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 6th 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.
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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-withcomposted-earth.html?src=cq0Gszr2RclTDGDJ-A6_Nw-1-1