Microbiology Flashcards
8 lectures on microbiology (179 cards)
1
Q
What did Robert Hooke do?
A
He was the first to observe microorganisms, after he invented the compound microscope. (1665)
2
Q
Who was the first person to view microorganisms in 1665?
A
Robert Hooke
3
Q
Who first viewed bacteria?
A
Antonie van Leeuwenhoek, he was a draper and wanted to check the quality of his fabrics, so made high quality lences. (1683)
4
Q
What did Antonie van Leewenjoek do?
A
First to view bacteria, he made high quality lenses to view the quality of his fabric. (1683)
5
Q
What did Louis Pasteur study?
A
He was a chemist. Interested in food spoilage, linked microbiology to this. (19th century)
He used experiments where he sterilised things to prove this, called the germ theory of life.
6
Q
What did Robert Koch study?
A
He was interested in linking disease to microorganisms. He developed multiple vaccines, and discovered microorgansism that were linked to specific diseases. (19th century)
7
Q
When did we start to appreciate the involvement of microorganisms in environmental and geochemical processes?
A
Late 19th/earth 20th century
8
Q
What did Sergei Winogradsky discover?
A
-Lithotrophy (form of metabolism using inorganic compounds)
-Sulfer Oxidising bacteria
-Nitrifying bacteria
-Autochthonous (slow growth rates) / zymogenous (rapidly grow then die back when nutrients are gone)
He also developed a lab technique called Enrichment culture
9
Q
Who developed Enrichment culture and what is it?
A
Sergei Winogradsky
Allows you to take a sample from an environment and put into a specific growth medium to increase the concentration of a particular population.
10
Q
What did Martinus Beijerinck discover?
A
-symbiotic nitrigen fixation
-sulfate reduction (sulfer for metabolism)
-viruses
- he used enrichment culture for his work
11
Q
What did Albert Kluyver and Corenlius Neil discover?
A
-microbial transformations of inorganic species
-phototrophic bacteria
-sulfide/sulfer oxidation
12
Q
What did Roger Stainer discover?
A
-transformation of organic chemicals
-and the metabolic diversity of Pseudomonas
13
Q
What is the most metabolically diverse group of bacteria?
A
Pseudomonas
14
Q
Why is a zymogenous plant?
A
bacteria typically show a population increase when a specific substrate is added, and their numbers decrease when the substrate is depleted.
Aka grow fast and then die off when run out of nutrients
15
Q
Define microorganisms…
A
Small; measured in thousandths of a mm
Usually free living, unicells (can form clusters)
e.g Fungi, Algae, Protozoa, Bacteria, Archaea
16
Q
What features is common in all cells?
A
-Cell envelope
-Nucleic acids
-Ribosomes
-Cytoplasm
17
Q
What type of cells are classed as Prokaryotic?
A
Bacteria and Archaea
18
Q
What type of cells are classed as Eukaryotic?
A
Fungi, Algae, Protozoa, Plants, Metazoa ect
19
Q
What are some important functions of cell membranes?
A
-barrier between cell and environment
-structural component of the cell
-site of crucial biochemical reactions
-fundamental to energy generation
20
Q
What a cell membranes made of?
A
Phospholipid bilayer.
2 fatty acids (hydrophonic tail) ESTER linked to a phosporylated glycerol (hydrophillic head)
21
Q
How do cell membranes in Archaea differ?
A
- Fatty acids are ETHER linked to phosphorylated glycerol (stability)
2.Fatty acids are often branched and cyclic isoprenoids ( 5 carbon groups) - Cyclic tetraether lipids can form a monolayer functionally identical to a lipid bilayer.
22
Q
Why do archaea membranes have ether links?
A
more stable to help resist more extreme conditions
23
Q
Describe the fluid mosaic model…
A
Lipid bilayer forms a lipid “bag” around cell. Contains proteins (structural,transport and catylitic) that “fload” in bilayer.
24
Q
What other lipid components can be found in the cell membrane?
A
Sterols-Eukaryotes (few bacteria)
Hopanoids- Euakryotes and Bacteria
25
What are Sterols and Hopanoids?
They're also lipid components that change the viscosity of the cell membrane. They disrupts the tight packing of FA tails. This will help cell to adapt to changes in temperature.
They are very stable molecules.
26
What organisms have cell walls made of cellulose (glucose) ?
-Plants
-Algae
some fungi
27
What organisms have cell walls made of Chitin?
Chitin= N-acetylglucosamine (monomer)
Fungi
28
What type of bacteria have calcium carbonate in their cell walls?
foraminifera and coccolithophorid algae
29
What type of bacteria have silica cell walls?
diatoms, radiolarians
30
What is n-acetyl glucosamine?
the polysaccharide monomer used in chitin
31
What are cell walls often constructed from?
Polysaccharides, (different monomers and bonds between sugars)
32
What types of cell walls often have a range of "novel" cell walls?
-Bacteria
-Archaea
33
What type of cell can often have Peptidoglycan as their cell wall?
Bacteria,
Polysaccharide chains cross linked with peptides.
34
what is the structure of peptidoglycan cell walls in bacteria like?
Polysaccharide chain cross linked with peptides.
polysaccharides; -n-acetlyglucosamine and n-acetylmuramic acid
-find amino acids in D and L form, and amino acids that are only found in these cell walls
35
What is a common cell wall found in Archaea?
1.Pseudopeptidoglycan
( N-acetylglucosamine, N-acetyl-talosaminuronic acid) with lots of different peptide links.
2. can also form cell walls with combination of glycoproteins, proteins and polysaccharides (forms S-layer)
36
What is the basis of 2 major groupings of Bacteria?
Cell wall structure (the gram stain)
37
What is the gram stain?
Test to distinguish two major groups of bacteria, gram positive/negative.
1. samples stained with crystal violet
2 treated with alcohol/acid
3.stained with second stain
purple=positive
pink=negative
38
Describe the cell envelope of Gram positive bacterial cells...
Outer wall of peptidolycan, an inner cell membrane (Purple)
39
Describe the cell evelope of Gram negative cells...
The outer wall of Lipipolysaccharide and protein, then a cell wall of peptidoglycan and then an inner cell membrane. (Pink)
40
What is a nucleoside?
Sugar and base but no phosphate group
41
Which bases are Pyrimidines?
Single ring:
-Cytosine
-Thymine
-Uracil (RNA)W
42
What bases are Purines?
Double rings:
-Adenine
-Guamine
43
Describe the structure of RNA...
Single stranded, contains intramolecular hydrogen bonds between complimentary bases and folds into a 3D structures
44
How many H bonds between Cytosine and Guamine?
3 H bonds
45
How many bonds are between Adenine and Thmine?
2 Hydrogen bonds
46
Organisms that live in high temperature environments are more likely to have a higher percentage of what DNA pairing>
Cytosine to Guamine, because they form 3 Hydrogen bonds instead of 2. Which allows the DNA molecule to be more stable.
47
In Eukaryotic cells where is RNA present?
Within the nucleus and the cytoplasm of the cell
48
Describe the structure of ribosomes...
-made of a large subunit and small subunit
-complex of over 50 proteins and 3 different rRNA molecules
They direct the process of translation.
49
What is the size of ribosomes in Prokaryotes and Eukaryotes?
Eukaryotes= 80s = 60s + 40 s
Prokaryotes= 70s = 50 s +30s
Svedberg unit (S) is a measurement used to characterize ribosomes, , based on their sedimentation rate during ultracentrifugation.
50
Describe the cytoplasm/cytosol...
It is the fluid within a cell
-many biochemical reactions occur
-contains crucial biochemicals for energy eneration/biosynthetic processes within the cell.
e.g ATP, NAD and NADP
51
What is the function of NAD/P?
It is an oxidant in biochemical reaction, its reduced form is NADH/NADPH.
It is used in energy metabolism
52
What are some cellular sturctures that are unique to Prokaryotes?
-pili and fimbriae
-sheaths
-polysaccharide capsules (glycocalyx)
-gas vesicles
-heterocysts
-endospores
53
What are pili?
Protein nodules.
Used to attach to surfaces on other organisms and non biological surfaces.
sex pili; can transfer exstra chromosomal plasmids to other prokaryotes.
54
What are gas vesicles?
Vesicles that hold gases. So organisms can alter buoyancy to move up and down water collum so move to correct deph for optimum wavelengths for photosynthesis.
55
What are Heterocysts?
Only found in some cyanobacteria (photosynthetic). Specilised function for fixation of nitrogen gas under anerobic environment as enzymes involved are inactivated in the presence of oxygen.
56
What is a polysaccharide capsule (gylcocalyx)?
Produced to provide a physical barrier from physical environments but also phagocytic cells.
57
What are endospores?
Produced by bacteria, (not used for disperasal), one cell produces one spore. It is a survival dormant structure, in response to extreme conditions. spores are very resistant. They will germinate again in favourable conditions.
58
What are sheaths?
Found in some prokaryotes. Prevents encasing of iron oxide. (provides a physical barrier)
59
How big do Prokaryotes and Eukaryotes tend to be in microns?
Prokaryotic; (1-5 Microns)
Eukaryotic; (2-200 Microns)
60
Where were the earliest microorganisms discovered?
They were found in fossil stromatolites around 3.5 billion years ago. However some argue 3.8 billion years ago in hydrothermal vents.
Hypothetically some found in hydrothermal vents in Mexico 4 billion years ago...
For some reason resembled cyanobacteria but deffo not as oxygenic photosynthesis not a thing yet
61
When was oxygenic photosynthesis believed to have evolved?
around 2.5-3 billion years ago
62
What are the 2 main classification systems of microorganisms?
-Whittaker's 5 kingdom system
-Woese's 3 kingdom system
63
What is included in Whittaker's 5 kingdom system?
-Platae
-Animalia
-Fungi
-Protista
-Monera
"my passionate fling pleasured all"
64
What is Whittakers 5 kingdom system based on?
Means of nutrition.
e.g photosynthetic, absorbtion, ingestion
65
What was included in Woese's 3 kingdom system?
-Archaea
-Bacteria
-Eukarya
66
What was Woese's 3 kingdom system based on?
Based on evolutionary relationships inferred from comparison of macromolecular sequence data from rRNA sequences.
67
Within the eukarya using Woese's 3 kingdom systems what 3 subdivitions of microorganisms are there?
-Fungi
-Protozoa
-Algae
68
What type of microorganisms do we find included in Fungi?
-moulds
-yeasts
-mushrooms
69
What are the characteristics of most Fungi?
-Most are aerobic (except yeast and cellulolytic remen fungi)
-mushrooms grow as filaments called Hyphae that form together into Mycelia
-Produce extracellular hydrolytic enzymes the decompose polymeric carbohydrates (Permits them to penetrate solid materials such as wood)
70
Why are Fungi important?
-Important in decomposition of complex organic material e.g plant tissue, chitin
71
How are fungi classified?
By the spores that they produce during sexual reproduction.
-Ascomycetes; Ascopores
-Zygomycetes; Zygospores. 2 come together from each mating type.
-Basidiomycetes; Basidiospores. Fruiting bodies.
-Deuteromycetes; No sexual spores.
72
What are the key features of Protozoa?
-unicellular eukaryotic
-much larger than bacteria
-include the marine protozoa Foraminifera (produce calcium carbonate frustules aka cell wall)
-organic matter decomposition
-control bacterial populations and carbon cycling by grazing (they act as predators)
-can enter symbiotic relationships with algae or methanogens
-can be pathogenic
73
What organsisms do we find in the Protozoa?
-Amoebae (Rhizaria, amoebozoa)
-Ciliates (alveolates)
-Flagellates (alveolates, diplomonads, kinetoplastids)
-Sporozoans,mainly pathogenic (alveolates, apicocomplexans)
74
What are the key features of Algae?
-eukaryotic photosynthetic organisms (chloroplasts for oxygenic photosynthesis)
-related to higher plants
-can be related to protozoa
-some are unicellular
-some are filamentous or colonial
-can be large multicellular organisms such as seaweeds such as phaeophyta (brown algae)
-play a crucial role in primary productivity,especially in aquatic systems and mineral cycling.
75
Eukaryotic Algae are not related to what type of algae?
They are not related to blue-green Algae as these are prokaryotic cynobacteria.
76
Do all types of eukaryotic algae carry out oxygenic photosynthesis?
Yes!
(not related to blue-green algae which are cyanobacteria)
77
Where did chloroplasts evolve from?
cyanobacteria (symbiotic relationship)
78
How do we classify Algae?
By their photosynthetic pigments.
79
Bacteria have huge metabolic diversity, give as many examples of this as you can...
-Heterotrophy
-Lithoautotrophy
-Lithoheterotrophy
-Lithotrophy
-Photoheterotrophy
-Photoautotrophy
-Photosynthesis
-many anaerobic mechanisms
80
What is Heterotrophy?
Organisms that cannot synthesize their own food and must ingest organic carbon from other organisms.
81
What is Lithotrophy?
Organisms that use inorganic substances (like hydrogen sulfide or ammonia) as electron donors to obtain energy.
82
What is Lithoautotrophy?
Organisms that derive energy from inorganic compounds and use carbon dioxide as their carbon source.
83
What is Lithoheterotrophyy?
Organisms that obtain energy from inorganic compounds but require organic compounds as a carbon source.
84
What is photoautotrophy?
Organisms that use light energy to convert carbon dioxide into organic compounds.
85
What is photoheterotrophy?
Organisms that use light for energy but cannot fix carbon dioxide and thus require organic compounds for carbon.
86
What are Cyanobacteria?
-Sometimes called blue green algae (however they're bacteria not Algae)
-Oxygenic photosynthesis
-evidence suggests that they gave rise to chloroplasts in photosynthetic eukaryotes.
87
What are the 5 types of bacteria i need to remember?
-cyanobacteria
-planctomycetes
-green sulfer bacteria
-proteobacteria (alpha beta... ect)
88
What are cyanobacteria?
-called blue green algae (not algae deffo bacteria)
-reason for chloroplasts (endosymbiosis)
-morphologically diverse
-photosynthetic
89
What are Planctomycetes?
Genre of bacteria.
(plantomyces, pireullula, gemmata and isophaera)
-normally lack peptidoglycan in cell wall
-free living, aquatic oligotrophs (organism that thrives in low nutrient environments) that divide by budding (not binary fission)
-include anaerobic ammonia- oxidizing bacteria (ANAMMOX)
90
What is Green Sulfer bacteria?
-anoxygenic photosynthetic bacteria that uses sulfide as the electron donor for CO2 fixation.
-they can grow at very low light intensity
-common in fresh water, marine sediments and stratified water bodies.
-can form external sulfer granuales via sulfer oxidation
91
What are Proteobacteria?
Type of bacteria that contains 6 sub classes.
Divided into a, b, y, d, e
-physiologically the most diverse bacterial group
92
What are the characteristics of alphaproteobacteria?
-autotrophs/heterotrophs
-nitrate oxidising bacteria (nitrobacter)
-methane oxidising bacteria (methylocytis, methylosinus)
-nitrogen fixing bacteria (rizobium)
-anoxygenic photosynthetic purple non sulfer bacteria
93
What are the characteristics of betaproteobacteria?
-autotrophs/heterotrophs
-autotrophic ammonia oxidising bacteria
(nitrosomonas, nitrosospira)
-contaminent degrading bacteria
(ralstonia,comamonas)
-perchlerate reducers
(dechloromonas, dechlorosoma)
94
What are the characteristics of gammaproteobacteria?
-autotrophs/heterotrophs
-nitrate oxidising bacteria
-ammonia oxidising bacteria
-methane oxidising bacteria
-chemolithtrophic bacteria
-versitile metal reducing bacteria
-contaminent degradation bacteria
-pseudomonas
-anoxygenic photosynthetic purple sulfer bacteria
95
what are the characteritics of deltaproteobacteria?
-autotrophs/heterotrophs
-mostle sulfate reducing bacteria
-some iron reducing bacteria (geobacter)
-sulfate reducing bacteria
96
What are the characteristics of the epsilonproteobacteria?
-autotrophs/heterotrophs
-chemolithotrophic bacteria
-ectosymbionts
-gut pathogens (helicobacter, campylobacter)
97
What group do we find anoxygenic pruple photosynthetic non-sulfer bacteria?
alphaproteobacteria,
gammaproteobacteria has sulfer
98
What group do we find anoxygenic pruple photosynthetic sulfer bacteria?
gammaproteobacteria
alphaproteobacteria have non sulfer
99
What are some key characteristics of Archaea?
-Ether linked isoprenoids in cell membrane
-Often found in extreme environments
There is evidence that the Eukarya evolved from witihn the Archaea
100
What are some examples of well know Archaea?
-Euryarchaeota
-Crewnarchaeota
101
What are the two divisions of archaea?
TACK and DPANN
102
What are some general features of archaea?
-distantly related to all other organisms
-evidence that the eukarya evolved from within the archaea
-unique properties (ether linked isoprenoid,branched, lipids, novel cell walls)
-can be found in extreme environment but also normal
103
What are some key features of the Euryarchaeota Archaea group?
group known as euryarchaeota
-Methanogens
-Extreme halophiles
-Thermoplasmatales
-Thermococcus
-Archaeoglobus
104
What are some key features of Crenarchaeota Archaea group?
-extreme thermophiles
-acidophilic thermophiles
-novel uncultured mesophiles
105
What are methanogens?
euryarchaeota (eukaryotic archaea) mostly!
Methanogens are a group of microorganisms belonging to the domain Archaea that produce methane as a byproduct of their metabolic processes. They play a crucial role in the carbon cycle, especially in anaerobic environments.
-they use simple substrates
106
what is an example of a non euryarchaeota methanogen?
First evidance of non eukaryotic was Bathyarchaeota, methanogenisis evolved before the divergence from euryarchaeota.
However also,verstraaetearchaetoa
107
What are Extreme Halophiles?
euryarchaeota (eukaryotic archaea)
-high salt tolerance
-require oxygen
-heterotrophic ( obtain nutrients by consuming other organisms or organic substances)
-can be found in ancient halo deposits, soda lakes,saturated brines
-often have unusual shapes
108
What are Thermoplasma?
genus of eukaryotic Archaea known for thriving in extreme environments characterised by high temperatures and low pH levels.
-need oxygen,acidophillic, heterotrophs
-no cell wall
-can be found in self heating coal piles
55 degrees, pH 2
109
What are Thermococcus?
Eukaryotic archaea.
-Microorganisms that thrive in extremely hot environments.
- Anaerobic fermentative heterotrophs.
-Circle shaped.
-Can be found in deep sea hydrothermal vent systems and hot oilfeild water
-reduce elemental sulfer
110
What are Archaeoglobus?
Eukaryotic archaea.
-hyperthermophillic sulfate reducers
-found in deep sea hydrothermal vents and oilfield water
111
What are the Crenarcheota?
Crenarchaeota are a group within the domain Archaea, known for their adaptability to extreme environments and significant roles in global ecosystems.
-extreme thermophiles
-require absence of oxygen
-some hetertrophic sulfate reducers
-can grow on hydrogen,sulfer ect
-most thermophillic organism know, don't grow below 88 degrees
-found in deep sea hydrothermal vents,hot springs
112
What are the key features of Viruses?
-non cellular
-Can be DNA or RNA, with a protein coat and some are encapsulated in a membrane
-reproduce using hoast cells' replication system
113
What is a bacteriophage?
A virus that infects bacteria
114
What 2 different life cycles do bacteriophage follow?
1.The lytic cycle
2.Lysogeny
115
Describe the lytic cycle that a bacteriophage may follow...
The virus infects a host cell, replicates its components, assembles new viruses, and ultimately causes the host cell to burst (lyse), releasing the newly formed viruses to infect other cells.
116
Describe the lysogeny cycle that a bacteriophage may follow?
The virus integrates its genetic material into the host cell's DNA, remaining dormant (as a prophage) and replicating along with the host cell's genome. Under certain conditions, the viral DNA may activate, leading to the lytic cycle.
117
what are the importances of viruses?
-control bacterial populations
-release and recycle organic matter via cell lysis
Virus infection is central to breakdown of blooms of algae, (Emiliania huxleyii), marine carbon cycling, release of climate related trace gases
118
What is transduction, and impact on cyanobacteria?
Viral transduction is a process by which viruses transfer genetic material from one cell to another.
can be used to infect cyanobacteria, photosynthesis can still occur which provides energy for viral production.
119
Give some examples of environmentally important cycles that microorganisms play a role in...
-carbon cycle
-nitrigen cycle
-sulfer cycle
-iron cycle
and more!
120
What roles may microorganisms take part in within environmental processes?
-primary production
-production/consumption of atmospheric gases
-acid mine drainage
-mineral formation
121
What is primary production?
The fixation of CO2 by autotrophs and its conversion to organic material. By plants, algae and cyanobacteria.
122
What is the importance of primary production?
-organic materials derived from photosynthesis drive geochemical processes e.g nitrate reduction
-produces fossil fuel reserves
-Silicate/carbonate mineral deposites are driven by algal primary productivity
123
Describe methane...
-CH4, majore green house gas
-most atmospheric methane produced via methanogens
124
What are the key features of anaerobic food chain?
-organic compounds often degraded by microorganisms interacting together.
-in absence of oxidants like nitrate or sulfate at the end of the food chain CO2/H2 or acetate converted to METHANE
125
What is biogenic methane?
Methane produced through biological processes, primarily by microorganisms known as methanogens.
-rumenant animals e.g cows
-natural wetlands
126
Describe Nitrous oxide...
-greenhouse gas (N2O)
-biogenically produced by the mostly anaerobic process of denitrification (breakdown of organic carbon in anaerobic conditions when microorganisms use nitrate as an oxidant)
127
What processes produce nitrous oxide?
1.denitrification;breakdown of organic carbon in anaerobic conditions when microorganisms use nitrate as an oxidant
2.nitrifying bacteria; ammonia oxidising bacteria
128
What is acid mine drainage? (AMD)
Acid mine drainage is an issue associated with mining activities, particularly coal and metal mining. When water interacts with sulfide minerals,exposed during mining.Leads to chemical reactions that produce sulfuric acid, resulting in acidic water with high concentrations of metals. The acidic water can contaminate nearby streams, rivers ect Can prevent photosynthesis, toxic to aquatic life
129
How does bacterial oxidation of iron sulfide minerals lead to acid mine drainage issues?
Bacterial oxidation significantly contributes to acid mine drainage (AMD) by accelerating the breakdown of sulfide minerals
130
What role do microorganisms play in mineral formation?
-sedimentary carbonates/silicates
-elemental sulfer deposites (sulfer oxidising bacteria)
-sulfer minerals (sulfer reducing bacteria)
-magnetite
131
How do some microorganisims create Magnetite?
They can precipitate magnetite from the reduction of ferric iron
132
To study microorganisms we may take samples from...
-soil
-water
-sediment
133
To process samples of microorganisms we may...
-homogenise (to make it uniform in composition)
-dilute
-concentrate
134
To determine the number of microorganisms in a sample we may...
Direct count, viable count
135
How could we do proxy measure of biomass of microorganisms?
use cell envelope contents such as lipids, ATP, or photosynthetic pigments
136
How could we measure the activity of microorganisms?
-isotopic techniques
-"specific" inhibitors to measure metabolic intermediates
-direct chemical measurements
137
what is enumeration?
establishing the number of something
138
What ways are there to enumerate pure lab cultures of microorganisms?
-microscopic examination (count)
-dry weight of known volume (biomass)
-optical density (spectrophotometre)
-counts of colonies on agar growth media
-measurement of specific biochemicals
139
Why is it hard to enumerate microorganisms in complex natural environments?
-presence of biological/ non biological particles and chemicals
-complex mixture of organisms present
140
Describe the "direct" count procedure to measure the number of microbes and give some problems with it...
-cells are counted directly (usually with microscope, gives highest estimate of cell numbers
problems;
-cannot distinguish cells that are alive/dead
-background debris can cause problems
-provides no information on organisms present, activity or physiological type
Good for large morphologically distinguishable cells. e.g fungi, algae
141
What equipment can you use with your microscope when using the "direct" counting method?
-often we use a modified microscope slide known as a counting chamber or on filterse.g Sedgwick-rafter cell, Haemocytometer
142
It is difficult to use the "direct" count method for fungi and other filamentous organisms
How do we then modify this procedure?
-add known amount of sample to mixed agar
-placed on a microscope slide and it sets
-then stained with dye
-determine length/volume of mycelium; this can then be used to determine biomass/biovolume
143
How do we modify the "direct" method when enumerating bacterial cells?
-may dilute sample
-fluorescent stain cells
-use a specific epifluorescence microscope (UV lights cells up)
144
What are commonly used stains for "direct" count?
-Acridine orange direct (nucleic acids,)
-DAPI-4,6-diamidino, -2 phenylindole
( A-T DNA stain)
-FITC (amino groups on proteins/sugars)
-SYBR (genral nucleic acid stain)
145
What is a flow cytometer?
automated cell counting. The sample is added to a fine stream of flowing liquid through the needle. Droplets pass by optical detector. Can also use the amount of light scatter to measure the size of the cell too!
146
What is the "viable" count procedure?
A viable count procedure is a technique used to estimate the number of living (viable) microorganisms in a sample. This method specifically counts only those cells capable of growing and forming colonies under defined conditions, thereby excluding dead or non-culturable cells.
147
What are some negative of the "viable" count procedure?
-detect only cells that can grow on lab growth media (selective to some extent, gives lower estimates of cell counts)
148
What does the "viable" count method rely on?
Technique relies upon the ability to separate cells into reproductive units (individual cells). However cells normally form "clumps". Hence viable cell counts measured in CFU's (colony forming units).
149
What two methods are there for "viable" count procedures?
1.Plate counts
2.MPN (most probable number) counts
150
How to do a viable plate count?
1.organisms grow on solid agar media
2.samples serially diluted
3.plates incubated in suitable conditions
4.count the number of colonies arising from viable cells
5.then scale up depending on dilution factor to find original number of cells
151
What do we do if we want to viable plate count oxygen sensitive organisms?
Mix sample with molton agar
152
What is a diagnostic growth media?
a media used to isolate, identify, and differentiate microorganisms based on their physiological and biochemical characteristics. e.g antibiotic resistance
153
How do we do viable MPN (most probable number) counts?
Serial Dilutions: Prepare a series of tenfold dilutions of your sample using sterile diluents.
Inoculation.Incubation: Incubate the tubes under appropriate conditions.
MPN Calculation: Record the number of positive tubes at each dilution level and use an MPN table or calculator to estimate the most probable number of microorganisms per unit volume of the original sample.
154
When would we use MPN viable count method?
It's particularly useful when dealing with samples that have low microbial counts or contain particulate matter that interferes with plate count methods. Also lithotropic organisms that grow poorly on solid media, but have high turnover of metabolic substrate.
155
What type of count method gives higher counts for the number of microorganisms?
Direct count procedures for microorganisms give counts 1-2 order of magnitude higher than bacterial viable counts.
156
How can we measure microbial activity using chemical measurments?
Measuring changes in conc. of chemicals.
e.g
-Nitrification; nitrate loss/nitrite gain
-Sulfate reducion; Sulfate loss/sulfide gain
-Mathane oxidation; methane loss
-Mathanogenisis; methane gain
-nitrigen fixation; acetylene
-denitrification-nitrous oxide loss/nitrogen gain
-metabolic avtivity- CO2 production
157
What are some negatives of using chemical measurements to measure microbial activity?
-Often have limited sensitivity, as limited by accuracy of concentration of each substance
-measures potentials ( providing ideal conditions in the lab) rather than situ rates (within their natural environment, reflecting the actual conditions)
-linked processes can affect measured rates
158
What 2 isotopic techniques can we use to measure microbial activity?
-Radiotracer
-stable isotope
159
What are the benefits of using radiotracer techniques to measure microbial activity?
-extremely sensitive
-only need small amounts of tracer
-minimises perturbation of conditions during measurement
HOWEVER strict safety requirements.
160
What are the positives and negatives of using stable isotopes to measure microbial activity?
-stable/safer
-less sensitive than radiotracer
161
How can we use radiotracers to measure microbial activity?
Radioactive isotopes used to measure microbial activity by tracking the incorporation of these isotopes into microbial cells or their metabolic products. The level of radioactivity correlates with the rate of microbial activity.
162
Why may using a radiotracer give an underestimation of cell activity.
-not all organisms may assimilate new radioactivly labled compounds during their processes.
163
What is microautoradiography?
Microautoradiography is technique used to detect metabolically active microorganisms. It involves incubating a sample with a radiolabeled substrate, allowing cells to incorporate the radioactive material during metabolic processes. After incubation, the sample is overlaid with a photographic emulsion sensitive to radiation. As radioactive decay occurs, it exposes the emulsion, creating silver grains that can be visualized under a microscope, indicating active cells.
164
How can we use radioactive carbon 14 to measure microbial activity?
Use radioactive organic compounds
165
What is a biometer flask?
flask designed to measure the CO₂ produced by microorganisms during the aerobic biodegradation of organic substances, particularly in soil samples
166
What is the most common stable isotope used for stable isotope techneques?
15N, often measuring the activity of nitrogen cycling processes.
167
How do we measure gaseous radioactive products?
Mass spectrometry.
Dissolved nitrogen species are reduced to nitrous oxide/dinitrogen gas to do this.
168
What inhibitor is used for sulfate reduction?
-Sodium molybdate
-Fluoracetate
169
What inhibitor is used for methanogenesis?
-Bromoehtane sulfonic acid
170
Can inhibitors effect more the one process?
Yes! they are not specific
171
Define a gene...
a sequence of nucleotides in DNA that codes for a functional protein
172
Define a chromosome...
Genetic element carrying genes essential to cellular function. Porkaryotes typically have one chromosome which is a circular DNA molecule. Eukaryotes typically have several, which are linear DNA molecules.
173
What is a promotor?
DNA sequence in front of gene that is needed to activate gene expression
174
What is a plasmid?
extrachromosomal DNA that is not essential for normal cellular functions. Usually contains things such as antibiotic resistance.
175
What are proteins?
macromolecules that have many functions. They consist of one or more polypeptides. can be for storage, support, transport, defence, cataylisis. They're composed of repeating units called amino acids.
176
Define gene expression...
The mechanism at the molecular level by which a gene is able to express itself in the phenotype of the organism.
177
What is liebig's law of the minimum?
growth of microorganisms—like bacteria or fungi—is limited by the essential nutrient in the shortest supply, even if all other necessary nutrients are abundant.
excess= algal blooms
limitation=hydrocabon degration e.g be lack of nitrogen and phosphate
178
What is shelfords law of tolerance?
success and distribution of an organism depend on a range of environmental conditions, each with minimum, maximum, and optimum levels that the organism can tolerate. Conditions outside this range can lead to stress or death
179
What adaptationas do organisms that live in super high temperaturs have?
-high g-c contents
-lots of proteins to stabilise dna
-lots of saturated fatty acids
-ether linked
-isoprnoid lipids
