La germinación empieza en el semillero.

Because germinación is a feminine noun in Spanish. Nouns ending in -ción are almost always feminine, so they take la in the singular.

• la germinación
• la nación
• la estación

So in this sentence, la germinación means the germination.

Empieza is the conjugated form of the verb empezar.

The subject of the sentence is la germinación, which is third-person singular, so the verb must also be third-person singular in the present tense:

• empezar = to begin / to start
• empieza = begins / starts

So:

• La germinación empieza... = Germination begins...

Because empezar is a stem-changing verb. In many present-tense forms, the e in the stem changes to ie.

Present tense of empezar:

• yo empiezo
• tú empiezas
• él/ella/usted empieza
• nosotros empezamos
• ellos/ellas/ustedes empiezan

So empieza is the correct form for la germinación.

Semillero usually refers to a place or container where seeds are sown so they can begin growing. Depending on context, it can mean:

• seedbed
• seed tray
• nursery bed
• a place where seedlings are started

In agriculture or gardening, en el semillero means something like in the seedbed or in the seed tray.

Because en is the normal preposition for location here, meaning in or in/at.

• en el semillero = in the seedbed / in the seed tray

Also, semillero is a masculine noun, so it takes el:

• el semillero

So the phrase breaks down like this:

• en = in
• el = the
• semillero = seedbed / seed tray

Yes. Comienza from comenzar is very similar to empieza from empezar.

Both are natural:

• La germinación empieza en el semillero.
• La germinación comienza en el semillero.

In most contexts, they both mean Germination begins in the seedbed/seed tray.

Yes, that is grammatically correct.

Spanish allows more flexibility in word order than English. Both versions are fine:

• La germinación empieza en el semillero.
• En el semillero empieza la germinación.

The second version puts more emphasis on where it begins.

A little, yes. La germinación is a noun, so the sentence sounds slightly more technical or scientific.

Compare:

• La germinación empieza en el semillero.
  = Germination begins in the seedbed.

• La semilla germina en el semillero.
  = The seed germinates in the seedbed.

The first talks about the process; the second talks about the seed itself.

A simple pronunciation guide:

• germinación → gehr-mee-nah-SYON
• empieza → em-PYEH-sah

A few helpful notes for Latin American Spanish:

• The ción ending is stressed on the last syllable: -ción
• The z in empieza is usually pronounced like s in Latin America
• The ie in empieza sounds like yeh

Spanish often uses the simple present where English might use either the simple present or the present progressive, depending on context.

So:

• La germinación empieza en el semillero
  can mean
• Germination begins in the seedbed
• Germination starts in the seedbed

If you specifically wanted is starting, Spanish would usually use a different structure, such as está empezando, but that would slightly change the feel of the sentence. The original sentence is a general statement, so the simple present is the most natural choice.