What's getting my Jerusalem Artichokes?

I just started harvesting Jerusalem Artichokes and every clump is affected with whatever it is shown in the pics I will attach. I have no idea what it might be. Fortunately it's just affecting maybe 10-15% of the clump. It seems to start on the surface as a smallish red stain and as it continues to consume the tuber it appears as a deep dark beet red rotting(on the surface) splotch.

It just looks like rot to me.

HARVEST
Tubers can be harvested 4 to 6 weeks after flowering. Even though the flowers are pretty, yields will be better if the flower buds are pinched off as they appear. In cooler areas with well-drained soils it is better to dig them only as you use them. In subtropical areas and poorly drained soils the tubers may rot if left in the ground once the tops die back, so it is better to dig the whole harvest at once. Tubers do not store well out of the ground. Take care to store them in slightly damp sawdust or sand in a dark place; or store them in a plastic perforated bag in the bottom of the fridge.

Link

Now 6a isn't tropical but maybe you have wet ground? Or if you want a much more dry and scientific article try this one on diseases of JA's Link That one describes the black rot as starting at the growth tips and working it's way inside, it also says it's more common on sandy soil so not waterlogged I would guess.

Sorry to hear of the disease issue, Gary, but may I offer thumbs up on the photos!?....very nice!  Given that you mentioned a red pigment and your photos show a glistening exudate within the rot, I'm going to suggest either a Fusarum fungal disease or Erwinia (carotavora?) bacterial disease.  On the one hand the gummy exudate suggests a bacterial *causal* agent, but it could also be that bacteria went to town within the tuber after a fungal disease made the initial cavity.  Erwinias and many Fusaria are associated with pinkish to red pigmentation, but it could also be that the infection is causing a response in the sunchoke that is depositing red pigmentation at the site of the infection.  

Unfortunately, I was not able to sample some of my yield earlier....the grounds froze up, but may thaw enough for me to dig a few up....I know I was getting some kind of insect borer in my 'chokes, but with the 40s slated for mid-week I may be able to dig some and see if anything similar is occurring here.  With the large sunflower industry locally, we also have Sclerotinia in the area, but I've not seen a huge problem on the sunchokes from this disease.  Will let you know what I find out if the dig is made.  In  the meantime, if you plan to dig up most of them and are going to replant next year, make sure to plant the cleanest stock....which may actually already have some resistance to the disease.  Controlling the diseases would be difficult without standard chemical fungicides and antibiotics unless there is a biocontrol for this scenario that I'm not aware of.  Good luck!

They are rotting. Rots thrive in soggy soil. Growing them in drier soil may help. Digging them earlier in the season may help.

Thanks all! I had dug some up a month ago and they had similar rot going on. Though I had planted in a slightly raised mound, the mounds did settle and they are in a relatively moist area. I have another tub which I haven't harvested yet, perhaps that will prove/disprove the 'too wet' theory as they should be high and dry.

Regarding saving for replanting.... is there a best method of storing them?

Gary Grata wrote:Regarding saving for replanting.... is there a best method of storing them?

I have already replanted my sunroots. They overwinter great. They are very susceptible to dehydration once dug, so storing in plastic in the refrigerator works well. I store mine in buckets on the back porch, which stays just above freezing.

Thanks Joseph... do you have an idea how long they might keep under best storage conditions? This is my first go around with them. Can I just leave some in the ground when I harvest? And thus avoid a separate planting and need to store?

At my place, sunroots cannot be thoroughly dug. No matter how much effort I put into it, there are always tubers that survive, and re-sprout in the spring. I have received reports that in gardens with high populations of subterranean mammals, that the sunroot tubers may be completely consumed if left in the ground overwinter.

Sunroots will survive till spring if kept cool and in a more or less sealed container. I often add a bit of coconut choir or peat to absorb moisture and stabilize any tubers that rot in storage.

Thanks for the help Joseph!

I, too, am finding this problem, and I'm also in 6a.  I know there's a late blight that affects tomatoes in this soil, so the mention of- was it fusarium- rings true.  My colony of sunchokes is elevated but the past two weeks have been very wet following a droughty August and September.  

My chokes did get a fungal disease several years back, and the supplier at Ronniger's (yes, so long ago that it was still Ronniger's) talked me through a treatment that got rid of it.  It was a drier rot than this and showed earlier, including a wilt. That disease hasn't shown in many years.

I have long dug them through the winter, at times when the soil thaws, because all storage I've tried so far allows them to rot, and I can't use up the huge yield before they go bad. My location's winters have gotten much milder over the past decades and it's unusual for the soil to stay frozen for long.

Here's a question I've got, though:  I have been intending to send a start to my friend in Sacramento, but I'm wondering if I should not do this, or if I should send anyway and advise her to take it to the local ag extension office before putting them out.  Many tubers are not visibly affected, and, of course, I'd send her some of those.  

Thanks.