Are soil bacteria harmful?

Question: I understand that millions of bacteria live in soil. Are they harmful? What are they doing?

Soil is rich in both the number and diversity of its microbial inhabitants. But most of the bacteria in soil can’t directly cause disease, as they don’t have the necessary biochemical abilities.

How many microbes?

It’s estimated that the number of bacteria in soil is more than 100 million per gram of soil (dry weight equivalent); we also estimate there are 6,000 to 8,000 different types of bacteria per gram of soil. More surprising is the fact that the structure of the population can vary in the landscape over relatively short distances. While many bacteria are technically mobile, in soil they are more likely found attached to the soil surface, and most of their movement is controlled by the water flowing through soil pores.

A natural community of bacteria growing on a single grain of sand. The image, taken using a scanning electron microscope (SEM), is courtesy of the Lewis Lab at Northeastern University. It was created by Anthony D'Onofrio, William Fowle, Eric Stewart, and Kim Lewis.

A natural community of bacteria growing on a single grain of sand. The image, taken using a scanning electron microscope (SEM), is courtesy of the Lewis Lab at Northeastern University. It was created by Anthony D’Onofrio, William Fowle, Eric Stewart, and Kim Lewis.

Soil bacteria live in small clumps called micro-colonies that are attached to the soil surface. These micro-colonies tend to be associated with small soil aggregates, and the combination offers a form of protection from drying and predators (primarily protozoa). It also enhances the opportunity for genetic exchange.

What are they doing?

Soil microorganisms are responsible for breaking down plant residues and other carbon (C) inputs and converting nitrogen (N) within the N-cycle. Because of their soil surface attachment strategy, their actions are also a fundamental part of the soil formation process.

In terms of activity and what soil bacteria are doing most of the time, we find that they are often “resting.” That’s because the large, bacterial population uses up the available nutrients quickly and then spends most of its time waiting for new food to arrive: residue inputs, fertilizers, waste materials, etc.

Ambient water and temperature conditions also have a major impact on the actions of the bacteria; they are the most negatively affected by low water availability and high temperatures. In general, the ideal conditions for plant growth are also the ideal conditions for microbial activity.

Making a living in lots of ways

Unlike humans, bacteria can use a diversity of energy (i.e., electron) and carbon sources. Yet, while the soil is rich in biological abilities, not all organisms can do everything. What this means is that the soil bacterial population as a whole (not one bacterium or bacterial species) has a vast array of enzymes at its disposal.

The soil bacterium Streptomyces growing on various culture media. Streptomyces is the largest genus of Actinobacteria; over 500 species have been described. Found mainly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct, "earthy" odor, which results from production of a volatile compound, geosmin. Photo: bacteriainphotos.com.

The soil bacterium Streptomyces growing on various culture media. Streptomyces is the largest genus of Actinobacteria; over 500 species have been described. Found mainly in soil and decaying vegetation, most streptomycetes produce spores, and are noted for their distinct, “earthy” odor, which results from production of a volatile compound, geosmin. Photo: bacteriainphotos.com.

For example, some parts of the soil bacterial community can capture electrons and energy directly from sunlight and take C from carbon dioxide; others can decompose plant and animal residues for electrons and take their C from the residue; still other members of the population can oxidize minerals like nitrogen for energy and “fix” their C from carbon dioxide.

Like the diversity they exhibit in securing their energy and carbon, bacteria also use a diverse number of electron acceptors as part of their energy production system (people, other animals, and plants use oxygen as their electron acceptor). For example, some bacteria “respire” oxygen (like we do) while others can use nitrate (NO3) or sulfate (SO3).

In some cases, a combination of electron acceptors can be used, depending on the ambient conditions. Other bacteria in soil are strictly anaerobic (live in oxygen-starved conditions) and ferment their food, while other anaerobes utilize minerals like iron as an electron acceptor.

The critical point is that the soil doesn’t contain just one type of bacteria or one set of abilities (enzymes). It’s also not full of pathogens, nor are all the bacteria in soil active all the time. Instead, soil activity changes with fluxes in moisture, temperature, and substrate input. In order to respond to an ever-changing array of inputs, the soil biology is biochemically (enzymatically) diverse in its ability to utilize foods and electron acceptors. This diversity gives soil its resilience.

–Answered by Ron Turco, Purdue University

 Have a question about soils? Post it as a comment below, or email us at soils-matter@soils.org

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8 responses to “Are soil bacteria harmful?

  1. Pingback: Bacteria in soil…is it harmful to humans? | Good Sweet Earth·

    • Dear Amon, great question, and we’ll make this a future Soils Matter blog post!! Due to the “living” nature of soils, they do change with time. SSSA developed 12 monthly themes to help educate the public about soils…July is Soils are Living month. Our YouTube channel (https://www.youtube.com/channel/UCcEbCxaahphQg7Cm-W849Rw) will feature a video with the same theme, and the Soils Matter blog posts will both be about creatures that live in the soil (and, thus, make it dynamic!)

    • Dear Amon, another fantastic question. Soil color is based on the parent material from which it came, how much soil organic matter is in the soil, and many other factors, including erosion and activity! We’ll make this a future blog post answer.

  2. Pingback: Turns out earthworms are doing more to fight climate change than most people·

  3. hello, I just want to know if there are harmful bacteria found in soil?what are some examples and where do we find them? Thanks.

    • Hi, this is on our topics for soil scientists to write about…and we’ll get them posted as soon as we can. Thanks for reading! SF

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