Bacteria in the Soil and Ground Water

Bacteria can be classified by their ability to use oxygen and by their function. We will examine the ways in which bacteria transform organic material in soil and water.


Bacteria are single-celled organisms that lack a nucleus or membrane-bound organelles. A diagram of a typical bacterium is shown at left.

Bacteria live all over the Earth, in both aquatic and terrestrial environments. There are even bacteria who live in clouds. Many types live in soil and we'll focus on these today.

Some types of soil bacteria are photosynthetic and make their own food. Others absorb and metabolize organic or inorganic compounds from the environment for energy.

Although some types of bacteria cause disease to humans, as well as to other animals and plants, most others have a beneficial effect on the environment.

Use of Oxygen

Bacteria can be classified based on their use of molecular oxygen.
  • Aerobic bacteria require oxygen. They frequently live in topsoil, where air spaces provide oxygen. These organisms oxidize organic molecules to provide energy and are important in the decomposition of organic matter in soil.

  • Anaerobic bacteria are poisoned by gaseous oxygen. Some of them obtain the energy they need through fermentation processes, for example by the fermentation of lactic acid (180 kJ/mol).

    C6H12O6 + 2 ADP + 2 phosphate 2 lactic acid + 2 ATP

    Other anaerobes use sulfate, nitrate, iron, manganese, mercury, and carbon monoxide as electron acceptors (in place of O2) in respiration.

  • Facultative anaerobes prefer growing in the presence of oxygen but can grow without it. They use oxygen in respiration when it is available but can switch to fermentation at other times.


  1. Autotrophic bacteria are photosynthetic or use other chemical reactions to produce energy. These include
      (a) cyanobacteria

      (b) green sulfur bacteria

      (c) purple sulfur bacteria

      (d) purple nonsulfur bacteria

    The sulfur bacteria are particularly interesting, because they use hydrogen sulfide as hydrogen donor, instead of water.

  2. Heterotrophic bacteria are aerobic consumers of simple carbon compounds. They convert organic matter in energy and other carbon compounds. Some of these break down pesticides and pollutants in soil. They also prevent the loss of nutrients from plant root zone

  3. Mutualists, such as nitrogen-fixing bacteria. form root nodules with plants such as soybeans, peanuts, clover, and some trees. They convert N2 to NH3, NH4+ with the enzyme nitrogenase.

  4. Soil pathogens are bacteria that cause disease in plants and animals.

  5. Lithotrophs or chemoautotrophs obtain energy from compounds of nitrogen, sulfur, iron or hydrogen instead of from carbon compounds. They are organisms involved in nitrogen cycling (see below). They also help to degrade nitrogen-containing pollutants.

Bacteria of the nitrogen cycle

Autotophic nitrifying bacteria change ammonium to nitrite then to nitrate. This is a preferred form of nitrogen for grasses and most row crops.

NH4+ NO2- NO3-

Nitrate is leached more easily from the soil, so some farmers use nitrification inhibitors to reduce the activity of one type of nitrifying bacteria.

Nitrifying bacteria are suppressed in forest soils, so that most of the nitrogen remains as ammonium.

Nitrosomonas: 2 NH4+ + 3 O2 2 NO2- + 4 H+ + 2 H2O + energy

Nitrobacter: 2 NO2 + O2 2 NO3- + energy

Denitrifying bacteria convert nitrate to nitrogen (N2) or nitrous oxide (N2O) gas. Denitrifiers are anaerobic and are active in saturated soils or inside soil aggregates.


These organisms are bacteria with a resemblance to fungi. They break down humic materials in soil with air. They are responsible for the characteristically earthy smell of freshly turned, healthy soil.

They decompose even recalcitrant compounds, such as chitin and cellulose.

Human antibiotics produced by actinomycetes organisms include streptomycin.

Oxidation of sulfur-containing compounds by bacteria

Photosynthetic bacteria, including purple sulfur bacteria and green sulfur bacteria, use electrons from the oxidation of H2S (instead of H2O) to reduce CO2 and make organic molecules.

Thiobacillus thioxidans oxidizes sulfur compounds to sulfuric acid with oxygen and aids sulfate uptake by plants. It also reduces nitrate and limits soil fertility.

Desulfovibrio desulfuricans reduces sulfate.

Soil bacteria are the most important sink for MeCl and MeBr on Earth. Methanotrophic bacteria are aerobic and use methane as their only carbon source, live in close association with plant roots. Other types of aerobic bacteria can use aromatic hydrocarbons as their sole carbon source.

Professor Patricia Shapley, University of Illinois, 2010