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Soil Bacteria

What do bacteria look like?

Most bacteria in soil are about one micron in length or diameter (there are a thousand microns in a millimetre). Some are slightly larger than this, up to several microns, and in rare cases even larger. Their size varies with their environment. Bacteria in environments that have high levels of nutrients may be larger than those in nutrient poor conditions.

The majority of bacteria in soil usually occur as single cells. Bacteria sometimes join together in chains or clusters. They mainly have one of two shapes - spheres (called cocci) and rods (called bacilli). Other bacteria have more varied shapes including spirals and long thin hyphae (although these are less common).

What do bacteria do in soil?

Bacteria are able to perform an extremely wide range of chemical transformations, including degradation of organic matter, disease suppression, disease, and nutrient transformations inside roots (e.g. reducing bacteria in roots, bacteria cause nitrogen fixation).

Azobacter, for example, is a genus of free-living bacteria that converts atmospheric nitrogen into ammonium, making it available for plant use. This process may only take place, however, if the following conditions are met:

  • An easily degradable carbon source is available
  • Any nitrogen compounds such as ammonium or nitrate, are not already in present in substantial concentrations
  • Soil pH levels are between 6 and 9
  • High levels of phosphorus are present
  • Very low levels of oxygen are present

Azobacter is inhibited by a large range of toxic mineral and organic compounds, but may tolerate relatively high salinity and their activities are enhanced in the presence of clays (Lavelle and Spain, 2001, p.212).

In general, bacteria are the organisms in soil that are mainly responsible for transforming inorganic constituents from one chemical form to another. Their system of external digestion means that some of the metabolites released by the use of extracellular enzymes may be used by other organisms, such as plants. The bacteria gain nutrients and energy from these processes and provide other organisms with suitable forms of chemicals they require for their own processes. For example, in the conversions of nitrate to nitrite, sulphate to sulphide and ammonium to nitrite.

Where do bacteria live in soil?

Bacteria are aquatic organisms that live in the water-filled pore spaces within and between soil aggregates. As such, their activities are directly dependent on relatively high soil water contents (Lavelle and Spain, 2001, p. 211).

Bacteria are normally found on the surfaces of mineral or organic particles or congregate around particles of decaying plant and animal debris. Most are unable to move and hence, their dispersion is dependent on water movement, root growth or the activity of soil and other organisms (Lavelle and Spain, 2001, p. 212).

What are rhizobia?

Rhizobia are one of the groups of microorganisms living in soil. They are single celled bacteria, approximately one thousandth of a millimetre in length. Rhizobia belong to a family of bacteria called Rhizobiaceae. There are a number of groups (genera and species) of bacteria in this family.

Rhizobia belong to a specific group of bacteria that form a mutually beneficial association, or symbiosis, with legume plants. These bacteria take nitrogen from the air (which plants cannot use) and convert it into a form of nitrogen called ammonium (NH4+), which plants can use. The nitrogenase enzyme controls the process, called nitrogen fixation, and these bacteria are often called "nitrogen fixers".

Rhizobia are found in soils of many natural ecosystems. They may also be present in agricultural areas where they are associated with both crop legumes (like soybean) and pasture legumes (like clover). Usually, the rhizobia in agricultural areas have been introduced at sowing by applying an inoculum to the exterior of the seeds as liquid formations or pellets.

Refer to ‘Soils are Alive’ newsletter Volume 1 Number 3 “Rhizobia” by Dr Krys Haq.

How are nodules formed on the roots of legumes?

The nodulation process is a series of events in which rhizobia interact with the roots of legume plants to form a specialised structure called a root nodule. These are visible, ball-like structures that are formed by the plant in response to the presence of the bacteria.

The process involves complicated signals between the bacteria and the host roots. In the first stages, the bacteria multiply near the root and then adhere to it. The small hairs on the root's surface curl around the bacteria and they enter the root. Alternatively, the bacteria may enter directly through points on the root surface. The method of entry of the bacteria into the root depends on the type of plant. Once inside the root, the bacteria multiply within thin threads. Signals stimulate cell multiplication of both the plant's cells and the bacteria and this repeated division results in a mass of root cells containing many bacterial cells. Some of these bacteria then change into a form that is able to convert gaseous nitrogen into ammonium nitrogen (that is, they can "fix" nitrogen). These bacteria are then called bacteroids.

The shape of the nodules is controlled by the plant and nodules can vary considerably - both in size and shape.

Most plants need specific kinds of rhizobia to form nodules. The rhizobia that form nodules on peas, for example, cannot form nodules on clover.

Nodulation can be impeded by low pH, Al toxicity, nutrient deficiencies, salinity, waterlogging, and the presence of root parasites such as nematodes or genetic incompatibility with the plant host (Lavelle and Spain, 2001 p.439).

Clover nodules

Peas innoculated with rhizobia

Why are nodules pink inside?

The nitrogenase enzyme is extremely sensitive to oxygen and is only active at low oxygen levels or anaerobic conditions. The physical structure of the nodule acts as a barrier to oxygen and the enzyme leghaemaglobin binds oxygen and transports it away from nitrogenase to respiratory sites. Leghaemoglobin gives the inside of nodules their reddish-pink colouring.

Lupin nodules

What are some of the other plant-bacterial associations that fix atmospheric nitrogen?

Associations between bacteria and plants that fix atmospheric nitrogen include an association between species of Frankia bacteria and several tree species such as those of the genera Casuarina and Allocasuarina. Another example is between that of Azospirillum and grasses.

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