Download Nitrogen-fixing bacteria/archaea

Introduction to
Soil Microbiology
and its role in the Nitrogen Cycle
Valery Lynn, iisme 2011
Day 1 - What is Soil?
• It’s not just Dirt!
• According to NASA, it’s a “living,
breathing world supporting
nearly all terrestrial life.”
Don’t believe it? Click
here to watch a video of
what lurks in a soil
sample.
Why is soil so important?
• Holds nutrients and water for plants and
animals
• Filters water that passes through it
• Can change the chemistry of water
• Foods we eat and most of the materials
we use for paper, buildings, and clothing
are dependent on soils
Why is soil so important? Cont.
• Plays an important role in the amount and
types of gases in the atmosphere
• Stores and transfers heat, which affects
the temperature of the atmosphere
• Fosters rich microbial populations that are
responsible for processes essential for life
on earth!
Soil Composition
• Soil is composed of particles that are
defined by size:
– Sand (largest particle size)
– Silt (intermediate size)
– Clay (smallest size)
• Soil is also composed of:
– Organic matter
– Biological organisms
www.jic.ac.uk/SCIENCE/molmicro/Azot.html
Soil Particles - Sand
• Largest particles
• Determines aeration
and drainage
characteristics
• Allows for air
spaces between soil
particles
www.microscopemicroscope.org/applications/sand/microsc
opic-sand.htm
Soil Particles - Silt
• Medium particles
• Easily transported
into water by
erosion
Soil Particles - Clay
• Smallest particles
• Displays plasticity
when mixed with
water
• Holds water in soil
Loam
• A mixture of equal
parts sand, silt, and
clay
• Considered the best
agricultural and/or
garden soil
• Has good drainage,
aeration for root
growth, and holds
water without
promoting rot
Soil is also composed of:
• Organic matter:
– Vegetation
– Animal
• Biological
organisms
– Bacteria
– Archaea
– Fungi/Mold
www.jic.ac.uk/SCIENCE/molmicro/Azot.html
Agricultural/Garden Soil
• Made of loam plus
organic matter
• Will have a healthy
variety of
microorganisms
• Most garden soil will
have 100 million to 3
billion bacterial cells in
just 1 gram!!!!!
www.jic.ac.uk/SCIENCE/molmicro/Azot.html
Activity 1
• Examine and
classify a soil
sample.
– Refer to your
worksheet to
complete Activity 1
Day 2 - Soil Biology
There are 3 Domains in Biological Taxonomy:
1. Archaea (pronounced Ark-ee-a)
2. Bacteria
3. Eukaryota
http://www.ucmp.berkeley.edu/alllife/threedomains.html
Bacteria
1. Prokaryote – single
celled
2. No membrane-bound
organelles
3. Double stranded circular
DNA
4. Cell walls containing
peptidoglycan
http://www.ucmp.berkeley.edu/alllife/threedomains.html
Eukaryota
1. Generally, multi-cellular
organisms are
eukaryotes – Plants,
Animals, Fungi
2. But, Protists are single
celled eukaryotes
3. Cells contain membranebound organelles
4. Double stranded linear
DNA
http://www.ucmp.berkeley.edu/alllife/threedomains.html
Archaea
• Archaea are prokaryotes (single-celled) that
were once classified as a type of bacteria.
• At first, scientists found them only in
extreme environments, like hot springs, acid
waters and salt lakes.
• But techniques in DNA sequencing have
shown that they are EVERYWHERE!
Archaea
• Genetic analysis of ribosomal RNA reveals that
Archaea are different from bacteria, even though
they may look alike.
Archaea
http://www.sdmags.net/2009/09/the-three-domainclassification-system/
Bacteria
http://en.wikipedia.org/wiki/Escherichia_coli
How are Archaea different from
Bacteria?
• Some genes are
closer to Eukaryotes
than to Bacteria.
http://www.cen.ulaval.ca/merge/index.php?url=11211
Unlike Bacteria - Some Archaea
can be flat or square shaped
http://www.ucmp.berkeley.edu/archaea/archaeamm.html
Different Cell Membranes
Archaea – contains
ether linkages
Bacteria and Eukaryotes –
ester linkages
Bacteria and
Eukaryotes – lipid
bilayer
Archaea – lipid
monolayer
http://en.wikipedia.org/wiki/Archaea
But, like Bacteria, Archaea have:
1. Cell walls – (but without
peptidoglycan)
2. Some have flagella
3. No membrane-bound
organelles
4. Double stranded circular
DNA
Bacteria and Archaea in Soil
and Water
• Both Bacteria and Archaea have been
found in soil and water (including the
ocean) all over the world.
• Most scientists use DNA techniques to
determine their presence in an
environment.
Bacteria and Archaea in Soil
and Water
• Research has shown that Bacteria and
Archaea are involved in a number of
processes that are crucial for the
environment.
• One such process is:
The Nitrogen Cycle!!!
Of all nutrients, nitrogen often has
the greatest effect on plant growth
• Nitrogen is a component for:
– Proteins
– Nucleic acids
– Chlorophyll
– Other important organic molecules
Nitrogen composes 80% of the
atmosphere and yet,
• Plants can suffer from nitrogen
deficiencies.
• Take a minute and discuss with your lab
partners how this could be possible.
• Have someone in your group write down a
plausible answer that you all agree on and
share with the class before going on.
Plants are Finicky!
• Atmospheric nitrogen is
gaseous (N2)
• But plants can only use
nitrogen in the forms:
N2
– Ammonium (NH4+), or
– Nitrate (NO3- )
NH4+ and NO3-
Did you figure it out?
• Here’s another one!
• Discuss with your group and write down
ways that atmospheric nitrogen (N2) could
be converted to ammonium (NH4+), or
nitrate (NO3- ).
Soil Microbes!
Look what they can do…
Atmosphere
N2
N2
Atmosphere
Soil
N2
Nitrogen-fixing
bacteria/archaea
Denitrifying
bacteria/archaea
H+
Nitrate and
nitrogenous
organic
compounds
exported in
xylem to
shoot system
(From soil)
Soil
+
NH4
NH3
(ammonia)
–
+
NH4
(ammonium)
Nitrifying
bacteria/archaea
NO3
(nitrate)
Ammonifying
bacteria/archaea
Organic
material (humus)
Figure 37.9
Root
The Nitrogen Cycle
• Nitrogen-fixing bacteria/archaea
– Nitrogen gas (N2)
Ammonia (NH3)
– (Add H+ from the soil and you’ve got (NH4+))
• Ammonifying bacteria/archaea
– Organic Material
Ammonium (NH4+)
The Nitrogen Cycle
• Nitrifying bacteria/archaea
– Ammonium (NH4+)
Nitrate (NO3-)
• Denitrifying bacteria/archaea
– Nitrate (NO3-)
Nitrogen gas (N2)
Each of these reactions are
catalyzed by a different enzyme
• Nitrogen-fixing bacteria/archaea
– Nitrogen gas (N2)
Ammonia (NH3)
Nitrogenase
• Ammonifying bacteria/archaea
– Organic Material
Ammonium (NH4+)
Gln Synthetase
Glu 2-oxoglutarate
aminotransferase
Each of these reactions are
catalyzed by a different enzyme
• Nitrifying bacteria/archaea
– Ammonium (NH4+)
Nitrate (NO3-)
Ammonia monooxygenase
• Denitrifying bacteria/archaea
– Nitrate (NO3-)
Nitrogen gas (N2)
Nitrate reductase
Check your work
• Work with your lab partners to finish
Worksheet 1 – Nitrogen Cycle
Day 3 – Review and Soil Sampling
Today we are going to:
1. Review some key concepts for Soil,
Microbiology, and the Nitrogen Cycle
2. Learn how to take a soil sample using
sterile technique
Concept Check #1
Answer the following question, then write out
an explanation for your answer.
1. Soil is made of nonliving matter.
a) True
b) False
Concept Check #1
Answer the following question, then write out
an explanation for your answer.
1. Soil is made of nonliving matter.
a) True
b) False
Concept Check #2
Answer the following question, then write out
an explanation for your answer.
2. A component of soil that helps improve
drainage is:
a)
b)
c)
d)
Sand
Silt
Clay
Microorganisms
Concept Check #3
Answer the following question, then write out
an explanation for your answer.
1. A component of soil that helps improve
drainage is:
a)
b)
c)
d)
Sand
Silt
Clay
Microorganisms
Concept Check #3
Answer the following question, then write out
an explanation for your answer.
3. Sediment from a stream surrounded by
farmland is likely to be high in:
a)
b)
c)
d)
Sand
Silt
Clay
Microorganisms
Concept Check #3
Answer the following question, then write out
an explanation for your answer.
3. Sediment from a stream surrounded by
farmland is likely to be high in:
a)
b)
c)
d)
Sand
Silt
Clay
Microorganisms
Concept Check #4
Answer the following question, then write out
an explanation for your answer.
4. The 3 main domains in biology are:
a)
b)
c)
d)
Animalia, Plantae, Bacteria
Animalia and Plantae, Algae, Archaea
Eukaryota, Animalia, Bacteria
Eukaryota, Archaea, Bacteria
Concept Check #4
Answer the following question, then write out
an explanation for your answer.
4. The 3 domains in biology are:
a)
b)
c)
d)
Animalia, Plantae, Bacteria
Animalia and Plantae, Algae, Archaea
Eukaryota, Animalia, Bacteria
Eukaryota, Archaea, Bacteria
Concept Check #5
Answer the following question, then write out an
explanation for your answer.
5. Processes in the nitrogen cycle:
a) Are only important to plants.
b) Move nitrogen from the atmosphere through soil
and water.
c) Are key to moving nitrogen from the atmosphere,
through soil and water, and back to the atmosphere.
d) Only makes nitrogen available to plants.
Concept Check #5
Answer the following question, then write out an
explanation for your answer.
5. Processes in the nitrogen cycle:
a) Are only important to plants.
b) Move nitrogen from the atmosphere through soil
and water.
c) Are key to moving nitrogen from the atmosphere,
through soil and water, and back to the atmosphere.
d) Only makes nitrogen available to plants.
Concept Check #6
Answer the following question, then write out
an explanation for your answer.
6. Processes in the nitrogen cycle are
catalyzed by:
a)
b)
c)
d)
Nucleic acids
Enzymes
Carbohydrates
Nitrogen
Concept Check #6
Answer the following question, then write out
an explanation for your answer.
6. Processes in the nitrogen cycle are
catalyzed by:
a)
b)
c)
d)
Nucleic acids
Enzymes
Carbohydrates
Nitrogen
Concept Check #7
Answer the following question, then write out
an explanation for your answer.
7. Most processes in the nitrogen cycle:
a)
b)
c)
d)
Occur in plants.
Occur in DNA.
Occur in bacteria and archaea.
Occur in the atmosphere.
Concept Check #7
Answer the following question, then write out
an explanation for your answer.
7. Most processes in the nitrogen cycle:
a)
b)
c)
d)
Occur in plants.
Occur in DNA.
Occur in bacteria and archaea.
Occur in the atmosphere.
How to take a sterile soil sample:
Baggie Technique
1. Use a clean shovel or spade to dig up a
clump of soil or stream sediment.
2. Invert the baggie and collect a handful of
soil or sediment from the inner part of the
clump (avoid the outer edges that have
touched the shovel or spade.
3. Label the baggie appropriately and
immediately refrigerate or place on ice.
How to take a sterile soil sample:
Bottle Technique
1. Use a clean shovel or spade to dig up a
clump of soil or stream sediment.
2. Use a sterile spatula or spoon to collect a
sample of soil or sediment from the inner
part of the clump (avoid the outer edges
that have touched the shovel or spade.
3. Place in a sterile bottle and label
appropriately.
4. Immediately refrigerate or place on ice.
Bibliography
1.
Campbell, N. & Reece, J. 2004. Biology 7th Edition - Benjamin Cummings
2.
Grubinger, V. SOIL MICROBOLOGY: A PRIMER, University of Vermont Extension
(http://www.uvm.edu/vtvegandberry/factsheets/SoilMicrobes.html)
3.
4.
•
Wikipedia: Sand (http://en.wikipedia.org/wiki/Sand)
Wikipedia: Silt (http://en.wikipedia.org/wiki/Silt)
Introduction to the Archaea: Life's extremists. . . http://www.ucmp.berkeley.edu/archaea/archaea.html