lecture 13 - environmental microbiology

Question 1

What do you need to build / run a microbe?

Answer 1

Structurally and morphologically very diverse
However, in terms of molecular composition they are not that different.
All microbes have an approximate function for biomass of
C5H7O2N
Also have traces of other things in them as well such as P, S, and metals.

Question 2

Explain the importance of carbon in microbes

Answer 2

Structural backbone of living matter.

Up to half the weight of a typical microbial cell (dry weight) is carbon.

Microbes obtain their carbon from either organic material or by photosynthesis

Autotrophs – Obtain carbon from carbon dioxide
Heterotrophs – Obtain carbon from organic compounds

Question 3

Explain the importance of nitrogen, sulphur and phosphorous in microbes

Answer 3

Microbes need N, S and P for the synthesis of proteins and nucleic acids.

Obtained from either organic (e.g. amino acids) or inorganic material (e.g. ammonium ions).

Some bacteria (cyanobacteria), can use gaseous nitrogen directly from the atmosphere (nitrogen fixation.)

e.g. Symbiotic nitrogen fixing bacteria (Rhizobium) found with legumes.

Question 4

Explain the importance of trace elements in microbes

Answer 4

Microbes require very small amounts of minerals such as iron, copper and zinc.

Essential for the activity of some enzymes.

Question 5

Explain the importance of organic growth factors in microbes

Answer 5

Organic growth factors are essential organic compounds that the microbes can’t synthesise.

e.g. Some microbes are incapable of producing certain vitamins, amino acids, purenes and pyrimidines.

Question 6

How does energy production take place in microbes?

Answer 6

Microbes are capable of using a wide range of methods for the production of energy.
Microbes can be defined based on their source of energy:
Phototrophs – obtaining energy from light
Chemotrophs –obtaining energy from chemical compounds (sometimes these are called heterotrophs although strictly this refers to carbon source)

Question 7

Describe microbial metabolism

Answer 7

Microbes share many metabolic pathways with plant and mammalian biochemistry, (e.g. TCA cycle, glycolysis, photosynthesis)

Microbes also have a large number of different biochemical pathways. These include:

Pathways that do not require oxygen as a terminal electron acceptor.

Able to use compounds that are not normally thought of as carbon or energy sources e.g. PCBs and crude oil.

In its simplest form metabolism can be thought of as either the production (catabolic) or use of (anabolic) ATP.

Question 8

What are the types of energy yielding metabolism?

Answer 8

Respiration

Fermentation

Question 9

What is respiration?

Answer 9

“Energy yielding metabolism in which the oxidation of a energy substrate involves an exogenous electron acceptor.

The participation of the exogenous electron acceptor results in the net oxidation of the energy yielding substrate being significantly greater than that obtained by fermentation”

An essential feature of respiration is the operation of an electron transport chain.

Question 10

Describe aerobic respiration

Answer 10

Uses oxygen as terminal electron acceptor.

Most people think of it as the TCA (or Krebs) cycle followed by the electron transport chain.

Question 11

Describe anaerobic respiration

Answer 11

Bacteria can respire in the absence of oxygen if some other suitable oxidant is available to act as electron acceptor.

Called anaerobic respiration

Requires a modified ETC in order to transport electrons to the new acceptor.

Many sulphur and nitrogen compounds can be used by a variety of bacteria.

Question 12

What is fermentation?

Answer 12

Microbes have the option of breaking down organic compounds without using respiration.

This is fermentation.

Fermentation is defined as pathways in which organic compounds serve as both electron donors and electron acceptors.

A variety of fermentative pathways are available to microbes.

The fermentable substrates include carbohydrates, organic acids and amino acids.

Question 13

Describe microbial pathways for the degradation of “unusual” compounds

Answer 13

Microbes extract energy from their environment and convert compounds into cell components using a highly integrated network of chemical reactions.

Defining “unusual”:
Not part of “central” metabolic pathways
Biological polymers
Xenobiotics – typically derived by human activity

Question 14

Describe how microbes are able to survive extreme conditions

Answer 14

Microorganisms are capable of surviving:
Lack of oxygen
Heat and cold
Acidity
Salinity
High pressure
Form spores that are capable of surviving for hundreds, if not thousands of years.
Can survive journeys into space and back.
Evidence to suggest that microbes may have (or maybe still be) present on Mars.

Question 15

Describe the role of microbes in the development of life on earth

Answer 15

Archaea were the first organisms to inhabit Earth approximately 3–4 billion years ago
Bacteria changed atmosphere to more like it is today and allowed evolution of other life to occur? Question is how did they start – Creation, Panspermia, or generation from organic compounds?

Question 16

Describe the role of microbes in biogeochemical cycles

Answer 16

Microbes modified conditions on earth to allow other life.

e.g. Cyanobacteria produced oxygen circa 3.8 billion years ago.

Role of microbes bigger than their interactions at a relatively local scale

Play roles on a worldwide scale

Question 17

Describe how mycorrhizae create a positive interaction between fungi and plants

Answer 17

A mutualistic relationship between fungi and plant roots

Mycorrhizae literally means “fungus root”

Fungi are integrated into structure of root

Highly specific and organised

Association lasts for prolonged periods
of time over several years

Fungus gets nutritional benefit from material produced by plant root in form of photosynthesis products

Plant benefits from nutrients supplied by the fungus particularly P and N

Enhanced uptake of water

Effectively increases length of feeder roots

Increased tolerance of environmental conditions e.g. temperature

Allow plant/fungal associations to occupy habitats they would not normally

Resistance to pathogens – fungal sheath acts as a barrier and some fungi produce antibiotics and volatile organic acids that are fungistatic

Tolerance of toxins

Failure of cleared tropical rainforest to produce crops is linked to P limitation due to farmers not using plants that use mycorrhizae

Mycorrhizae allow P recycling from plant biomass as there is little in way of humic material as this is rapidly broken down

Question 18

Describe how lichens create a positive association between fungi and algae/cyanobacteria

Answer 18

Symbiosis between Fungi (usually Ascomycota) and Algae or Cyanobacteria
Type of mutualism
Fungi – is the consumer (mycobiont)
Algae or Cyanobacteria – is the producer (phycobiont)

There are 3 major types of lichen - crustose, fruticose, foliose

Algal and fungal members of lichen form distinct layers
Grow slowly and able to colonise habitats that other organisms can’t
Resistant to extremes of temperature and desiccation
Can produce organic acids to break down rock
Some can fix atmospheric nitrogen.
Structure is quite complex and varies between species.

Reproduce via vegetative (asexual) processes or by producing dispores (combined algal and fungal spore) although fungal partner can sometimes reproduce sexually.

Question 19

Give an example of positive interactions between microbes and animals

Answer 19

Interactions between fungi and animals can be beneficial

e.g. Cellulose degradation

Cellulose is abundant in nature, but most herbivorous animals can’t digest it

Rely on enzymes produced by fungi

Question 20

What are ruminants?

Answer 20

Protozoa, fungi and bacteria contribute to the digestion of the cellulose that the animal eats.

Microbes benefit from food supply and constant environment

Animal benefits from break down products of cellulose and microbial biomass

Question 21

Describe the role of gut microbiota as commensals

Answer 21

Vast range (and number) of microbes live in the gastrointestinal tract.

Traditionally thought to help with expanding nutrient sources, producing essential vitamins and carrying out xenobiotic metabolism

Diet, lifestyle, antibiotics, hygiene, genetics and immune status change microbial composition, with various consequences: chronic inflammation, metabolic dysfunction

Now linked to

Development and maturation of the intestinal epithelium
Changes to the immune system of the host
Organ morphogenesis
Tissue homeostasis
Bone mass
Obesity
Behaviour

Evidence for cross-species homeostatic interaction between the host and its microbiota.