It could be a hot spring, but it could also be a Xenomoray. It may have buried itself to avoid the nitrogen in the air, or as part of a crash when it left the time stream warp (or whatever it should be called) together with Makoto. Perhaps whatever absorbs the gaseous nitrogen inside Souboutei transports it into the soil? That could explain the strange plant-like pillars: they might absorb the nitrogen in the air, transport it to its "roots" (whatever those are: perhaps the Moray itself) and then expel it into the soil, which the puppets then transport away in order to unearth the Moray. Or, something else absorbs the nitrogen, expels it into the soil, and then the soil is transported and used to supply the plant pillars (or something plant-like elsewhere) with nitrogen so that they may grow. Where would they grow? Say, into the roof of Souboutei, where they could absorb rain? Or to spread through the wooden structure to reinforce it against attack?
Shit is muy misteriosa.
https://www.gardeningknowhow.com/garden-how-to/soil-fertilizers/nitrogen-nodules-and-nitrogen-fixing-plants.htm