Learning Guide: Introduction to Chemistry and Microbiology, Concepts of Hydrology PDF

LEARNING GUIDE Week No.: 2 TOPIC/S: INTRODUCTION TO CHEMISTRY AND MICROBIOLOGY CONCEPTS...

LEARNING GUIDE Week No.: 2 TOPIC/S: INTRODUCTION TO CHEMISTRY AND MICROBIOLOGY CONCEPTS OF HYDROLOGY I. EXPECTED COMPETENCIES: Upon completion of this material you should be able to do the following: 1. Describe basic concepts of chemistry and microbiology in environmental engineering 2. Explain basic concepts of hydrology in environmental engineering II. CONTENT/TECHNICAL INFORMATION: Introduction Tools and concepts from biology and chemistry are used to address a wide range of issues pertaining to environmental media. Environmental chemistry deals with pathways and rates of chemical transformations of organic compounds (both synthetic and biologically derived) and elements in the periodic table. Microbial ecology and engineering microbiology address microbial populations, changes in populations and ecosystems in space and time, the effects of microorganisms in naturally occurring and engineered systems, and behavior and consequences of pathogenic organisms. While ecology seeks to explore populations and phenomena in the present, as influenced by human activities, and to develop an understanding of ecosystem change over time. The Department of Environmental Health and Engineering seeks to understand foundational principles of these systems and apply this knowledge to elucidate linkages between environmental chemical and microbial exposures with human health outcomes. To mitigate environmental health and engineering challenges, research in these disciplines takes the interdisciplinary approach of interfacing with environmental and public health practitioners, researchers, scientists and environmental engineers. Methods of Expressing Concentration The two methods of expressing the concentration of a constituent of a liquid or gas are: 1. Mass/volume The mass of solute per unit volume of solution (in water chemistry). This is analogous to weight per unit volume; typically, mg/L = ppm (parts per million) 2. Mass/volume The mass of solute per unit volume of solution (in water chemistry). This is analogous to weight per unit volume; typically, mg/L = ppm (parts per million) If the density of a solution = p = (kg/L) and concentration of a constituent in mg/L = C A1 = (mg/L) and concentration of a constituent in ppm = C A2 = (mg/ml) then rearranging, p if p = 1kg/l, then CA1= CA2 i.e. the concentration of a constituent in ppm mg/kg = concentration of a constituent in mg/L For most applications in water and wastewater environments, p =1 kg/L. For applications in the air environment, Eq. (3.1) does not hold. The use of mg/L is most common in water applications as the volume of the solution is usually determined as well as the mass of the solute. The unit ppm is typically used in sludges or sediments. Example 3.1 Express the concentration of a 3 per cent by weight CaSO4 solution in water in terms of mg/L and ppm. Example 3.2 If a litre solution contains 190 mg of NH4+ and 950 mg of NO3-, express these constituents in terms of nitrogar (N). At the beginning of this section concentration in terms of mass or weight for a fixed weight or volume of solution is discussed, e.g. 1 L or 1 kg. Chemists sometimes prefer to use the concentration term mole, which is the mass of a constituent which is numerically equal to the molecular weight of the constituent. For instance: 1 gram mole of methane (CH4) = 18 g of methane Where 1 mole is that amount of a constituent which contains the Avogadro number of molecules. Therefore, the mole notation does not refer to a fixed weight but to a fixed number of particles. In the mole context there are four entities of concentration: where n is the number of protons denoted in an acid-base reaction or is the total change in valence in an oxidation reduction reaction. If two different solutions have the same normality, they will react in equal proportions, i.e. VANA = VBNB where VA, VB are the volumes of solutions A and B, and N A, NB are the respective normalities.  𝑛𝑜.𝑜𝑓 𝑚𝑜𝑙𝑒𝑠 𝑜𝑓 𝑠𝑜𝑙𝑢𝑡𝑒 Mole Fraction X = 𝑡𝑜𝑡𝑎𝑙 𝑚𝑜𝑙𝑒𝑠 𝑜𝑓 𝑠𝑜𝑙𝑢𝑡𝑖𝑜𝑛 Stoichiometric Examples If the gas methane is burned with oxygen to produce carbon dioxide and water, the reaction is Oxygen (0) is an 'element' of atomic weight 16, hydrogen is also an element with atomic weight 1 and carbon is an element of atomic weight 12. An element is defined as 'a pure substance which cannot be split into any simpler pure substance'. They are usually classified into metals and non-metals. Methane (CH4) is a 'compound' of molecular weight 16. Carbon dioxide is a compound of molecular weight 44 and water is a compound of molecular weight 18. A compound is defined as 'a pure substance composed of two or more elements, combined in fixed and definite proportions in a chemical reaction'. The `molecular weight' is the sum of the atomic weights of all the constituent atoms. The molecular weight of methane is 16. A 'mole' has the Avogadro number (6.023 x 1023) of molecules and is expressed as: 𝑚𝑎𝑠𝑠 𝑖𝑛 𝑔 g mole = 𝑚𝑜𝑙𝑒𝑐𝑢𝑙𝑎𝑟 𝑤𝑒𝑖𝑔ℎ𝑡 Example 3- In the treatment of potable water, an aluminium sulphate solution is used as a coagulant to produce an aluminium hydroxide (sludge) floc (see Chapter 11 for details). Compute the amount of sludge produced if 100 kg of alum coagulant is used daily. The stoichiometric analysis is as follows. 594 g of alum produces 156 g of alum hydroxide sludge and so. 100 kg of alum used daily produces 26 kg of alum hydroxide sludge. PHYSICAL AND CHEMICAL PROPERTIES OF WATER Water is never pure, except possibly in its vapor state. Water always contains impurities, which are constituents of natural origin. Frequently, water contains contaminants, which are constituents of anthropogenic origin. For instance, the presence of the chemical impurities of calcium and magnesium ions (Ca2± and Mg2±) in groundwater are usually of natural origin, being due to the dissolution of these minerals from the soil and underground rocks. However, the presence of the nitrogen compounds of ammonia nitrogen (NH4), nitrite (NO2-) or nitrate (NO3-) in groundwater is possibly due to pollution from agricultural fertilizers, agricultural liquid wastes, sewage or industrial wastewaters. In environmental engineering, water is of central interest due to its many varied occurrences and uses, including. Surface freshwaters in rivers and lakes and groundwaters when used as drinking water Surface freshwaters as used in fish and other fauna habitats Surface freshwaters as used for anthropogenic liquid discharges Surface freshwaters and groundwaters as used for irrigation Surface waters as used for recreation Surface waters as used for navigation The acceptability of a water for its defined use depends on its physical, chemical and biological properties, and sometimes on whether these properties can be modified to suit the defined use. The composition of water is the end result of many possible physical and/or chemical and/or biochemical processes. Physical properties are reflection of the chemical contents. They have temporal and spatial variations in natural water along two periods. The physical properties of water have a given appearance. 1- Color: Pure water is colorless. Dissolved organic material from decaying vegetation (algae, and humus compounds) and certain inorganic matter for example increasing concentrations of dissolved (Fe and Mn) ions, measured in (ppm) causes color in water. The color is estimated by comparing sample color with a standard solution color (1.245 gm of chloro-platinium potassium added to 1.0 gm of crystalline cobalt chloride in one-liter distilled water 2- Odor: released from any water may be due to decreases in the dissolved oxygen (DO2), presence of organic pollution, and presence of phenols and hydrogen sulfide (H2S). Pure water is odorless. Quantitative determinations of odor have been developed based on the maximum degree of dilution that can be distinguished from odor-free water. 3- Taste: may be due to increases in the total dissolved solids (TDS), carbonate hardness, decreased dissolved oxygen (DO2), and excessive bacterial activity, there are no accepted method devised for measuring tastes (Todd, 1980). All above characteristics are subjective sensation which can be defined only in terms of the experience of a human being. 4- Temperature (ToC): Temperature affects the geochemical and chemical reactions. It effects the acceptability of a number of other inorganic constituents and chemical contaminants that may affect taste. Temperature of groundwater is constant relatively and increases with the depth, it has effects on the hydro geochemical reactions. 5- Turbidity: The turbidity is the measure of suspended and colloidal matter in water such as silt, clay, organic matter and microscopic organisms, also it depends on the structural conditions like flow regime and weathering, and the total suspended solids (TSS). Measurement are often based on the length of the light path passes through the water sample till the image of a flame of a standard candle disappear, turbidity units is either FT(formazan turbidity units) , or JFU ( Jackson turbidity unit). In lakes and rivers, it can be measured using Secchi disk method. Ideally, normal turbidity should be below 1 Nephelometric turbidity Unit NTU (WHO, 1997).  5- Hydrogen Ion Concentration (pH): pH is the negative logarithm of hydrogen ion activity and its value expresses the intensity of the activity or alkalinity condition of water under normal condition temperature (T°C) and pressure. Most reactions in gas/water/rock systems involve or are controlled by the pH of the system, it related to taste, and odor problems. PH-value in natural water is affected by the concentration of bicarbonate and carbonate ions. The pH value for all water samples is in the optimum range (6.5-8.5). According to (WHO, 2006), some water samples are described as alkaline water, and the others are close to neutral. The water in a pure state has a neutral (pH=7), while the rain has a natural acidic pH of about 5.6 because it contains CO2 and SO2. It measured by pH Electrode meter, or Acidity Index paper. 6- Radioactivity: Water sources can contain radionuclides of natural and artificial origin (i.e. human made). Water may contain radioactive substances (“radionuclides”) that could present a risk to human health. Radioactivity comes from several naturally occurring elements (including K-40, Ra226, Ra-228, U-234, U-238 and Pb-210 ), and human-made sources is present throughout the environment such as :radionuclides discharged from nuclear fuel cycle facilities, manufactured radionuclides (produced and used in unsealed form in medicine or industry) entered into drinking- water supplies as a result of regular or incidental discharges, and radionuclides released in the past into the environment, including drinking water sources. Some chemical elements present in the environment are naturally radioactive. Earth is constantly bombarded by highenergy particles originating both from the sun and from outside the solar system. Collectively, these particles are referred to as cosmic radiation. Everybody receives a dose from cosmic radiation, which is influenced by latitude, longitude and height above sea level. Inorganic Chemical Properties of Water Included among the chemical processes influencing the quality of water described by Dojlido and Best (1993) are the chemical processes of: Acid—base reactions Exchange processes between the atmosphere and water Precipitation and dissolution of substances Complex actions/reactions Oxidation—reduction reactions Adsorption—desorption processes Major ions the major ionic species in some natural waters are listed in Table 3.1. It is seen that all-natural waters contain dissolved ionic constituents in varying amounts. The dominant ion in rainwater is chloride, as rainwater is largely derived from seawater. The predominant ionic species in either surface waters or groundwaters is that of bicarbonate and the dominant divalent ionic species are usually calcium and magnesium. In seawater, chlorides and to a lesser extent sodium predominate. Details of each element, occurrence, significance and method of determination are given in Dojlido et al. (1993). Minor ions in addition to the major ionic species found in natural waters, there may also be minor ionic species. Table 3.2 lists these. They are classified as minor since their concentrations are in the order of ppb (parts per billion) or ppt (parts per trillion), while major ions are more typically in ppm concentrations. Silica, Si02 -The presence of silica (a non-ionic mineral) along with calcium, magnesium, iron and aluminium can cause scaling in boilers. Most natural waters contain less than 5 mg/L of Si02, although higher values up to 100 mg/L have been reported. Silica can potentially be a limiting mineral in the process of surface water eutrophication. Silicon (Si) is a constituent of aquatic plants and animals in their skeletal structure. The concentrations in surface waters reduce in summertime due to its uptake by the accelerated growth of aquatic phytoplankton organisms in water, which is fuelled by sunlight and nutrients (phosphate). In Chow Valley Lake near Bristol, UK, the winter levels of Si02 were 6 mg/L, and in May during the spring plankton growth the values were reduced to 3.5 mg/L (Dojlido and Best, 1993) Nutrients The two nutrients of importance in water/wastewater are nitrogen and phosphorus. They are both essential nutrients for plant and organism growth, but in excess they can be undesirable, often leading to eutrophication. Nitrogen This is one of the basic components of proteins and in water it is used by the primary producers in cell production. Nitrogen exists in nine valence states. The largest amount of nitrogen is the atmosphere, as 78 per cent by volume. Nitrates in drinking water are harmful, and upper limit values of 40 mg NO3— -N/L are typical for drinking water. For surface waters for salmonoids the upper limits are typically 1 mg NO3 -N/L. Phosphorus This is an important nutrient in the aquatic environment and in freshwaters is most often the limiting nutrient of cultural eutrophication. Phosphorus was introduced to detergents in 1935 and is also a key crop fertilizer component. Phosphorus occurs in all living organisms and is important for cellular activity. Bones contain about 60 per cent Ca3(PO4)2 and about 2 per cent of dry weight of protoplasm is phosphorous. About 80 per cent of phosphate production is in fertilizers. Other uses are chemicals, soaps, detergents, pesticides, alloys, animal feed supplements, catalysts, lubricant and corrosion inhibitors (Dojlido et al., 1993). Phosphates are present in surface waters as a result of weathering and leaching of phosphorus-bearing rocks, from soil erosion, from municipal sewage, industrial wastewater effluent, agricultural runoff and atmospheric precipitation. The most commonly occurring compounds of phosphorus in water are: Gross chemical properties of water—inorganic The gross chemical properties of water that are in widespread use when relating a water quality, be it drinking water, wastewater or river water, are: pH Alkalinity and acidity Hardness Conductivity pH - pH is defined as the negative log (base 10) of the hydrogen ion concentration and is unitless pH = —log[H+] Water dissociates slightly into hydrogen ions (H±) and hydroxide ions hydroxyl ions as per the following equation: Alkalinity and acidity 'Alkalinity', the capacity of water to accept H± ions, is a measure of its acid neutralizing capacity (ANC) and is often described as the buffering capacity. Similarly, 'acidity' is a measure of the base neutralizing capacity (BNC). Alkalinity and acidity are capacity factors of a water. Fig. 2.3 The pH Scale Hardness- is expressed principally by the sum of the divalent metallic cations, Ca2+ and Mg2+. These cations react with soap to form precipitate and with other ions present in water to form scale in boilers. The ions causing hardness to have their origin in soil and geological formations. Table 3.4 lists the dominant ionic species, all responsible for hardness. Hardness is a water parameter used in potable water (not wastewater). Traditionally, hardness was calculated in mg/L as CaCO3 (similar to alkalinity) or as meq/L. Table 3.5 is a qualitative listing of waters rated on hardness. Carbonate hardness or temporary hardness (TH) since this form is removed on prolonged boiling:  Carbonate hardness = E (bicarbonate+ carbonate) alkalinity. This is so, when alkalinity is< total hardness Non-carbonate hardness (NCH Conductivity Electrical conductivity or, as it is more commonly called, conductivity, is a measure of the ability of an aqueous solution to carry an electric current. The electric current is conducted in the solution by the movement of ions and so the higher the number of ions (i.e. the greater the concentration of dissolved salts) the higher the ionic mobility and so the higher the magnitude of conductivity. Chemically pure water does not conduct electricity since the only ions present are H+ and OH+and so the conductivity of very pure water is about 0.05 µS/cm (microsiemens/cm). On the other hand, a seawater with high salts has a conductivity of about 40 000 µS/cm. SOIL CHEMISTRY Although often taken for granted and, seemingly, not as valued as water and air, without soil, life on this planet would not exist. Soil is important for the production of food; the maintenance of carbon, nitrogen, and phosphorus balances; and for the construction of building materials. Chemically, soil is a mixture of weathered rocks and minerals; decayed plant and animal material (humus and detritus); and small living organisms, including plants, animals, and bacteria. Soil also contains water and air. Typically, soil contains about 95% mineral and 5% organic matter, although the range in composition varies considerably. The concentrations of chemicals in soil are given in mass units: parts per million, milligrams per kilogram, or micrograms per kilogram. The units vary somewhat based on the magnitude of the mass of chemical present per unit mass (usually kilograms) of soil. For ex- ample, when dealing with carbon, the concentration is usually given in percent because carbon generally accounts for about 1 to 25% of soil material. On the contrary, when working with nutrient concentrations (e.g., nitrogen, phosphorus, etc.) units of milligrams per kilogram are used. When working with many hazardous wastes, whose concentrations are usually small, we use units of parts per billion or micrograms per kilogram. The movement of ionic nutrients such as nitrate, ammonia, and phosphate is governed by ion-exchange reactions. For example, sodium ions may be attached to the soil surface by elec trostatic interactions. If water containing calcium is passed through the soil, the calcium will be preferentially exchanged for the sodium according to this reaction: By this reaction, two sodium ions are released for every ion of calcium exchanged, thus maintaining the charge balance. Thus, an important characteristic of soil is its exchange capacity. Exchange capacity is, essentially, the extent to which a unit mass of soil can exchange a mass of a certain ion of interest. Exchange capacity (reported in units of equivalents of ions per mass of soil) is an important characteristic of soil in terms of its ability to leach ions such as magnesium, calcium, nitrate, and phosphate. Another important process that occurs in soils is sorption. Sorption is essentially the attachment of a chemical to either the mineral or organic portions of soil particles and includes both adsorption and absorption. Van der Waals forces, hydrogen bonding, or electrostatic interactions can result in the attachment of chemicals to the soil surface. In some cases, covalent bonding can actually result, and the chemical is irreversibly bound to the soil. With low concentrations of pollutants, sorption can be described mathematically by a linear expression. The partition coefficients of various organic pollutants can vary over at least eight orders of magnitude, depending predominately on the chemical characteristics of the pollutant, but also on the nature of the soil itself. With most neutral organic chemicals, sorption occurs predominately on the organic frac tion of the soil itself (as long as the fraction of organic material on the soil is “significant”). In these cases, ATMOSPHERIC CHEMISTRY The atmosphere is a thin envelope of gases that surround the Earth’s surface, held in place by gravity. As one moves higher in elevation, the Earth’s gravitational forces decrease, and the density of these gases also decreases. The composition of air varies with location, altitude, anthropogenic sources (e.g., factories and cars), and natural sources (e.g., dust storms, volcanoes, forest fires). The concentrations of some gases vary less than others. The essentially “nonvariable” gases make up approximately 99% (by volume) of the atmosphere. Of the vari able gases, water vapor, carbon dioxide, and ozone are the most prevalent. Table 2–8 lists these gases and their volume percents. The atmosphere is divided into several layers on the basis of temperature. The layer clos est to the Earth’s surface, the troposphere, extends to approximately 13 km. The temperature in this layer decreases with increasing altitude. It is estimated that 80–85% of the mass of the atmosphere is in the troposphere. The next layer is the stratosphere, which extends to an altitude of approximately 50 km. Within the stratosphere, the temperature increases with increasing altitude until it reaches approximately 0°C at the stratopause (the boundary between the stratosphere and the mesosphere). The temperature increase in the stratosphere is due to the absorption of ultraviolet radiation and the resulting heat given off by the reactions that occur. The troposphere and stratosphere contain approximately 99% of the mass of the atmosphere. In the next layer, the mesosphere, which extends to approximately 80 km, the temperature decreases with increasing altitude until it reaches a temperature of approximately −80°C. The outermost envelope around the Earth is the thermosphere, another region in which the temperature increases with increasing altitude. One of the major differences between aqueous and atmospheric reactions is the importance of gas-phase and photochemical reactions in the latter. One of the most important gas-phase photochemical reactions that occurs in the troposphere is the formation of ozone from the reaction of ultraviolet radiation, hydrocarbons, and nitrogen oxides (NOx). Another critical set of reactions is the absorption of infrared radiation by carbon diox- ide (CO2 ), methane (CH4 ), nitrous oxide (N 2 O), and the fluorinated gases (which include hydrofluorocarbons, perfluorocarbons, sulfur hexafluoride, and nitrogen trifluoride). This latter group of chemicals are sometimes used as alternatives for chemicals that deplete stratospheric ozone. Because of the ability of these gases to absorb infrared radiation and therefore warm the troposphere, they are referred to as greenhouse gases. Of the first three chemicals listed above, carbon dioxide accounts for most of the emissions in the U.S. Because of the different extents to which these chemicals absorb infrared radiation, they are often reported in units of CO 2 - equivalents (which is defined as the ratio of the accumulated radiative forcing within a specific time horizon caused by emitting 1 kilogram of the gas, relative to that of the reference gas CO 2). SOIL CHEMISTRY Soils are porous media formed at the earth's surface by the process of weathering over long periods, contributed to by biological, geological and hydrologic phenomena. Soils differ from rocks in that their build up over time shows layers of different soil types on top of each other, with definite vertical stratification. Soils are considered as multicomponent, open, biogeochemical systems containing solids, liquids and gases. Being open systems, they are subject to fluxes of mass and energy with the atmosphere, biosphere and hydrosphere, and their composition is spatially highly variable and also changes with time (Sposito, 1989). Soils are made up of three phases of solids, liquids and gases (including air and water vapour). The composition of each phase depends on the climate, moisture content, closeness to the surface and a host of other factors. Soils may also be organic or inorganic, but usually a combination of both. Organic soils may contain a vastness of microbial activity. Ten grams of soil may contain a microbial population equal to that of the earth's human population. One kilogram may contain as much as 500 billion bacteria, 10 million actinomycetes and 1 billion fungi, with a length of root system in the first metre for a single plant of up to 600 km. Therefore, because of the different phases in a soil sample, the microbial population, the vast number of elements and of minerals and heterogeneity of structure, soils are a dynamic domain. It is because of these and other phenomena of transport of soils from area to area that the physics and chemistry of soils is undoubtedly most complex, much more so than that of air or water. Microbiology Microbiology is the study of microorganisms – biological entities too small to be seen with the unaided eye. Most major advances in microbiology have occurred within the past 150 years, and several important subdisciplines of microbiology have developed during this time, including microbial ecology, molecular biology, immunology, industrial microbiology and biotechnology. Microorganisms of various types exist in all three domains of life (the Bacteria, Archaea and Eukarya), and they are by far the most abundant life forms on Earth. Microscopic biological agents include bacteria, archaea, protists (protozoa and algae), fungi, parasitic worms (helminths) and viruses. Although a small percentage of microorganisms are harmful to certain plants and animals and may cause serious disease in humans, the vast majority of microorganisms provide beneficial services, such as assisting in water purification and the production of certain foods, and many are essential for the proper functioning of Earth’s ecosystems. BACTERIA AND ARCHAEA Environmental engineering and science would not be the fields we know without bacteria and archaea; in fact the world would be very different without these organisms. The collective mass of all bacteria and archaea exceeds that of all eukaryotes by at least an order of magnitude. More bacteria and archaea can be found living in a spadeful of soil than the total number of people who have ever lived. Activated sludge tanks and trickling filters that clean wastewater (see Chapter 11) would not work without these organisms. The carbon, nitrogen, sulfur, and phosphorus cycles would come to a grinding halt without bacteria and archaea. As such, it is imperative that we dedicate a section of this chapter to these important organisms. Archaea In the traditional five-kingdom classification system, single-celled microorganisms (formally called prokaryotes) are placed in the Monera kingdom. In the three-domain system, these organ- isms are grouped either as Bacteria or Archaea. As mentioned earlier, Archaea are essentially living fossils, formed within a billion years after the Earth was formed. Archaea are not bacteria (hence the name Archaebacteria is no longer used); their genes differ significantly from those of bacteria. However, both Archaea and Bacteria have one major circular chromosome, although both may have smaller rings of DNA called plasmids, which contain only a few genes. The cell membrane of Archaeans are not made of the same lipids as found in other organisms; instead, their membranes are formed from isoprene chains. Archaea are very small, usually less than 1 μm long. Like true bacteria, Archaea come in many shapes. They may be spherical, a form known as coccus, and these may be perfectly round or lobed. Others are rod shaped, known as bacillus, and may be short bar-shaped rods to long and whiplike. Some unusual Archaea are triangular-shaped or even rectangular like a postage stamp. Bacteria Some of the characteristics of bacteria are presented above as these organisms are compared to Archaea. Like Archaea, the three main shapes bacteria take are cocci, bacilli, or spirilli (spiral shaped). Bacteria also grow in distinctive patterns. For those in pairs, the prefix diplo- is used. For example, cocci bacteria that aggregate in pairs are referred to as diplococci. The prefix staphylo- is used for cells that aggregate in clusters resembling bunches of grapes. Those that arrange in a chain are referred to with the prefix strepto-. As mentioned above, most bacteria have a cell wall made of peptidoglycan, which consists of polymers of modified sugars cross-linked with short polypeptides. The polypeptides vary with the species. The cell wall maintains the shape of the cell, protects it from harsh environ- ments, and prevents the cell from bursting in hypotonic solutions. FUNGI The mushrooms you ate for dinner, the persistent mold that grows on your shower curtain, and the yeast that was added to the bread used to make your sandwich are all members of this group. Fungi are saprophytic heterotrophic eukaryotes, feeding by releasing digestive enzymes that break down complex organic chemicals into forms that they can absorb. Fungi play an impor- tant role in recycling nutrients. Most fungi are multicellular, although a few, including yeasts, are unicellular. Some fungi, such as those that cause Dutch elm disease, athlete’s foot, and ringworm, are parasitic. Other fungi live in a symbiotic relationship. For example, some fungi live on plant roots, absorbing inorganic nutrients from the soil and releasing them to the plant roots. The fungus benefits in that it obtains organic nutrients from the plant. Fungi reproduce both sexually and asexually. Fungi are divided into four phyla: Chytridiomycota, Zygomycota, Ascomycota, and Basidiomycota. There is a fifth phyla, Deuteromycota, imperfect fungi, which contains a collection of species that do not fit into the four main phyla. VIRUSES Viruses are not living organisms; they do not have cytoplasm, organelles, or cell membranes. They do not respire or carry out other life processes. So what are they? Viruses are infectious particles consisting of nucleic acid enclosed in a protein coat, called a capsid. The genome of viruses is made up of double-stranded DNA, single- stranded DNA, double-stranded RNA, or single-stranded RNA. Thus, viruses are classified as either DNA viruses or RNA viruses. The smallest virus has only four genes, the largest has several hundred. Protozoa Protozoa, meaning “first animals,” are single-celled, eukaryotic organisms. Most are aerobic chemoheterotrophs that ingest or absorb their food. The 30,000 or so species of protozoa vary greatly in shape, from the microscopic Paramecium to the thumb-sized shell-covered marine forms. Many protozoa, especially those that are parasitic, have complex life cycles. In some cases, the different forms taken during the life cycle have caused biologists to mistakenly be- lieve that the same organism was two or more different species. The protozoa are divided into some 18 phyla, including Zoomastigina, Dinomastigota, Sarcomastigophora, Labyrinthomor- pha, Apicomplexa, Microspora, Ascetospora, Myxozoa, and Ciliophora. Algae Algae are photoautotrophic protists that contain pyrenoids, organelles that synthesize and store starch. Almost all species are aquatic. Algae may be unicellular, colonial, filamentous, or multi- cellular. Algae are classified into six phyla based on the type of chloroplasts and pigments they contain, their color (which is related to their pigments), food storage, and the composition of their cell wall. Environmental applications of microorganisms Microorganisms play critically important roles in the environment. We have already considered the key roles that microbes play in nature’s major nutrient cycles. But in addition to these more or less continuous activities, microorganisms have been exploited for purifying wastewaters and for cleaning pollution in the environment, a process called bioremediation. Sewage and other wastewaters must be treated before they can be released into natural waterways. This is because without treatment, the massive influx of organic matter and mineral nutrients would trigger extensive microbial growth and O2 consumption, causing die-offs of plants and animals and diminishing the aesthetic and recreational value of the water. To deal with the high nutrient load of wastewaters, elaborate treatment facilities are used to stimulate the activities of complex microbial communities to remove as much organic carbon and other polluting nutrients (such as nitrates and phosphates) from the wastewaters as possible. Following treatment, the water can then be safely released into rivers or other bodies of water. To produce potable drinking water, additional treatment is necessary to remove as many potentially pathogenic microorganisms and remaining toxic substances as possible. Drinking water production includes the coagulation and filtration of already high-quality surface or subsurface waters followed by disinfection with chlorine and transport of the water through water mains to the consumer. The entire process of drinking water production must be carefully performed and monitored to prevent breakdowns that can lead to incidents of serious waterborne illness, such as cholera or typhoid fever. When pollution of the environment occurs, either from natural events or from the activities of humans, microorganisms can be harnessed to clean up the mess. Microbial bioremediation is typically the most cost-effective method of removing environmental pollutants and, in many cases, it is the only practical way to accomplish the job. Bioremediation is grounded in the astounding diversity of metabolic reactions capable in the microbial world. Thus, if some pollutant, such as crude oil, is spilled in the environment, oil-consuming microbes applied to the spill site can clean up the mess by oxidising hydrocarbons in the oil to CO2. In a similar manner, microbes that can degrade pesticides, such as insecticides and herbicides, are beneficial in keeping these poisonous substances from accumulating in the environment and damaging plants and animals that were not the original targets of these agents. Although not every substance that humans have created is biodegradable (e.g. teflon is not), the vast majority of pollutants are, and it is through the activities of microorganisms that these undesirable substances are converted into compounds that can enter the natural nutrient cycles. Humans owe a considerable debt to the microbial world for keeping planet Earth habitable and healthy. If cyanobacteria had never become established on Earth, then the oxygen we breathe and depend on would never have been produced. And if it were not for microbes today, the everyday activities of humans would eventually damage the environment beyond its capacity to sustain human life. The microbial world is clearly the foundation of the biosphere, and thus the science of microbiology, which attempts to understand this unusual world, may be our most relevant biological science today. FUNDAMENTALS OF HYDROLOGY The availability of water is critical to maintaining ecosystems, as well as for communities, industry, agriculture, and commercial operations. The presence (or lack) of water at sufficient quantity and quality can significantly affect the sustainability of life. It is therefore important for the engineer and environmental scientist to have a solid understanding of our water supply and its distribution in nature. Hydrology is a multidisciplinary subject that deals with the question of how much water can be expected at any particular time and location. The application of this subject is important to ensuring adequate water for such purposes as drinking, irrigation, and industrial uses, as well as to prevent flooding. Surface water hydrology focuses on the distribution of water on or above the earth’s surface. It encompasses all water in lakes, rivers, and streams, on land and in the air. Groundwater hydrology deals with the distribution of water in the earth’s subsurface geological materials, such as sand, rock, or gravel The Hydrological Cycle The hydrological cycle describes the movement and conservation of water on earth. This cycle includes all of the water present on and in the earth, including salt and fresh water, surface and groundwater, water present in the clouds and that trapped in rocks far below the earth’s surface. Water is transferred to the earth’s atmosphere through two distinct processes: (1) evapora- tion and (2) transpiration. A third process is derived from the two and is called evapotranspi- ration. Evaporation is the conversion of liquid water from lakes, streams, and other bodies of water to water vapor. Transpiration is the process by which water is emitted from plants through the stomata, small openings on the underside of leaves that are connected to the vas- cular tissue. It occurs predominantly at the leaves while the stomata are open for the passage of carbon dioxide and oxygen during photosynthesis. Because it is often difficult to distinguish between true evaporation and transpiration, hydrologists use the term evapotranspiration to describe the combined losses of water due to transpiration and evaporation. WATER BALANCE The water balance or water budget is the accounting of water for a particular catchment, region or even for the earth as a whole. As seen in the preceding sections, the hydrologic cycle considers all the phenomena of water phases in a qualitative description. The water balance is the quantitative account of the hydrologic cycle. The input to the cycle is precipitation, either as rainfall, snow or sleet. The precipitation is distributed as surface runoff, evaporation, infiltration to the unsaturated zone, changing its storage, and deep percolation to the saturated zones. The equation for the water balance, which is the conservation of mass in a lumped or averaged hydrological system on a regional or catchment scale is Equation assumes that there is no 'flow' across catchments. While this is correct for surface water, it is not always possible to verify that there is zero flow in the subsoil regions across catchment boundaries, i.e. no interflow. If Eq. (4.1) is averaged over the hydrologic year (in northern temperate climates this is typically 1 October to 30 September), there may be no significant change in AS or AG. Thus P=R+E and so E=P—R ENERGY BUDGET The energy received at the earth's surface is essentially all solar (shortwave) radiation. Some of this energy is reflected back from the earth's surface to the atmosphere, and some penetrates the earth. The earth also re-radiates some of the solar energy. Like the water budget, the energy balance is the accounting of the distribution of the incoming shortwave solar radiation from space, through the atmosphere and onto the earth's surface of land and ocean. The energy balance also accounts for the outgoing long wave terrestrial radiation from the earth's surface. This distributes to evaporation flux, sensible heat flux and net radiant emission by the surface. What is of most interest to hydrology is the net incoming radiation at the earth's surface and the subsequent partitioning of this energy (measured in watts/m2 ) to evaporation, sensible heat and heat absorbed by the soil. The quantity of radiant energy remaining at the earth's surface is known as the net radiation, Rn, typically in units of watts/m2, and is measured by a simple instrument called a net radiometer. For a simple lumped system, the energy budget is expressed as INFILTRATION Infiltration is the process by which water on the ground surface enters the soil. Infiltration is governed by two forces, gravity, and capillary action. While smaller pores offer greater resistance to gravity, very small pores pull water through capillary action in addition to and even against the force of gravity. Infiltration rate in soil science is a measure of the rate at which a particular soil is able to absorb rainfall or irrigation. It is measured in inches per hour or millimeters per hour. The rate decreases as the soil becomes saturated. If the precipitation rate exceeds the infiltration rate, runoff will usually occur unless there is some physical barrier. It is related to the saturated hydraulic conductivity of the near-surface soil. Evaporation and Evapotranspiration Evaporation (transformation of liquid water to water vapor) and transpiration (water vapor emission from plant surfaces) are outflow processes of water budgets. Evapotranspiration (ET) is the combined process of water surface evaporation, soil moisture evaporation, and plant transpiration. Stormwater management applications may include water surfaces (e.g., pond, wetland, etc.), vegetation, or both, and therefore may require an estimation of evaporation, transpiration, or both to estimate water level changes between storms. For example, a wetland system includes vegetation, open water surfaces, and exposed moist soils. The combined effects of water surface evaporation, soil moisture evaporation, and plant transpiration for this system are often significant components of annual water budgets. Evaporation tends to lower water level in a pond or wetland over time, and evapotranspiration acts to dry out the soil before the next storm. During storms, however, evaporation and evapotransporation are typically not significant compared to precipitation, discharge and infiltration, and are often not considered. Evapotranspiration is a function of meteorological conditions, such as air temperature, wind speed, relative humidity, and solar radiation; and of evaporating/transpiring surface conditions, such as albedo (i.e., fraction of reflected incident sunlight), water temperature, roughness, and water availability. The effective surface conditions of plants are especially complex. Stomata openings in plant leaves are essential for the movement of water vapor and other gases. The number of these openings varies with plant type. The size of these openings varies with changes to the pressure in plant cells resulting from water stress and other factors. Often the complexity of plant canopies is simplified by considering only potential evapotranspiration. Potential ET occurs when the water availability in the soil does not influence ET. Therefore, the complexity associated with water stress is not needed to determine ET. Water stress can be minimized by irrigation systems. Reference plant ET is used to further simplify the determination of ET. (Reference plant ET is the potential ET for a standard reference plant.) The two most widely used reference plants are alfalfa and grass. Reference plant ET allows the impact of meteorological variables to be assessed using relatively constant plant conditions. Complexities related to time-varying vegetal cover and water stress do not need to be considered. The conversion of reference plant ET to potential ET for different plant types is done using plant or crop factors. Hydrologic Instrumentation Hydrological methods and equipment measure the movement of water. These methods are used to paint role of a water body in the bigger picture of an ecosystem or environment. As meandering streams carve new paths, hydrological equipment can be used to determine how much sediment is being moved downriver, or whether a flood event will cause structural damage to a bridge or dam. Hydrology is even used to determine how quickly or how far pollution or invasive species might spread based on flow rates and dye studies. Whether a project consists of level and discharge readings, or studying ocean currents, hydrology is focused on water quantity and movement as whole, rather than the internal properties of a particular body of water. Low Flow Low flow is the "flow of water in a stream during prolonged dry weather," according to the World Meteorological Organization. Many states use design flow statistics such as the 7Q10 (the lowest 7-day average flow that occurs on average once every 10 years) to define low flow for setting permit discharge limits. Urban Hydrology Urban hydrology is a science investigating the hydrological cycle and its change, water regime and quality within the urbanized landscape and zones of its impact. Urban hydrology is a link in a number of sciences dealing with the problems of ecology, environmental protection, conservation and rational use of the water resources of the Earth. The problems of studying the influence of urbanization on the hydrological cycle present an issue of international cooperation of scientists that has been especially fruitful for the last 40 years. Groundwater Groundwater, water that occurs below the surface of Earth, where it occupies all or part of the void spaces in soils or geologic strata. It is also called subsurface water to distinguish it from surface water, which is found in large bodies like the oceans or lakes or which flows overland in streams. Both surface and subsurface water are related through the hydrologic cycle (the continuous circulation of water in the Earth-atmosphere system). Groundwater, water that occurs below the surface of Earth, where it occupies all or part of the void spaces in soils or geologic strata. It is also called subsurface water to distinguish it from surface water, which is found in large bodies like the oceans or lakes or which flows overland in streams. Both surface and subsurface water are related through the hydrologic cycle (the continuous circulation of water in the Earth-atmosphere system). Ground water is water that fills pores and fractures in the ground, much as milk fills the voids within bits of granola in a breakfast bowl (Figure 2). The top of ground water is called the water table. Between the water table and the land surface is the unsaturated zone or vadose zone. In the unsaturated zone, moisture is moving downward to the water table to recharge the ground water. The water table can be very close to the surface (within a few feet), or very deep (up to several hundred feet). In most California regions, the water table is between 10 and 100 feet below the land surface (in some Southern California desert basins it is as deep as 300 feet) PROGRESS CHECK REFER TO INSTRUCTOR REFERENCES: Textbook/s: Mackenzie L. Davis Susan J. Masten., (2002), Principles of Environmental Engineering and Sciences J. Glynn Henry, Gary W. Heinke, Environmental Science and Engineering 2 nd Edition Terence J. McGhee, Water Supply and Sewage 6 th Edition Clair N. Sawyer, Perry L. McCarthy, Gene, F. Parkin, Chemistry for Environmental Engineering 4th Edition.