In a nutshell, "the nature can also be used. A universe is something you can identify and describe. We normally think about the one we live in. It is countable. We do not normally think of a universe other than ours. Nature can be countable or not. If you are speaking generally about it as in the universe, it is more of an idea and hence uncountable. Nature can also be countable and use "the when something specific is mentioned. So we can talk about the nature of a tiger, or the nature of the Sahara desert. So you could write about "the nature of the universe we live in" Similarly you can use water as a countable noun. The water of the Dead Sea is saltier than the water of the Mediterranean Sea.

'The' is not used for 'uncountable' nouns, like water, or in this example, nature. 'I have one water' is wrong and has no meaning because you cannot count water; is it the same with nature. However, 'universe' is countable! even though there is only one (that we are aware of!) It is the only universe, but it is a discrete entity, so we can count it, and it does take the article 'the'. For the same reason we use 'the' when talking about 'the Internet' - there is only one, but it is countable - but we don't use 'the' with the word 'cyberspace', which refers to the concept of an area where computers operate the Internet, and is not countable.