Chapter 13

Question 1

4 examples of free-living nitrogen fixers + what they required

Answer 1

1. Beijerinckia
2. clostridium: stricly anaerobes
3. azotobacter: strict aerobes. The enzyme is protected by a very high rate of O2 consumption, which keeps the intracellular environment anaerobic
4. cyanobacteria: only some species are capable of N2 fixation. MAJOR nitrogen-fixing organisms in nature. They produce energy by oxygenic photosynthesis, oxygen is produced in the cell

• widespread in soil, require a soil rich in organic matter to provide energy for nitrogen fixation
• produce ammonia that can be used by plants (NH3, dissolves in water to produce ammonium NH4)

Question 2

3 characteristics of cyanobacteria

Answer 2

1. nitrogen fixation occured in specialized anaerobi cells (heterocysts), which lack photosystem II (does not produce O2)
2. the heterocysts have a thick cell wall that slow down the diffusion of O2
3. the regular cells provide the heterocysts with carbohydrate (pyruvate)

Question 3

3 characteristics of symbiotic nitrogen fixers

Answer 3

• the mutualistic relationship between leguminous plants and nitrogen-fixing bacteria is one of the most important symbioses known
• ex of legumes: alfafa, soybean, peas, beans, clovers
• rhyzobium is the best known nitrogen-fixing bacteria engaging in these symbioses

Question 4

colonization of legume roots by nitrogen-fixation bacteria leads to what

Answer 4

to the formation of root nodules that fix nitrogen

Question 5

6 steps of nodule formation

Answer 5

1. Recognition and attachment of bacterium to root hairs (ex: rhizobial cell)
   
   2. Excretion of nod factors by the bacterium causing root hair curling
   3. Bacterial invasion of the root hair
   4. Travel to the main root via the infection thread (tube composed of cellulose)
   5. Formation of bacteroid state within plant cell (swollen and misshapen bacteria-fix N2). Surrunded by plant cytoplasm
   6. Continued plant anc bacterial division, forming the mature root nodule

Question 6

2 other characteristics nodule formation

Answer 6

• Oxygen levels are controlled by the O2-binding protein leghemoglobin, produced by plant cells.
• Bacteroids are a terminal structure and cannot be shed in the environment. The nodules contain regular Rhizobium cells that serve to inoculate the environment

Question 7

2 characteristics of nitrogen-fixation in Sierra Mixe Maize

Answer 7

1. Nitrogen fixation in aerial roots through the mucilage-associated microbiota:
   
   • Plan can acquire 29%-82% of its nitrogen from the air
   • At least some of this N is fixed by bacteria in the mucilage
     2. Mucilage: viscous sugar-rich fluid secreted by some plants:
   • Diverse community of bacteria
   • Including N fixers (ex: rhizobiaceae)

Question 8

5 implications of N cycle for agriculture

Answer 8

1. Most plants will use nitrogen compunds produced by free-living nitrogen fixers or by other organisms during ammonification (organic-N = NH4+; e.g. urine)
   
   • Good for farmers, don’t havd to use as much fertilizer
     2. Nitrate is more soluble than ammonium and is more readily available to plants
   • Plants can be use both ammonium and nitrate
     3. Source of nitrate: nitrifying bacteria: NH3=NO2-=NO3-
   • Requires O2
   • Competition between nitrifiers and plants for NH3
     4. If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which promotes denitrification: NO3- = NO2- = NO = N2O = N2
   • This is bad for plants and farmers!!
     Anaerobic conditions also promote sulfur and sulfate reduction which produce H2S (toxic for plants)

Question 9

what is hummus

Answer 9

dead plant material that is resistant to decomposition. keep water and nutrients in the soil. Good for soil fertility

Question 10

4 compositions of the soil + soil can be divided into 2 broad groups

Answer 10

the losse outer material of Earth’s surface, distinct from bedrock (solid rock)

4 compositions:

• water and air (50%)
• inorganic material matter (40% of soil volume)
• organic matter (5%)
• living organisms

2 broad groups:

1. mineral soils: derived from rock weathering (breaking down of rocks) and other inorganic materials
   - predominate most terrestrial environments
2. organic soils: derived from sedimentation in bogs and marshes

Question 11

4 different zones of the soil

Answer 11

1. O horizon: layer of undecomposed plant materials
   
   2. A horizon: surface soil (high in organic matter, dark in color, is tilled for agriculture; plants and large numbers of microorganisms grow here, microbial activity high)
   3. B horizon: subsoil (minerals, humus, and so on, leached from soil surface accumulate here; little organic matter; microbial activity detectable but lower than at A horizon
      C Horizon: soil base (develops directly from underlying bedrock; microbial activity generally very low)

Question 12

2 roles of bacteroidetes

Answer 12

1. extract soil microbial community DNA

2. isolate, sequence and analyze 16S rRNA genes

Question 13

most important factors for microbial activity at the subsurface and at the surface

Answer 13

surface: the availability of water is the most important factor influencing microbial activity in surface soils
ex: sand = 0.1-2 mm particules so water drained too quickly
silt: 0.002-0.1 mm paritcules so retain water to the right extent
clay: less than 0.002 mm so water retained too well, soil become anoxic

subsurface environment: nutrient availability

Question 14

4 things parasites are responsible for

Answer 14

• production of humus
• nitrogen fixation
• cycling of nutrients (C,N,S)
• release of minerals from soil particles (production of acids from organic compunds solubilize the minerals)

Question 15

what is mycorrhizae and rhizosphere

Answer 15

rhyzosphere: soil that surrunds plant roots and receive plant secretions
- mycorrhizae: association of fungi with plant roots

Question 16

N2 fixation:
2 free-living aerobic
3 free-living anaerobic
3 symbiotic

Answer 16

aerobic:

1. cyanobacteria
2. azotobacter

anaerobic:

1. clostridium
2. purple and green phototrophic bacteria
3. methanobacterium (archaea)

symbiotic:
1. rhizobium
2. bradyrhizobium
3, frankia

Question 17

steps of nitrogen cycle

Answer 17

1. nitrogen from the atmosphere (N2)
2. consume by nitrogen-fixing bacteria living in legume root nodule and nitrogen-fixing soil bacteria
3. from nitrogen-fixing soil bacteria, there is the ammonification (transformation into NH4+)
4. nitrification by nitrifying bacteria: transform NH4+ into nitrites (NO2-)
5. nitrifying bacteria transform into nitrates (NO3-)
6. 2 ways of nitrates:
   - assimilation by plants which will be consume by animals and decomposed by decomposers (aerobic and anaerobic fungi and bacteria)
   - denitrifying bacteria transform it into atmospheric nitrogen (N2)

Question 18

4 characteristics of the nitrogen fixationr reaction

Answer 18

• reaction is catalyzed by nitrogenase complex (metal cofactors)
• 8 electrons (from pyruvate) are required, 2 are lost as H2 in the process
• ammonia is the final product and is used to produce AA
• dinitrogenase reductase is inhibted in the presence of oxygen