Managing Microbes in the Garden

 in Garden

I control almost all my airborne molds and insect pests with a ridged 5 week organic spray cycle that I described in my post about organic gardening basics.  However, not every pest comes from above. If you have ruled out all other causes and put on ample compost, but your plants are still not producing to potential, It’s time to talk about soil microbes.  

First and foremost make sure you put a good layer of compost every time you plant a bed, you can’t be sure you have a bad microbe if your soil isn’t well nourished to begin with.

Every region has different good and bad soil microbes, and in the tropics I’ve found the most common microbial pest is soil nematodes. Root Knot nematodes are endemic to the region and cause the plants to be much smaller and produce little to no fruit. It is a terrible bug to have and I put my brain to solving it the most organic way possible. The techniques I learned and share here can be used again any nematode that you diagnose in your garden.

If your soil freezes completely each year, you probably have never heard of nematodes because they die off year after year. However in Southern states and tepid climates these little microbes suddenly become a big deal.  While I’m speaking from Southern gardenin experience today, if you live in a northern place and have an undiagnosed problem, soil microbe management isn’t a bad step to take.

Bad Microbes Identification
Plants will grow slowly and likely be dwarfed.
Fruit will ripen slowly or unevenly.
When removing the plant the roots will have visible warts or knots.

First Steps
Do not compost plants with signs of nematode disease, have them removed with the trash or place them far away from where you plant. Nematodes will spread any place you put down these roots.

Consider moving your garden.
Nematodes can’t move, but you can. If you have enough space you may consider trying 5-10 feet away, if no one has garden in your space before there is a good chance your nematodes haven’t spread yet.

Under no circumstance should you move soil you think has bad microbes.
Either treat it, or leave it.  

Methods of Control
Once you have removed all the infected plants and roots you can treat the soil.

1. Ground Cover
This was my first line of defense, because I have a 4 season garden many of my beds were already planted when I found out about my nematode problem. I wasn’t sure how far into the garden the issues persisted but I went ahead and assumed all my soil was infected.

Ground cover became my best friend in my already planned areas. I seeded dozens of marigolds throughout the garden in front of or behind plants depending on where I had room. Marigold roots are toxic to nematodes but won’t affect your other plants. Plus you have the benefit of wonderful golden flowers. If you have already planted or have enough room for ground cover I highly suggest this method pest control.

2. Plant resistant crops

I didn’t want to be without harvests as I healed my garden, therefore in my next rotation for most of the beds I planted beet roots and kale that are less susceptible to soil nematodes. I did not plant anymore watermelon, tomatoes or eggplant that are some of the most susceptible plants.

3. Solarization

Then I started the long task of treating my soil thoroughly for all microbe pests. Since I had just moved into the house I wasn’t sure about how they treated the soil before me. Many people recommended I pour hot boiling water over the ground where I was going to plant. This is a very common and useful technique to rapidly de-microbing your soil. However, you will also be killing the small bugs and worms that happened to be there at the same time. After solarization or hot boiling water you have to replenish your soil of nutrients and healthy positive microbes. The second negative is that bugs are much slower to come back after a hot water bath.

Therefore, solorazing is environmentally friendly and the most ethic method of pest and fungus control I’ve found.
Albeit a slow method, when done correctly it is also highly effective.

How to Solarize: 
You will need clear plastic, painter plastic works well.
A black or white plastic will not allow the temperature to rise enough for this method, choose only clear plastic.

Water the bed deeply before starting and remove any weeds or old plants. Till the soil if time allows.

Cover the beds with the clear plastic and weigh down the sides with stones or bricks. It’s okay to either be directly on the soil or a few inches above it like in my raised beds, both work.

Within a couple of days humidity should begin to build on the inside of the plastic.
The environment should remin humid for the rest of treatment, if you notice the plastic has dried out before the time is up water the edges and under the plastic where you are able.

Leave the plastic for a minimum of 4 weeks during summer sun and up to 3 months.
If you start in spring sun you may want to leave the plastic 6 or more weeks.
Your goal is to heat the ground to between 98-126 degrees fahrenheit.
Within 4 weeks you will have treated the top soil, the longer you leave the plastic the deeper in the soil you will treat.

After Treatment
Aftercare is the most important time because now your soil is bare of all microbes. The bugs and worms will come back soon but I like to make a really good encouraging environment for them.

My favorite method is direct composting.
After you remove the plastic spread a thick layer of fresh kitchen scraps over the soil. I usually keep a weeks worth of scraps depending on the size of my bed. If you don’t create a lot of compost you can collect it in the freezer during solorization until you have enough.

Cover the kitchen scraps with cardboard and weight down the corners with rocks.
Leave this for 4 weeks or up to 3 months depending on your weather conditions until all the food scraps have turned into soil and the cardboard is breaking down.

If it isn’t completely broken down, you can leave the cardboard and cut holes into it when ready to plant new baby seedlings.

Compost Tea

If you are pressed for time or solarized only a small amount of soil, compost tea is another method of replenishing nutrients. You can either buy this as a liquid at your local organic nursery or make it yourself.

To make compost tea
Soak 5 big handfuls of fresh compost in a 5 gallon bucket of water for 24-48 hours.
Water your plants with this mixture.

If you can afford the space and time, a bed treated with solarization should be solarized for 3 months and then left fallow for 3 months to replenish the soil nutrients.


Here are some other soil microbes to familiarize yourself with as you are diagnosis your plant’s problem.


More about control of nematodes

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