lecture 13 - environmental microbiology Flashcards
What do you need to build / run a microbe?
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.
Explain the importance of carbon in microbes
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
Explain the importance of nitrogen, sulphur and phosphorous in microbes
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.
Explain the importance of trace elements in microbes
Microbes require very small amounts of minerals such as iron, copper and zinc.
Essential for the activity of some enzymes.
Explain the importance of organic growth factors in microbes
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.
How does energy production take place in microbes?
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)
Describe microbial metabolism
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.
What are the types of energy yielding metabolism?
Respiration
Fermentation
What is respiration?
“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.
Describe aerobic respiration
Uses oxygen as terminal electron acceptor.
Most people think of it as the TCA (or Krebs) cycle followed by the electron transport chain.
Describe anaerobic respiration
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.
What is fermentation?
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.
Describe microbial pathways for the degradation of “unusual” compounds
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
Describe how microbes are able to survive extreme conditions
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.
Describe the role of microbes in the development of life on earth
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?
Describe the role of microbes in biogeochemical cycles
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
Describe how mycorrhizae create a positive interaction between fungi and plants
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
Describe how lichens create a positive association between fungi and algae/cyanobacteria
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.
Give an example of positive interactions between microbes and animals
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
What are ruminants?
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
Describe the role of gut microbiota as commensals
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.
