Treating diseased soil

Hi.  This year I have learned tons and managed to get a good harvest from my limited space.  Part of my success was a  a huge and varied tomato harvest, which was a delight since I didn't plant any tomatoes.  They were volunteers from my compost.  Ditto for the cantaloupe although they split after tropical storm rainfall.

The problem?  Brown spot everywhere by the end.  Not only my tomatoes but the wineberries I have growing on the edge of my woods, ornamental plants, and neighboring trees.  I may have cucumber beetles;  my head is spinning trying to figure out all the disease and pests  that have appeared.  Neem oil and copper fungicide (I was told these are okay in organic gardens) have kept things in check up till now. I have purchased some resistant varieties of seed which may or may not help.  Next planting season will see drip irrigation which will also improve things.

I have raised beds.  Do I have to replace all the soil?  Some beds are near the woods and I have found diseased leaves falling into my garden.   I can relocate them, but not far enough to completely eliminate the risk.  I have purchased a mix with "mycorrhizal fungi, trichoderma and a diverse mix of bacterial species" to inoculate the soil with , but I have also heard of covering beds with black plastic to sterilize, which would negate the inoculant.  Also, I think it is too late in the season (zone 7) to get and extended period of hot weather.  My compost isn't ready yet to introduce to the soil.

Do I toss this soil to an unused pile in my back yard and start over (expensive)?  In the next week, I plan to plant a few varieties of garlic to overwinter,; should I just give it a try after adding the inoculant?

Shaking my head.  Despite the difficulties and come what may, I still love all of this lifestyle.  

Susan Mené wrote:

I have raised beds.  Do I have to replace all the soil?

In my opinion, I would not. Disease is a symptom of an imbalance.

Some beds are near the woods and I have found diseased leaves falling into my garden.   I can relocate them, but not far enough to completely eliminate the risk.

Unfortunately it will be impossible to eliminate any risk. Spores are literally everywhere and it is how nature works. Fear not, you mention two things that will greatly help you, which I have quoted below.

I have purchased a mix with "mycorrhizal fungi, trichoderma and a diverse mix of bacterial species" to inoculate the soil with , but I have also heard of covering beds with black plastic to sterilize, which would negate the inoculant.  Also, I think it is too late in the season (zone 7) to get and extended period of hot weather.  My compost isn't ready yet to introduce to the soil.

Introducing those mycorrhizae and trichoderma among other bacterium will greatly assist in providing balance in your soil. I personally do not recommend the black plastic route. It is impossible to sterilize a soil via this method, and I believe the most any person can achieve is some degree of sanitization near the very surface of the soil. The compost your making, when produced from aerobic decomposition, will also greatly benefit your soil and the plants you choose to grow in it. This also adds biological diversity, carbon and food for the kinds of soil bacteria and fungi we want in a healthy soil.

Do I toss this soil to an unused pile in my back yard and start over (expensive)?  In the next week, I plan to plant a few varieties of garlic to overwinter,; should I just give it a try after adding the inoculant?

I personally would not toss the soil and start over. What I suggest is using your inoculant and compost, and also mulching the surface of the soil with some hay or straw or wood chips. This mulch arrests falling raindrops and allows rain to trickle into the soil. Aside from other benefits such as preventing a surface crust, it keeps raindrops from splashing soil particles onto the leaf surfaces of plants, which can result in soil borne bacterial and viral pathogens infecting a plant if the plant is in a state of stress and not growing in it's optimal healthy state.

Shaking my head.  Despite the difficulties and come what may, I still love all of this lifestyle.  

Yes, with every challenge is an opportunity to do things differently and improve techniques. After 25 years of gardening, I'm still learning.

In addition to what has already been suggested, it might help to have the diseases and arthropod pests identified. A disease that causes brown spots on leaves is unlikely to be the same pathogen across diverse kinds of plants. It is possible that you have a few different diseases/pests at work, which may respond to different management practices. Also, something like uniform leaf damage can reflect a nutrient deficiency or similar in the soil, pointing your efforts more toward soil building than toward pest management. Most state "land grant" universities have plant pest diagnostics clinics that can be quite helpful in both identification and management recommendations.

I love the fact that you are already doing natural selection and creating your own cultivars. Out of the tens thousands of seeds that went into your compost only 100 or so of them. Survived the winter and compost and grew, even less gave you wonderful produce.

You want to keep seeds from those ones and esp ones that had the least amount of brown spots. They are the most disease-resistance ones, they will be good to next years breading program, in addition to whatever local/regional cultivars that you are able to get.

The probably could have been as simple as too much water/humidity and so next year you can try try watering less or at a different time of the day.

You could also try outcompeting the bad microbes by doing a foliar spray with aerated compost tea (worm compost, molasses, chitin/insect frass, compost, mushroom slurry, vigorous/healthy plant soil).  

James Freyr,Andy Jenson,S benS Benki, Thank you for all the explanations, advise and suggestions!  I can't believe what a wealth of information is available on these forums.

Great responses from experienced gardeners! I'll add one from a peer beginner.

I am also a bit discouraged by how much disease and pest damage I see in my garden, but we just started, we are still learning our own habits and deficiencies as we learn about the plants. I am trying to keep my head up and count my losses as lessons learned.

Also even if a plant has a disease or pest damage it can often still produce a harvest that's good to eat, and I've read that saving seeds from survivors not only selects for strong resistance but those pressures can actually cause the plants to develop resistance in the first generation of offspring. I can't verify that yet, but it's encouraging to hear!

Okay, I didn't execute that  "quote/unquote" thing above correctly.  

Also even if a plant has a disease or pest damage it can often still produce a harvest that's good to eat,

I harvest like my life depends upon it, obviously discarding the questionable.    The abundance of good produce  harvested from brown-spot plants was impressive, especially tomatoes (various types)I froze them whole by the gallon until I time to process them, vacuum sealing/freezing the pureed tomatoes over canning this year because it was quicker and I use them often.  I don't have enough harvest to need massive canning days/weeks, but I learned how several years ago and I never have to throw away excess.  

One year later, all of these responses are still helpful.  Thanks!