Chapter 1: Environmental Biology

1. Microorganisms in the environment

All organisms may be placed into one of three categories with respect to their part in the global flow of energy:

Producers: autotrophs that obtain energy from the sun or chemical sources (e.g. green plants, photosynthetic bacteria, chemolithotrophic bacteria). They use the energy to synthesise organic material from carbon dioxide and water. Consumers: heterotrophs that derive energy through the consumption of other organisms (producers or other consumers). They may serve as a link between the primary producers and the decomposers. Decomposers: organisms that break down the remains and waste products of producers and consumers, obtaining energy and releasing nutrients, including CO2, that can be reused by the producers.

1.1

The Carbon cycle

1.2.

The Nitrogen cycle

1.3.

The Sulphur cycle

1.4.

The Phosphorus cycle

2. Biodegradation
2.1. Biodegradation: Biodegradation is the process by which organic substances are broken down into smaller compounds by the enzymes produced by living microbial organisms. The microbial organisms transform the substance through metabolic or enzymatic processes. Biodegradation processes vary greatly, but frequently the final product of the degradation is carbon dioxide or methane. Organic material can be degraded aerobically, with oxygen, or anaerobically, without oxygen. 2.2. Aerobic Biodegradation Aerobic biodegradation is the breakdown of organic contaminants by microorganisms when oxygen is present. More specifically, it refers to occurring or living only in the presence of oxygen; therefore, the chemistry of the system, environment, or organism is characterized by oxidative conditions. Many organic contaminants are rapidly degraded under aerobic conditions by aerobic bacteria called aerobes. Aerobic bacteria (aerobe) have an oxygen based metabolism. Aerobes, in a process known as cellular respiration, use oxygen to oxidize substrates (for example sugars and fats) in order to obtain energy. Before cellular respiration begins, glucose molecules are broken down into two smaller molecules. This happens in the cytoplasm of the aerobes. The smaller molecules

then enter a mitochondrion, where aerobic respiration takes place. Oxygen is used in the chemical reactions that break down the small molecules into water and carbon dioxide. The reactions also release energy.

2.3.

Anaerobic Biodegradation Anaerobic biodegradation is the degradation of compounds by microorganisms in

the absence of oxygen. Anaerobic processes are used for treating wastewater with high concentrations of biodegradable organic materials, such as concentrated domestic wastewater, biosolids, animal manure slurry, and food processing wastes. The process is described by the following four steps: Hydrolysis: large polymers are broken down by enzymes. Fermentation: Acidogenic fermentations are most important, acetate is the main end product. Volatile fatty acids are also produced along with carbon dioxide and hydrogen.

Acetogenesis: Breakdown of volatile acids to acetate and hydrogen. Methanogenesis: Acetate, formaldehyde, hydrogen and carbon dioxide are converted to methane and water

3. Indicator Microorganisms for Water Quality

3.1. Fecal indicator bacteria: Fecal indicator bacteria are used to assess the quality of water because they are not typically disease causing, but are correlated to the presence of several waterborne disease-causing organisms (pathogens). The concentration of indicator bacteria is a measure of water safety for body-contact recreation or for consumption. For fecal contamination, indicator organisms should:

Be easily detected using simple laboratory tests. Generally not be present in unpolluted waters. Appear in concentrations that can be correlated with the extent of contamination. Have a die-off rate that is not faster than the die-off rate of the pathogens of concern.

Indicator bacteria are usually harmless, more plentiful, and easier to detect than pathogens. Methods are not currently available to culture or enumerate all the diseasecausing organisms that might be present in natural waters. Indicators vary in their ability to reliably predict potential risks to human health. Some indicators have been shown to have a greater statistical relationship to disease than others. Despite variability in the ability of indicators to reliably predict potential risks to human health, EPA studies indicate that enterococci and E. coli are the most effective available primary indicators for predicting the presence of gastrointestinal illness-causing pathogens, and for marine waters, enterococci is most appropriate. 3.2. Identification and enumeration methods

1. Wash thoroughly with soap and water. Invert the sample for 30 sec, approximately 25 times, to make sure that it is well-mixed.

2. Using sterile buffered dilution water, prepare at least 3 serial dilutions of the sample.

3. Use a sterile pipette to transfer 10 ml of each serial dilutions of the sample into tubes

4. Invert the tube several times to thoroughly mix the sample with the nutrient medium. After the last inversion, make sure the inner vial is full of liquid with no air bubbles.

5. Place the tubes in the incubator at 350C. After one hour, invert the tubes to remove trapped air in the inner vials. Loosen the caps slightly before returning the tubes to the incubator.

6. After 24 hours, examine the inner vials for gas. The presence of gas is an indication of coliform. If tubes are cloudy but have no gas bubbles, check the tubes for fluorescence.

7. If the solution shows fluorescence, the test is positive for E. coli. If the tube does not fluoresce, return the tubes to the incubator and examine again after a total of 48 (3) hours. Compare the fluorescence of the sample tubes to a tube containing a known E. coli culture to make a positive confirmation.

8. After 48 (3) hours, use a longwave ultraviolet (UV) lamp to check the tubes for fluorescence. Examine the tubes in a dark area. If the solution shows fluorescence, the test is positive for E. coli. If there is no fluorescence, the test is negative for E. coli.

4. Disinfection
4.1. Disinfection: Disinfection refers to the partial destruction of disease-causing organisms. All the

organisms are not destroyed during the process. The fact that all of the organisms are not destroyed differentiates disinfection from sterilization, which is the destruction of all organisms. 4.2. Disinfection mechanisms: The five principal mechanisms that have been proposed to explain the action of disinfectants are (1) damage to the cell wall, (2) alteration of cell permeability, (3) alteration of the colloidal nature of the protoplasm, (4) alteration of the organism DNA or RNA, and (5) inhibition of enzyme activity.

4.3.

Chlorine Chlorine is one of the most commonly used disinfectants for water disinfection. Chlorine can be applied for the deactivation of most microorganisms and it is relatively cheap. In a vacuum chlorinator, chlorine gas is pulled from the cylinder into the source water by a vacuum. The vacuum is created by water flowing through the injector and creating a negative head. This negative head forces open the pressure regulating valve on the cylinder and allows chlorine gas to flow out of the cylinder and into the chlorinator. Once the gas has entered the chlorinator, the chlorine feed rate is measured using an indicator known as a rotameter. Just beyond the rotameter, the chlorine gas flows past a regulating device which is used to adjust the chlorine feed rate. Then the chlorine gas is pulled into the injector, also known as an ejector. The injector consists of a pipe filled with flowing water. The flowing water pulls chlorine into the water, both chlorinating the source water and creating a vacuum in the chlorine line which pulls more chlorine gas out of the cylinder. This type of chlorinator is also known as a solution feeder since the chlorine gas is dissolved into a small amount of source water, which is then piped into the main line of water to be chlorinated. Vacuum chlorinators are very safe since any break in the line with disrupt the vacuum and close the pressure regulating valve. As a result, chlorine leaks are very uncommon. 4.4. Ultraviolet radiation Ultraviolet light is electromagnetic radiation with wavelengths shorter than visible light. UV can be separated into various ranges, with short range UV (UVC) considered germicidal UV. At certain wavelengths UV is mutagenic to bacteria, viruses and other micro-organisms. At a wavelength of 2,537 Angstroms (254 nm) UV will break the molecular bonds within micro-organismal DNA, producing thymine dimers in their DNA thereby destroying them, rendering them harmless or prohibiting growth and reproduction.

Chlorine Generator

Schematic diagram of the UV and UV-TiO2 disinfection systems

5. Phytotechnology
5.1. Phytotechnolgy describes the application of science and engineering to study problems and provide solutions involving plants. Although the term is not widely used, it is useful in promoting a broader understanding of the importance of plants and their beneficial role within both societal and natural systems. Underlying this concept is the use of plants as living technologiesto help address environmental challenges. Phytotechnology applications employ ecological engineering principles and are considered to be ecotechnologies. Hence phytotechnologies are based on the science of ecology and consider the ecosystem as an integral component of human and societal interventions involving the natural environment. A related term is biotechnology, which refers to the application of science and engineering to study problems and provide solutions involving living beings. The term biotechnology can also refer to the manipulation of the genetic structure of cells to produce modified organisms with an augmented capacity to perform certain functions. Defining Phytotechnology
eco = living systems, ecological PHYTO = plant, flora, vegetation bio = life, of living beings, biological TECHNOLOGY = the application of science and engineering to study problems and provide solutions ecotechnology = the application of science and engineering to study problems and provide solutions involving ecological systems PHYTOTECHNOLOGY = the application of science and engineering to study problems and provide solutions involving plants biotechnology = the application of science and engineering to study problems and provide solutions involving living beings

Just as there are many different applications of biotechnology, there are also many different applications of phytotechnology. Some of these applications are well established in sectors such as medicine, agriculture and forestry to name a few. There are also many important environmentally related applications. The environmentally beneficial applications of phytotechnologies can generally be divided into five categories: augmenting the adaptive capacity of natural systems to moderate the impacts of human activities; preventing pollutant releases and environmental degradation; controlling pollutant releases and environmental processes to

minimize environmental degradation; remediation and restoration of degraded ecosystems; and incorporating indicators of ecosystem health into monitoring and assessment strategies. The integrated ecosystems management component of this focuses on the use of phytotechnologies to augment the capacity of natural systems to absorb impacts. The prevention component involves the use of phytotechnologies to avoid the production and release of environmentally hazardous substances and/or the modification of human activities to minimize damage to the environment; this can include product substitution or the redesign of production processes. The control component addresses chronic releases of pollutants and the application of phytotechnologies to control and render these substances harmless before they enter the environment. The remediation and restoration component embodies phytotechnologies and methods designed to recuperate and improve ecosystems that have declined due to naturally induced or anthropogenic effects. The monitoring and assessment component involves the use of phytotechnologies to monitor and assess the condition of the environment, including releases of pollutants and other natural or anthropogenic materials of a harmful nature.

Environmentally Beneficial Applications of Phytotechnologies

5.2 .

Phytotechnology applications include: The use of plants to reduce or solve pollution problems that otherwise would be more harmful to other ecosystems. An example is the use of wetlands for wastewater treatment.

The replication of ecosystems and plant communities to reduce or solve a pollution problem. Examples are constructed ecosystems such as ponds and wetlands for treatment of wastewater or diffuse pollution sources.

The use of plants to facilitate the recovery of ecosystems after significant disturbances. Examples are coal mine reclamation and the restoration of lakes and rivers. The increased use of plants as sinks for carbon dioxide to mitigate the impacts of climate change. Examples of this are reforestation and afforestation. The use of plants to augment the natural capacity of urban areas to mitigate pollution impacts and moderate energy extremes. An example is the use of rooftop vegetation, or greenroofs.