Here is an extract from an article from a wonderful site for beginners in soil microbiology http://www.artemisthai.com
Before reading this article, here’s two short paragraphs of the needs of soil.
Soil microorganisms (Flora & Fauna), just like higher plants depends entirely on soil for their nutrition, growth and activity. The major soil factors which influence the microbial population, distribution and their activity in the soil are
1. Soil fertility 2. Cultural practices 3. Soil moisture 4. Soil temperature
5. Soil aeration 6. Light 7. Soil PH (H-ion Concentration) 8. Organic matter 9. Food and energy supply 10. Nature of soil and 11. Microbial associations.
Why Do We Need Soil Bacteria?
Soil bacteria are the primary digestive system of the soil. Their activity is responsible for almost 90% of all biological and chemical actions. For instance, key macronutrients such as nitrogen, sulphur and phosphorus all require microbial transformation in the root zone to make them more available to the plant. Soil bacteria transform nutrients from “forms not usable by the plant” to “forms usable by the plant”. Again, soil microbes improve aeration by loosening dense and compacted soils. Water is then able to better infiltrate and percolate. Most important, soil bacteria decompose organic waste materials such as leaves and manure into organic humus, which stores both moisture and nutrients. Further, microbes can balance soil acidity and alkalinity, create the carbon dioxide plants need, as well as produce vitamins, toxins, and hormones that both feed and protect the plant system.
What Do Bacteria Do In the Soil?
Soil micro-organisms are living, breathing organisms and, therefore, need to eat. They compete with plants for nutrients including Nitrogen, Phosphorus, Potassium and micronutrients as well. They also consume amino acids, vitamins, and other soil compounds. Their nutrients are primarily derived from the organic matter they feed upon. The benefit is that they also give back or perform other functions that benefit higher plant life.
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.
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.
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.
What Are Rhizobia?
Rhizobia are one of the groups of micro-organisms 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 innoculum to the exterior of the seeds as liquid formations or pellets.
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, water logging, and the presence of root parasites such as nematodes or genetic incompatibility with the plant host.
Affects of Soil Micro-organisms on Plant Health and Nutrition
Soil micro-organisms, sometimes spelled as soil micro-organisms, are a very important element of healthy soil. Knowing what microbes in soil eat, the conditions they thrive in and the temperatures that they are most active in is important in organic gardening and organic lawn care. From a practical standpoint, it boils down to organic matter, but not just any organic matter. These facts below will help you plan your activities around the time they are most beneficial. Below is a partial list of important functions they perform.
Soil Micro-Organisms Are Responsible For:
- Transforming raw elements from one chemical form to another. Important nutrients in the soil are released by microbial activity are Nitrogen, Phosphorus, Sulphur, Iron and others.
- Breaking down soil organic matter into a form useful to plants. This increases soil fertility by making nutrients available and raising CEC levels.
- Degradation of pesticides and other chemicals found in the soil.
- Suppression of pathogenic micro-organisms that cause diseases. The pathogens themselves are part of this group, but are highly outnumbered by beneficial microbes.
Types of Micro-organisms in Soil
There are several types of micro-organisms in soil that benefit plants. Together they make up an immense population of living organisms. One teaspoon of soil may contain millions of various types. Below is a list of common soil micro-organisms found throughout the world.
These are small, single cell organisms that make up the single most abundant type of microbe. They have a very wide range of conditions that they live in from the Arctic wastelands to the steaming waters of volcanic hot springs. In soils, they multiply rapidly under the proper conditions. When conditions are wrong for one species, it is right for another. This is not always a good thing since a balance is what is required.
The largest microbe group in terms of mass. Some fungi are beneficial, called mycorrhiza, that form a symbiotic relationship with plant roots, either externally or internally. Within the fungi group are pathogen fungi. These are disease causing fungi, some of which can be quite devastating to plants.
Small single cell microbes that feed on bacteria.
Necessary for the breakdown of certain components in organic matter.
Beneficial groups such as blue-green algae, yellow-green algae and diatoms. Some of these can produce their own energy through photosynthesis.
What is Organic Matter?
It is a variety of natural substances including decomposed leaves, grass clipping, shed roots, wood chips, etc. Humus (well decomposed organic matter) is the richest source for plant growth. Organic matter comes in many different nutrient levels, especially Nitrogen. While soil microbes need carbon (C) to live, they also need the nitrogen contained in organic matter. Therefore, the Carbon to Nitrogen ratio (C:N) is very important.
Problems with Low Nitrogen Organic Matter
Organic matter low in Nitrogen will also have a slower breakdown rate than organic matter with higher nitrogen levels. The microbes will consume the Nitrogen element first and the grass will get what is left over. So, organic matter high in carbon and low in Nitrogen will provide little nitrogen to the grass. However, if another N source is applied over the organic matter, it will speed up the decomposition.
Therefore, the rule of thumb is to choose an organic matter with higher levels of nitrogen. Anything lower than four percent (4%) Nitrogen with high Carbon content should be considered a soil amendment and not a fertilizer.
How Temperature Affects Soil Microbe Activity
Soil Microbe activity is dependent on soil temperatures. For simplicity, all essential soil microbes are classified into the three different temperature ranges they are most active in.
Psychrophiles: Active in temperatures less than 68 degrees.
Mesophiles: Active in temperatures between 77 degrees and 95 degrees. This makes up the largest group of soil microbes and the range most activity charts are based on.
Thermopholes: Active in temperatures from 115degrees to 150 degrees. From a plant and landscape view, this group will rarely apply.
Since the primary group contains Mesophiles, this has a great influence on the degree of soil microbe activity. Areas where the temperatures are warm most of the year, organic matter can be consumed very quickly. Tropical rainforests are so lush in part because of consistently warm temperatures, which promote fast breakdown of organic matter and the release of nutrients into the soil.
Cooler areas, such as Canada and parts of Europe, that have extended periods of cool weather below 77 degrees will benefit far less from the additions of organic matter. This is because far fewer microbes are active in that temperature range. It is possible to build unhealthy levels of organic matter if you follow the example of those in warmer climates.
The scientific rule is this: With every 18 degree rise in temperature, from 32 degrees to 95 degrees, there is a 1.5 to 3.0 % increase in microbial activity.
Remember, the food availability to microbes, the quality of organic matter, soil types, pH level, percent of Nitrogen, etc. will also have an effect on microbial activity level.
Soil pH Factor
Most soil micro-organisms can tolerate a wide range of soil levels. However, bacteria favours a neutral to slightly alkaline soil up to 8.0. When pH drops below 6, fungi begin to dominate as bacteria finds it less favourable.
Just as temperature levels stimulate different soil microbes, so does soil moisture. Some are obvious. Persistent, damp conditions with heavy shade will promote the growth of algae while hindering microbes that thrive in sunny locations. Proper lawn watering requires deep watering so that the soil is wet 4 inches deep. Shallow watering means only the surface is wet. It dries out quickly and can greatly hinder soil microbes.
Oxygen Levels Necessary for Healthy Microbes
There is a balance to everything, including oxygen in soil. Compacted soil will have less oxygen and less water holding capacity. Clay soil consists of extremely tiny particles, even smaller than silt. Clay with proper structure can have sufficient oxygen, but it can also compact easily. Since soil micro-organisms consume oxygen, but low oxygen soils will quickly deplete what oxygen it has and lower the soil microorganism levels. In lawns, deeply water to a level of 4 inches deep and allow it to dry before watering again. The deeper soil will remain moist at sufficient levels. Shallow watering means when the surface moisture is gone there is no moisture deeper to support a healthy microbe population.
What are Fungi?
Fungi are primarily organisms that cannot synthesise their own food and are dependent on complex organic substances for carbon. Specialized fungi can be pathogenic on the tissues of plants, while others form mutually beneficial relationships with plants and assist in direct nutrient supply to the plants (e.g. mycorrhizal associations).
Many fungi play a very important role in the recycling of important chemical elements that would otherwise remain locked up in dead plants and animals. In the decomposition of plant debris, certain fungi are particularly important because of their ability to derive their carbon and energy requirements from the break down of dead and decaying plant cell walls, cellulose and lignin. They are much less dependent on water than other micro-organisms, but interactions with other microbes, temperature and nutrient availability will have an effect on their activity. Fungal activity is greatest in decomposing leaves and wood, and tends to diminish in the later stages of decomposition when bacteria become more dominant.
Fungi vs Bacteria: Their Different Roles in the Decomposition of Organic Matter
Even though a high proportion of both fungi and bacteria are decomposers in the soil, they degrade plant residues differently and have different roles in the recycling of nutrients. This is partly due to their different choice of habitats within the soil and the different types of organic matter they consume.
Fungi are generally much more efficient at assimilating and storing nutrients than bacteria. One reason for this higher carbon (C) storage by fungi lies in the chemical composition of their cell walls. They are composed of polymers of chitin and melanin, making them very resistant to degradation. Bacterial membranes, in comparison, are phospholipids, which are energy-rich. They degrade easily and quickly and function as a food source for a wide range of micro-organisms.
The different proportions of C and N (i.e. different C:N ratios) of bacteria and fungi might also play a role in the mineralisation and immobilisation processes of nutrients in the soil. Due to their structure and C:N ratio between 7:1 and 25:1, fungi need a greater amount of carbon to grow and reproduce and will therefore ‘collect’ the required amount of carbon available for this from the soil organic matter. Bacteria, however, have a lower C:N ratio (between 5:1 and 7:1) and a higher nitrogen requirement and take more nitrogen from the soil for their own requirements.