根 and 茎: identifying roots and stems
Read plant parts and the targets of watering or cutting precisely.
The state of roots
根 (ね) means root. 「土の中に根が伸びています」 says roots are extending through the soil.
「根を傷つけないように植え替えました」 describes transplanting with care not to damage the roots. ように gives the purpose of that care.
The appearance of stems
茎 (くき) means stem. 「茎が長くなりました」 says the stem grew longer.
「茎の下の部分を切りました」 identifies the lower part of the stem as what was cut. It does not include cutting away all the roots.
Comparing parts
「根は残っていますが、茎は折れています」 says the roots remain but the stem is broken. Do not merge the whole plant's condition into one state.
「茎ではなく、根の近くに水をやりました」 places watering near the roots rather than the stem. Read this as a location contrast, not as gardening instructions.
Does 「茎の下の部分を切りました」 mean all roots were also cut off?
Show the answer and why
No. Only the lower stem section is specified; the roots' state is separate.