linen (flax) is less viable.
A big thing to consider overall is that long-season crops invariably do not do great in indoor hydroponics, so you need to look at short season crops - herbs, leafy greens like lettuce, sometimes beans etc. Anything that's longer season will struggle indoors. This is a huge consideration, there's a reason so much of successful hydroponics is done outside, grow lights can only do so much.
As an example, if I were contemplating something like this, I'd grow all green short season crops in hydroponics, and everything else indoors in recycled/composted soil, with an interest in using textiles for both the hydroponics (it helps), and also as dry matter in the compost (it helps), which would open me up to more options and introduce interesting dynamics like...experiments in what grows better in hydro or soil, or arguments over what 'deserves' soil more if it's in smaller quantities or alternative what 'deserves' hydroponics more.
Make sure when you're searching that you're restricting your searches to 'what grows best in indoor hydroponics' and not just 'hydroponics.' Because the word "indoor" takes so many plants out of the equation. Presumably some science developments would help with some things, but disease vectors are rough.
Anyway it's a huge subject! With many different theories etc. there's no single 'this is definitely what always grows best in hydroponics' (like, do you have hard or soft water, can they chemically treat the water, does it have an excess of calcium or lime, how are they dealing with build up, etc.) Water from different places in the same country can impact hydroponics systems very differently!! And obviously some water with some minerals is going to be better for some plants and worse for others (plants usually like a very specific Ph to grow in, and not all plants share that same Ph).