Pass auf, sonst stolperst du über die Wurzel.

Because aufpassen is a separable verb.

• Infinitive: aufpassen = to pay attention / to watch out
• In a main clause, the prefix auf- separates and goes to the end:
  • Ich passe auf.
  • Du passt auf.
• In the imperative, you also separate it:
  • Pass auf!

So Pass auf! is the normal imperative form of aufpassen.

German imperative sentences usually leave out the subject pronoun.

So instead of saying:

• Du pass auf

German normally says:

• Pass auf!

This is just like English often saying Watch out! instead of You watch out!

If you do include du, it sounds more marked or emphatic:

• Pass du auf! = You be the one who watches out!

But in a normal warning, Pass auf! is the standard form.

This is the informal singular imperative of passen / aufpassen.

For many verbs, German can drop the final -e in the imperative. So:

• passe auf → pass auf

In modern spoken German, the shorter form is very common and natural.

So:

• Pass auf! = standard everyday German

You may still sometimes see the longer form Passe auf!, but Pass auf! is much more common.

Sonst here means otherwise or or else.

So the structure is:

• Pass auf, sonst ...
• Watch out, otherwise ...
• Watch out, or else ...

It introduces the consequence of not doing what was just said.

Examples:

• Beeil dich, sonst verpasst du den Zug.
  Hurry up, otherwise you'll miss the train.
• Lern, sonst fällst du durch.
  Study, otherwise you'll fail.

Because sonst takes the first position in the clause, and in a German main clause the finite verb must come second.

So the second clause is structured like this:

• sonst = position 1
• stolperst = position 2
• du = after the verb

That is why you get:

• ..., sonst stolperst du ...

not:

• ..., sonst du stolperst ...

This is a very common German word-order pattern:

• Heute gehe ich nach Hause.
• Dann kommt er später.
• Sonst wird es teuer.

Stolperst is the 2nd person singular present tense form of stolpern (to trip / stumble).

Conjugation:

• ich stolpere
• du stolperst
• er/sie/es stolpert

Since the sentence is addressing du, the correct form is:

• du stolperst

So:

• sonst stolperst du ... = otherwise you’ll trip ...

German often uses the present tense where English may use will in translation.

German frequently uses the present tense to talk about the future, especially when the future is clear from context.

So:

• sonst stolperst du über die Wurzel

literally looks like:

• otherwise you trip over the root

but naturally means:

• otherwise you'll trip over the root

German could also use wirst stolpern, but that would usually sound heavier and less natural here.

There are two things going on here:

1. Wurzel is a feminine noun

So its article is:

• nominative: die Wurzel
• accusative: die Wurzel

In this case, nominative and accusative look the same.

2. stolpern über takes über + accusative

When German says to trip over something, it normally uses:

• über + accusative

Examples:

• Er stolpert über einen Stein.
• Sie stolpert über die Tasche.

So here:

• über die Wurzel = over the root

Here, yes, it means a root in the ground, like a tree root that you could trip over.

But Wurzel can also mean other things in different contexts, for example:

• square root in math: die Quadratwurzel
• the root or origin of something: die Wurzel des Problems

In this sentence, though, the physical meaning is the one that fits.

It can mean both, depending on context.

In this sentence, because there is an immediate danger:

• Pass auf, sonst stolperst du ...

it is closest to:

• Watch out
• Be careful

In other contexts, aufpassen can also mean pay attention:

• Pass im Unterricht auf.
  Pay attention in class.

So the exact English translation depends on the situation.

Yes, very natural.

A native speaker would easily say:

• Pass auf, sonst stolperst du über die Wurzel.

It sounds like a normal spoken warning to one person you address as du.

Some close alternatives would be:

• Pass auf, du stolperst sonst über die Wurzel.
• Vorsicht, sonst stolperst du über die Wurzel.
• Achtung, sonst stolperst du über die Wurzel.

But the original sentence is completely normal and idiomatic.