Environmental Pollution Control Microbiology - Chapter 7 pdf

The solid particles form layers or clumps with open void spaces between the different soil particles.. The water that cannot enter the soil void spaces moves across the soil surface by g

Chapter 7

SOIL MICROBES

Soil is an interesting medium for growing microorganisms It contains various nutrients that the microbes need for their metabolism Unfortunately, the nutrients

are not always readily available Soil is not a homogeneous material, but rather is a heterogeneous material Soil consists of ground rock particles, clay particles, and

silt particles in various combinations and with varying amounts of water The solid particles form layers or clumps with open void spaces between the different soil particles Microorganisms cannot penetrate the solid soil particles They can live on the surface of the particles, provided there are adequate nutrients and water for their growth Organic matter discharged from living organisms on the soil surface provides the major nutrients for the microorganisms in the soil The upper layer of soil provides the best environment for growing microorganisms Bacteria, fungi, actinomycetes, algae, protozoa and nematodes can be found in organic rich soil The soil environment determines the specific microbes that can grow and their numbers The seasons of the year produce the most important environmental variables with both temperature and moisture changes

SOIL CHARACTERISTICS

Engineering courses dealing with soils are concerned more with the physical characteristics of soils than with their chemical characteristics Both the physical and the chemical characteristics of soil are important in developing a proper understanding of soil microbiology Natural forces such as wind, rain, freezing, thawing and pressure help form soil Rocks are slowly broken into small particles,

50 n to 1 mm, known as sand As the particles decrease in size to between 2 ^ and

50 u, they are called silt Particles less than 2 (j in size are known as clay All of these particles are essentially quartz, SiO2, with various chemical contaminants The primary chemical contaminants include iron, aluminum, calcium, magnesium, potassium and sodium Since potassium and sodium are monovalent cations that are more soluble than the divalent calcium and magnesium cations or the trivalent iron and aluminum cations, soil particles contain lower sodium and potassium concentrations than the other cations

As soil particles decrease in size, they are more chemically reactive The three common clays: kaolinite, montmorillonite and illite have layers of silica joined by aluminum, iron, magnesium and potassium and their hydroxides Kaolinite clays consist of layers of silica and aluminum hydroxide Montmorillonite has water layers between sheets of aluminum hydroxide and silica Loss of the water during dry weather causes the montmorillonite to shrink When wetted with water, the dehydrated montmorillonite expands Illite has potassium ions binding the layers of silica The clays can change properties by ionic displacement of the active cations Other soil particles include mica (a potassium oxide-aluminum oxide-silicate combination), calcite (calcium carbonate crystals), gypsum (calcium sulfate) and hematite (ferrous oxide)

Organic matter also contributes to the structure of soil Organic matter deposited on the soil surface undergoes biological decomposition by various groups of microorganisms, eventually forming humus Humus is complex organic material that is relatively stable, accumulating in the upper layer of soil particles Humus is dark brown in color and consists of polymers of benzene and oxygen in ether linkages Humus has carboxyl radicals that allow it to react as an organic acid The polymers in humus also have some nitrogen links The various hydrophilic groups allow humus to attract and hold moisture Humus gives soil some of its structural properties and is important in the cultivation of plants Overall, soil is a mixture of relatively inert, inorganic particles and organic humus

The upper layers of soil contain about 50% solid matter and 50% void space The solid soil particles provide the structure for soil As forces are applied to the soil surface, the forces are distributed through the solid particles to keep the soil structure from collapsing Application of concentrated forces on the soil surface causes the soil to compact with a reduction in void space Moving down through the soil, larger particles are encountered Eventually, solid rock is reached There are many places in the world where solid rock is at the ground surface and there is

no normal soil Over time, the environment is continuously wearing down the solid rock and producing smaller particles that eventually become soil

Precipitation is one of the main forces helping to create and change soil Rainfall is the most common form of precipitation Snow, sleet and hail are different forms of precipitation Precipitation varies widely across the world's landmasses both as to time and intensity Precipitation determines which areas of the world can sustain life and which areas cannot

The hydrologic cycle determines how water moves through the environment Energy from the sun evaporates large quantities of water from the oceans As the water vapor rises in the atmosphere, it cools and condenses into clouds Atmospheric pressure differences create winds that move the clouds over land masses When the clouds move into colder temperatures, the moisture condenses into rain droplets and falls to the ground Some areas receive considerable rain on

an annual basis and produce large quantities of plants that can be used as a source

of food Other areas do not receive significant precipitation, creating desert areas with little vegetation Desert areas cannot support much life unless water is imported from the wet areas Figure 7-1 illustrates the various aspects of the hydrologic cycle

EVAPORATION CONDENSATION PRECIPITATION

Figure 7-1 SCHEMATIC DIAGRAM OF THE HYDROLOGIC CYCLE

In regions near the north and south poles the seasons vary widely over the course of

a year During the winter period, temperatures drop and precipitation occurs as snow, sleet or hail If the ground surface has sufficient heat, the frozen precipitation melts and acts the same as rain If the ground surface temperature is

below freezing, the precipitation remains frozen and accumulates on the ground surface until the temperature rises above freezing Except in areas very close to the north and south poles, the accumulated frozen precipitation melts and becomes fluid, the same as rain

When precipitation is formed, the water droplets come into contact with the various gases and particulates in the atmosphere The water absorbs some of the gases and collects the particulates, cleansing the air of contaminants These contaminants move with the water and react with the particles in the soil as well as with the plants growing in the soil The initial precipitation is more contaminated than the later precipitation that falls in air already cleansed of contaminants Precipitation is nature's way of cleaning the air The lack of alkalinity in pure precipitation allows the absorbed carbon dioxide from the atmosphere to produce carbonic acid and depress its pH Industrial discharges of nitrous oxides and sulfur dioxide into the atmosphere can cause the pH of precipitation to become quite acidic Collection of alkaline soil particles in precipitation causes the pH to increase Chemical analyses

of precipitation can provide considerable data as to its contact with industrial pollution and natural contaminants Once precipitation reaches the soil surface, it collects varying quantities of contaminants, depending on the soil characteristics Precipitation that reaches the ground surface is partially evaporated by the heat of the sun, returning back to the atmosphere as water vapor Part of the precipitation runs into the soil void spaces Gravity pulls the water down through the interconnecting void spaces in the soil Plants, growing on the surface of the soil remove some of the water as it moves past their root structures Plants obtain many

of their nutrients from the water in the soil As the water moves through the plants,

it carries nutrients to the various cells The water taken up by the plants is returned

to the atmosphere by transpiration from the plant leaves The water that cannot enter the soil void spaces moves across the soil surface by gravity to rivers and lakes If the velocity of water flow is very high, the water can pickup soil particles and move them into the rivers and lakes Soil movement by rapid surface runoff results in erosion of the soil and loss of plant nutrients By modifying the soil surface to reduce the velocity of surface runoff, loss of soil can be prevented This

is the basis of most agriculture soil conservation programs

As rain begins, water runs into the void spaces and fills the voids Continued rain

results in most of the water running off over the soil as surface water When the

rain stops, the water drains out of the void spaces into the lower soil layers The soil particles remain coated with water as a result of surface tension forces This attached water determines the moisture content of the soil and reduces the void space available for air As the sun heats the soil surface, the attached water is slowly evaporated, increasing the void space and reducing the soil moisture

content Since the sun's heat cannot penetrate very deep, the lower soil layers retain moisture for a longer period of time than the upper layers of the soil The soil with

attached water and air void spaces is considered unsaturated, as far as water is

concerned The water moves downward by gravity until it reaches an impervious layer that prevents it from moving deeper The water builds up over the impervious

layer, creating a saturated water zone The increasing water level above the

impervious layer creates a pressure that causes the water to move along the path of least resistance Accumulation of a large layer of water over the impervious layer

results in an aquifer that can be used as a source of groundwater Groundwater can

be tapped by placing a well into the saturated water zone and pumping the water to the land surface where it can be used The key to successful use of groundwater is having greater recharge than pumpage A porous media structure is required for the water to move easily as the hydraulic gradient is created Dense soil particles create resistance to the flow of water through the aquifer, limiting their value as water supplies except for individual homes

Some aquifers are located between two impervious layers The recharge area is located at the soil surface in a coarse media that eventually becomes sandwiched between two impervious layers The water pressure in the aquifer can increase with the slope of the terrain Drilling a well into the subsurface aquifer allows the water

to rise in the well pipe in proportion to the water pressure and the resistance of the water pipe When the water pressure is sufficient, the water may actually flow out the top of the pipe without being pumped In other cases the water may rise up into the pipe, requiring only a little energy to pump the water to the surface These

pressurized aquifers are called artesian aquifers Excessive removal of water from

an artesian aquifer will result in loss of pressure, requiring more work to pump the water to the ground surface

Aquifers have gravel and rock media to minimize the resistance to water flow, hi areas with large limestone deposits the water moves through fractures in the limestone Carbon dioxide in the water can react with the limestone to produce soluble calcium bicarbonate Over time the loss of calcium carbonate from the limestone leaves an ever-increasing hole Many large caverns have been formed in limestone regions as a result of water slowly dissolving the limestone Clay soils do not make good aquifers, as the particles are too small for rapid water movement Many clay soils swell when wetted, reducing the void spaces between particles Clay soils can create impervious layers that prevent the passage of water The groundwater will move across the clay surface until it reaches the end of the clay deposit and moves downward again In some aquifers the water is trapped in small pockets Recharging aquifers is essential for continued use of groundwater as water supplies

Groundwater continues to move slowly until it comes to the soil surface and becomes surface water or it reaches the ocean under the surface The point where

the groundwater comes to the soil surface is called a spring Springs can be classified as continuous or intermittent, depending on the flow characteristics.

Spring water quickly becomes surface water Surface waters that collect in streams and rivers move more rapidly than groundwater, as it flows back to the ocean The large volumes of water that are continuously recycled through the environment have created many major rivers that drain large land masses The major rivers form inland waterways that stimulate economic development to sustain the areas through which they flow These waterways are used for water supplies as well as for waste disposal They are used for transportation and recreation Agriculture and industries find the major rivers very attractive It is not surprising that these rivers carry large amounts of the suspended soil and dissolved chemicals from the drainage basins into the oceans The heavy silt particles settle out, creating deltas as they enter the oceans and slow their velocity The dissolved chemicals accumulate and became part of the ocean salts With continuous evaporation of water from the oceans, the soluble salts slowly increase their concentrations

MICROORGANISMS

Moisture, nutrients and particulate surfaces are essential for the growth of microorganisms in the soil The gaseous atmosphere in the void spaces is also important in microbial growth The majority of microorganisms in soil are aerobic, requiring unsaturated conditions Only anaerobic organisms grow in soils saturated with water

BACTERIA

The wide diversity of metabolism, together with the small size of bacteria permits them to grow in soils that contain significant amounts of nutrients The surface of the soil screens out most particulates, allowing only small colloidal particles and soluble nutrients to pass with the water into the soil voids Plowing the soil surface can mix large organic particles into the soil and create an environment for microbial growth to the depth of the plow Plant roots penetrate the soil, seeking water and nutrients for growth These plant roots provide additional surfaces for microbial attachment and subsurface organics for growth Because the environment changes rather drastically in the soil, sporeforming bacteria tend to be most common When environmental conditions become too difficult for normal growth, the bacteria form spores and remain dormant until the environment returns to proper conditions for normal growth The diversity of nutrients found in the soil stimulates bacteria that can completely metabolize the organics to carbon dioxide,

water and cell mass under aerobic conditions Alexander found Pseudomonas, Bacillus, Arthrobacter, Clostridium, Achromobacler, Micrococcus and Flavobacterium as the most common bacteria in organic soils Nitrifying bacteria

are also widely distributed in soils since the decomposition of proteins releases

ammonia nitrogen, providing the Nitroso- bacteria with food for their metabolism Conversion of ammonia nitrogen to nitrite nitrogen provides nutrients for the

Nitro-bacteria, allowing them to oxidize the nitrite nitrogen to nitrate nitrogen The production of nitrous acid assists in the dissolving of minerals in the soil If the nitrous acid is not neutralized, the low pH will limit further bacteria metabolism, preventing oxidation of the nitrite ions to nitrate ions Other inorganic metabolizing

bacteria include the sulfur oxidizing bacteria, Thiobacillus, and several different

iron oxidizing bacteria The sulfur oxidizing bacteria generate sulfuric acid that also dissolves minerals in the soil The normal organic metabolizing bacteria and the nitrifying bacteria do not compete for nutrients, but do compete for oxygen Many of the soil bacteria are facultative with the ability to shift from aerobic metabolism to anaerobic metabolism as the dissolved oxygen is depleted

The air in the void spaces in the unsaturated zone contains a finite amount of oxygen This oxygen is in equilibrium with the dissolved oxygen in the water layer attached to the surface of the soil particles As the bacteria metabolize the organic matter in the soil, the dissolved oxygen in the water is reduced and more oxygen is transferred from the void space into the water Over time the oxygen in the air is reduced, slowing the rate of oxygen transfer into the water Near the ground surface the void spaces are in direct contact with atmospheric air that can continuously replenish the oxygen as fast as it is used Thus, the bacteria near the ground surface are always metabolizing aerobically, unless they are saturated with water Moving deeper into the soil, gas exchange with the atmosphere becomes more difficult Depletion of the oxygen results in a pressure decrease; but the production of carbon dioxide results in a pressure increase The net effect is dependent on the reaction of the carbon dioxide with minerals in the soil When the carbon dioxide reacts with soil minerals, very little carbon dioxide will be released as a gas to replace the oxygen that was used With a pressure differential in the void space, gas will move

to produce equal pressure Without a chemical reaction between the carbon dioxide and minerals in the soil, the carbon dioxide will be released as a gas into the void space In this case, there will be no significant pressure difference to cause the gases to flow in any direction Molecular forces will cause the gases to move at a very slow rate, not allowing the void spaces at the lower levels to maintain aerobic conditions Water movement through the void spaces is the primary mechanism for renewing the oxygen in the void spaces As the water enters the voids and fills the voids, the gases are compressed and form bubbles that are carried downward until they reach pressure equilibrium As the rain slows and the water pressure decreases, the bubbles may move upward towards the soil surface Eventually, the

bubbles rise to the soil surface Atmospheric air moves into the new void spaces at the surface, replenishing the oxygen

Carbon dioxide produced by aerobic metabolism is more soluble in water than oxygen Once the water attached to soil is saturated with carbon dioxide, the excess carbon dioxide is discharged into the void spaces Carbon dioxide in water forms carbonic acid that reacts with minerals in the soil to form bicarbonate salts Carbonic acid reacts with insoluble calcite particles to form calcium bicarbonate that is soluble and moves with the successive flow of water past this area of soil The insoluble calcite crystals in the soil will slowly disappear over time, leaving larger void spaces Water moving through the soil is now more mineralized

Having picked up calcium ions, the water is considered to be harder than it was

before the calcium ions were solubilized Ammonia nitrogen reacts very readily with carbonic acid, forming ammonium bicarbonate Magnesium and iron also react to form soluble bicarbonate salts Thus, microbial metabolism in the soil affects the mineral quality of the groundwater that is produced by successive infiltration of precipitation The geology of the rocks in any given area determines the potential for minerals to be dissolved by the groundwater Fortunately, the dissolution of minerals is slow and passes without much notice except for the minerals appearing in the groundwater

Bacteria metabolism results in the production of new cell mass in proportion to the organic matter metabolized The new bacteria are retained in the water layers attached to the surface of soil particles Surface tension forces hold the water layers

on the surface of the soil particles As the bacteria age and lose motiliry, they use their pili to become attached to the soil particle surfaces Over time, microbial growth may completely cover the soil particle The force of water moving through the void space may force some of the dispersed bacteria deeper into the soil environment Unfortunately, the deeper environment is not as suitable for sustaining biological life as the upper environment The bacteria die off and become part of the humus material in soil It takes a long time for the humus material to accumulate in the deeper layers Humus materials form more rapidly at the soil surface because of the greater amounts of available organics and more rapid metabolism The bacteria continue to grow as long as the environment permits Unfortunately, the bacteria located next to the soil particle surface cannot obtain sufficient nutrients and shift entirely to endogenous respiration as other bacteria grow over them Slowly, the bacteria die and become part of the inert organics in the soil, helping to retain water and hold the particles together If the bacteria are unable to find suitable electron acceptors for endogenous respiration, they simple remain in an inert state until a suitable electron acceptor becomes available

Nitrogen fixing bacteria are one of the more interesting groups of bacteria found in soil These bacteria have the ability to take nitrogen gas from the atmosphere and fix it into ammonia nitrogen in their cell proteins Unfortunately, nitrogen fixation requires considerable energy and occurs only when ammonia, nitrite, or nitrate

nitrogen is not available in the soil Rhizobium is a symbiotic bacteria that fixes atmospheric nitrogen when grown in conjunction with legumes Rhizobium forms

nodules on the root structure of the legumes Air in the soil around the roots supplies the nitrogen gas for the bacteria; while the legume supplies carbohydrate

energy for the bacteria When the Rhizobium cells die and undergo lysis, ammonia

nitrogen is released and made available to the legumes for their growth At the end

of growing season, the legumes are plowed into the soil where they are decomposed by bacteria and fungi The protein nitrogen from the legumes is released as ammonia nitrogen for use by crops the next growing season The use of legumes is an important method for replenishing nitrogen removed by other crops

Clostridium and Azotobacter are two free-living, nitrogen-fixing bacteria that are found in the soil Clostridium are anaerobic bacteria that fix atmospheric gas in the absence of dissolved oxygen Azotobacter are aerobic bacteria that can fix

atmospheric nitrogen in the presence of adequate dissolved oxygen Nitrogen fixing bacteria are very important microorganisms in nitrogen deficient soils

Water saturated soil cannot obtain much oxygen from the atmosphere and quickly becomes anaerobic Swamps tend to be formed when the soil is continuously saturated Facultative bacteria will be readily found in saturated soils, but their metabolism will be slow under anaerobic conditions Strict anaerobic bacteria will grow over time If the environment is satisfactory, sulfate-reducing bacteria will produce sufficient hydrogen sulfide to reduce the O-R-P of the soil to a point where the methane-producing bacteria can grow The methane produced under these

conditions has been called swamp gas Anaerobic environments tend to make many

heavy metals soluble as salts of organic acids On the other hand, the hydrogen sulfide produced by sulfate reducing bacteria can convert the soluble heavy metal salts to insoluble metal sulfides and prevent their movement in the water It is not surprising that many heavy metals are found in soil as insoluble sulfide salts The solubilities of the metallic sulfide salts range from 10~16 for MnS to 10~53 for HgS Data on the numbers of active bacteria in soil are highly variable and should be used with care So many environmental factors enter into the bacteria counts that the data have little validity on a quantitative basis Part of the problem is many bacteria in soil form spores that allow the bacteria to survive until placed into a good nutrient environment The various plating media do not distinguish between spores and vegetative cells Direct microscopic counts using fluorescent dyes have been the developed to measure vegetative cells; but many of the fluorescent dyes are not as specific in the soil environment as in the laboratory environment where

they were first developed One can find bacteria populations from 103/g soil to

109/g, if the data of Martin and Focht are valid Chapelle found data that indicated that direct counts gave the highest numbers and that the counts of active bacteria varied with the media used to cultivate the bacteria Since the soil environment is not uniform like water, adjacent samples from the same soil will not have the same number of living cells Care should be used with the collection of single samples as well as with the cultivation media Valid data can only be obtained with large numbers of samples, grown on various media and analyzed statistically These reasons help explain why soil bacteriology remains an uncharted area of microbiology

FUNGI

The fungi find the upper layers of soil conducive for growth As strict aerobes, the fungi are only able to grow when there is adequate oxygen in the water Fungi are not good at competing with bacteria for nutrients Under the right conditions they are able to compete quite well If the pH of soil is acidic, fungi have an advantage over bacteria If the soil is low in nitrogen, fungi are able to produce more protoplasm than bacteria on the limited nitrogen Fungi can also grow under less moist conditions than bacteria Fungi reproduce by spore formation, making it much easier to distribute cell material for future growth than the simple binary fission of bacteria The large number of spores permits the fungi to grow better than bacteria when soil samples are placed into nutrient media Fungi will overgrow bacteria in most laboratory media Fungi mycelium will quickly cover the media surface exposed to air In soil the fungi filaments grow over the soil particle surface and help to hold soil particles together

The large quantity of plant residues deposited on the soil surface provides the nutrients needed by certain species of fungi Lignin is a complex aromatic polymer that combines with cellulose in higher plant tissue to protect the plant tissue from premature biodegradation A number of fungi have the ability to metabolize the lignin and the cellulose in dead plant tissue, returning these materials back into the

environment as basic components The white-rot fungi, Phanerochaete chrysoporium, are common fungi capable of metabolizing both lignin and cellulose Most of the soil fungi belong to the Fungi imperfecti, a large group of

diverse fungi whose complete life cycle has not been sufficiently observed to permit proper classification Yeasts are a special group of fungi that will also be found in soils Martin and Focht, as well as Ehrlich, indicated that the number of fungi cells range from 103/g soil to 106/g soil There is no doubt that fungi are important to the overall soil microbiology