Wait, did I do it wrong?
Shape manipulation is manipulate the chakra you use to form objects, Nature manipulation is turn ones raw chakra into a more advanced chakra, elemental chakra, it can form fire chakra, wind chakra, lightning chakra, earth chakra and water chakra, it can also be used even more advancedly, with Kekkei Gekkais, to combine two or more of the basic elemental chakras to form a much more powerful one.
Each person has an affinity to certain types of elemental chakra, usually related to where they're born, people from Konoha most likely will have fire affinity, Suna wind, Kumo lightning, Iwa earth and Kiri water.
A nature and shape manipulation technic will be more strong than only a shape manipution one, taking for example Rasengan, Rasengan is a strong jutsu that is A rank and has a massive destructive power with only shape manipulation, now, by adding nature manipulation, wind chakra in the manga, it becomes Fuuton: Rasenshuriken, which is much, much more stronger than the regular rasengan, now being S-Rank.
There is also the Ying and Yang manipulation, which is used for regular ninjutsus, like shadow clones, clan jutsus, and it's own technics, like Izanagi, Izanami, etc.