Tuesday, March 26, 2013

Soil Remediation and Anaerobic Bacteria

"We know more about the movement of celestial bodies than about the soil underfoot." - Leonardo Da Vinci, circa 1500's

Ew! Today I realized my barrel of soil has gotten too wet and developed an atrocious odor (like sewage). I am happy because I am excited that there are (or were) living organisms in my soil, but I need to know if they are helpful or harmful and if they are no good, how to make them go away.

First, I wanted to know: what is making this smell?

Observations: Dark black soil on top of grey soil. Very foul smelling - more like sewage than sulfurous (rotten eggs). Very wet- still visible standing water (a centimeter or so).

Possible culprits:
Anaerobic bacteria
Decaying organic matter (there is a lot of peat moss mixed in the barrel)
Too acidic

Possible solutions:

1) Dry out soil to expose to oxygen
2) Adding more organic matter and keep aerated
3) Add pulverized limestone or other basic material (e.g. eggshells) to balance the pH

Can I use this soil again?
I will find out as I go.


"Your problem is poor drainage. Soil that stays wet for long periods of time get lots of anaerobic bacteria operating in them and those kinds of bacteria produce offensive odors, just what you are smelling. A simple mehtod to test a soils drainage capability is to dig a 1 foot square hole 1 foot deep and fill it with water. Once that water drains away refill the hole and time how long it takes for that water to drain away. If it takes longer than 6 hours for the 2nd pail of water to drain corrective action is required, adding lots of organic matter to the soil to open up the soils pores so water can flow through. One garden I did that test to once took 4 days for the first pail of water to drain away and the "gardener" did not understand why her plants kept dying on her." 

"Types of Harmful Bacteria

Gardeners refer to beneficial soil bacteria as probiotics. Harmful bacteria are called proteobacteria. A very large group, proteobacteria includes many bacteria that also affect humans, such as Vibro cholarae, the root cause of cholera. Xanthomonas campestris, one example of proteobacteria, works in the soil to fix nitrogen and forms useful compounds for platn growth; however, it also causes black rot in Arabidopsis and Brassicas. Bacteria that cause rot in plants do so by blocking the vessels that carry water to the various parts of the plant.

Effects on Humans

According to Types of Bacteria, there are no recorded cases of bacteria being passed from a plant to a person that results in an infection. The bacteria affecting plants are highly specific. People working with soils should understand that while most bacteria are beneficial, the potential exists for contact with harmful bacteria. The potential for catching tetanus exists, despite the reduced risk resulting from frequent immunizations. Soil contaminated with fecal matter can harbor E. coli 0157, according to Soil-Net. Although rare, anthrax can also exist in the soil. It is recommended that gardeners wear gloves and wash hands thoroughly after working in garden soil.

Fixing Good Bacteria

Beneficial bacteria can be fixed into the soil to help reduce harmful bacteria. In most instances of bacterium-based disease, the recommended action is to avoid planting the specific species of plant affected for several seasons in the affected area. The nurturing of beneficial bacteria in the soil may help to eliminate the risk from harmful bacteria. Anecdotal evidence points to the removal of damaging bacteria through the heating of the soil by use of black plastic mulching. Frequent turning and aeration of the soil may help to reduce tetanus, which thrives in oxygen-free environments. However, methods that reduce harmful bacteria often remove beneficial bacteria as well. Starter bacterial inocula are available to help diversify the bacterial species in the soil. Fish emulsion, green plant material and sugars help increase the full range of beneficial bacteria"

What do Soil Bacteria Do?

Decomposer Bacteria

Soil bacteria along with fungi are the primary decomposer in the soil. That means they breakdown virtually everything f®om your lunch to a Mac Truck. They, along with fungi, are the workhorses of the compost pile.

Nitrogen Fixing Bacteria

Nitrogen is essential for life. It is present in all amino acids which make up protein and the nucleic acids of RNA and DNA. While Nitrogen is very plentiful, about 79% of our air is made of nitrogen gas, plants can only use the nitrogen if it is fixed or combined making ammonia or NH4 or Nitrates NO3. All the nitrogen we need we get either directly or indirectly from plants. And almost all of the nitrogen plants need is provided by nitrogen fixing bacteria.

Actinomycetes or Actinobacteria

These bacteria seem almost like a hybrid of a bacteria and a fungi. They look more like fungi but their inner structure is bacterial.
These elegant microbes are responsible for decomposing tough to decompose material, fixing nitrogen in association with certain plants and for many of the most important antibiotics we use in medicine today.

Cryptobiotic Crusts and Cyanobacteria

Ever wonder how it all began. Some clues might be found by studying the blue-green algae or cyanobacteria. These bacteria are able to make food from air, sunshine and water and fix nitrogen. They along with other hardy bits of life - fungi, mosses and lichens - create very young soils called cryptobiotic soils.