That's exactly what I was thinking - too dense of a soil, not enough sun and drainage. I don't know if they're salvageable, but you have to get rid of that rot and dust the cleaned-out-completely area with something like flowers of sulphur (available at a compounding pharmacist's) or cinnamon. That rot may seep down into the stem. I'd carefully monitor the plants to see if it's not spreading - if it isn't, keep them in the ground. If it's not, remove the plants from the ground and treat the roots for rot (if any). You're going to have to remove them anyway to improve the soil - I'd suggest raised beds if you want to keep them in that location.

Ok thanks. How do you suggest getting rid of the rot? Just pull out all rotted leaves and then treat with sulfur? Or something more aggressive?

Yes, arm yourself with a knife and cut out, if needed (don't rip the leaves out if they don't want to come out easily). You have to remove all of the questionable tissue too. Can you limit the water intake until it's warmer?

I would add LOTS of grit to the soil and make a good mound of draining soil.

My suggestion of a raised bed would incorporate a form of treated 2x4 or 2x6 as a base for the bed - you could then paint them to match the house's paint.

I'm in Austin. Those yuccas are incredibly hardy even in the heavy clay soil here (I recall from my earlier years growing up there that San Antonio has somewhat lighter soil on average than Austin's heavy pack caliche). If it's planted in the ground, then amendment for drainage shouldn't be necessary even in clay. The rostrata do very well in full sun, but don't usually sulk too much in shade. But yours looks pale as though in response to too little light but in my experience they typically grow slowly in response to shade rather than produce pale new growth. The dark areas at the base of new leaves do look like rot. Fingers crossed that it isn't affecting the trunk.

I do notice, however, that you've got a large area of rockscaping. I'm wondering if there's a layer of landscape fabric beneath that rock covering up the soil. That may very well be limiting oxygen exchange and slowing water permeation as well as drying- making for poor root conditions. After a year or so of fabric coverage, the soil microbiology will effectively die off as will any roots. Large trees can usually work around it, but perennials and annuals will almost always suffer.

They also appreciate having the faded leaves pruned off. Too heavy of a skirt allows moisture to trap against the trunk after heavy rain events, especially so close to your house where wind flow is limited. I've cleaned up yuccas in similar conditions and found lots of mold, mildew, soft rotting leaf bases and colonies of roaches/ ants/ beetles living in clumps of those old leaves.

So before breaking ground and bringing in soil, I'd check to make sure any landscape fabric isn't choking the root system (at least a 3x3 area should be free of fabric to allow good root development. And perhaps trim the dead leaves, though I know some people like the straw skirt aesthetic. But if you do a bit of exploration and surgery to remove any rot, you would have to remove those leaves first anyway to get a good look at the trunk. Check for any wobbling. Healthy yucca roots don't usually allow for any budging.

If you do find the soil is pretty dead, you can treat with liquid seaweed every couple weeks to promote beneficial bacteria and fungi repopulation.

Thanks for all the advice everyone. I've started the process of removing all of the top leaves. Unfortunately, the rot did extend all the way to the center of the spear, and the first 3in or so of the trunk is rather spongy to touch. The rocks were overlying fabric, so I removed that. The trunk itself is very sturdy, not wobbly at all. I guess the question I have is, can you expect a yucca to recover from rot that appears to extensively cover the entire top as in this case? I don't like the idea of giving up, but I also don't want to waste a whole lot of time and effort if its a lost cause. Is there a role to sawing off the rotted section (or is this a species that would not regrow after that kind of intervention?

If a plant has rot at the top, you've got to wonder what is going on below the surface. Ditch the landscape fabric, at least over the root zone. Here's another thread that may be helpful.

http://forums.gardenweb.com/discussions/2083473/yucca-rostrata-bud-rot

It may sprout an offshoot or maybe two somewhere along the trunk once the rot is resolved. However, I doubt this really stays in line with what you had chosen aesthetically and it will probably take a year before anything noticeable happens. It may be best to replace with a healthy plant. You could also replant this guy somewhere less visible to see if it recovers.

The soil looks pretty tragic. The almost black, fine, texture-less stuff that almost looks like moist ash. That's what I'm used to seeing under landscape fabric that's been in place for years, though your bed doesn't look that old. At least your skullcap, feather grass and firecracker ferns don't look that long established. But I suppose that could have to do with soil quality beneath the fabric impacting them as well.

I would run an irrigation check if you have a system for your lawn. There may be some overspray that could have been wetting the crown on a regular schedule, which could definitely set rot on a succulent in cooler temperatures.

I'd personally 1) check irrigation and adjust if necessary, 2) trim away more of the dead leaves to open up more air circulation, and 3) give it a week for the rotty areas to dry up before attempting a whack.

The rot may be superficial and not systemic and a week's wait won't put a nail in the coffin, but give clue as to how much is infected. Also, if the rot is driven by a fungal infection, sunlight and air circulation may clear it up (the crown doesn't look completely mushy to me). There's a bit of a chance that with our pretty good forecast, slight rot may dry, callous and begin healing itself. It won't ever grow from the top of the crown, though. If you do whack, best to do it on a diagonal so water won't collect on the cut surface. It won't be easy to make a super smooth cut, a saws all with a brand new sterilized blade would probably be the best option. And I'd also remove all dead leaves to clear way for new offsets (otherwise, trapped moisture may cause the same demise for the new growth).

If you do replant, I would strongly suggest amending the root zone with liquid seaweed a few days prior and then on a twice a month schedule until the gallon of seaweed is used up. Your other plantings would probably also appreciate some (and a bit of fabric clearing- you can push rocks back into place on top of soil to cover up). Both skullcap and firecracker fern "run" along and just under the soil surface and spread that way as well as by rooting anywhere the stems stay in contact with soil.

You can get liquid seaweed (or soil activator, a different product but with the same purpose) at Lowe's. A gallon of concentrate is about $15 and should last you quite a while even with regular use.

Will do. I will try to transplant the yucca to a different part of the yard that gets more sun and less water. Here's a few shots of the plant sans-skirt. The rest of the plant seems very solid without any give when I press on any part of the trunk. I did find a few mushy roots in the soil however. Don't know if any of that has any prognostic significance?

I'd get it out of that earth NOW! If it's salvageable, your recovery efforts have to incorporate, IMO, remediation from both ends. In case you don't know, the roots are not long, but they are strong and fibrous. So, use a digging bar to dig a ringed trench 8" or so away from the trunk. Proceed to under the plant and remove the whole root ball to a place you can chip away at the dirt and then hose it all off. Dry it as much as you can and bring it inside to a warm place, if possible, so it can dry out further and you can work on the root ball. You'll definitely want a fungicide and you might want pruning seal. I hope it will make it, but those symptoms you describe proscibe delay in treatment at the root ball.

Alright, on the job. I pruned back a few roots that were somewhat squishy, but over all, most of the roots are very firm. How long would you recommend leaving the root ball exposed prior to replanting, and what do you recommend as fungicide? Neem Oil? Thanks again!

If at all possible I'd root it again inside, with a heating mat or someplace that the surface is warm. If that's not doable, wait a month or so and replant into the ground, which in the meantime has been amended / improved for better porosity (maybe Austin's warmer than I suspect, but I don't think it's going to do any growing until the ground is at least 50F). I'd recommend flowers of sulfur - cheap, available, and useful in a number of healing applications. Clean out the rootball, after it dries, of the dead stuff.

I have had Y rostratas rot on me in Austin. It was a clay based humus. Other yuccas like Y.alifolia,Yucca recurvifolia, Yucca glorious, Yucca filmantosa are better for Austin clay areas.. I have also had Y. rostrata roast and dry out west of town during the drought when I first put them in.. They are from the chihuahua desert . Here is a link from Central Texas Gardener.

Yucca Rostrata advice for Central Texas

I would keep cutting off the rot from the top cleaning your knife after each cut till you get to untainted firm flesh. then powder the fresh cut with cinnamon or sulphur.