Ask Mr. Smarty Plants

Because Armillaria mellea is a mushroom and a non-vascular (does not have internal food and water conducting tissues possessed by "true" plants) fungi, we are unfamiliar with how it interacts with other plants. From MushroomExpert.com, Armillaria mellea: The Honey Mushroom, gives you much more information on that than we could. From that article, here is an extract that locates the plant and its target hosts:

"The classic honey mushroom, Armillaria mellea, turns out to be limited to roughly the eastern half of North America, from about the Great Lakes to the Gulf Coast and the East Coast--and perhaps to northern California, where it has been reported. It usually grows in clusters on hardwoods, but is occasionally found on conifers. It has a fairly smooth cap, a sturdy ring on the stem, and fused stem bases that are tapered to points. Under the microscope, it has basidia that are not clamped at their bases."

Oakland, on the San Francisco Bay appears to be in USDA Hardiness Zones 10 to 11, approximately in the middle of the state; that is considered Northern California.

There are two members of the Thuja genus native to North America:

Thuja occidentalis (Arborvitae) - this USDA Plant Profile shows that it does not grow west of Minnesota nor in any of the southeastern United States

Thuja plicata (Western arborvitae) - USDA Plant Profile indicates it grows in 3 counties in Northern California, but these maps can become out of date. Pictures from Google.

So, you have one plant (Thuja occidentalis (Arborvitae) that should not be growing in your area at all, and one  (Thuja plicata (Western arborvitae)  plus the Armilleria mellea that might not grow in your area. It is always essential, before you purchase a plant, to determine if it belongs in the area where you are gardening. If you have Thuja plicata (Western arborvitae) our webpage on that plant states that it is very resistant to rot. Since we do not know the answers to these questions, we will proceed as best we can on what you should do next. If a local expert has made the diagnosis we will defer to that, since we are not on the spot, and probably wouldn't know which is what, if we were on the spot.

We made all the above comments to help you understand that perhaps the selection of a conifer such as Thuja for your area may have been the original mistake. Our second thought is that, although this perhaps does not constitute a complete monoculture, 100' of the same plant is certainly inviting trouble if they all contract the same problem and/or transmit it among themselves. We are going to go to our Recommended Species section, select on Northern California on the map, and then choose "tree" from the drop-down menu on General Appearance. You may also, in that right hand sidebar on the page, indicate soil moisture and amount of sun available. We will do a sample list for you, and recommend that you read each webpage on the specific tree and also follow the link at the bottom of the page to Google on that plant and, using the same method, make choices of your own. If your plants have a disease carried in the soil, you will have to find plants whose roots can withstand whatever is causing the rot. We also suggest you contact the people at the University of California Extension Office, Alameda County, to see if they know what is going on. We could find no conifers native to your area; perhaps they don't like that warmth and low altitude.

From our Native Plant Image Gallery:

Thuja occidentalis

Cercocarpus montanus var. glaber

Cornus sericea ssp. sericea

Quercus agrifolia

Umbellularia californica