First is lost to space second is actually destroyed. Most other elements can be recycled.
Arguably genetic/linguistic diversity might also count. Because the rate of creation of new species and languages is slower than the rate of their destruction.
And finally total useful energy supply of the universe.
Plutonium is not a natural resource, it's manufactured in nuclear reactors.
Also, as it turns out operation of nuclear reactors generates Helium (an alpha particle is a Helium nucleus). Realistically we're not running out of Helium, there are lots of sources for it.
Uranium 235 / 238 supply's are finite so Plutonium is finite. I used it as an example because of it's decay rate forcing the issue also, using depleted uranium in ammunition is "sustainable" even if there are limits on it's use as a fuel. More specifically Plutonium-238 has a half-life of 88 years and emits alpha particles. It is a heat source in radioisotope thermoelectric generators, which are used to power some spacecraft.
Anyway, Man made production of Helium is no where near our current usage levels. Granted, if the world total energy supply was generated by fusion the numbers would be closer.
Energy density by mass (MJ/kg) Deuterium-tritium fusion = 337,000,000 MJ /kg, total worldwide energy consumption was 474 exajoules (474×10^18 J) = 1,406,528.19 kilograms / extraction efficiency.
I had hoped for something more forceful. Helium and plutonium are quite obscure and we can do without.
You are probably right about genetic and linguistic diversity. Though we can also do with less, if necessary.
I am not sure about the useful energy supply of the universe. I suspect its true, but we probably do not know whether the universe at large behave like a thermodynamically closed system.