I really like the core mechanic - seeds with 2 functions, and with offensive, defensive, and puzzle-solving abilities. (not to backseat design, but) Maybe lower the number of seeds (possibly by merging some) or offer only a few for each level to avoid overwhelming the player with choice and having them never use most of them, thus forgetting about them when a puzzle requires something specific. It would also be good to introduce the seed types slowly, but not so slowly it's boring, maybe 2 per level (ideally staggered) until they have them all, or make them use the ones they have more, and introduce them slowly (which requires quite a lot of levels). If you want to let the player know about the scientific principles behind the seeds (since it seems important to the group), but you don't want to distract the player with it if they don't care, you could have information panels or descriptions when/if you find them.
While the game is very planty, and very plant-a-seed-ey, there's not much of a clearly environmental message; there's more to the climate than plants, and more to industrialisation than robots, but I think that putting your focus into making a better game rather than a better messaged game is a good move, at least in this case.
There also seem to be 2 different narratives, either you're a forest spirit manifested to reclaim the land, or you're a gardener recruited into an organisation to collect seeds, which then gets distracted by Moonsanto (good name, legally distinct). Both seem like pretty good narratives, and they're not necessarily contradictory (there could be some possession or something), but it would be good to clear up.
This might be strange to say in a game jam, but this is the most "game" of a game I've seen so far, which is definitely a positive. I greatly look forward to playing this at the end of the jam, as it actually sounds like it will be quite fun