Topic 12 - Environmental microbiology

Question 1

What is biotic and abiotic?

Answer 1

living and non-living.

Question 2

What is biosphere?

Answer 2

It includes all ecosystems such as:
atmosphere which is the air. this is difficult for microbes as it lacks nutrients/moisture/surfaces and is mainly for the dispersal of spores.
lithosphere which is soil or earth’s crust
hydrosphere which is water - marina/fresh

Question 3

What are extremophiles?

Answer 3

Microbes which live in extreme environments which includes extreme pH’s, temperature and salinity.

Question 4

What are examples of extreme habitats?

Answer 4

Salt lakes which have bacterohodospin and high temperatures in very deep oceans with high pressures

Question 5

What is symbiosis?

Answer 5

When two different organisms live together in close association which is beneficial to one or both of them.

Question 6

What are examples of symbiosis?

Answer 6

Ruminants - have bacteria in their rumen which enables the animal to digest cellulose.
Mycorrhizae - have a close association with fungi and plants as they contribute to plant growth

Question 7

What is mycorrhizae?

Answer 7

Fungi that lives in plant roots in a mutualism relationship as that plants extend the surface area via hyphae roots and the fungi receives carbohydrates from the plant. This drastically increases the plant growth.

Question 8

What is biogeochemical cycles?

Answer 8

It is the recycling of chemical elements (via oxidation and reduction) between biotic and abiotic environment.

Question 9

What is soil microbiology?

Answer 9

mineral particles - 51% (clay, silt, sand and gravel)
organic matter - 9% (plant and animal derived)
pore space - 40% (water and air)
living organisms - 1%

Question 10

What is the mature soil profile?

Answer 10

O horizon - layer of undecomposed plant materials
A horizon - surface soil which is high in organic matter and where plants and microbes grow
B horizon - minerals, humus from soil accumulate here, there is little living matter, microbial activity lower than A horizon
C horizon is the soil base which develops directly underneath bedrock and microbial activity is very low

Question 11

What is a rhizosphere?

Answer 11

The microecological zone in direct proximity of plant roots.

The distance between them is either on or within 5mm of the root to allow for microbial growth.

Question 12

What are examples of bacteria which inhabit soil?

Answer 12

Chemoheterotrophic - Pseudomonas, Arthrobacter, Streptomyces and bacillus.
Chemoautotrophic - nitrobacter, thiobacillus

Question 13

What is environmental microbiology?

Answer 13

The study of microbe interactions in their natural habitats

Question 14

What causes the sweet earthy smell after rain?

Answer 14

Stretomyces as it releases a compound called geosmin which can be detected by the human nose.

Question 15

List the fungi properties for soil inhabitation.

Answer 15

• fungi has the ability to better tolerate desiccation than bacteria
• carbon recyclers/decomposers (saprophytes)
• predominant genera: Mucor, Pencillium, Aspergillus
• seen as moulds and yeasts in soil

Question 16

Cyanobacteria properties in soil

Answer 16

• blue geen algae/bacteria
• important for carbon cycling (photosynthetic)
• widely found in soil and water
• can fix nitrogen (seen in rice paddies)
• heterocytes are specialised nitrogen fixing cells with low oxygen to protect nitrogenase enzyme
• cynanobacteria can be environmentally harzardous, toxic blooms in water (Microcytis aeruginosa has toxins which can kill people and animals).

Question 17

Apart from free soil at the very surface where would you find high levels of organic matter and bacteria in soil?

Answer 17

Rhizosphere

Question 18

How would the nutrition and respiration of microbes change with depth in soil?

Answer 18

There is more anaerobic bacteria; sulphur (sulphate reducing bacteria) and methanogens (archae) with increasing depth.

Question 19

What are the different methodologies when it comes to growing and studying soil?

Answer 19

• Isolation and identification
• Enumeration (counting)
• Metagenomic (sequence of DNA, which is cheap but difficult to interpret)
• Biological activity
• Cultivation (only 10% of soil species is cultivable)

Question 20

What are isolation techniques?

Answer 20

• Selective media which discourages the growth of unwanted products by adding inhibitory compounds, e.g. addition of streptomycin and rose bengal allows for fungal growth but inhibits bacterial growth
• Enrichment media which is an addition of a substrate which encourages growth of organism in interest, e.g. adding cellulose as the sole carbon source which allows for microbes which can break down cellulose to grow while others cant

Question 21

What are examples of isolation medias?

Answer 21

MacConkey’s agar which is selective for enteric bacteria due to bile salts
Enrichment broth which is a liquid medium which greatly increases small numbers

Question 22

What biogeochemical cycle is much publicised as contributing to global warming?

Answer 22

The carbon cycle - greenhouse gases

Question 23

Main source of carbon in cellulose forming mass of a forest?

Answer 23

0.04% CO2 in atmosphere

Question 24

Why is lightening important in the nitrogen cycle?

Answer 24

The high energy breaks down N2 which reacts with oxygen (nitrous oxide) and becomes dissolved in rain as nitrates = fixed nitrogen.
Accounts for 5-7% of earth total nitrogen fixation per year. nd

Question 25

Outline the nitrogen cycle.

Answer 25

Living organisms have 10 - 15% N
Global turn over os 10^9 to 10^10 tonnes per year
Cycling is mainly through chemical reactiosns
N2 is the most stable form of nitrogen

Question 26

What is soil nitrogen compose of?

Answer 26

• Amino acids (20-50%)
• Amino sugars (5 -10%)
• Purine and pyrimidine bases (1%)
• Inorganic nitrogen (2%)

Question 27

What is ammonification?

Answer 27

• also called mineralisation
• deamination of AA’s which releases ammonia gas (NH3)
• NH3 solidifies in water presence = NH4+ (ammonium) in dry soil NH3 is lost in the atmosphere
• extracellular enzymes of fungi and bacteria
• ammonium is used up by other microbes or oxidised to NO3

Question 28

What is nitrification?

Answer 28

it is the biological oxidation of ammonia to nitrate which are preferentially assimilated by plants.
- ammonium is chemically stable under acidic conditions and not easily leached out of soil and it may be toxic to plants over a certain level.
There are 2 steps depending on the different groups:
nitrosomonas
2NH4+ + 3O2 —–> 2NO2 + 4H+ + 2H2O
Nitrobacter
2NO2 + O2 —-> 2NO3

Question 29

What is denitrification?

Answer 29

biological reduction of nitrate or nitrite to nitrogen or nitrous oxide
NO3 —> NO2- —> N2O —> N2
it leads to decrease of oil fertility
occurs at pH 5, high temp and anaerobic conditions (water logged soils)
caused by pseudomonas, bacillus and achromobacter

Question 30

What is nitrogen fixation?

Answer 30

This is seen in symbiotic relationships, in root nodules.
Rhizobium - gram negative rods found in peas, alfalfa, beans, lucerene and glover.
Bradyrhizobium - gram negative rods which are in soy beans and lupins.
Franka- actinomycete which is in alder trees and casuarina\