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Kenneth Todar, PhD
Beneficial Effects of Microorganisms
Microbes are everywhere in the biosphere, and their presence invariably affects the environment that
they are growing in. The effects of microorganisms on their environment can be beneficial or harmful
or inapparent with regard to human measure or observation. Since a good part of this text concerns
harmful activities of microbes (i.e., agents of disease) this chapter counters with a discussion of the
beneficial activities and exploitations of microorganisms as they relate to human culture.
The beneficial effects of microbes derive from their metabolic activities in the environment, their
associations with plants and animals, and from their use in food production and biotechnological
processes.
Nutrient Cycling and the Cycles of Elements that Make Up Living Systems
At an elemental level, the substances that make up living material consist of carbon (C), hydrogen
(H), oxygen (O), nitrogen (N), sulfur (S), phosphorus (P), potassium (K), iron (Fe), sodium (Na),
calcium (Ca) and magnesium (Mg). The primary constituents of organic material are C, H, O, N, S, and
P. An organic compound always contains C and H and is symbolized as CH 2O (the empirical formula for
glucose). Carbon dioxide (CO2) is considered an inorganic form of carbon.
The most significant effect of the microorganisms on earth is their ability to recycle the primary
elements that make up all living systems, especially carbon (C), oxygen (O) and nitrogen (N). These
elements occur in different molecular forms that must be shared among all types of life. Different
forms of carbon and nitrogen are needed as nutrients by different types of organisms. The diversity of
metabolism that exists in the microbes ensures that these elements will be available in their proper
form for every type of life. The most important aspects of microbial metabolism that are involved in
the cycles of nutrients are discussed below.
Primary production involves photosynthetic organisms which take up CO 2 in the atmosphere and
convert it to organic (cellular) material. The process is also called CO 2 fixation, and it accounts for a
very large portion of organic carbon available for synthesis of cell material. Although terrestrial plants
are obviously primary producers, planktonic algae and cyanobacteria account for nearly half of the
primary production on the planet. These unicellular organisms which float in the ocean are the "grass
of the sea", and they are the source of carbon from which marine life is derived.
NASA receives data from the Terra and Aqua satellites which measures net primary
productivity on Earth. These false-color maps represents the rate at which photosynthetic
organisms absorb carbon out of the atmosphere. The yellow and red areas show the highest
rates, ranging from 2 to 3 kilograms of carbon taken in per square meter per year. The
green, blue, and purple shades show progressively lower productivity. Tropical rain forests
are generally the most productive places on Earth. However, primary productivity near the
seas surface over such a widespread area of the Earth makes the ocean roughly as
productive as the land. http://earthobservatory.nasa.gov/Newsroom/NPP/npp.html
Some habitats like this cactus community in the Sonoran Desert, rely on nitrogen-fixing
bacteria at the base of the food chain as the source of nitrogen for maintenance of cell
material. Every plant in this scene depends ultimately on biological nitrogen fixation.
http://helios.bto.ed.ac.uk/bto/microbes/nitrogen.htm
Oxygenic photosynthesis occurs in plants, algae and cyanobacteria. It is the type of photosynthesis
that results in the production of O2 in the atmosphere. At least 50 percent of the O2 on earth is
produced by photosynthetic microorganisms (algae and cyanobacteria), and for at least a billion years
before plants evolved, microbes were the only organisms producing O 2 on earth. O2 is required by
many types of organisms, including animals, in their respiratory processes.
Nitrogen is one of the primary nutrients critical for the survival of all living organisms.
Although nitrogen is very abundant in the atmosphere, it is largely inaccessible in this
form to most organisms. This article explores how nitrogen becomes available to
organisms and what changes in nitrogen levels as a result of human activity means to
local and global ecosystems.
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Introduction
Nitrogen is one of the primary nutrients critical for the survival of all living organisms. It is a necessary component of
many biomolecules, including proteins, DNA, and chlorophyll. Although nitrogen is very abundant in the atmosphere
as dinitrogen gas (N2), it is largely inaccessible in this form to most organisms, making nitrogen a scarce resource
and often limiting primary productivity in many ecosystems. Only when nitrogen is converted from dinitrogen gas into
ammonia (NH3) does it become available to primary producers, such as plants.
In addition to N2 and NH3, nitrogen exists in many different forms, including both inorganic (e.g., ammonia, nitrate)
and organic (e.g., amino and nucleic acids) forms. Thus, nitrogen undergoes many different transformations in the
ecosystem, changing from one form to another as organisms use it for growth and, in some cases, energy. The major
transformations of nitrogen are nitrogen fixation, nitrification, denitrification, anammox, and ammonification (Figure 1).
The transformation of nitrogen into its many oxidation states is key to productivity in the biosphere and is highly
dependent on the activities of a diverse assemblage of microorganisms, such as bacteria, archaea, and fungi.
Nitrogen Fixation
Nitrogen gas (N2) makes up nearly 80% of the Earth's atmosphere, yet nitrogen is often the nutrient that limits primary
production in many ecosystems. Why is this so? Because plants and animals are not able to use nitrogen gas in that
form. For nitrogen to be available to make proteins, DNA, and other biologically important compounds, it must first be
converted into a different chemical form. The process of converting N2 into biologically available nitrogen is called
nitrogen fixation. N2 gas is a very stable compound due to the strength of the triple bond between the nitrogen atoms,
and it requires a large amount of energy to break this bond. The whole process requires eight electrons and at least
sixteen ATP molecules (Figure 2). As a result, only a select group of prokaryotes are able to carry out this
energetically demanding process. Although most nitrogen fixation is carried out by prokaryotes, some nitrogen can be
fixed abiotically by lightning or certain industrial processes, including the combustion of fossil fuels.
Genes for nitrogenase are globally distributed and have been found in many aerobic habitats (e.g., oceans, lakes,
soils) and also in habitats that may be anaerobic or microaerophilic (e.g., termite guts, sediments, hypersaline lakes,
microbial mats, planktonic crustaceans) (Zehr et al. 2003). The broad distribution of nitrogen-fixing genes suggests
that nitrogen-fixing organisms display a very broad range of environmental conditions, as might be expected for a
process that is critical to the survival of all life on Earth.
Nitrification
Nitrification is the process that converts ammonia to nitrite and then to nitrate and is another important step in the
global nitrogen cycle. Most nitrification occurs aerobically and is carried out exclusively by prokaryotes. There are two
distinct steps of nitrification that are carried out by distinct types of microorganisms. The first step is the oxidation of
ammonia to nitrite, which is carried out by microbes known as ammonia-oxidizers. Aerobic ammonia oxidizers convert
ammonia to nitrite via the intermediate hydroxylamine, a process that requires two different enzymes, ammonia
monooxygenase and hydroxylamine oxidoreductase (Figure 4). The process generates a very small amount of
energy relative to many other types of metabolism; as a result, nitrosofiers are notoriously very slow growers.
Additionally, aerobic ammonia oxidizers are also autotrophs, fixing carbon dioxide to produce organic carbon, much
like photosynthetic organisms, but using ammonia as the energy source instead of light.
Reaction 1 converts ammonia to the intermediate, hydroxylamine, and is catalyzed by the enzyme ammonia
monooxygenase. Reaction 2 converts hydroxylamine to nitrite and is catalyzed by the enyzmer hydroxylamine
oxidoreductase.
2010 Nature Education All rights reserved.
Unlike nitrogen fixation that is carried out by many different kinds of microbes, ammonia oxidation is less broadly
distributed among prokaryotes. Until recently, it was thought that all ammonia oxidation was carried out by only a few
types of bacteria in the genera Nitrosomonas, Nitrosospira, andNitrosococcus. However, in 2005 an archaeon was
discovered that could also oxidize ammonia (Koenneke et al. 2005). Since their discovery, ammonia-oxidizing
Archaea have often been found to outnumber the ammonia-oxidizing Bacteria in many habitats. In the past several
years, ammonia-oxidizing Archaea have been found to be abundant in oceans, soils, and salt marshes, suggesting
an important role in the nitrogen cycle for these newly-discovered organisms. Currently, only one ammonia-oxidizing
archaeon has been grown in pure culture, Nitrosopumilusmaritimus, so our understanding of their physiological
diversity is limited.
The second step in nitrification is the oxidation of nitrite (NO2-) to nitrate (NO3-) (Figure 5). This step is carried out by a
completely separate group of prokaryotes, known as nitrite-oxidizing Bacteria. Some of the genera involved in nitrite
oxidation include Nitrospira, Nitrobacter, Nitrococcus, andNitrospina. Similar to ammonia oxidizers, the energy
generated from the oxidation of nitrite to nitrate is very small, and thus growth yields are very low. In fact, ammoniaand nitrite-oxidizers must oxidize many molecules of ammonia or nitrite in order to fix a single molecule of CO2. For
complete nitrification, both ammonia oxidation and nitrite oxidation must occur.
Anammox
Traditionally, all nitrification was thought to be carried out under aerobic conditions, but recently a new type of
ammonia oxidation occurring under anoxic conditions was discovered (Strous et al. 1999). Anammox (anaerobic
ammonia oxidation) is carried out by prokaryotes belonging to the Planctomycetes phylum of Bacteria. The first
described anammox bacterium was Brocadiaanammoxidans. Anammox bacteria oxidize ammonia by using nitrite as
the electron acceptor to produce gaseous nitrogen (Figure 6). Anammox bacteria were first discovered in anoxic
bioreactors of wasterwater treatment plants but have since been found in a variety of aquatic systems, including lowoxygen zones of the ocean, coastal and estuarine sediments, mangroves, and freshwater lakes. In some areas of the
ocean, the anammox process is considered to be responsible for a significant loss of nitrogen (Kuypers et al. 2005).
However, Ward et al. (2009) argue that denitrification rather than anammox is responsible for most nitrogen loss in
other areas. Whether anammox or denitrification is responsible for most nitrogen loss in the ocean, it is clear that
anammox represents an important process in the global nitrogen cycle.
Denitrification
Denitrification is the process that converts nitrate to nitrogen gas, thus removing bioavailable nitrogen and returning it
to the atmosphere. Dinitrogen gas (N2) is the ultimate end product of denitrification, but other intermediate gaseous
forms of nitrogen exist (Figure 7). Some of these gases, such as nitrous oxide (N2O), are considered greenhouse
gasses, reacting with ozone and contributing to air pollution.
Ammonification
When an organism excretes waste or dies, the nitrogen in its tissues is in the form of organic nitrogen (e.g. amino
acids, DNA). Various fungi and prokaryotes then decompose the tissue and release inorganic nitrogen back into the
ecosystem as ammonia in the process known as ammonification. The ammonia then becomes available for uptake
by plants and other microorganisms for growth.
Summary
Nitrogen is arguably the most important nutrient in regulating primary productivity and species diversity in both
aquatic and terrestrial ecosystems (Vitousek et al. 2002). Microbially-driven processes such as nitrogen fixation,
nitrification, and denitrification, constitute the bulk of nitrogen transformations, and play a critical role in the fate of
nitrogen in the Earth's ecosystems. However, as human populations continue to increase, the consequences of
human activities continue to threaten our resources and have already significantly altered the global nitrogen cycle.
Kuypers, M. M. M. et al. Massive nitrogen loss from the Benguela upwelling system through anaerobic ammonium
oxidation. Proceedings of the National Academy of Sciences of the United States of America 102, 64786483 (2005).
Risgaard-Petersen, N. et al. Evidence for complete denitrification in a benthic foraminifer. Nature 443, 9396 (2006).
Strous, M. et al. Missing lithotroph identified as new planctomycete. Nature 400, 446449 (1999).
Vitousek, P. M. et al. Human alteration of the global nitrogen cycle: sources and consequences. Ecological
Applications 7, 737750 (1997).
Vitousek, P. M. et al. Towards an ecological understanding of biological nitrogen fixation. Biogeochemistry 57, 145
(2002).
Ward, B. B. et al. Denitrification as the dominant nitrogen loss process in the Arabian Sea. Nature 460, 7881 (2009).
Zehr, J. P. et al. Nitrogenase gene diversity and microbial community structure: a cross-system
comparison. Environmental Microbiology 5, 539554 (2003).
Bacteria and Archaea and the Cycles of Elements in the Environment (page
4)
(This chapter has 4 pages)
Kenneth Todar, PhD
Figure 4.The Phosphorus Cycle. Plants, algae and photosynthetic bacteria can absorb phosphate (PO 4)
dissolved in water, or if it washes out of rocks and soils. They incorporate the PO 4 into various organic forms,
including such molecules as DNA, RNA, ATP, and phospholipid. The plants are consumed by animals wherein
the organic phosphate in the plant becomes organic phosphate in the animal and in the bacteria that live with
the animal. Animal waste returns inorganic PO4 to the environment and also organic phosphate in the form of
microbial cells. Dead plants and animals, as well as animal waste, are decomposed by microbes in the soil.
The phosphate eventually is mineralized to the soluble PO4 form in water and soil, to be taken up again by
photosynthetic organisms.
The biological activity at the surface of the lake and at the bottom of the lake may have a lot to do
with what will be going on in the middle of the water column, especially near the interface of the
aerobic and anaerobic zones. This area, called the thermocline, is biologically very active. Bacterial
photosynthesis, which is anaerobic, occurs here, using longer wave lengths of light that will penetrate
the water column and are not absorbed by all the plant chlorophyll above. The methanotrophs will stay
just within the aerobic area taking up the CH 4 from the sediments as a carbon source, and returning it
as CO2. Lithotrophic nitrogen and sulfur utilizing bacteria do something analogous: they are aerobes
that use NH3and H2S from the sediments, returning them to NO 3 and SO4.
http://textbookofbacteriology.net/environment_4.html
Biology I
B. Fleming
Ecology: Nutrient Cycling
Overview:
Presents the four primary nutrient cycles (water, carbon, nitrogen, and phosphorous)
through discussion and an interactive PowerPoint presentation in a 50 minute class
period.
Objectives:
Content Standards
Students describe how carbon and soil nutrients cycle through
selected ecosystems (Michigan Benchmarks LEC III.5-5)
Technology Standards
Teacher demonstrates introductory knowledge, skills, and
understanding of concepts related to technology (ISTE NETS I.A.).
Teacher identifies and locates technology resources and evaluates
them for accuracy and suitability (ISTE NETS II.C.)
Activities:
5 min.
20 min.
Assessment.
Phosphorous Cycle. Have students look at the map and try to
describe what they think is happening, based on the cycles they
have just learned about. (This is a simple cycle, with two separate
parts. Have them choose a branch and just describe that one, or
do both if time permits.)
Question: What would happen in the Nitrogen Cycle if the nitrogenfixing bacteria were not working properly? Describe the impact on
both producers and consumers.
Question: Hypothetical scenario: Grandma Johnson had very
sentimental feelings toward Johnson Canyon, Utah, where she and
her late husband had honeymooned long ago. Her feelings toward
this spot were such that upon her death she requested to be buried
under a creosote bush overlooking the canyon. Trace the path of
a carbon atom from Grandma Johnsons remains to where it could
become part of a hawk. Note: hawk dig not dig up and consume
Grandma Johnsons remains.
10 min.
Homework.
Students should complete classwork and any other work appropriate
at this point in the unit.
http://www.britannica.com/EBchecked/topic/572740/sulfur-cycle