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My juniper is yellowing and I believe it has root rot. i recently cut the trunk a bit and found brown under neath that confirmed this. Also the roots appear to be black. What is the best treatment to save this tree?

It is quite normal for shoots to die but there is too much on the plant. Lack of water or lack of sun also. I hope you are not keeping it inside, that is the killer.

nope it is outside on the balcony. it is deteriorating fast. certainly not lack of water or sun as I also have a light above it just in case of low sun days.

I see you have an automated watering system ? ( the tubes) I also see a lot of moss. Both things combined mean you can not see how wet your substrate/soil is. Take away the moss and water only when soil feels dry to the touch.
But if it is deteriorating fast it could be too late, coniferous species show signs of distress very long after they have problems or have died.

Looks like you are training it. Where do you live? If it’s the northern hemisphere it’s not the time to trim its roots. Plants are way too active during the summer.

Tell us what you did exactly.