Botany
Welcome to Botany page
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Effect of Nitrogen on Organic Matter
Excess nitrogen applications stimulate increased microbial activity that speeds organic matter decomposition. The extra nitrogen narrows the ratio of carbon to nitrogen in the soil. The native soil carbon to nitrogen ratio (C:N ratio) is around 12:1. At this ratio, populations of decay bacteria are kept at a stable level When large amounts of inorganic nitrogen are added, the C:N ratio is reduced, which increases the populations of decay organisms and allows them to decompose more organic matter. While soil bacteria can efficiently use moderate applications of inorganic nitrogen accompanied by organic amendments (carbon), excess nitrogen causes bacteria populations to explode, decomposing existing organic matter at a rapid rate.
Composting
Biological treatment of waste solids is a process which involves the transformation of organic material (plant matter) through decomposition into a soil-like material called compost. Invertebrates (insects and earthworms), and microorganisms (bacteria and fungi) help in transforming the material into compost, but we will examine this next week.
Composting is a natural form of recycling that continually occurs in nature. It is also an ancient practice, composting is mentioned in the Bible several times and can be traced to Marcus Cato, a farmer and scientist who lived in Rome 2,000 years ago. Biological treatment is not only used to treat plant material, but also used to process other wastes. For example, it is also used to process sewage sludge, industrial wastes, and agricultural and food processing wastes.
Today there are several different reasons why composting remains an invaluable practice. Yard and food wastes make up approximately 50% of the waste stream in Australia. Composting most of these waste streams would reduce the amount of municipal solid waste (MSW) requiring disposal by almost a half, while at the same time provide a nutrient-rich soil amendment. Compost added to gardens improves soil structure, texture, aeration, and water retention. When mixed with compost, clay soils are lightened, and sandy soils retain water better. Mixing compost with soil also contributes to erosion control, soil fertility, proper pH balance, and healthy root development and disease resistance for plants.
The standard means of disposal for most yard and food waste include landfilling and incineration. These practices may not be as environmentally or economically sound as composting. Yard waste which is landfilled breaks down very slowly due to the lack of oxygen. As it decomposes, it produces methane gas and acidic leachate, which are both environmental problems (as mentioned in last weeks lecture). Landfilling organic wastes also takes up landfill space needed for other wastes. Incinerating moist organic waste is inefficient and results in poor combustion, which disrupts the energy generation of the facility and increases the pollutants that must be removed by the pollution-control devices. Composting these wastes is more effective and is usually a less expensive means of managing organic wastes. It can be done successfully on either a large or small scale, but the technique and equipment used differ.
Decomposition occurs naturally anywhere plants grow. When a plant dies, its remains are attacked by microorganisms and invertebrates in the soil, and it is decomposed to humus. This is how nutrients are recycled in an ecosystem. This natural decomposition can be encouraged by creating ideal conditions. The microorganisms and invertebrates fundamental to the composting process require oxygen and water to successfully decompose the material. The end products of the process are soil-enriching compost, carbon dioxide, water, and heat. Composting is a dynamic process which will occur quickly or slowly, depending on the process used and the skill with which it is executed.
Passive Composting:
Composting can survive most forms of benign neglect, especially if a one/to/two year wait for compost is acceptable. A neglected pile of organic waste will inevitably decompose, albeit slowly. This has been referred to as “passive composting,” because little maintenance is performed.
Active or “Fast” Composting:
Under optimum conditions and with frequent turning, usable compost can be produced in as little as four to six weeks. This method requires attention to the following three items:
- aeration, by turning the compost pile
- moisture
- the proper carbon to nitrogen (C:N ratio).
Attention to these elements (active or “Fast” composting) will raise the temperature to around 55 &endash; 60°C, and ensure rapid decomposition in the pile.
Decomposers
Decomposers are the microorganisms and invertebrates that accomplish the composting process. These naturally occurring microorganisms accomplish much of chemical decomposition in the material being composted. These microorganisms include bacteria, molds/fungi, actinomycetes and protozoa. The invertebrates involved in the physical decay of the material are mites, millipedes, insects, earthworms and snails. This process consists of breaking up of the material resulting the movement of the microorganisms from one area to another.
The Decomposition Process
In the process of composting, microorganisms break down organic matter and produce carbon dioxide, water, heat, and humus, the relatively stable organic end product. Under optimal conditions, composting proceeds through three phases:
- the mesophilic, or moderate-temperature phase, which lasts for a couple of days,
- the thermophilic, or high-temperature phase, which can last from a few days to several months, and finally,
- a several-month cooling and maturation phase.
Different communities of microorganisms predominate during the various composting phases. Initial decomposition is carried out by mesophilic microorganisms, which rapidly break down the soluble, readily degradable compounds. The heat they produce causes the compost temperature to rapidly rise.
As the temperature rises above about 40°C, the mesophilic microorganisms become less competitive and are replaced by others that are thermophilic, or heat-loving. At temperatures of 55°C and above, many microorganisms that are human or plant pathogens are destroyed. Because temperatures over about 65°C kill many forms of microbes and limit the rate of decomposition, compost managers use aeration and mixing to keep the temperature below this point.
During the thermophilic phase, high temperatures accelerate the breakdown of proteins, fats, and complex carboydrates like cellulose and hemicellulose, he major structural molecules in plants. As the supply of these high-energy compounds becomes exhausted, the compost temperature gradually decreases and mesophilic microorganisms once again take over for the final phase of “curing” or maturation of the remaining organic matter.
Bacteria
Bacteria are the smallest living organisms and the most numerous in compost; they make up 80 to 90% of the billions of microorganisms typically found in a gram of compost. Bacteria are responsible for most of the decomposition and heat generation in compost. They are the most nutritionally diverse group of compost organisms, using a broad range of enzymes to chemically break down a variety of organic materials.
Bacteria are single-celled and structured as either rod-shaped bacilli, sphere-shaped cocci or spiral-shaped spirilla. Many are motile, meaning that they have the ability to move under their own power. At the beginning of the composting process (0-40°C), mesophilic bacteria predominate. Most of these are forms that can also be found in topsoil.
As the compost heats up above 40°C, thermophilic bacteria take over. The microbial populations during this phase are dominated by members of the genus Bacillus. The diversity of bacilli species is fairly high at temperatures from 50-55°C but decreases dramatically at 60°C or above. When conditions become unfavorable, bacilli survive by forming endospores, thick-walled spores that are highly resistant to heat, cold, dryness, or lack of food. They are ubiquitous in nature and become active whenever environmental conditions are favorable.
At the highest compost temperatures, bacteria of the genus Thermus have been isolated. Composters sometimes wonder how microorganisms evolved in nature that can withstand the high temperatures found in active compost. Thermus bacteria were first found in hot springs in Yellowstone National Park and may have evolved there. Other places where thermophilic conditions exist in nature include deep sea thermal vents, manure droppings, and accumulations of decomposing vegetation that have the right conditions to heat up just as they would in a compost pile.
Once the compost cools down, mesophilic bacteria again predominate. The numbers and types of mesophilic microbes that recolonize compost as it matures depend on what spores and organisms are present in the compost as well as in the immediate environment. In general, the longer the curing or maturation phase, the more diverse the microbial community it supports.
Actinomycetes
The characteristic earthy smell of soil is caused by actinomycetes, organisms that resemble fungi but actually are filamentous bacteria. Like other bacteria, they lack nuclei, but they grow multicellular filaments like fungi. In composting they play an important role in degrading complex organics such as cellulose, lignin, chitin, and proteins. Their enzymes enable them to chemically break down tough debris such as woody stems, bark, or newspaper. Some species appear during the thermophilic phase, and others become important during the cooler curing phase, when only the most resistant compounds remain in the last stages of the formation of humus.
Actinomycetes form long, thread-like branched filaments that look like gray spider webs stretching through compost. These filaments are most commonly seen toward the end of the composting process, in the outer 10 to 15 centimeters of the pile. Sometimes they appear as circular colonies that gradually expand in diameter.
Fungi
Fungi include moulds and yeasts, and collectively they are responsible for the decomposition of many complex plant polymers in soil and compost. In compost, fungi are important because they break down tough debris, enabling bacteria to continue the decomposition process once most of the cellulose has been exhausted. They spread and grow vigorously by producing many cells and filaments, and they can attack organic residues that are too dry, acidic, or low in nitrogen for bacterial decomposition.
Most fungi are classified as saprophytes because they live on dead or dying material and obtain energy by breaking down organic matter in dead plants and animals. Fungal species are numerous during both mesophilic and thermophilic phases of composting. Most fungi live in the outer layer of compost when temperatures are high. Compost molds are strict aerobes that grow both as unseen filaments and as gray or white fuzzy colonies on the compost surface.
Protozoa
Protozoa are one-celled microscopic animals. They are found in water droplets in compost but play a relatively minor role in decomposition. Protozoa obtain their food from organic matter in the same way as bacteria do but also act as secondary consumers ingesting bacteria and fungi.
Rotifers are microscopic multicellular organisms also found in films of water in the compost. They feed on organic matter and also ingest bacteria and fungi.
Aerobic versus Anaerobic Microorganisms
Aerobic organisms thrive at oxygen levels greater than 5 percent (fresh air is approximately 21 percent oxygen). They are the preferred microorganisms for composting because they provide the most rapid and effective breakdown or organic materials. Anaerobes thrive when the compost pile is oxygen deficient–referred to as an anaerobic condition. Anaerobic microorganisms: Anaerobic microorganisms are undesirable in a compost pile because they create unpleasant odors. The most common product of anaerobic decomposition is hydrogen sulfide, which smells like rotten eggs. Other anaerobic decomposition products, such as cadaverine and putrescine, also result in offensive odors. Anaerobic processes can generate acids and alcohols that are harmful to plants.
Aerobic microorganisms: Among all the microorganisms at work in a compost pile, the aerobic bacteria are the most important initiators of decomposition and temperature increase in the compost pile. Psychrophilic bacteria work in the lowest temperature range and have an optimum temperature of about 12°C. Mesophilic bacteria thrive at temperatures between 21°C and 37°C. Thermophilic bacteria are heat-loving and thrive in a range between 45°C and 68°C. Each category includes numerous strains of bacteria.
The initial temperature of the compost pile usually reflects the ambient air temperature. If the initial temperature is less than 21°C, psychrophilic bacteria begin decomposition. This activity produces a small amount of heat and an increase in pile temperature that creates an environment for dominance by mesophilic bacteria. The mesophilic bacteria accelerate the decomposition and further increase the pile temperature to create an environment where the thermophiles can thrive. Eventually as the thermophilic bacteria in the pile decline and the temperature decreases, mesophilic bacteria again become dominant.
While high temperatures are advantageous for killing harmful pathogenic organisms and weed seeds, moderate temperatures encourage the growth of mesophilic bacteria–the most effective decomposers. If the organic material being composted is not diseased and does not contain seeds, there is no need to be concerned about achieving high temperatures. Many decomposers die or become inactive if the temperature rises above 140oF. The rise and fall of temperature during the compost process will depend on the material being composted and the composting method used. Given the high temperatures required for rapid composting, the process will inevitably slow down during the winter months in cold climates. Compost piles often steam in cold weather.
Factors Affecting The Composting Process
All organic material will eventually decompose. The speed at which it decomposes depends on these factors:
- carbon to nitrogen ratio of the material
- amount of surface area exposed
- moisture
- aeration, or oxygen in the pile
- temperatures reached in compost pile
- outside temperatures
Carbon-to-Nitrogen Ratios
Carbon and nitrogen are the two fundamental elements in composting, and their ratio (C:N) is significant. The bacteria and fungi in compost digest or “oxidize” carbon as an energy source and ingest nitrogen for protein synthesis. Carbon (often referred to as “browns”) can be considered the “food.” Nitrogen (often referred to as “greens”) can be considered as the digestive enzymes.
The bulk of the organic matter should be carbon with just enough nitrogen to aid the decomposition process. Ideally, the ratio should be roughly 30 parts carbon to 1 part nitrogen (30:1) by weight. Even though this ratio is deemed “ideal,” one doesn’t always generate materials in tidy ratios. Thus, as long as a pile has 1) an adequate carbon source or “browns,” 2) is not overloaded with “greens” and 3) is well mixed, successful compost is possible. Adding 34 kg of nitrogenous material for every 100 kg of carbonaceous material should be satisfactory for efficient and rapid composting. The composting process slows if there is not enough nitrogen, and too much nitrogen may cause the generation of ammonia gas which can create unpleasant odors. Leaves are a good source of carbon; fresh grass, manures and blood meal are sources of nitrogen.
Surface Area
Decomposition by microorganisms in the compost pile occurs when the particle surfaces are in contact with air. Increasing the surface area of the material to be composted can be done by chopping, shredding, mowing, or breaking up the material. The increased surface area means that the microorganisms are able to digest more material, multiply more quickly, and generate more heat. It is not necessary to increase the surface area when composting, but doing so speeds up the process. Insects and earthworms also break down materials into smaller particles that bacteria and fungi can digest.
Aeration
The decomposition occurring in the compost pile takes up all the available oxygen. Aeration is the replacement of oxygen to the center of the compost pile where it is lacking. Efficient decomposition can only occur if sufficient oxygen is present (aerobic decomposition). It can happen naturally by wind, or when air warmed by the compost process rises through the pile and causes fresh air to be drawn in from the surroundings. Composting systems or structures should incorporate adequate ventilation.
Turning the compost pile is an effective means of adding oxygen and brings newly added material into contact with microbes. It can be done with a compost turning fork (similar to a pitchfork) a shovel, or a special tool called an “aerator,” designed specifically for that purpose. If the compost pile is not aerated, it may produce an odor symptomatic of anaerobic decomposition.
Moisture
Microorganisms can only use organic molecules if they are dissolved in water, so the compost pile should have a moisture content of 40-60 percent. If the moisture content falls below 40 percent the microbial activity will slow down or become dormant. If the moisture content exceeds 60 percent, aeration is hindered, nutrients are leached out, decomposition slows, and the odor from anaerobic decomposition is emitted. The “squeeze test” is a good way to determine the moisture content of the composting materials. When squeezing a handful of material it should feel damp like a well wrung sponge. A pile that is too wet can be turned or can be corrected by mixing in dry materials.
Temperature
Microorganisms generate heat as they decompose organic material. A compost pile with temperatures between 32°C &endash; 60°C is composting efficiently. Temperatures higher than 60°C inhibit the activity of many of the most important and active microorganisms like cool temperatures and will continue the decomposition process, though at a slower pace. Serious composters can use a temperature probe or soil thermometer to monitor the temperature of their compost piles.
On-Site Composting
On-site or “backyard” composting can be done using a variety of different systems, enclosures, or containers. On-site composting eliminates the environmental and economic costs of the heavy equipment used to bring yard materials to a composting site and manage the piles. Composting systems or bins can be constructed at home or purchased commercially. Depending on where you live, you may have a problem with rodents if they are seeking a warm place for nesting or the food from your pile. If so, an enclosed space or bin is advisable. The methods employed will vary somewhat depending on the system you choose, but the principles and purpose remain the same. This is true for large-scale composting projects as well.
Large-Scale Composting
Some municipalities collect yard trimmings, leaves and grass separated from trash at the curbside similar to the way recyclables are collected. This material is taken to a central location and formed into compost windrows, triangular-shaped rows from 1 to 2.5m high and as long as necessary. Turning for aeration is done about once a month using a front-end loader or other type of heavy equipment made specifically for that purpose. The temperature and moisture are checked twice a week. The finished compost may be sold, given away, or used by the municipality in public works projects. Large-scale composting carries a greater environmental cost than onsite or “backyard” composting, but not nearly as high as if yard trimmings are disposed of in landfills. In Rhode Island, large-scale composting operations are regulated by the Department of Environmental Management.
Conclusion
The art of composting has been part of our global culture since ancient times. The basic principles are quite simple, and adhering to them will result in an efficient and successful outcome. Studies have shown that home composting can divert an average of 700 lbs. of material per household per year from the waste stream. Composting is an excellent way to manage certain wastes responsibly and prevent the wasting of natural resources; while at the same time it produces a high quality and inexpensive soil amendment.
Biological treatment of waste solids is a process which involves the transformation of organic material (plant matter) through decomposition into a soil-like material called compost. Invertebrates (insects and earthworms), and microorganisms (bacteria and fungi) help in transforming the material into compost, but we will examine this next week.
Composting is a natural form of recycling that continually occurs in nature. It is also an ancient practice, composting is mentioned in the Bible several times and can be traced to Marcus Cato, a farmer and scientist who lived in Rome 2,000 years ago. Biological treatment is not only used to treat plant material, but also used to process other wastes. For example, it is also used to process sewage sludge, industrial wastes, and agricultural and food processing wastes.
Today there are several different reasons why composting remains an invaluable practice. Yard and food wastes make up approximately 50% of the waste stream in Australia. Composting most of these waste streams would reduce the amount of municipal solid waste (MSW) requiring disposal by almost a half, while at the same time provide a nutrient-rich soil amendment. Compost added to gardens improves soil structure, texture, aeration, and water retention. When mixed with compost, clay soils are lightened, and sandy soils retain water better. Mixing compost with soil also contributes to erosion control, soil fertility, proper pH balance, and healthy root development and disease resistance for plants.
The standard means of disposal for most yard and food waste include landfilling and incineration. These practices may not be as environmentally or economically sound as composting. Yard waste which is landfilled breaks down very slowly due to the lack of oxygen. As it decomposes, it produces methane gas and acidic leachate, which are both environmental problems (as mentioned in last weeks lecture). Landfilling organic wastes also takes up landfill space needed for other wastes. Incinerating moist organic waste is inefficient and results in poor combustion, which disrupts the energy generation of the facility and increases the pollutants that must be removed by the pollution-control devices. Composting these wastes is more effective and is usually a less expensive means of managing organic wastes. It can be done successfully on either a large or small scale, but the technique and equipment used differ.
Decomposition occurs naturally anywhere plants grow. When a plant dies, its remains are attacked by microorganisms and invertebrates in the soil, and it is decomposed to humus. This is how nutrients are recycled in an ecosystem. This natural decomposition can be encouraged by creating ideal conditions. The microorganisms and invertebrates fundamental to the composting process require oxygen and water to successfully decompose the material. The end products of the process are soil-enriching compost, carbon dioxide, water, and heat. Composting is a dynamic process which will occur quickly or slowly, depending on the process used and the skill with which it is executed.
Passive Composting:
Composting can survive most forms of benign neglect, especially if a one/to/two year wait for compost is acceptable. A neglected pile of organic waste will inevitably decompose, albeit slowly. This has been referred to as “passive composting,” because little maintenance is performed.
Active or “Fast” Composting:
Under optimum conditions and with frequent turning, usable compost can be produced in as little as four to six weeks. This method requires attention to the following three items:
- aeration, by turning the compost pile
- moisture
- the proper carbon to nitrogen (C:N ratio).
Attention to these elements (active or “Fast” composting) will raise the temperature to around 55 &endash; 60°C, and ensure rapid decomposition in the pile.
Decomposers
Decomposers are the microorganisms and invertebrates that accomplish the composting process. These naturally occurring microorganisms accomplish much of chemical decomposition in the material being composted. These microorganisms include bacteria, molds/fungi, actinomycetes and protozoa. The invertebrates involved in the physical decay of the material are mites, millipedes, insects, earthworms and snails. This process consists of breaking up of the material resulting the movement of the microorganisms from one area to another.
The Decomposition Process
In the process of composting, microorganisms break down organic matter and produce carbon dioxide, water, heat, and humus, the relatively stable organic end product. Under optimal conditions, composting proceeds through three phases:
- the mesophilic, or moderate-temperature phase, which lasts for a couple of days,
- the thermophilic, or high-temperature phase, which can last from a few days to several months, and finally,
- a several-month cooling and maturation phase.
Different communities of microorganisms predominate during the various composting phases. Initial decomposition is carried out by mesophilic microorganisms, which rapidly break down the soluble, readily degradable compounds. The heat they produce causes the compost temperature to rapidly rise.
As the temperature rises above about 40°C, the mesophilic microorganisms become less competitive and are replaced by others that are thermophilic, or heat-loving. At temperatures of 55°C and above, many microorganisms that are human or plant pathogens are destroyed. Because temperatures over about 65°C kill many forms of microbes and limit the rate of decomposition, compost managers use aeration and mixing to keep the temperature below this point.
During the thermophilic phase, high temperatures accelerate the breakdown of proteins, fats, and complex carboydrates like cellulose and hemicellulose, he major structural molecules in plants. As the supply of these high-energy compounds becomes exhausted, the compost temperature gradually decreases and mesophilic microorganisms once again take over for the final phase of “curing” or maturation of the remaining organic matter.
Bacteria
Bacteria are the smallest living organisms and the most numerous in compost; they make up 80 to 90% of the billions of microorganisms typically found in a gram of compost. Bacteria are responsible for most of the decomposition and heat generation in compost. They are the most nutritionally diverse group of compost organisms, using a broad range of enzymes to chemically break down a variety of organic materials.
Bacteria are single-celled and structured as either rod-shaped bacilli, sphere-shaped cocci or spiral-shaped spirilla. Many are motile, meaning that they have the ability to move under their own power. At the beginning of the composting process (0-40°C), mesophilic bacteria predominate. Most of these are forms that can also be found in topsoil.
As the compost heats up above 40°C, thermophilic bacteria take over. The microbial populations during this phase are dominated by members of the genus Bacillus. The diversity of bacilli species is fairly high at temperatures from 50-55°C but decreases dramatically at 60°C or above. When conditions become unfavorable, bacilli survive by forming endospores, thick-walled spores that are highly resistant to heat, cold, dryness, or lack of food. They are ubiquitous in nature and become active whenever environmental conditions are favorable.
At the highest compost temperatures, bacteria of the genus Thermus have been isolated. Composters sometimes wonder how microorganisms evolved in nature that can withstand the high temperatures found in active compost. Thermus bacteria were first found in hot springs in Yellowstone National Park and may have evolved there. Other places where thermophilic conditions exist in nature include deep sea thermal vents, manure droppings, and accumulations of decomposing vegetation that have the right conditions to heat up just as they would in a compost pile.
Once the compost cools down, mesophilic bacteria again predominate. The numbers and types of mesophilic microbes that recolonize compost as it matures depend on what spores and organisms are present in the compost as well as in the immediate environment. In general, the longer the curing or maturation phase, the more diverse the microbial community it supports.
Actinomycetes
The characteristic earthy smell of soil is caused by actinomycetes, organisms that resemble fungi but actually are filamentous bacteria. Like other bacteria, they lack nuclei, but they grow multicellular filaments like fungi. In composting they play an important role in degrading complex organics such as cellulose, lignin, chitin, and proteins. Their enzymes enable them to chemically break down tough debris such as woody stems, bark, or newspaper. Some species appear during the thermophilic phase, and others become important during the cooler curing phase, when only the most resistant compounds remain in the last stages of the formation of humus.
Actinomycetes form long, thread-like branched filaments that look like gray spider webs stretching through compost. These filaments are most commonly seen toward the end of the composting process, in the outer 10 to 15 centimeters of the pile. Sometimes they appear as circular colonies that gradually expand in diameter.
Fungi
Fungi include moulds and yeasts, and collectively they are responsible for the decomposition of many complex plant polymers in soil and compost. In compost, fungi are important because they break down tough debris, enabling bacteria to continue the decomposition process once most of the cellulose has been exhausted. They spread and grow vigorously by producing many cells and filaments, and they can attack organic residues that are too dry, acidic, or low in nitrogen for bacterial decomposition.
Most fungi are classified as saprophytes because they live on dead or dying material and obtain energy by breaking down organic matter in dead plants and animals. Fungal species are numerous during both mesophilic and thermophilic phases of composting. Most fungi live in the outer layer of compost when temperatures are high. Compost molds are strict aerobes that grow both as unseen filaments and as gray or white fuzzy colonies on the compost surface.
Aerobic versus Anaerobic Microorganisms
Aerobic organisms thrive at oxygen levels greater than 5 percent (fresh air is approximately 21 percent oxygen). They are the preferred microorganisms for composting because they provide the most rapid and effective breakdown or organic materials. Anaerobes thrive when the compost pile is oxygen deficient–referred to as an anaerobic condition. Anaerobic microorganisms: Anaerobic microorganisms are undesirable in a compost pile because they create unpleasant odors. The most common product of anaerobic decomposition is hydrogen sulfide, which smells like rotten eggs. Other anaerobic decomposition products, such as cadaverine and putrescine, also result in offensive odors. Anaerobic processes can generate acids and alcohols that are harmful to plants.
Aerobic microorganisms: Among all the microorganisms at work in a compost pile, the aerobic bacteria are the most important initiators of decomposition and temperature increase in the compost pile. Psychrophilic bacteria work in the lowest temperature range and have an optimum temperature of about 12°C. Mesophilic bacteria thrive at temperatures between 21°C and 37°C. Thermophilic bacteria are heat-loving and thrive in a range between 45°C and 68°C. Each category includes numerous strains of bacteria.
The initial temperature of the compost pile usually reflects the ambient air temperature. If the initial temperature is less than 21°C, psychrophilic bacteria begin decomposition. This activity produces a small amount of heat and an increase in pile temperature that creates an environment for dominance by mesophilic bacteria. The mesophilic bacteria accelerate the decomposition and further increase the pile temperature to create an environment where the thermophiles can thrive. Eventually as the thermophilic bacteria in the pile decline and the temperature decreases, mesophilic bacteria again become dominant.
While high temperatures are advantageous for killing harmful pathogenic organisms and weed seeds, moderate temperatures encourage the growth of mesophilic bacteria–the most effective decomposers. If the organic material being composted is not diseased and does not contain seeds, there is no need to be concerned about achieving high temperatures. Many decomposers die or become inactive if the temperature rises above 140oF. The rise and fall of temperature during the compost process will depend on the material being composted and the composting method used. Given the high temperatures required for rapid composting, the process will inevitably slow down during the winter months in cold climates. Compost piles often steam in cold weather.
Factors Affecting The Composting Process
All organic material will eventually decompose. The speed at which it decomposes depends on these factors:
- carbon to nitrogen ratio of the material
- amount of surface area exposed
- moisture
- aeration, or oxygen in the pile
- temperatures reached in compost pile
- outside temperatures
Carbon-to-Nitrogen Ratios
Carbon and nitrogen are the two fundamental elements in composting, and their ratio (C:N) is significant. The bacteria and fungi in compost digest or “oxidize” carbon as an energy source and ingest nitrogen for protein synthesis. Carbon (often referred to as “browns”) can be considered the “food.” Nitrogen (often referred to as “greens”) can be considered as the digestive enzymes.
The bulk of the organic matter should be carbon with just enough nitrogen to aid the decomposition process. Ideally, the ratio should be roughly 30 parts carbon to 1 part nitrogen (30:1) by weight. Even though this ratio is deemed “ideal,” one doesn’t always generate materials in tidy ratios. Thus, as long as a pile has 1) an adequate carbon source or “browns,” 2) is not overloaded with “greens” and 3) is well mixed, successful compost is possible. Adding 34 kg of nitrogenous material for every 100 kg of carbonaceous material should be satisfactory for efficient and rapid composting. The composting process slows if there is not enough nitrogen, and too much nitrogen may cause the generation of ammonia gas which can create unpleasant odors. Leaves are a good source of carbon; fresh grass, manures and blood meal are sources of nitrogen.
Surface Area
Decomposition by microorganisms in the compost pile occurs when the particle surfaces are in contact with air. Increasing the surface area of the material to be composted can be done by chopping, shredding, mowing, or breaking up the material. The increased surface area means that the microorganisms are able to digest more material, multiply more quickly, and generate more heat. It is not necessary to increase the surface area when composting, but doing so speeds up the process. Insects and earthworms also break down materials into smaller particles that bacteria and fungi can digest.
Aeration
The decomposition occurring in the compost pile takes up all the available oxygen. Aeration is the replacement of oxygen to the center of the compost pile where it is lacking. Efficient decomposition can only occur if sufficient oxygen is present (aerobic decomposition). It can happen naturally by wind, or when air warmed by the compost process rises through the pile and causes fresh air to be drawn in from the surroundings. Composting systems or structures should incorporate adequate ventilation.
Turning the compost pile is an effective means of adding oxygen and brings newly added material into contact with microbes. It can be done with a compost turning fork (similar to a pitchfork) a shovel, or a special tool called an “aerator,” designed specifically for that purpose. If the compost pile is not aerated, it may produce an odor symptomatic of anaerobic decomposition.
Moisture
Microorganisms can only use organic molecules if they are dissolved in water, so the compost pile should have a moisture content of 40-60 percent. If the moisture content falls below 40 percent the microbial activity will slow down or become dormant. If the moisture content exceeds 60 percent, aeration is hindered, nutrients are leached out, decomposition slows, and the odor from anaerobic decomposition is emitted. The “squeeze test” is a good way to determine the moisture content of the composting materials. When squeezing a handful of material it should feel damp like a well wrung sponge. A pile that is too wet can be turned or can be corrected by mixing in dry materials.
Temperature
Microorganisms generate heat as they decompose organic material. A compost pile with temperatures between 32°C &endash; 60°C is composting efficiently. Temperatures higher than 60°C inhibit the activity of many of the most important and active microorganisms like cool temperatures and will continue the decomposition process, though at a slower pace. Serious composters can use a temperature probe or soil thermometer to monitor the temperature of their compost piles.
On-Site Composting
On-site or “backyard” composting can be done using a variety of different systems, enclosures, or containers. On-site composting eliminates the environmental and economic costs of the heavy equipment used to bring yard materials to a composting site and manage the piles. Composting systems or bins can be constructed at home or purchased commercially. Depending on where you live, you may have a problem with rodents if they are seeking a warm place for nesting or the food from your pile. If so, an enclosed space or bin is advisable. The methods employed will vary somewhat depending on the system you choose, but the principles and purpose remain the same. This is true for large-scale composting projects as well.
Large-Scale Composting
Some municipalities collect yard trimmings, leaves and grass separated from trash at the curbside similar to the way recyclables are collected. This material is taken to a central location and formed into compost windrows, triangular-shaped rows from 1 to 2.5m high and as long as necessary. Turning for aeration is done about once a month using a front-end loader or other type of heavy equipment made specifically for that purpose. The temperature and moisture are checked twice a week. The finished compost may be sold, given away, or used by the municipality in public works projects. Large-scale composting carries a greater environmental cost than onsite or “backyard” composting, but not nearly as high as if yard trimmings are disposed of in landfills. In Rhode Island, large-scale composting operations are regulated by the Department of Environmental Management.
Conclusion
The art of composting has been part of our global culture since ancient times. The basic principles are quite simple, and adhering to them will result in an efficient and successful outcome. Studies have shown that home composting can divert an average of 700 lbs. of material per household per year from the waste stream. Composting is an excellent way to manage certain wastes responsibly and prevent the wasting of natural resources; while at the same time it produces a high quality and inexpensive soil amendment.
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Nutrient Cycling by Soil Microbes
Soil microbes exert much influence in controlling the quantities and forms of various chemical elements found in soil. Most notable are the cycles for carbon, nitrogen, sulfur and phosphorus, all of which are elements important in soil fertility, and as we know today, may be involved in global environmental phenomena. The mineralization (i.e. the conversion of organic forms of the elements to their inorganic forms) of organic materials by soil microbes liberates carbon dioxide, ammonium (which is rapidly converted to nitrate by soil microbes), sulfate, phosphate and inorganic forms of other elements. This is the basis of nutrient cycling in all major ecosystems of the world. John Burroughs once said, “Without death and decay, how could life go on?” No doubt, he was referring to the mineralization of nutrients from dead animals and plants. We now know that soil microbes accomplish this task with remarkable zeal and that in the process a substantial part (perhaps as much as one third) of the decomposing materials are converted to the bodies of soil microbes. This pool of microbial biomass constitutes a portion of the soil organic matter which turns over (cycles) fairly quickly and therefore represents a “fertility buffer” in the soil. Don’t forget that the liberation of carbon dioxide through microbial respiration makes possible the continued photosynthesis (i.e. carbon dioxide fixation) by algae and green plants which in turn produce more organic materials which may ultimately reach the soil, thereby completing the cycle.
In the world’s agricultural soils, the source of our food supply, mineralization of nitrogen by soil microbes is a most important process. In those soils not receiving external inputs of fertilizer nitrogen (e.g. most forested lands and many grasslands) the liberation of ammonium from organic debris makes possible the continued growth of new plant matter. Therefore, it is the soil microbial population which controls the productivity of these soils if other environmental factors (moisture, temperature) are suitable. In fact, fertilization of a soil represents our attempt to balance the competition between plants and soil microbes for available soil nitrogen. Nitrogen tied-up (assimilated into cell constituents) in microbial cells is not available for plants or other microbes until that tissue has been decomposed by other microbes. In other words, nitrogen contained in tissues is said to be immobilized. Microbes are the keys for the remobilization of these nutrients. These mineralization/immobilization phenomena are common to all the elements but typically they are only agriculturally important for the macronutrients such as nitrogen, phosphorus and sulfur.
Aside from their role in controlling the rates of production of inorganic forms of nitrogen and sulfur, soil microbes, in particular soil bacteria, can control the forms of the ions in which these nutrients occur. For example, ammonium (NH4+) in the soil is usually rapidly oxidized by bacteria first to nitrite (NO<SUB<2< sub>-) and then to nitrate (NO3-) which may readily leach through soil. Ammonium is oxidized to nitrite and then to nitrate by the bacteria Nitrosomonas and Nitrobacter, respectively. Thus, bacteria can influence the form and, thereby, the retention of nitrogen in the soil. Similarly, reduced sulfur compounds such as thiosulfate, elemental sulfur and even iron pyrite (FeS2, “Fool’s Gold”) can be oxidized to sulfuric acid by soil bacteria. The bacteria which accomplish the oxidation of reduced nitrogen and sulfur compounds use these materials as energy sources to drive their metabolism. Unlike the decomposer microbes which use organic carbon compounds from organic matter for energy and to make cell matter (e.g. they are called heterotrophs), these specialized bacteria called chemoautotrophs obtain their carbon for cell synthesis from carbon dioxide or from dissolved carbonate.
There are many genera of bacteria that can oxidize reduced sulfur compounds. However, much of this activity, especially the oxidation of sulfur and pyrite, can be attributed to bacteria of the genus Thiobacillus (thio = sulfur; bacillus = rod-shaped bacterium). Thiobacillus thiooxidans can oxidize elemental sulfur to sulfuric acid. Sulfur, therefore, can be used to decrease the pH of an alkaline soil. Thiobacillus ferrooxidans attacks both the iron and sulfur in iron pyrite, generating sulfuric acid and dissolved iron in the process. This is also the basis of acid mine drainage associated with the mining of coal throughout the world.
The long-term application of ammonium-based fertilizers can likewise result in the acidification of agricultural soils through bacterial nitrification (the conversion of ammonium to nitrate with the concurrent production of acidity). Thus, we see that certain environmental problems can arise from the activities of these chemoautotrophic soil bacteria.
Another important aspect of nutrient cycling is that under certain circumstances nitrogen and sulfur may be converted to gaseous forms (volatilized) and lost to the atmosphere. Nitrogen in the form of nitrate can be converted to gases such as nitrous oxide (N2O) and dinitrogen (N2) through the process of denitrification (the bacterial reduction of NO3- to N2O or N2) by soil bacteria under anaerobic conditions. A consequence of denitrification is that nitrogen, a precious nutrient for plants, is lost from the soil. On the other hand, this process is a useful way to remove excess nitrate from wastewater.
Sulfur in the form of sulfate (SO4-2) is used by anaerobic bacteria like the genus Desulfovibrio which convert it to hydrogen sulfide gas (H2S). Hydrogen sulfide reacts with metal ions and forms very insoluble metallic sulfides like pyrite (Fe2S). In fact, it is probable that the pyrites associated with coal seams were deposited by the action of these bacteria eons ago. The black color of salt marsh soils and the rotten egg smell associated with them are a result of the activities of the sulfate-reducing bacteria in these habitats. They attest to the occurrence of anaerobic conditions. Sulfur volatilization from soil represents loss of a plant nutrient as well as a contribution of atmospheric sulfur which may contribute to the phenomenon of acid precipitation.
We mentioned above that nitrogen can be lost from agricultural soils as well as from other ecosystems. Fortunately, this “leak” in the terrestrial nitrogen cycle can be at least partially replaced through another important biological process called biological nitrogen fixation. In this process, which is unique to bacteria and a few other microbes, notably the cyanobacteria (blue-green algae), atmospheric dinitrogen (N2) is captured and converted to plant-available forms. Biological nitrogen fixation is carried out by free-living bacteria and cyanobacteria and by symbiotic microorganisms in a wide variety of mutualistically symbiotic associations with higher plants.
The most useful and probably the most widely recognized example of symbiotic nitrogen fixation is that of the Rhizobium – legume root-nodule symbiosis. Soil bacteria belonging to the genera Rhizobium and Bradyrhizobium (and a few others) are capable of inducing the formation of nodules on roots of specific legumes (plants like peas, beans, peanuts, soybeans, alfalfa etc.) and fixing large quantities of nitrogen in these structures. In the nodule, the bacteria are supplied with carbon sources (photosynthate from the plant) that they need in order to fix nitrogen. In return for this carbon, the bacteria fix atmospheric nitrogen which is converted to amino acids used by the plant for growth. The result of this unique plant-microbe partnership is that many legumes are self-sufficient for nitrogen, that is, they are nearly independent of a supply of nitrogen from the soil. It is no wonder that these plants are cultivated all over the world as sources of food, fiber and forage. Nearly two-thirds of the world’s nitrogen supply is from biological nitrogen fixation. Legumes have been used since the beginning of recorded history as “soil improving” crops known as “green manures”. Green manuring is the practice of growing a legume species for the sole purpose of returning it to the soil to serve as a source of nitrogen for an ensuing crop.
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++ Diploma course 2008 microbiology (botany)
By Prof. Dr. Mahmoud Hazaa
Faculty of Science – Benha University- Egypt
email mhazaa@benhascience.com
It’s all in the teamwork
How do microbes “learn” to defeat antibiotics? That’s a feverishly important question in an era of mounting resistance to life-saving drugs. Unfortunately, the answers are disturbing.
“Molecular biology is telling us … what the resistance mechanisms are, although we don’t know all the details,” says microbiologist Julian Davies of the University of British Columbia. Most people probably figure that bacteria rely on mutations to gain resistance to antibiotics.
Here’s new information on the number of bacteria on Earth.
Mutations do come into play when drug manufacturers modify an existing antibiotic to overcome resistant bugs. In that case, the bacteria already possess a gene to defeat the antibiotic, and it mutates to regain mastery over the modified antibiotic.
How do microbes “learn” to defeat antibiotics? That’s a feverishly important question in an era of mounting resistance to life-saving drugs. Unfortunately, the answers are disturbing.
“Molecular biology is telling us … what the resistance mechanisms are, although we don’t know all the details,” says microbiologist Julian Davies of the University of British Columbia. Most people probably figure that bacteria rely on mutations to gain resistance to antibiotics.
Here’s new information on the number of bacteria on Earth.
Mutations do come into play when drug manufacturers modify an existing antibiotic to overcome resistant bugs. In that case, the bacteria already possess a gene to defeat the antibiotic, and it mutates to regain mastery over the modified antibiotic.
Bacteria acquire genes for resistance in three ways.
1. In spontaneous mutation, bacterial DNA may change spontaneously, as indicated by the starburst. Drug-resistant tuberculosis arises this way.
2. In a form of microbial sex called transformation, one bacterium may take up DNA from another. Penicillin-resistant gonorrhea (defined) results from transformation.
3. Most frightening, however, is resistance acquired from a small circle of DNA called a plasmid. Plasmids can flit between bacteria of various types — they generally must be touching — and carry multiple resistance. In 1968, 12,500 Guatemalans died in an epidemic of Shigella diarrhea, caused by a microbe harboring a plasmid that conferred resistances to four antibiotics!
But bacteria do something much more clever than just mutating. That’s chancy, so bacteria prefer to share biochemical secrets — resistance genes — that enable them to resist or destroy antibiotics.
This diabolical bartering can occur in a couple of ways.
1. Some bacteria share plasmids — small chunks of DNA, like mini-chromosomes — that exist outside the main chromosomes. This sharing can leap broad divisions in bacterial phylogeny (defined). It’s almost as if a cow could lend a crow a gene and teach it to grow teeth.
2. Gene cassettes are genes that can be spliced in the chromosomes (defined). While the mechanism is kind of complex, it can be compared to an expedition to a shopping mall, Davies says. Genes called integrons code for enzymes called integrases that can splice those cassettes into chromosomes or other genetic material where they become functional. That makes the integrons function something like a shopping cart, Davies says.
If bacteria can obtain resistance merely by accepting gene cassettes, then, like shoppers in a video store who aren’t sure if they’ve seen their first selection, bacteria can pick up several cassettes and obtain resistance to several antibiotics. Furthermore, says microbiologist Abigail Salyers of the University of Illinois, “Bacteria also integrate resistance to disinfectants or to pollutants in these clusters. Thus disinfectant use or pollution can select for antibiotic resistance, which could be exactly what Merri Moken was finding back at the start of our story.
From the human point of view, the problem with this kind of resistance is its permanence. Once lodged inside the chromosome or plasmid, these resistance genes are distributed as normal genes to all daughter (defined) cells. “Origin and Interstate Spread…” in the bibliography gives a detailed picture of how a deadly bug that causes tuberculosis gained resistance to many antibiotics.
Mechanisms
So far, we’ve talked generally about resistance without painting a good picture of how it works. And here we’re in for yet another surprise, yet more evidence of what might be called the microbial mind. It turns out that antibiotic resistance is part of a larger picture of the way microbes defend themselves against chemical threats in their environment.
It seems that these defense mechanisms are strangely similar across many kinds of organisms — and many threats. “The issue of resistance is converging from the human infectious disease and agricultural angles,” says plant pathologist Jo Handelsman, “whether the microbe is trying to protect itself against antibiotics, fungicides, insecticides, herbicides, even antiviral agents.” Handelsman, who studies the interaction of fungi and bacteria at the University of Wisconsin-Madison, points to more similarities. “At the molecular level, there are only a few mechanisms of resistance: change the target molecule, inactivate or decompose the drug or pesticide, sequester (defined) the drug or pesticide, or keep it out of the cell” to begin with.
Let me see your sources
All in all, it makes sense that microbes would have defenses. After all, during their billions of years on the planet, they’ve overcome countless chemical hazards. But what is the source of the antibiotic resistance genes in the first place?
Probably the organisms that originally produced the antibiotics.
While this might sound odd, it’s logical. Assume that I, a lowly bacterium, make some kind of chemical that, say, destroys bacterial cell walls. Wouldn’t I need some kind of chemical defense against what kids sometime call “my own medicine?”
This supposition is not only logical, it may even be true, says Davies. “We find resistance genes in the streptomycetes (bacteria that produce many antibiotics) that have exactly the same biochemical function as the resistance genes” in samples from hospital patients. And since the gene sequences are similar — but not identical — it’s tempting to think that the genes jumped between species, although Davies admits “we can’t yet prove it.”
Jumping genes
Salyers, who studies this process of gene jumping between species, says bacteria have many tricks for moving resistance genes. For one thing, they seem to be able to cause other bacteria to start genetic swap meets: When a DNA resistance plasmid released by a bacterium is accepted by another bacterium, the recipient may be stimulated to release its own plasmid, a process called retrotransfer. “This transfer capability gives bacteria the ability to sample DNA from other bacteria,” Salyers says. To her, the relationship represents a new form of symbiosis (defined).
As if this prospect of bacteria ganging up to defeat antibiotics were not alarming enough, recognize that this generosity extends beyond members of their own species, Salyers says. “Just about any bacterium can get genes from just about any other bacterium.”
What is the evidence for this movement? Scientists are finding distantly related bacteria with resistance genes whose DNA sequences (defined) are 95 to 99 percent identical. Although it’s extremely improbable by chance alone, it’s a strong suggestion — but not proof — that the genes have a common origin.
But don’t forget that the bacterial anti-antibiotic toolkit also includes multiple mutations, which could explain what’s happened in New York City, where a deadly drug-resistant tuberculosis has been on the rampage.
microbial enzymes is required as a lecture for me