You can invest a maximum of 31 books in your geologist. All skills have three levels excepts for the highest three (Lucky Find, Natural Born Digger, Nature's Gift), those only have one. Since the three highest skills require 30 books invested in the levels below, you can only choose one of these
Type: Manuscript
Hidden Stone Stash
Natural Copper Vein
Two Marble in One *
Quality Copper Mineshafts
Natural Stone Vein
Type: Tome
Natural Marble Vein
Copper Mining Surplus
Two Iron in One *
Quality Coal Mineshafts
Tendentious Geologist
Gold Mining Surplus
Type: Codex
Hidden Coal Stash
Iron Mining Surplus
Natural Gold Vein
Two Coal in One *
Quality Gold Mineshafts
Ore Collector
Lucky Find
Natural Born Digger
Nature's Gift
* The bonus deposit will NOT benefit from other skills that can upgrade these kind of deposits