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Mmm sorry to disagree but not great advise, in my opinion the best option is grind out the stumps for the reasons below.

Honey fungus(a common disease)lives on old tree stumps and can use them as a food supply allowing rhizomorphs (often known to gardeners as ‘bootlaces’) to spread to other trees from infected roots through the soil. Best to remove infected stumps then.
As for spores being spread by stump grinding, well spores are only created by the fruiting bodies or mushrooms. The wind will have done a good job of spreading these already and the atmosphere is full of billions of fungal spores which are even capable of surviving space travel!! .
The longer an infected stump is left in the ground the more spores it will create so my advise would be to remove the stump.
As for needing to remove or grind out the entire stump including all roots, depends on weather you are so paranoid about the remaining roots becoming infected with diseases that you would want a large part of your garden ripped apart, remembering that the roots of a tree will spread out as far or if not further than its branches.
Now to the need to grind the Stump to "remove the whole core right down until it reaches fresh soil". Large tree stumps can send down tap roots to a depth of 6ft, No domestic size stump grinding machine on the market is capable of going down this far, most will do 1 ft max.
Alternatively dig out the stump and dispose of at land fill or burn?
1. Have you tried digging out a stump recently? more than a few inches in diameter and you may be having a rethink after a couple of hours digging!! From experience 6 ton diggers struggle to pull out anything above a few feet in diameter. Most Landscapers will use a local stump grinding service instead of digging.
2. Have you ever tried burning a stump? I'm betting that when the fires gone out then that big old stump will still be a big old stump, they don't burn well.
3. Take the stump to land fill? OK have you tried lifting a large tree stump(with all the roots of course, oh and the soil and stones which is stuck to it) into the back of your nice clean hatchback? maybe a rethink there??

"A fungicide will need to be applied to the soil to cleanse before replanting" Well lets see what the RHS has to say..."There are no chemicals available for control of honey fungus" fungicides don't work and may even disrupt important symbiotic relationships between trees and beneficial fungi which help the tree to draw in nutrients.
"Next, take out all of the chippings because it can lead to severe nutrient deficiency in new plants and shrubs." Well its not the best idea anyway to plant a tree in exactly the same spot as the soil will already be lacking in nutrients which will have been used by the previous tree. Any disease which infected the previous tree will be still in the soil no matter what you do. Yes remove the wood chip if you want to replant as not much will grow in wood chip!! Wood chip can be used as a mulch or composted, different types of fungi live in wood chip and you will find that honey fungus for example will not survive in a wood chip pile. Man has invented such things as fertilizers which contain nutrients this could be mixed with some new compost or top soil and filled into the hole and then replanting can take place, a few remaining wood chips mixed in here are not going to kill new plants!!
The long and short of it is don't worry about diseases affecting other plants every woodland in Britain will be full of honey fungus, they have been for thousands of years and the trees are not all dying are they?? most diseases will only affect weak, damaged or dying trees and plants.

So stump grinding is the best option, it is inexpensive, fast, doesn't break your back, allows quick replanting or re-turfing and leaves you with some wood chip that you can use around the garden or turn into compost. If any one would like more advise then feel free to email me.
Scott
Simply Stumps
scott@simplystumps.co.uk


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