Chapter 6 : The Ecological Importance of Microbes Microorganisms are found everywhere on earth. The adult human body, for example, contains 3 pounds or more of microbial biomass. The discovery of environmental microorganisms that invade the human body resulted in the development of the field of environmental microbiology. Environmental microbiology can be defined as the study of microorganisms with in all ecosystems and their beneficial or detrimental effects on human welfare, and is more of an applied field of microbiology. The field of environmental microbiology is different from, however related, microbial ecology which involves the interactions between microorganisms and other organisms in the air, soil, or water. In this chapter we will explore how humans rely on microorganisms for life, as we know it, to exist. Microorganisms play the majority role in biogeochemical cycles that occur on earth. Imagine the earth as having a living skin, the soil is a thin layer of organic and inorganic material that covers a large portion of earth. The soil is crucial for human life and can contain billions of microorganisms in a very small amount of material. In this medium is where many of the biogeochemical cycles take place. Cycles such as the carbon, nitrogen, phosphorus, and sulfur cycles are microbial driven and occur in the soil and water. As you have learned these elements are required for life, as they are found in the macromolecules in cells. Since, the goal of all organisms is to pass on genetic material, organisms must acquire or make nutrients in order to reproduce. The Carbon Cycle Carbon is the fundamental element for life, this element is found in all organic molecules in the body. Primitive earth (before life evolved) did not have much if any carbon available in a fixed form to sustain life. The majority of carbon was found as inorganic carbon dioxide in the atmosphere. How do we go from an earth filled with inorganic carbon to one rich in organic carbon? The answer to that is microorganisms, early microbes began removing carbon dioxide from the atmosphere through a carbon fixation process called photosynthesis. Cyanobacteria, a photosynthetic bacteria, and algae, a photosynthetic eukaryote, along with plants (which have symbiotic cyanobacteria in the cells that do the photosynthesis) begin the carbon cycle and are considered primary producers. You will see that every human depends on the primary producers for life to exist. Primary producers are also called autotrophs, which basically means to make their own food. Autotrophic organisms covert carbon dioxide into organic molecules through photosynthesis, these organic molecules are used for building cell components such as cell walls. In fact what many people do not realize is that the material you observe in a plant is largely carbon based and was once carbon dioxide in the atmosphere. When you burn a plant or other carbon based material, by- products of combustion include carbon dioxide and therefore you are in a sense completing the carbon cycle. There are other types of autotrophy, however, we will focus on photosynthesis as our primary example in this textbook. As a result of carbon fixation through
photosynthesis the organism releases oxygen as a product, which we and other aerobic respiring organisms rely on for life. In fact the majority of oxygen we use was produced by cyanobacteria beginning approximately 2.5-3 billion years ago when they first evolved. For about 200 million years these cyanobacteria produced oxygen, which was quickly captured by dissolved iron. Evidence of this resulted in banded iron formations (BIFs) in fossilized sediments. Image ID: 137487155 Figure 8.1. Fossilized banded iron formation. During that 200 million year time period the earth remained largely anaerobic. Following the period, oxygen began accumulating in the atmosphere changing earth forever; it is thought huge populations of anaerobic bacteria went extinct at this time. As you can see we rely on autotrophs for oxygen, however, humans rely on autotrophic plants as well. Even if you are a strict meat eater, that cow that you eat will eat plants, which fix carbon from the atmosphere. The so called meat eater is considered to be a consumer. Consumers or heterotrophs rely on the activities of autotrophs and utilize the organic materials produced by the autotroph for growth. The organic carbon we consume is incorporated into our cells and will largely remain with us until we die (we really are what we eat!). If you think about it the carbon in our bodies has been through countless organisms throughout the evolution of earth. As a result of consumption by the consumers we release carbon dioxide as a by- product of metabolism, we just completed another carbon cycle! When an organism does indeed perish a decomposition process takes place (this does not happen on its own) but microorganisms are involved. Fungi and bacteria are largely considered decomposers, which digest and utilize the carbon from the remains of primary producers and consumers. As a result of decomposition bacteria and fungi release carbon dioxide as a product (figure 8.2). By now you should have a better appreciation for microorganisms and other autotrophs as they set the stage for human existence. Consider the earth without decomposers, how would the world look? Image ID: 151017485 Figure 8.2. The carbon cycle. Nitrogen Cycle Nitrogen is an important element for all organisms, nitrogen makes up approximately 14% of the dry weight of a cell and is found in amino acids which make up proteins and nucleic acids which make up a cells DNA and RNA. Nitrogen is said to be a growth- limiting nutrient if a cell does not have nitrogen available then the cell cannot grow. The majority of nitrogen on earth is found in the atmosphere as a gas, roughly 78% of atmospheric gases. Nitrogen gas (N2) is not a usable form for organisms to incorporate into their cells.
Nitrogen Fixation Nitrogen is made available to organisms through lightning strikes, which causes nitrogen gas and water (H2O) to react to form ammonia (NH3) and nitrates (NO3). Precipitation would then carry these molecules to the ground, which organisms can then utilize. This process of nitrogen fixation through lightning strikes only makes up a small amount of available nitrogen on earth. Prokaryotic microbes called diazotrophs complete the majority of nitrogen gas fixation. Diazotrophs can be found free living in the soil, in the water (cyanobacteria), or with a symbiotic relationship with certain plants. Plants such as legumes that include beans, alfalfa, and peas have nodules in their root system that house diazotrophs for nitrogen fixation. Nitrogen fixation is a very energy intensive process performed by a special enzyme called nitrogenase, this enzyme converts N2 gas into ammonia NH3 and requires approximately 16 molecules of ATP for every 1 molecule of nitrogen that is fixed from the atmosphere. The free- living diazotrophs were extremely important for the evolution of all life forms. If it were not for these nitrogen- fixing organisms the amount of nitrogen available would not support life, as we know it (figure 8.3). Ammonification Not all microbes are capable of fixing nitrogen from the atmosphere the majority of microbes obtain their nitrogen from a decomposition process called ammonification. Ammonification is the process of decomposing organic nitrogen (usually amino acids) to obtain nitrogen. The proteins of dead organisms are degraded to remove the amine group from the amino acid creating ammonia. In moist environments ammonia is converted to ammonium (NH4+), both ammonia and ammonium are available forms of nitrogen for organisms to utilize. Have you ever wondered why your cat litter box smells like ammonia or perhaps your chicken coop? The ammonia smell is from bacteria decomposing proteins in the animal waste. Nitrification Nitrification occurs when bacteria called nitrifiers oxidize ammonium (NH4+) to form nitrite (NO2- ) and ultimately form Nitrate (NO3- ). Nitrate is an available source of nitrogen used by plants for growth. Take a look at a bag of fertilizer and usually you will see nitrogen in the form of potassium nitrate or ammonium nitrate, which you add to your garden to support plant growth. Industrial processes are capable of fixing nitrogen into forms plants can utilize, before modern fertilizers farmers relied (and still do) on bacterial processes to support plant growth. You might already see a cycle developing, nitrogen gas was in the atmosphere, then fixed into a form available to a microbe, microbes degrade proteins from dead organisms, nitrifiers convert ammonium to nitrate. Denitrification The nitrogen cycle is completed when available nitrogen is returned to a gas. This is completed through an anaerobic process when nitrate is used as a terminal electron acceptor. Denitrifiers convert Nitrate (NO3- ) to Nitrite (NO2- ), some organisms such
as those from the genus Pseudomonas can then convert nitrite to nitrogen gas, therefore completing the nitrogen cycle. These processes largely take place in the soil, now imagine you fertilize your lawn with a nitrogen rich fertilizer, the grass will surely absorb some of the nitrogen. However, a large amount of the fertilizer is utilized by bacteria and converted back to nitrogen gas. Now imagine if you bag your lawn clippings and have a truck pick up your yard waste as many cities do, that money you spent to fertilize your lawn is now being carted away to a dump that turns that into compost. What microbial processes would occur in your soil if you mulched your lawn clippings? Would you need to fertilize very often? mage ID: 151017518 Figure 8.3. The Nitrogen cycle. Applied Environmental Microbiology Understanding bacterial growth requirements and microbial adaptation has allowed scientists to use microbes for beneficial processes. One field that has emerged using microbes for beneficial purposes is the field of bioremediation, which uses microbes to degrade or de- toxify harmful pollutants. The pollutants can be introduced to the environment by accident (oil spill), on purpose (insecticides), or by convenience of disposal. Certain man made (synthetic) compounds are similar to what is found naturally in the environment and can be easily degraded since organisms in the environment have enzymes capable of recognizing the compound. Other synthetic compounds such as certain herbicides are referred to as xenobiotics, which is a term used for compounds that persist in the environment for a long period of time (Figure). Xenobiotics persist in the environment since microorganisms do not recognize the synthetic compound as food, therefore they do not have enzymes that will degrade the compound.
Figure 8.4. 2,4- D and 2,4,5- T are both herbicides, 2,4- D is readily broken down in the environment. 2,4,5- T is considered a xenobiotic since it will persist over time in the environment. (Image made by author) The most known application is using microbes to clean up oil spills. Since oil is a hydrocarbon and microbes need carbon for growth we can stimulate microbes to eat the oil by adding nutrients to a contaminated site, referred to as biostimulation. The nutrients added would be the growth limiting element nitrogen (no nitrogen=no growth) and other elements such as potassium and phosphorus, therefore natural bioremediation is basically applying fertilizer to a contaminated area (Figure). Other types of bioremediation involve the addition of microbes not normally present in a population, this type of remediation is referred to as bioaugmentation.
Figure 8.5: Bioremediation of a contaminated shoreline following the Exxon Valdez oil spill. This is an example of biostimulation, by the addition of nutrients the amount of oil degraded is easily observed. (Image from Microbiology: A human perspective 6 th edition, Nester et.al. Chapter31 Figure 31.11 page 750 Waste Water Treatment Townships with large enough populations rely on underground sewer systems to flow waste water from the home to a treatment facility. Rainwater and snow melt will also make its way to the same treatment plant. The plant will remove most of the pollutants and microbes and release the treated water back into the environment. However, some pollutants can be released in very low concentrations such as prescription medications. Occasionally there are lapses in the removal of harmful microbes such was the case in Milwaukee, WI in 1993, 400,000 people were infected with an intestinal parasite Cryptosporidium parvum which causes watery diarrhea. Diarrhea caused by this parasite can result in the loss of 10-15 liters of fluid a day! The wastewater at the treatment facility is collected in large underground wells. The remaining steps are outlined below: Primary Treatment: a process to physically remove large waste materials that will settle out of the water.
The water is pumped from the wells to the treatment facility where it is sprayed with aluminum sulfate or ferric chloride, which are coagulants. The coagulants help remove phosphorus from the wastewater for removal. Upon entry into the treatment facility the liquid is screened to remove large solid material. Large skimmers remove scum and floating waste that was not removed by the screens. The remaining solids are allowed to settle out of solution forming sludge and are removed from the water and flows to the secondary treatment tanks. Secondary Treatment: There are 4 different methods that can be utilized and all of them are biological processes used to convert the solids suspended in sewage into inorganic compounds. Microbial growth is encouraged, allowing aerobes to degrade organic compounds to carbon dioxide and water. Toxic or hazardous materials can drastically affect this process. Activated sludge treatment: Large numbers of microbes are inoculated into the wastewater from previous sludge treatment applications. The sludge is aerated delivering large amounts of oxygen to stimulate aerobic growth. Following aeration the suspended particles are allowed to settle where it is then removed. Water is then disinfected by chlorine, UV light, or Ozone and released into a nearby river or lake. Trickling Filtration: Used at small treatment facilities. A large rotating arm will spray sewage over a bed of gravel and rocks or plastic. The surfaces develop biofilms that degrade organic materials Filtered water is sent to a sedimentation tank to remove sludge. Water is then disinfected by chlorine, UV light, or Ozone and released into a nearby river or lake. Lagoons: Contaminated wastewater is deposited into shallow ponds or lagoons. Water remains for several days. Cyanobacteria and Algae grow and provide oxygen for aerobic bacteria to degrade the sewage. Water is then disinfected by chlorine, UV light, or Ozone and released into a nearby river or lake. Artificial Wetlands: Same principle as lagoons with more advanced designs providing habitat for birds and other wildlife while treating sewage. Water is then disinfected by chlorine, UV light, or Ozone and released into a nearby river or lake.
Advanced Treatment: Involves the removal of ammonia, nitrates, and phosphates. All three chemicals can stimulate the growth of algae and cyanobacteria leading to large masses of surface scum. Figure 8.6. Basic schematic of sewage treatment. Kendal Hunt Image Microbial Ecology 19.15. Municipal Drinking Water Treatment Water is pumped into large reservoirs and solids are allowed to settle. Water is filtered through a thick bed of gravel. This removes many microorganisms such as protozoa and bacteria. Additional filtration through activated charcoal will remove organic chemicals. These chemicals may be harmful or give the water a bad taste. Microorganism form biofilms on the filter materials and remove carbon and nitrogen from the flowing water. Lastly the water will be treated with disinfectants such as chlorine, UV light, or ozone to kill remaining harmful microbes. The treated water makes its way to your home.
Treatment of Solid Wastes The sludge mentioned during the treatment of wastewater is largely sent to landfills where it is buried along with other household and industrial waste. Landfills pose a large problem: run off of rain water can contaminate ground water, take up large amounts of space, pollute the nearby air with methane and other noxious smells, and decrease property values to name a few. One way to combat growing landfills is by composting. Composting is a natural decomposition process that takes household food waste and turns it into a natural fertilizer. Microbial metabolism inside of the piled waste creates heat. Temperatures will reach upwards of 60 degrees Celsius and pathogens are killed. Thermophilic bacteria will not be harmed and will continue to decompose the organic waste. If the pile is frequently aerated by mixing the pile, the compost can be complete in about 6-7 weeks. http://www.shutterstock.com/pic- 160161059/stock- photo- compost- with- composted- earth.html?src=cq0gszr2rcltdgdj- A6_Nw- 1-1