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MICR222 > Module One > Flashcards

Module One Flashcards

1
Q

what is the physiology of organisms?

A

Genomes
Proteins
Metabolism
Growth and reproduction

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2
Q

what allows organisms to survive in an environment?

A

traits of the organism

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3
Q

what do we need to understand in order to understand an organism?

A

physiology
ecology
evolution

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4
Q

what do we need to know in order to understand the planet?

A

how microbes respond at a cellular level and how they respond to an environments

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5
Q

how old is planet earth?

A

~4.5 billion years old

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6
Q

how long have humans been around compared to the earth?

A

0.02%

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7
Q

what was the first form of life on the planet?

A

microbes

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8
Q

how long have microbes been on the earth compared to the earth’s life?

A

88% of its existence

for 50% of the time they were the only organism

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9
Q

what created the first oxygen on earth?

A

microbes

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10
Q

what was the environment of early earth?

A

anaerobic environment

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11
Q

what are the major changes in the earth’s atmosphere linked to?

A

microbes

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12
Q

what is the common ancestor of all life on earth?

A

LUCA

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13
Q

what does LUCA stand for?

A

Last Universal Common Ancestor

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14
Q

what can we learn from the fact that all life stems from one common ancestor?

A

by understanding one group of cells we can learn things about another group of cells because we are all related

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15
Q

what is the similarity between all life domains?

A

all three domains of life have common biochemistry
they have shared architecture
common basic mechanisms of biochemistry

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16
Q

what are the major components of cells?

A

membranes
nucleic acids (DNA/RNA)
proteins

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17
Q

what are the basic components of life?

A

CHONSP

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18
Q

what are the CHONSP elements?

A 
Hydrogen
Carbon
Oxygen
Nitrogen
Sulfur
Phosphorus
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19
Q

what are the features of CHONSP elements?

A

all can form covalent bonds (stable)

-more than one link is possible (except in H)

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20
Q

why is water so important for life?

A

chemical reactions occur in a solvent and water is the universal solvent

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21
Q

what did the Miller-Urey Experiment show?

A

-Succeeded in creating many organic molecules, most essential amino acids, and most nucleic acid bases

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22
Q

what was the conclusion of the Miller-Urey Experiment?

A

the organic building blocks of life are generated in the probable atmosphere of early earth

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23
Q

what was the environment of early earth?

A

Anoxic
High Temp
High UV
Alternative energy forms, radiant, geothermal, electric-discharge

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24
Q

what are the tendencies of early molecules?

A

aggregates

membrane-like interfaces

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25
Q

what are the types of self-assembled membranes?

A

coacervates
micelles
liposomes

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26
Q

What did the formation of early membranes allow?

A

formed a semi-permeable membrane that allows the formation of chemical gradients and allows the harvesting of energy from these gradients

forms different environments for reactions to occur

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27
Q

why is DNA the nucleic acid that the genome is most commonly stored in?

A

DNA is more stable

-less reactive in the presence of oxygen

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28
Q

what is the prebiotic world (chemistry)?

A

Precursors -> Nucleotides -> Random RNAs -> Ribozymes

this is a very random and rare occurrence

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29
Q

what is the RNA world (biology)?

A

Precursors -> Nucleotides -> Ribosymes

Ribozymes become recombinases
Ribozymes form polymerases
Ribozymes facilitate Nucleotide synthesis
Ribozymes reduce reliance on precursors

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30
Q

where did the first organisms live?

A

at the bottom of the ocean in thermal vents

Likely surviving on inorganic nutrients

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31
Q

what are the features of the first organism?

A

anaerobic

Chemolithotrophic (FeS and H2S)

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32
Q

what was the likely metabolism of the first organism?

A

FeS + H2S –> FeS2 +H2

the resulting H2 could have been used to drive a primitive ATPase with S as a potential electron acceptor

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33
Q

what is the panspermia hypothesis?

A

Alternative explanations for life or life-forming compounds

Carbonaceous meteorites may have brought the prebiotic seeds of life to early earth

No evidence to date to convincingly support this idea

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34
Q

what has shaped the current planet earth?

A

major transformations in the microbial world

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35
Q

How do gradients cause speciation?

A

gradients cause different niches which create different habitat types that different species can evolve to enhance

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36
Q

what are four types of gradients that can be caused by bacteria?

A

oxygen gradient
nutrient gradient
pH gradient
chemical gradients

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37
Q

how is an oxygen gradient formed by microorganisms?

A

oxygen is consumed faster than the rate of diffusion

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38
Q

what speciation can an oxygen gradient cause?

A

aerobes
fermenters
anaerobes

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39
Q

what speciation can a nutrient gradient form?

A

Metabolically active cells

Starving cells, dormant cells, VBNC cells, persisters, and dead cells

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40
Q

how does a nutrient gradient form?

A

the further away from the nutrient source, the fewer nutrients there are

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41
Q

how is a pH gradient formed by microorganisms?

A

microorganisms consuming and producing waste products

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42
Q

how do microbes create gradients?

A

as they grow

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43
Q

what do the gradients create?

A

gradients create a diversity of habitats

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44
Q

what is an example of experimental evidence that supports evolution?

A

Single E.coli inoculated and grown in glucose-limited media in a chemostat environment.
the glucose limitation introduced competition and so evolution of the E.coli to metabolize different growth rates and uptake of glucose.

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45
Q

what is a chemostat?

A

liquid culture maintained at a steady nutrient state

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46
Q

what are the three ways to classify microorganisms?

A

Taxonomy
Function
Metabolism

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47
Q

what are the three classification systems of organisms?

A

Biological
Phenetic
Cladistic (phylogenetic)

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48
Q

what is the biological classification system?

A

grouped based on their ability to breed. If they can breed and produce offspring that can only reproduce then they are considered the same species

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49
Q

why does the biological classification system not work for microbes?

A

microbes are asexual and do not require a mate to reproduce

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50
Q

what is the phenetic classification system?

A

grouped based on overall physical similarity with no account of evolutionary history

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51
Q

what is the disadvantage of the phenetic classification system?

A

liable to make errors due to convergent evolution. Microbes are also very similar to each other physically.

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52
Q

what is the cladistic (phylogenetic) classification system?

A

grouping based on evolution from a shared ancestor (clade) as determined from a shared trait
Can be deduced by comparing their base or amino acid sequences

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53
Q

what are the issues with the cladistic (phylogenetic) classification system?

A

Liable to ignore useful descriptive traits by being too focused on one evolutionary trait or gene

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54
Q

how does the cladistic (phylogenetic) classification system work?

A

The more similar the genomes of two organisms the more closely related they are

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55
Q

what is a molecular clock?

A

A molecular clock is a gene whose DNA sequence can be used as a comparative temporal measure of evolutionary divergence

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56
Q

what is the most commonly used molecular clock?

A

16S ribosomal gene (encodes the RNA sequence for the small ribosomal subunit)

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57
Q

why is the 16S ribosomal gene a good molecular clock?

A

universally conserved

Every living creature needs to make proteins

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58
Q

what are the properties of molecular clocks?

A
  1. Found in all living organisms
  2. Maintains its function amongst all organisms (has the same selection pressure in all organisms)
  3. Highly conserved, with multiple hypervariable regions (allows an anchor but also allows observation of evolution)
  4. Sufficient length (enough information)
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59
Q

what was the genealogical tree before pre-16s rRNA taxonomy?

A
  1. increasing complexity further away from the root

2. Man at top of the pyramid

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60
Q

who proposed the three domains of life?

A

Carl Woese

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61
Q

what are the three domains of life?

A

Eubacteria
Eukaryotes
Archaebacteria

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62
Q

what is the Eocyte hypothesis (two domain hypothesis)?

A

Implies that the closest relative to eukaryotes is one, or all of the TACK Archaea

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63
Q

what are TACK Archaea?

A

TACK archaea and eukaryotes share genes not found in other archaea

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64
Q

what are some examples of microbial species?

A 
Bacteria
Archaea
Fungi
Algae
Protozoa
Viruses
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65
Q

how many species of fungi are there?

A

> 70,000 species described

estimated ~6 million exist

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66
Q

what is an example of decomposer fungi?

A

saprophytic fungi

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67
Q

what do decomposer fungi do?

A

convert dead organic material into fungal biomass, carbon dioxide, and small molecules, such as organic acids.

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68
Q

what is absorptive nutrition?

A

describes a way of obtaining energy and nutrients in which digestive enzymes are secreted into a substrate, then smaller, easily assimilated molecules are absorbed through the cell membrane

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69
Q

what is an example of mutualist fungi?

A

Mycorrhizal fungi

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70
Q

what is the function of mycorrhizal fungi (mutualist)?

A

Colonize plant roots. In exchange for carbon from the plant, mycorrhizal fungi help solubilize phosphorus and bring soil nutrients (phosphorus, nitrogen, micronutrients, and perhaps water) to the plant.

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71
Q

what are the three groups of fungi?

A

Mutualist
decomposer
pathogens

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72
Q

what is the function of pathogenic fungi?

A

cause reduced production or death when they colonize roots and other organisms

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73
Q

what are some examples of root-pathogenic fungi?

A

Verticillium
Pythium
Rhizoctonia

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74
Q

what are some definitions of species?

A

Taxonomic rank

A group of organisms capable of interbreeding and producing fertile offspring of both genders

A separately evolving lineage that forms a single gene pool

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75
Q

what is the issue with speciation?

A

the long-standing failure of biologists to agree on how we should identify species and how we should define the word ‘species’

There is no one species definition

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76
Q

how are different organisms defined as species?

A

different phyla of organisms are defined as species in different ways

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77
Q

what is the definition of a prokaryotic species?

A

defined as “a category that circumscribes a (preferably) genomically coherent group of individual isolates/strains sharing a high degree of similarity in (many) independent features, comparatively tested under highly standardized conditions

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78
Q

what is the definition of a bacterial species?

A

a genomically coherent group of organisms

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79
Q

why are there issues with defining a species?

A

evolution is a continuum and so species will always have other organisms that are almost identical but are defined as different species

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80
Q

what is the phenotypic consistency between two organisms that defines them as the same species?

A

70% of DNA-DNA binding and over 97% of 16s ribosomal RNA gene-sequence identity

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81
Q

what are the features of the prokaryotic species definition?

A

Arbitrary
anthropocentric
rooted in practical necessity

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82
Q

what are the historical definitions of a bacterial species?

A 
growth characteristics (morphology, gram stain, growth medium)
Diseases caused
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83
Q

what are the issues with historical bacterial species definitions?

A

those that do not cause disease

they are useful identifiers but have no ecological or evolutionary meaning

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84
Q

what does the DNA-DNA hybridization comparison show?

A

phenotypic and genotypic differences

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85
Q

what does DNA-DNA hybridization measure?

A

the degree of genetic similarity between complete genomes by measuring the amount of heat required to melt the hydrogen bonds between the base pairs that form the links between the two strands of the double helix of the duplex DNA

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86
Q

what is the benefit of DNA-DNA hybridization classification?

A

provided a standardized means for identifying and classifying prokaryotes that lack well-defined morphological or phenotypic characteristics

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87
Q

when does DNA-DNA hybridization show the same species?

A

> 70% = SAME species

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88
Q

what are the issues with DNA-DNA hybridization (DDH)?

A
  1. Unclear how it relates to whole-genome relatedness
  2. It is time-consuming
  3. Carried out properly by a few laboratories
  4. Ill-suited for rapid identification
  5. Only suited for pair-wise comparison
  6. the Previous classification must be present
  7. Unavailable for non-culturable organisms
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89
Q

how many prokaryotic cells are culturable?

A

only 1-2%

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90
Q

what is the comparison between 16s rRNA sequencing and DNA-DNA hybridization?

A

No organisms sharing <97% sequence similarity at 16S meet the DDH criteria of >70%

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91
Q

what are the limitations of 16s genome vs. DNA-DNA hybridization?

A

Many examples of organisms with >97% similarity at 16s with <70% DDH
The rule only works to confirm differences not similarities

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92
Q

what are the limitations of 16s rRNA gene comparison?

A
  • lack resolution compared to DDH
  • Cannot discriminate between highly related species… >97% similarity
  • does not relate to metabolic capabilities
  • relies on a single gene
  • 16s rRNA can be too conserved (slow evolution)
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93
Q

what is ANI?

A

average nucleotide identity
-a new method of comparison

allows many genomes to be compared at the same time

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94
Q

what is the correlation between DDH and ANI?

A

70% DDH = 95% ANI

Good correlation between DDH and ANI

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95
Q

what are the issues in DDH and ANI comparison?

A
  1. We are simply updating the way we measure and compare differences
  2. No biological definition/explanation for why we sue 95% ANI or 70% DDH
  3. Biased classification system
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96
Q

16s genomes sequence vs. ANI?

A

> 95% ANI = >98.5% 16s rRNA

Good correlation between DDH, ANI and 16s

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97
Q

what is Multilocus Sequence typing (MLST)?

A

A method for the genotypic characterization of prokaryotes at the infraspecific level, using the allelic mismatches of a small number (usually 7) of housekeeping genes

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98
Q

what is the purpose of multilocus sequence typing (MLST)?

A

designed as a tool in molecular epidemiology and used for recognizing distinct strains with named species

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99
Q

what is Multilocus sequence analysis (MLSA)?

A

a method for the genotypic characterization of a more diverse group of prokaryotes (including entire genera) using the sequences of multiple protein-coding genes

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100
Q

what are ecotypes?

A

Populations that are genetically cohesive and ecologically distinct

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101
Q

what are the pros of MLSA?

A
  • higher resolution
  • uses multiple genes
  • whereas 16 s rRNA gene analysis provides a genus classification, MLSA gives a species or lower
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102
Q

what are the cons of MLSA?

A
  • genes must be single copy
  • must all be present in all the organisms being analyzed
  • what constitutes a species
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103
Q

what is metabolism?

A

the sum total of all chemical reactions that occur in a cell.
the balance between catabolic and anabolic reactions

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104
Q

what is a catabolic reaction?

A

energy-releasing metabolic reactions (breaking down bonds that store energy to release the energy)

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105
Q

what is an anabolic reaction?

A

energy-requiring metabolic reactions (building things from simpler products, this requires energy)

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106
Q

what is the issue with our knowledge of metabolism?

A

mosy knowledge of microbial metabolism is based on the study of laboratory cultures

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107
Q

what are nutrients?

A

supply of monomers (or precursors of) required by cells for growth

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108
Q

what are macronutrients?

A

nutrients required in large amounts, make up a large percentage of the cell

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109
Q

what are micronutrients?

A

nutrients required in trace amounts in the cell

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110
Q

why are CHONSPs important in the cell?

A

stable enough but not too stable to breakdown

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111
Q

how are micronutrients utilized in the cell?

A
  • Many are cofactors or part of the catalytic site of enzymes
  • Transition metals (can have more than one charge state) -> role in mediating redox reactions)
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112
Q

what is energy defined by?

A

units of kilojoules (kJ), a measure of heat energy

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113
Q

what is Gibbs free energy?

A

the energy released that is available to do work

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114
Q

what is the first law of thermodynamics?

A

energy can be changed from one form to another, but it cannot be created or destroyed. The total amount of energy and matter in the Universe remains constant, merely changing from one form to another

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115
Q

what is an exergonic reaction?

A

Release free energy

  • cell respiration
  • catabolism
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116
Q

what is an endergonic reaction?

A

Require free energy

  • active transport
  • cell movements
  • anabolism
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117
Q

what is the function of ATP?

A

is released in the catabolic reaction and used to drive anabolic reactions

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118
Q

what is oxidation?

A

loss of electrons

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119
Q

what is reduction?

A

gain of electrons

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120
Q

what is the most energy-rich state?

A

the more negative the element the more energy that it has

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121
Q

what is the electron donor?

A

the substance oxidized in a redox reaction

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122
Q

what is the electron acceptor?

A

the substance is reduced in a redox reaction

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123
Q

how does a redox reaction occur?

A

occurs in two pairs (two half-reactions)

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124
Q

how are redox reactions used in biology?

A

we can tap into the flow of electrons from one compound to another

  • energy can be stored in bonds, and used at a later time
  • Or, be used immediately as an energy source
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125
Q

what are the most common macronutrients?

A

metals and most common transition metals

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126
Q

what are the two classes of electron carriers?

A 
Prosthetic groups (attached to enzymes)
Coenzymes (diffusible) NAD+ , NADP
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127
Q

what is the most common energy currency?

A

ATP

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128
Q

how does ATP work as an energy source?

A

ATP bonds can be broken again later to release energy

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129
Q

what are the different types of energy sources?

A

Chemoorgnaotroph (organic molecules)
Chemolothotroph (inorganic molecules)
Phototroph (light)

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130
Q

what are the different carbon sources?

A

Autotroph (CO2)

Heterotrophs (organic molecules)

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131
Q

what are the different electron sources?

A

Organotroph (organic molecules)

Lithotrophs (inorganic molecules)

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132
Q

what is the most efficient terminal electron acceptor?

A

oxygen

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133
Q

what are the two functions of the citric acid cycle?

A

energy harvesting

Carbon harvesting through creating intermediates

134
Q

what are the features of anaerobic respiration?

A

the use of electron acceptors other than oxygen

  • dependent on electron transport, generation of a proton motive force, and ATPase activity
  • Less energy released compared to aerobic respiration
135
Q

how many ATP molecules are released from full energy production aerobic respiration?

A

38

136
Q

why is oxygen the best terminal electron acceptor?

A

while the other electron acceptors are good at capturing electrons, the electron transport chain is simpler with oxygen

137
Q

what is involved in amino acid biosynthesis?

A
  • Carbon skeletons come from intermediates of glycolysis or citric acid cycle
  • Ammonia is incorporated by glutamine dehydrogenase or glutamine synthetase
  • Amino group transferred by transaminase and synthase
138
Q

what are the technological advances in microbiology?

A

Direct cell counts
Culturing
16s surveys
Metagenomics

139
Q

how do microscopic and culture enumerations differ?

A

by orders of magnitude

140
Q

reasons for culture number difference?

A

different nutritional requirements
Cells may be in a non-dividing state
Organisms may rely on other organisms (cannot grow alone- obligate)

141
Q

what is selection bias?

A

most people will pick organisms that will stand out

142
Q

what is enrichment bias?

A

each culture media selects for only a few organisms

Microorganisms cultured in the lab are frequently only minor components of the microbial ecosystem

143
Q

what are the reasons that some organisms are hard to culture?

A
  • nutrients available in the lab culture are typically much higher than in nature (can be toxic to some cells)
  • Narrow set of conditions
  • selects for organisms that can grow alone
144
Q

how do we minimize the effect of cellular competition in culture?

A

dilution of the inoculum

Eliminate rapidly growing, but quantitively insignificant, weed species

145
Q

what is the issue with PCR analysis of microbial communities?

A

need to have information about the genome of the microorganism to create a primer

Primers can also have a bias towards certain microorganisms

146
Q

what are the results of PCR phylogenetic analyses?

A

several phylogenetically distinct prokaryotes are present
-rRNA sequences differ from those of all known laboratory cultures
Molecular methods conclude that less than 0.1% of bacteria have been cultured

147
Q

what is the rare biosphere?

A

a concept describing the observation that a very large proportion of the taxa in microbial communities are extremely uncommon

massive diversity at low abundance

148
Q

what did 16s genome analysis enable when compared to prior technology?

A

prior techniques lacked the resolution to detect rare biosphere

149
Q

what is the genome?

A
  • the entire complement of genetic information

- includes genes, regulatory sequences, and noncoding DNA

150
Q

what is genomics?

A

the discipline of mapping, sequencing, analyzing, and comparing genomes

151
Q

what is bioinformatics?

A

the multidisciplinary field that combines biology, computer science, information engineering, mathematics, and statistics to analyze and interpret biological data

152
Q

what defines the biology of a particular organism?

A

complement of genes, but genomes are also molded by an organism’s lifestyle

153
Q

what does bioinformatics explore?

A

gene functions
who carries what genes
where are these genes/organisms found

154
Q

what is comparative genomics?

A

Many genes can be identified by sequence similarity to genes found in other organisms (comparative analysis)

Comparative analyses allow for predictions of metabolic pathways and transport systems

155
Q

what are hypothetical proteins?

A

uncharacterized ORFs; proteins that likely exist but whose function is presently unknown

  • likely encode nonessential genes
  • in E.coli, many predicted to encode regulatory or redundant proteins
  • considered to be biological ‘dark matter’
156
Q

what is the issue with metagenomics?

A

to separate the individual genomes

157
Q

what is metagenomics?

A

the total sequence of DNA from a total sample of DNA (unbias)

158
Q

what are the pros of metagenomics?

A
  • detects as many genes as possible
  • Yields picture of gene pool in environment
  • can detect genes that are not amplified by current PCR primers
  • Powerful tool for assessing the phylogenetic and metabolic diversity of an environment
159
Q

what is total DNA extraction?

A
  • environmental single-gene surveys

- Shotgun studies of all environmental genes

160
Q

what is metagenomic DNA sequencing?

A
  • identify common genes within a community

- identify genome contents favored by current environmental conditions

161
Q

what is the difference between 16s surveys and metagenomics?

A

16s is not metagenomics

-a survey of a particular gene that uses PCR

162
Q

what is the cascade of omics?

A 
Genomics
Transcriptomics
Proteomics
Metabolomics
Glycomics; Lipidomics; Fluxomics
163
Q

what is a transcriptome?

A

the entire complement of RNA produced under a given set of conditions

164
Q

what can be learned from RNA experiments?

A
  • an expression of specific groups of genes under different conditions
  • an expression of genes with unknown function; can yield clues to possible roles
  • comparison of gene content in closely related organsims
  • identification of specific organisms
165
Q

what is proteomics?

A

Genome-wide study of the structure, function, and regulation of an organism’s proteins

166
Q

what is metabolomics?

A

The complete set of metabolic intermediates and other small molecules produced in an organism

167
Q

what effects the unknowns in a microbial community?

A

the more diverse the ecosystem, the more unknowns you will find

168
Q

what is the new type of phototrophy?

A

Light-driven ion pumps of bacteria that assist in the generation of ATP in the absence of photosynthesis

-prototype in bacteriorhodopsin

169
Q

where are proteorhodopsin found?

A

in every single body of water

170
Q

what is the mechanism of proteorhodopsin energy generation?

A

several forms exist, each tuned to the absorption of different wavelengths of light

171
Q

what are the variants of proteorhodopsin?

A

abundant in all GOS samples
a total of 2,674 putative proteorhodopsin genes were detected
variation in the residues responsible for light absorptive properties was strongly correlated with the origin of the sample

172
Q

what are the stages from individual organisms to a biosphere?

A 
Individual
Population
Community
Ecosystem
Biome
Biosphere
173
Q

how was microbiology established?

A

by studying disease-causing organisms

174
Q

how do most microorganisms live?

A

in communities of other microbes

175
Q

what are the types of competition?

A

direct or indirect

176
Q

what is the direct competition?

A

the competition that involves direct physical contact

177
Q

what is interference competition?

A

direct; physical fighting over resources

178
Q

what is the indirect competition?

A

use of resources or other things before another organism

179
Q

what is the exploitative competition?

A

indirect, competition through consuming scarce resources

180
Q

what are the patterns of competition via differential resource capture?

A

as one organism depletes its resources, its numbers decline and they lose its competitive advantage, and then the other organism that needs lower levels of nutrients can thrive

181
Q

what is the pattern of competition exclusion via chemical aggression?

A

Production of an antibiotic that kills the other. One organism dies and the other lives

182
Q

what is the effect of competition modulated by plant defense responses?

A

The plant will select for one organism to the detriment of another

183
Q

what is the effect of niche specialization in space?

A

Competition is not always static
Two organisms that share the same niche but not at the same time

Community changing over space and time

184
Q

what are the two ecological processes?

A

Stochastic

deterministic

185
Q

what is a stochastic ecological process?

A

processes occur at random. No set rules, so predictions are not possible. Outcomes will be impossible to determine

186
Q

what is a deterministic ecological process?

A

processes follow a consistent set of rules. Implies that given some input and parameters, the output will always be the same. You can easily predict what will happen once you know the rules and the conditions in the ecosystem

187
Q

how is initial colonisation deterministic?

A

most likely invaded by cells from nearby land masses

188
Q

how is initial colonisation stochastic?

A

the species of organisms from the nearby landmass is random

189
Q

what determines which organisms dominate an ecosystem?

A

determined by competition/cooperation outcomes

190
Q

what happens to a new niche over time?

A

as time passes, and conditions change (due to the colonization of the organisms) it allows new niches to open up, allowing the replacement of species

191
Q

what is ecological succession?

A

change in species composition observed upon a disturbance that opens up niches for colonization

192
Q

what are the two types of ecological succession?

A

Primary and secondary

193
Q

what is primary succession?

A

environments are colonized for the first time (e.g. after a volcanic eruption)

194
Q

what is secondary succession?

A

occur in established systems when a disturbance (e.g. N deposition) reduces diversity leading to a renewed succession thanks to newly available resources or removal of competition

195
Q

what is the driving force of microbial succession?

A

gradients

196
Q

what are gradients?

A

can be metabolic side effects (fewer substrates, change in pH)
Or purposely generated metabolites (bacteriocins, antibiotics)

197
Q

what is a disturbance?

A

processes/events which affect the species composition, structure, and function within an ecosystem

  • disturbances can have both positive and negative effects
  • can be drivers of change and increased diversity
  • can also collapse a community
198
Q

what are the two ways to respond to a disturbance?

A

resistance

resilience

199
Q

what is resistance?

A

Staying essentially unchanged despite the presence of disturbances

200
Q

what is resilience?

A

Returning to the reference state (or dynamic) after a temporary disturbance

201
Q

what are the stages of plant succession?

A
  1. bare rock
  2. mosses, grasses
  3. grasses, perennials
  4. woody pioneers
  5. Fast-growing trees
  6. climax forest
202
Q

what is the life history strategy?

A

the general survival strategy used by a microbe to ensure species viability
-dictates the conditions under which a microbe can not only survive, but thrive

203
Q

what are the features of r strategists?

A
  • don’t compete well
  • need lots of resources
  • major “skill” is high reproduction
  • do not depend on others
  • have extreme population fluctuations
204
Q

what is an example of an r strategist?

A

Pseudomonas

205
Q

what are the features of K strategists?

A
  • excel in competitive environments (low resources)
  • efficient but slow growing
  • stable population
  • often require interaction with other organisms to survive
206
Q

what are marine microbial blooms?

A

transient events that typically last for several weeks and are large enough to be visible from space

207
Q

what is the community succession from diatom blooms?

A

once the diatoms die, their biomass provides nutrients for other bacteria

208
Q

what are the factors that affect community succession?

A

competition
cooperation
disturbances

209
Q

what is parasitism?

A

one member in the relationship is harmed and the other benefits

210
Q

what is mutualism?

A

both species benefit

211
Q

what is commensalism?

A

one species benefits and the other is neither harmed nor helped

212
Q

what are social cheaters?

A

Individuals in a population that benefits from the cooperative behavior of other individuals without themselves contributing to cooperation

213
Q

what is the function of protozoa?

A

dissolve the microbes and eat them

214
Q

how do fungi gain energy?

A

by consuming organic material, dead or alive

215
Q

what is the nutrient level of salt water?

A

nutrients are limited

216
Q

what does limited nutrients cause?

A

competition

217
Q

what selects for different microbial conditions in the ocean?

A

Physical and chemical conditions

Diversification (gradients drive conditions for an organsim)

218
Q

what is the general surface temperature of the ocean?

A

surface (~35 degrees)

seasonal fluctualtions no more that 20 degrees

219
Q

what is the general temperature. ofthe ocean belwo 100m?

A

0-5 degrees

220
Q

what is the pH of the ocean?

A

8.3-8.5

221
Q

how is the pH of of the ocean changing with cliamte change?

A

rising CO2 levels are causing ocean acidification , the pH is decreasing

222
Q

why is oxygen important for microbial growth?

A

is a major electron acceptor for many microbes

223
Q

where are the regions in the ocean with near 0 oxygen at the surface?

A

in the tropics and around coasts

224
Q

why are the regions in the tropics low in surface oxygen?

A

the higher the temperature of the water the less oxygen that can be dissolved in it

225
Q

why are coastal regions low in oxygen?

A

they are high in nutrients and so can support a lot of life and the oxygen gets used up quickly,

226
Q

what changes with the depth of the ocean?

A

temperature
pressure
light

227
Q

what determines an microbes survival?

A

the availability of energy

228
Q

what are microbial energy sources?

A

chemical

light

229
Q

what wavelength of light penetrates furthest into the ocean?

A

blue light

230
Q

what is the difference between the open ocean and coastal water light penetration?

A

light penetrates deeper into the open ocean

231
Q

why does light not penetrate as far in coastal water?

A

more sediment in the water and so the light is more likely to scatter

232
Q

where do photoautotrophs live in the ocean?

A

in the surface waters

233
Q

what is the function of photoautotrophs in the ocean?

A

they capture light energy and then transfer this light energy to other organsims when they are eaten or through their waste products

234
Q

how much of the marine energy is produced by phytoplankton?

A

> 90%

235
Q

how does phytoplankton provide energy to other organsims?

A

they act as a carbon source

236
Q

how does light effect productivity of life?

A

as light diminishes with depth, so does productivity

237
Q

what is the microbial carbon pump (MCP)?

A

the microbial transfer of organic carbon from labile (easily degradable) to refractory (recalcitrant or non-degradable) states

238
Q

what is the life cycle of carbon stored by microorgansims?

A

microorganisms transfer energy from matter
They die and, make the nutrients available to other organisms
Most of the carbon is released into the water
Some are released into the air as carbon dioxide

239
Q

what is the biological carbon pump?

A

The biological pump refers to the export of phytoplankton-derived POM from the surface oceans ro deeper depths via sinking

240
Q

what is the function of the biological carbon pump?

A

energy transfer and carbon transfer from the surface to the depths of the ocean

241
Q

how does the rate of microbial growth differ with ocean depth?

A

at the top microbes are fast-growing

at the bottom, they are very slow growing

242
Q

what are proteorhodopsins?

A

membrane-bound proteins that change physical shape when exposed to light

243
Q

what is rhodopsin?

A

membrane-embedded protein that absorbs a photon, causing a physical change

244
Q

what does the conformational change in rhodopsin cause?

A

A cause a proton, or halide ion, to be translocated from one side of the cell to the other

can also be sued to initiate a signal or cascade, or can be used to directly power several energy-requiring celluralrfunctions

245
Q

how do rhodopsins differ?

A

they respond differently to different wavelengths of light

246
Q

what are the features of proteorhodopsin?

A

isolated deep in the photic zone (75-100m) and is blue light absorbing

when isolated from closer to the surface the light absorbancy is different (green and/or blue)

247
Q

how is light important for ocean microbial growth?

A

light-driven processes sustain and control the flow of external energy into the global ocean

248
Q

what are the three different types of photosynthesis?

A

oxygenic photosynthesis (OP)
Anaerobic anoxygenic photosynthesis (AnAnP)
Aerobic anoxygenic photosynthesis (AAnP)

249
Q

what is oxygenic photosynthesis?

A

classic photosynthesis

250
Q

what is anaerobic anoxygenic photosynthesis?

A

hydrogen sulfide is instead of water

does not produce oxygen

251
Q

what is aerobic anoxygenic photosynthesis?

A

wide variety of sources

organisms often have a very flexible metabolism

252
Q

what are the other two light-driven processes?

A

rhodopsin-based

phytochrome-based

253
Q

what do rhodopsin-based and phytochrome-based processes require?

A

carbon to be produced by other organisms

254
Q

how does transcription of proteorhodopsin and photosynthesis genes differ?

A

transcription is tightly synchronized to the day/night cycle

255
Q

what is the role of Prochlorococcus?

A

further establishes synchrony of microbes by pulses of organic carbon

256
Q

what are the subtropical front zone (STFZ) and MOTS?

A

the transition zone between multiple water sources

257
Q

what is linked to MOTS transections?

A

changes in physiochemical, nutrient, and biological parameters

258
Q

how are microbial communities trales of space/time?

A

using 16s sequencing

259
Q

what drives microbial seasonality?

A

phytoplankton blooms in surface waters

260
Q

what changes in the water seasonally?

A

Chl levels change throughout the year in surface waters

This change is linked to changes in productivity, even in deep water

261
Q

what is a living bioreactor?

A

the symbiotic rumen microbiome

262
Q

what is New Zealand’s milk production annually?

A

3% of the world’s milk

16 billion liters/year

263
Q

how much of NZs meat production is exported?

A

> 82%

264
Q

why are the numbers of animals in the world increasing?

A

step rise in the number of animals due to the increasing population of humans and an increase in the demand for food

265
Q

what makes an animal a ruminant?

A

they have a rumen

266
Q

what are the features of a rumen?

A

has multiple chambers

harbors microbes that feed the animal

267
Q

how does a rumen create a mutualistic environment?

A

the microbes in the rumen feed the animal

the animal feed the microbes in the rumen

268
Q

what is the interaction between a ruminant and microbes?

A

the microbes and the ruminant have a symbiotic relationship

269
Q

what are the four chambers of the rumen?

A

Rumen
Reticulum
Omasum
Abomasum

270
Q

what is the rumen (chamber one)?

A

this is where food is churned in a rotary motion and fermentation takes place (9-12 hours)

271
Q

what is the reticulum (chamber two)?

A

used for regurgitation of food “chewing the cud” to increase the surface area for microbial attack

272
Q

what is the omasum (chamber three)?

A

acts as a filtering device to regulate the type of digest that enters the Abomasum

273
Q

what is the abomasum (chamber four)?

A

true acidic stomach. Secretes gastric juices (e.g. mucus, pepsin, and HCl). Protein is denatured. Site of bacterial protein assimilation by the animal

274
Q

what are the important features of the rumen?

A

large size
High constant temperature
Anaerobic environment

275
Q

why is a large rumen important?

A

important for retention of food for microbial attach

276
Q

why is a high constant rumen temperature important?

A

39 degrees
6.5 pH
carefully controlled habitat

277
Q

why is an anaerobic rumen important?

A

supports microorganisms in “symbiotic association”. Considerable capacity to digest cellulose.
Anaerobic fermentation

278
Q

why are the microbes in the rumen so important to the animal?

A

because the animal does not have the enzymes required to breakdown cellulose but the microbes do
this means that the cow can get energy from cellulose, only if the microbes are present
without them, it would die

279
Q

why is the animal so important to the microbes in the rumen?

A

the animals provide the microbes with their food source on a high scale level through masticated feed (grass)

280
Q

how is energy from the microbes “paid” to the animal?

A

in the form of volatile fatty acids (VTFs)

281
Q

what are the types of microbes that provide energy to the ruminant?

A

homoacetogens

282
Q

what are the microbes that convert wasted energy into methane?

A

methanogens

283
Q

what are the cellulose-degrading microbes in the rumen?

A

Fibrobacter succinogenes

Ruminococcus albus

284
Q

what are the starch degraders in the rumen?

A

Bacteroides ruminocola

Streptococcus bovis

285
Q

what are the lactate degraders in the rumen?

A

Megasphaera elsdenii

286
Q

what are the methanogens in the rumen?

A

Methanobrevibacter ruminantium

287
Q

what can shape the composition of microbes in a rumen?

A

species

diet

288
Q

what is most rumens comprised of microbially?

A

Prokaryotes (cellulose, starch, lactate degraders, and methanogens)
Protozoa
Fungi

289
Q

what are the key products created by the microbes that benefit the cow?

A

Acetic acid
Propionic acid
Butyruc acid

290
Q

what are the microbial processes that occur in the rumen?

A

Hydrolysis (cellulolysis, amylolysis)

Fermentation

291
Q

what are the microbial waste products of rumen microbes?

A

CO2
CH4
H2O

292
Q

what is the final carbon and energy source of the cow procided by the microbes in the rumen?

A

Volatile fatty aicds (VFA)

293
Q

what else are the microbes in the rumen used for?

A

once they pass into the small bowl of the ruminant they provide ~90% of the requirements of amino acids and vitamins

294
Q

what is syntrophy/cross-feeding?

A

metabolic interaction between dependent microbial partners

Also called obligately mutualistic metabolism

295
Q

what is an example of syntrophy?

A

inter-species hydrogen transfer

production of H2 by one organisms and H2 consumption by another

296
Q

what happens in the rumen without methanogens?

A

glucose undergoes glycolysis through bacterial metabolism and hydrogen is produced as a by-product

the build-up of hydrogen inhibits fermentation

297
Q

which part of fermentation does the build-up of H2 inhibit?

A

the oxidation of NADH and H+

298
Q

what is the role of methanogens in the rumen?

A

Methanogens take CO2 and H2 and convert it into CH4 (methane) which is then released via respiration
H2 no longer builds up and fermentation can proceed

299
Q

what is an example of a microbe in the rumen that produces H2?

A

Ruminococcus albus

300
Q

what are the features of methanogens?

A

rumen methanogens are hydrogenotrophic (hydrogen eaters)

301
Q

How are methanogens beneficial to the ruminant?

A

they keep the partial pressure of H2 low and therefore fermentations are directed towards the formation of organisms acids (ACETATE) used by the animal

302
Q

how can the level of methanogens be measured?

A

methanogens are autofluorescent

303
Q

what is the benefit of syntrophic relationships?

A

They allow reactions that are not energetically feasible for one of the microbes acting alone to be possible

304
Q

what is IHT?

A

interspecies hydrogen transfer

305
Q

what is interspecies hydrogen transfer?

A

refers to the syntrophic process by which one organism transfers hydrogen to another

306
Q

what are the benefits of interspecies hydrogen transfer?

A
  • keeps fermentation directed towards short chain volatile fatty acids like ACETATE
  • without it H2 accumulates and inhibits fermentation leading to animal malnutrition
307
Q

what is an example of a short-chain volatile fatty acid?

A

ACETATE

308
Q

what are the main events that caused an increase in carbon emissions?

A
  1. Mechanization, water power, steam power

2. Mass production, assembly line, electricity

309
Q

how can we try and reduce agriculture’s impact on methane production?

A

identify inhibitors to control the growth of methanogens

310
Q

what is soil made from?

A

minerals (inorganic nutrients)
Air (O2 and other gases)
water
organic material (live and dead biomass)

311
Q

what are the components of soil?

A

pore space (40-60%)

  • air (20-30%)
  • water (20-30%)

Soil solids (~50%)

  • Mineral (45%)
  • Organic (5%)
312
Q

what is igneous rock?

A

rocks formed when magma (molten rock) from the interior of the earth cools and solidifies

313
Q

what is metamorphic rock?

A

the heat and pressure of the earth’s interior transform igneous rock and sedimentary rocks into metamorphic rocks

314
Q

what is sedimentary rock?

A

atmospheric agents erode and transport igneous rock to the seabed, where they are compressed and merged with others into sedimentary rock

315
Q

what is weathering?

A

the means by which soil, rocks, and minerals are changed by physical, chemical, and biological processes

316
Q

what factors can influence the development of specific soil?

A
  1. Parent material
  2. climate
  3. living organisms
  4. Topography
  5. time
317
Q

what are the types of rocks that can result from weathering?

A 
clay
silt
sand
granule
pebble
cobble
boulder
318
Q

what are the stages of transition from soil to rock?

A 
residual soil
fully weathered
strongly weathered
weak weathered
slightly weathered 
intact rock
319
Q

how do microbes affect the formation of soil?

A

introduction of microbes starts the enable the rock to sustain life
weeds add carbon which provides a direct source of energy and activity

the organic layer is directly proportional to the amount of biomass

320
Q

what are the features of desert soil?

A

Aridisol forms in deserts. Rainfall is so low that no O-horizon forms and soluble minerals accumulate in the B-horizon

321
Q

what are the features of temperate soil?

A

Alfisol forms in temperate climates. An O-horizon forms and less-soluble materials accumulate in the B-horizon

322
Q

what are the features of tropical soils?

A

Oxisol forms in tropical climates where percolating rainwater leaches all soluble minerals, leaving only iron- and aluminum-rich residues

323
Q

what are the factors that affect soil development?

A
  1. Climate: rainfall and vegetation
  2. slope
  3. substrate
  4. pH (most observed)
324
Q

what are the six categories for soil classification?

A 
order
suborder
great group
subgroup
family
series
325
Q

What is soil taxonomy based on?

A

morphogenetic soil classification system using diagnostic horizons and features to infer pathways of soil genesis and formation

326
Q

what are some of the features/components of soil?

A 
Silt/clay particles
microbes
POM
pore space
virus
fungi
organic matter binder and pore space
mycorrhizal fungal hyphae
plant root
327
Q

what are the six functions of soil?

A
  • the extraction of raw materials and water
  • physically supporting buildings and other man-made structures
  • the production of biomass
  • filtration, buffering, storage, and chemical/biochemical transformations
  • the preservation of biodiversity or potentially useful genetic material
  • the preservation of geogenic and cultural heritage
328
Q

what factors can affect the nitrogen transforming pathways?

A
  • pH
  • Moisture
  • Carbon availability
  • genetic potential
  • other microbe related factors
329
Q

what is involved in nitrogen-fixing?

A

many organisms and many different genes

330
Q

what can pH act to regulate?

A

Emissions
Denitrification
Community composition

pH has a direct and indirect effect

331
Q

what is the effect of urine patches?

A

create a unique environment, with new rules

pH control on emissions abolished

332
Q

what are the effects of urea?

A

urea induces

  • a decrease in community diversity
  • a shift in community composition

MICR222 (1 decks)

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