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BIO 315 > Module 4 - Microbial Ecosystems > Flashcards

Module 4 - Microbial Ecosystems Flashcards

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1
Q

What is the foundation of microbiology?

A

The study of microbes in pure culture as a pure species

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2
Q

What is the problem with pure cultures?

A

Microbes in nature do not exist under these ideal laboratory experiments

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3
Q

How do microbes live in nature?

A

As complex communities that exchange nutrients, waste products, and genetic material

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4
Q

How many of the total microbes are culturable?

A

Very few (vast majority are not culturable)

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5
Q

What does CFU stand for?

A

Colony forming unit

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6
Q

What is a CFU used for?

A

An estimation of the number of viable bacteria in a sample

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7
Q

How is CFU calculated?

A

The number of colonies that grow from a sample on solid media

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8
Q

Why does CFU refer to the number of bacteria in a sample?

A

Each individual bacterial cell can form one colony

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9
Q

Which environment has the lowest number of culturable bacteria?

A

Seawater

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10
Q

What is an ecosystem?

A

A community of living organisms in conjunction with nonliving components of the environment interacting as one system

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11
Q

What is life on Earth (generally)?

A

A collection of ecosystems

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12
Q

What does an ecosystem consist of?

A

A community of organisms interacting with each other and the environment

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13
Q

What does an ecosystem include?

A

Both biotic and abiotic factors

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14
Q

What are biotic factors?

A

Other organisms

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15
Q

What are abiotic factor?

A

Nonliving components, such as gases, minerals, and water

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16
Q

What defines an ecosystem?

A

The network of interactions between the biotic and abiotic factors

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17
Q

How can organisms in an ecosystem be categorized?

A

Based on their roles in terms of energy flow

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18
Q

What are the three groups of organisms, in terms of energy flow?

A

Producers, consumers, and decomposers

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19
Q

What are producers?

A

Organisms that capture energy and put it in a useable form

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20
Q

What is one of the major processes done by producers?

A

Photosynthesis

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21
Q

What does photosynthesis do?

A

It drives the incorporation of inorganic carbon (CO2) into organic molecules

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22
Q

True or false: photosynthesis is the only way communities can obtain energy

A

False: while the most common, photosynthesis is not the only way to obtain energy

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23
Q

What is a guild?

A

A group of organisms that carry out similar processes (but are not necessarily genetically similar)

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24
Q

What is microbial ecology?

A

The study of interactions of microbes with their surroundings

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25
Q

How do microbes interact with other organisms?

A

They may alter their metabolic activity based on competition from other organisms

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26
Q

What is the result of microbes interacting within their environment?

A

They work to modify their environment based on their metabolism

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27
Q

What is a niche?

A

The specific functional role of an organism within an ecosystem

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28
Q

What does a niche include?

A

The physiological interactions with the habitat and other organisms

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29
Q

How do microorganisms like to exist?

A

Within microenvironments

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30
Q

What are the characteristics of a microenvironment?

A

Conditions such as oxygen, pH, light, or nutrients may exist over a small distance

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31
Q

What happens when a microenvironment changes?

A

The microbes must also change in order to survive

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32
Q

What does the fitness of a microbe depend on?

A

Adaptation to the environment, and modifying metabolism through gene expression (use different nutrients to produce energy and biomass)

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33
Q

Where do microbes tend to grow?

A

On solid surfaces (biofilms)

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34
Q

What is a biofilm?

A

A collection of one or more types of microorganisms that can grow on many different surfaces

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35
Q

What is the purpose of a biofilm?

A

To allow bacteria to interact and support each other

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36
Q

Which microorganisms can produce biofilms?

A

Bacteria, fungi, and protists

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37
Q

What are some examples of biofilms?

A

The goo in the shower drain, and the plaque on teeth

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38
Q

What holds a biofilm together?

A

Extracellular polysaccharides

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39
Q

When are biofilms important in terms of humans?

A

When a human wants to rid a surface of microbes

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40
Q

How fast can a biofilm start forming?

A

Within minutes of a surface being introduced to a microbial-filled fluid

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41
Q

What is the first step of biofilm formation?

A

Specific bacteria bind to the surface and form the primary layer

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42
Q

What happens in biofilm formation after the primary layer is formed?

A

Secondary bacteria bind and secrete EPS

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43
Q

What does EPS stand for?

A

Exopolysaccharide

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44
Q

What is the function of EPS?

A

Helps protect biofilm, and form water-filled channels for transport of nutrients and wastes

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45
Q

What is an example of appendaged bacteria?

A

Caulobacter

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46
Q

What is special about Caulobacter?

A

It is specialized to attach to the surface and form the primary layer of biofilms

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47
Q

What is an example of EPS?

A

Colanic acid and alginate

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48
Q

What bacteria secretes colanic acid?

A

E. coli K 12 strain

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49
Q

What strains of E. coli were used to study the role of colanic acid?

A

A wild type strain, and a mutant strain that could not produce colanic acid

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50
Q

What is the result when wild type E. coli were grown in the biofilm experiment?

A

They formed a biofilm

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51
Q

What is the result when mutant E. coli were grown in the biofilm experiment?

A

They were able to attach to the surface, but not form a biofilm

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52
Q

What was the conclusion of the experiments studying E. coli biofilm formation?

A

Colanic acid was necessary for biofilm formation, but it was not necessary for cell attachment

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53
Q

How do bacteria know when to secrete EPS?

A

Through chemical signaling

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54
Q

What does the chemical signaling do during biofilm formation?

A

It assesses population density, and changes gene expression profiles

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55
Q

What is one clinical example of a biofilm?

A

The biofilm produced during cystic fibrosis

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56
Q

What bacteria is responsible for cystic fibrosis?

A

Pseudomonas aeruginosa

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57
Q

What does P. aerunginosa do in the lungs?

A

It attaches to epithelial cells, forms microcolonies, and secretes alginate

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58
Q

What is alginate?

A

An EPS secreted by P. aerunginosa during biofilm production

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59
Q

What is the advantage of a biofilm in cystic fibrosis?

A

Protect the bacteria from the immune system, and leads to increased antibiotic resistance

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60
Q

What are culturable bacteria?

A

Bacteria that can be grown in a lab environment

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61
Q

True or false: if all the bacteria could be collected, they could be cultured

A

False: they may not be active in the environment at the time of isolation

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62
Q

True or false: individual species live in isolation of their natural environment

A

False: they are complicated interactions between an individual and its environment

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63
Q

What are the two broad objectives in studying microbial ecosystems?

A
  1. How many types of microorganisms are present (biodiversity)
  2. What are their interactions/effects in the ecosystem
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64
Q

What is the estimate for the total number of bacterial and archaeal cells?

A

~10^30 cells

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65
Q

What can be said about cell number and biomass in terms of microorganisms?

A

There is a lot of biomass production and cellularity from non-eukaryal cells

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66
Q

What is one technique to grow bacteria isolated from the environment?

A

The enrichment method

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67
Q

What is an example of a type of bacteria that can be isolated through the enrichment culture method?

A

Nitrogen fixing bacteria (Azotobacter)

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68
Q

What are nitrogen fixing bacteria and what do they do?

A

Aerobic microbes that can bind to atmospheric nitrogen and release ammonium ions

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69
Q

What type of microbe is Azotobacter?

A

Nitrogen fixing bacteria

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70
Q

What is the significance of nitrogen fixing bacteria?

A

They can take nitrogen from an unusable source (atmospheric nitrogen) and turn it into a useable source for plants (ammonium ions)

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71
Q

In general, what is needed to grow bacteria in the laboratory?

A

A source of nitrogen

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72
Q

What happens if growth media without nitrogen is used?

A

Only bacteria that can use atmospheric nitrogen can grow in the growth media

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73
Q

How can nitrogen fixing bacteria be isolated?

A

By using nitrogen deprived media, so only the nitrogen fixing bacteria can survive on the atmospheric nitrogen

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74
Q

What is the purpose of the enrichment culture method?

A

To promote the growth of desired microbes over undesired cells

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75
Q

Why might microbes need to be cultured through an enrichment culture method?

A

They may be rare in the population, or may grow slowly

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76
Q

What are cultivation-independent techniques?

A

Techniques that can identify organisms that cannot be cultured

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77
Q

What are some examples of cultivation-independent techniques?

A

Direct sequencing, metagenomics, DGGE, TRFLP, FISH, and flow cytometry

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78
Q

How does direct sequencing work?

A

A DNA sample is extracted from the environment, and amplified through PCR. The 16S rRNA gene can then be sequenced for identification

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79
Q

How can unknown organisms be identified through direct sequencing?

A

By comparing the sequence to existing databases

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80
Q

What is an application of direct sequencing?

A

It can be used to estimate the relative number of each type of organism present in the sample

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81
Q

If 25/100 sequenced clones match E. coli genome sequence, approximately how many of the organisms in the sample were E. coli?

A

25%

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82
Q

What is metagenomics?

A

The study of genetic material recovered directly from environmental samples

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83
Q

What are some other names for metagenomics?

A

Environmental genomics, ecogenomics, or community genomics

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84
Q

What are the steps of metagenomics?

A
  1. DNA is extracted, isolated, and digested with restriction enzymes
  2. DNA fragments are ligated into plasmids
  3. Plasmids are transformed into bacterial cells to prepare a metagenomic library
  4. These sequences can be studied
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85
Q

How can a metagenomic library be studied?

A

Through sequencing and/or functional analysis

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86
Q

What does DGGE stand for?

A

Denaturing gradient gel electrophoresis

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87
Q

What does TRFLP stand for?

A

Terminal restriction fragment length polymorphism

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88
Q

What does FISH stand for?

A

Fluorescent in situ hybridization

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89
Q

What do DGGE, TRFLP, FISH, and flow cytometry all have in common?

A

They are all cultivation-independent techniques

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90
Q

How much of the Earth’s surface is covered with water?

A

2/3

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91
Q

Where is most of the water on Earth found?

A

In oceans (marine environments)

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92
Q

True or false: all water ecosystems are the same

A

False: a freshwater ecosystem is very different from a marine ecosystem

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93
Q

How much of the marine biomass is microbes?

A

98%

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94
Q

How much of ocean water is composed of salts?

A

3.5%

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95
Q

What are the common salt ions found in the oceans?

A

K, Ca, Mg, and Na

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96
Q

What is the highest salt found in the ocean?

A

NaCl (75%)

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97
Q

True or false: aerobic respiration can occur in oceans

A

True: the oceans are an oxic environment

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98
Q

What nutrients are low in the oceans?

A

Nitrogen, phosphorus, and iron

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99
Q

What is an example of an environment with oligotrophy?

A

The ocean

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100
Q

What is oligotrophy?

A

Living in an environment with very low levels of nutrients

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101
Q

What characteristics define an oligotroph?

A

Slow growth and low rates of metabolism

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102
Q

How can marine growth be increased?

A

By increasing the amount of nutrients

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103
Q

What happens if marine microbes are overfed?

A

This can lead to anoxic water conditions (dead zones)

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104
Q

What are dead zones?

A

Areas without enough oxygen to support much eukaryal life

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105
Q

How many identified dead zones are on the planet?

A

400

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106
Q

What is the largest dead zone on the planet?

A

The Baltic Sea

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107
Q

What has a direct connection with dead zone formation?

A

Agricultural activities

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108
Q

What are phytoplankton?

A

Microscopic marine plants

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109
Q

What is the functional role of phytoplankton?

A

They provide food for a wide range of sea creatures

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110
Q

What process do phytoplankton undergo?

A

They undergo photosynthesis based on the chlorophyll they have

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111
Q

How much of all photosynthetic activity do phytoplankton make up?

A

1/2

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112
Q

What limits the photosynthesis by phytoplankton?

A

Limited concentrations of nitrogen and phosphorus

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113
Q

What are synthetic fertilizers rich in?

A

Nitrogen and phosphorus

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114
Q

How does the Mississippi River lead to dead zones?

A

Fertilizers from farmland drain into the river, which drains into the Gulf of Mexico

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115
Q

What is the result of increased nitrogen and phosphorus in the water?

A

Phytoplankton bloom, increasing the amount of energy and organic carbon available

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116
Q

What happens when phytoplankton blooms?

A

There is a growth in heterotrophic microbes

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117
Q

What happens when there is a growth in heterotrophic microbes in the water?

A

They use up oxygen through cellular respiration, and create hypoxic conditions

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118
Q

True or false: dead zones have no life

A

False: they still have an active community of microbes, but not much eukaryal life

119
Q

How do microbes survive in dead zones?

A

Not sure, but they may adapt to the low oxygen environment

120
Q

What is the concentration of microbes in the ocean water?

A

100 million cells per mL

121
Q

Compared to the microbes, how many viruses live in the oceans?

A

10x more viruses than microbes

122
Q

How are the zones of the ocean divided?

A

Based on depth

123
Q

What are the three zones of the ocean?

A

Surface zone, mid-water zone, and deep sea zone

124
Q

What characterizes these three zones?

A

Amount of light, temperature, and pressure

125
Q

True or false: light can penetrate the surface zone

A

True: it is the topmost layer

126
Q

How deep is the surface zone?

A

0-200m

127
Q

What are the primary producers in the surface zone?

A

Phytoplankton

128
Q

What is an example of phytoplankton?

A

Cyanobacteria

129
Q

What is a heterotroph?

A

An organism that cannot create its own food, and must take in organic substances

130
Q

How is carbon and energy distributed to the other ocean layers?

A

Through zooplankton (consumers) feeding on phytoplankton, and virus mediated lysis

131
Q

What organisms are heterotrophs?

A

Most bacteria, and all protists, fungi, and animals

132
Q

How deep is the dark mid-water zone?

A

200-4000m

133
Q

What is the temperature of the dark mid-water zone?

A

2-3 C

134
Q

True or false: photosynthesis can occur in the mid-water zone

A

False: sunlight does not reach this zone, so photosynthesis is not possible

135
Q

What materials do microorganisms feed on in the mid-water zone?

A

Organic matter produced by primary producers in the surface zone

136
Q

What is the major characteristic of the deep sea zone?

A

High pressure (1000x higher than sea level)

137
Q

What is the depth of the deep sea zone?

A

Average depth is 3500m, with the deepest being 11000m

138
Q

What types of organisms can live in the deep sea zone?

A

Piezophiles

139
Q

What are piezophiles?

A

Organisms that can live in high pressure environments (also called barophiles)

140
Q

What helps maintain the fluidity of the plasma membrane in piezophiles?

A

High levels of polyunsaturated fatty acids

141
Q

What is the importance of polyunsaturated fatty acids?

A

They help keep the plasma membrane of piezophiles fluid

142
Q

How much of the primary production reaches the sea floor?

A

1%

143
Q

True or false: primary production that reaches the sea floor is likely to biodegrade

A

False: biodegradation is unlikely

144
Q

How come biodegradation is unlikely for primary production that reaches the sea floor?

A

Due to the cold conditions and lack of oxygen

145
Q

What is the result of primary production not biodegrading on the sea floor?

A

A rich sediment is formed on the sea floor

146
Q

What is the significance of the rich sediment on the sea floor?

A

This can be oil or gas reserves, which can be used by humans

147
Q

How does the proportions of archaeons and bacteria change with depth in a marine environment?

A

The proportion of archaeaons increase

148
Q

True or false: there are more archaeons than bacteria in the oceans

A

True: DNA sequencing suggests that there may be more archaeons than bacteria

149
Q

Approximately how many virions live in the oceans?

A

~10^30 (10x more than microbes)

150
Q

What is the role of viruses in the ocean ecosystem?

A

They supply the ecosystem with nutrients

151
Q

How do viruses supply the ocean ecosystem with nutrients?

A

By lysing cyanobacteria, nutrients are released into the environment

152
Q

What nutrients are released when lysing cyanobacteria?

A

Fragments of the plasma membrane, DNA, and proteins

153
Q

True or false: little is known about viruses in the marine ecosystem

A

True: little is known about their replication cycles and their ecological impacts

154
Q

True or false: viruses are integral to the proper functioning of the ecosystem

A

True: without viruses, the ecosystem would not function

155
Q

What is needed to study the physiological and metabolic needs of microbes?

A

They need to be grown in pure cultures

156
Q

How come microbes from the sea water cannot be cultured easily?

A

They cannot survive the high concentration of nutrients in the lab media

157
Q

What do commercial marine isolation medias contain?

A

Elemental profiles similar to sea water

158
Q

What are commercial marine isolation medias good for?

A

Isolating microbes

159
Q

What are commercial marine isolation medias not good for?

A

Replicating the growth conditions of the natural habitat

160
Q

What types of microbes are hard to culture?

A

Those adapted to oligotrophic conditions

161
Q

How can some metabolic properties of microbes that live in sea water be studied?

A

Through metagenomics

162
Q

What is the consequence of oligotrophic microbes?

A

They have a low yield of biomass, and do not support visible colonies

163
Q

What technique is used to grow oligotrophic microbes from sea water?

A

Dilution-to-extinction

164
Q

What is dilution-to-extinction?

A

A method to grow oligotrophic microbes from sea water

165
Q

What are the steps of dilution-to-extinction?

A
  1. A sea water sample is collected, and microbes are counted using a microscope
  2. The sample is diluted so few cells remain in aliquot
  3. Autoclaved sea water is inoculated with diluted aliquots
  4. All samples that show growth are mixed in one bottle
166
Q

True or false: dilution-to-extinction involves multiple tubes

A

True: multiple aliquots are needed to dilute the sample

167
Q

What happens once a big bottle is generated from the dilution-to-extinction method?

A

The cells are centrifuged and analyzed

168
Q

How are terrestrial ecosystem divided?

A

Into various biomes

169
Q

What is a biome?

A

Categories of ecosystems based on vegetation characteristics

170
Q

What abiotic factors distinguish biomes?

A

Temperature and precipitation

171
Q

What are the primary producers in terrestrial biomes?

A

Plants

172
Q

How do plants provide nutrients to the soil?

A

Through microbial decomposition and photosynthesis derived root exudates

173
Q

What is important for the functioning of terrestrial ecosystems?

A

The heath of the soil

174
Q

What is soil?

A

A thin band over the surface of Earth

175
Q

How is soil formed?

A

Through microbial decomposition of plant and animal matter

176
Q

What happens to plant and animal matter that is decomposed?

A

It combines with abiotic material to form soil

177
Q

Where does the abiotic material to make soil come from?

A

The weathering of rocks

178
Q

How do plants contribute to soil?

A

Through excreting nutrients from plant roots

179
Q

How are the layers of soil determined?

A

Through depth

180
Q

How does organic matter vary in the soil?

A

It is highest in the uppermost layer, and decreases with depth

181
Q

What are the layers of soil (in order from highest to lowest)?

A

O horizon, A horizon, B horizon, C horizon, bedrock

182
Q

Where is the C horizon located?

A

Closest to the bedrock

183
Q

What is the composition of the C horizon?

A

Primarily inorganic material

184
Q

What is another name for the B horizon?

A

Subsoil

185
Q

What is the composition of the B horizon?

A

It contains some organic matter

186
Q

What is another name for the A horizon?

A

Topsoil

187
Q

What is the composition of the O horizon?

A

The organic matter on the soil surface

188
Q

How come topsoil has the most organic material?

A

Due to its proximity to plant roots and decomposing biomass

189
Q

Where are microbial activity and numbers highest in a terrestrial ecosystem?

A

Near the surface (topsoil)

190
Q

What is the rhizosphere?

A

The area of soil immediately surrounding plant roots

191
Q

What is the composition of the rhizosphere?

A

Large amounts of organic carbon

192
Q

How come the rhizosphere has large amounts of organic carbon?

A

Due to the excretion of plant exudates

193
Q

What is the composition of plant exudates?

A

Sugars, sugar alcohols, and organic acids

194
Q

True or false: there are more microbes in the rhizosphere compared to the bulk soil

A

True: a large amount of microbes are found in the rhizosphere

195
Q

How come there are more microbes in the rhizosphere than the bulk soil?

A

Due to the high nutrients from the plant exudates present here

196
Q

What occurs at the rhizosphere?

A

A symbiotic relationship between plants and microbes

197
Q

How do plants benefit microbes?

A

More carbon from plants means more growth of microbes

198
Q

How do microbes benefit plants?

A
  1. Production of hormones that stimulate growth
  2. Production of antibiotics to control plant pathogens
  3. Fixation of atmospheric nitrogen into a form usable by plants
  4. Solubilization of phosphates to be taken up by plant roots
199
Q

True or false: different soil conditions can have different microbial communities

A

True: these different conditions can alter the microbial ecosystem

200
Q

How do microbes decide how to adapt the environment to keep growing there?

A

Based on the nutrient availability

201
Q

How has human activity impacted terrestrial ecosystems?

A

Dangerous chemicals get mixed into the soil

202
Q

What is bioremediation?

A

The process of using microbes to clean up contaminants

203
Q

True or false: no microbes can naturally degrade human waste

A

False: some natural microbes can degrade waste, but many commercial chemicals do not come from natural processes

204
Q

What is an example of bioremediation?

A

The use of hydrocarbon degrading microbes in petroleum-contaminated areas

205
Q

What are xenobiotics?

A

Chemicals that are not normally found in nature

206
Q

What is the danger of xenobiotics?

A

They are usually toxic, carcinogenic, or mutagenic (bad for human health)

207
Q

What are PAHs and PCBs derived from?

A

Petroleum

208
Q

What are some examples of xenobiotics?

A

PAHs, PCBs, TNT, and TCE

209
Q

What does PAH stand for?

A

Polycyclic aromatic hydrocarbons

210
Q

What does PCB stand for?

A

Polychlorinated biphenyls

211
Q

What does TCE stand for?

A

Trichloroethylene

212
Q

What does TNT stand for?

A

2,4,6-trinitrotoluene

213
Q

In the future, what will potentially happen with contaminated areas?

A

Microbes may evolve to break down these chemicals

214
Q

What is the problem with waiting for microbes to evolve to clean up contaminated areas?

A

This will take too much time

215
Q

How can contaminated areas be cleaned up without microbes?

A

Physically removing the contaminant, or incineration

216
Q

What is the problem with physically removing the contaminant from an area, or incineration?

A

It can be expensive and not practical

217
Q

What is the problem with natural biodegradation?

A

It is slow and often limited by lack of oxygen

218
Q

How come natural biodegradation is limited by the lack of oxygen?

A

The best degradation enzymes require oxygen to function

219
Q

What is biostimulation?

A

Providing oxygen and other nutrients to enhance the activity of microbes

220
Q

What can be dome to overcome the problems of natural biodegradation?

A

Biostimulation

221
Q

What is bioaugmentation?

A

The addition of a microbe that is known to degrade a particular contaminant

222
Q

What is cometabolism?

A

The addition of a nutrient that stimulates a broad substrate-range degradation pathway

223
Q

How come Earth can be seen as a “microbial world”?

A

Microbes has a majority of the biomass, carbon, and other nutrients compared to other forms of life

224
Q

What does a consumer do?

A

Ingests stored photosynthetic energy

225
Q

What does a decomposer do?

A

Breaks down dead organic matter and recycles the components back into the environment

226
Q

What are some examples of guilds?

A

Anoxygenic phototrophs, or thermophilic methanogens

227
Q

What is chemosynthesis?

A

The use of elements such as hydrogen sulfide to create energy

228
Q

How do organisms without light obtain energy?

A

Through chemosynthesis

229
Q

What is one chemical formula for chemosynthesis?

A

CO2 + O2 + 4H2S –> CH2O + 4S0 + 3H2O

230
Q

Where does the energy to fix carbon come from in chemosynthesis?

A

The oxidation of hydrogen sulfide (H2S)

231
Q

What defines a niche?

A

The type, quality, and quantity of sustaining resources

232
Q

How come two organisms cannot occupy the same niche?

A

One organism will outcompete the other and take over that niche

233
Q

What is the focus of studying microbes in nature?

A

Which metabolic types of microbes are present (not necessarily taxonomy)

234
Q

True or false: taxonomy implies metabolism

A

False: while there are some weak correlations, they do not hold generally

235
Q

What is oxidation?

A

Removing electrons from a compound

236
Q

What is reduction?

A

Adding electrons to a compound

237
Q

How does a biofilm lead to more growth?

A

Nutrients stick to the biofilm, so it can support more growth than microbes in bulk fluid

238
Q

What is another name for EPS?

A

Extracellular polymeric substances

239
Q

Besides EPS, what can be found in a biofilm?

A

Extracellular proteins and DNA

240
Q

What does quorum-sensing do?

A

Allows for coordinated signaling of microbes in a biofilm

241
Q

What is a Winogradsky column?

A

A column that allows for the study of microbial diversity

242
Q

How does a Winogradsky column work?

A

Mud from a swamp or pond is added to a clear cylinder, which is then exposed to light

243
Q

What is the result of the Winogradsky column?

A

Different microbes will proliferate at different levels of the column

244
Q

What microbes are at the top of the Winogradsky column?

A

Aerobic cyanobacteria

245
Q

What microbes are in the middle of the Winogradsky column?

A

Green and purple sulfur bacteria

246
Q

What microbes are at the bottom of the Winogradsky column?

A

Anaerobic sulfur-reducing bacteria

247
Q

How can the different microbes be visualized in a Winogradsky column?

A

Based on differences in coloration

248
Q

How can traditional cultivation approaches be used to get specific microbes?

A

By adding specific molecules to help growth

249
Q

What molecules can be added to traditional cultivation approaches to help in growth?

A

Quorum-sensing molecules, siderophores, and vitamins

250
Q

What do siderophores do?

A

Helps microorganisms acquire iron

251
Q

What part of the rRNA is used to determine phylogeny?

A

The hypervariable regions

252
Q

How can primers be used with 16S rRNA?

A

They can be used to identify all rRNA, or only rRNA from specific taxons

253
Q

What is the problem with direct sequencing of rRNA genes?

A

The primers may be biased, and it may be hard to extract DNA

254
Q

What is SIP?

A

A cultivation-independent method to analyze microbes in a community

255
Q

What does SIP stand for?

A

Stable isotope probing

256
Q

What are the two types of SIP?

A

DNA-SIP and RNA-SIP

257
Q

True or false: metagenomics lead to the sequencing of an entire organism

A

True: this creates a DNA library for that organism

258
Q

True or false: metagenomics requires cloning

A

False: the genes can be sequenced directly, without a cloning step

259
Q

Outside of the microbial world, what is the standard measure of diversity?

A

The number of species

260
Q

What does OTU stand for?

A

Operational taxonomic unit

261
Q

What is an OTU?

A

Any group of organisms that share at least 97% small subunit rRNA gene sequence identity

262
Q

What are some problems with OTU?

A

Low abundance can lead to noise

263
Q

What is microbial dark matter?

A

Genomes recovered from poorly explored microbes

264
Q

Besides cyanobacteria, what are some examples of phytoplankton?

A

Diatoms (Thalassiosira) and dinoflagellates (Ceratium)

265
Q

True or false: cyanobacteria can fix nitrogen

A

True: this is important for the marine ecosystem

266
Q

What is commonly found in marine bacteria?

A

Proteorhodopsin

267
Q

What is the general question with cultivation-independent methods?

A

Who is there

268
Q

What is the general question with cultivation-dependent methods?

A

What do they do

269
Q

How do freshwater environments differ from marine environments?

A

Freshwater environments contain much higher nutrients and organic matter due to runoff

270
Q

Why are lakes separated into zones?

A

Based on the temperature dependent density of water

271
Q

What are the three zones of a lake (in order of increasing depth)?

A

Epilimnion, thermocline, and hypolimnion

272
Q

What is the epilimnion?

A

An oxic, warmer low-density water environment

273
Q

What is the hypolimnion?

A

An anoxic, colder high-density water environment

274
Q

What is the thermocline?

A

A thin region where temperature and density rapidly changes

275
Q

True or false: photosynthesis can occur in the hypolimnion

A

True: sunlight can reach this layer, so photosynthesis can occur

276
Q

Why do some lakes mix?

A

Based on water from the bottom of the lake freezing and rising to the top

277
Q

What is the importance of mixing the layers of a lake?

A

It redistributes nutrients

278
Q

How is soil categorized taxonomically?

A

Based on physical characteristics

279
Q

What is the texture of a soil?

A

The proportion of particle sizes that make up the mineral components of the soil

280
Q

What is the importance of soil texture?

A

It is important in water retention and the concentration and interconnectedness of soil microbial communities

281
Q

What can be said about soils with larger particle sizes?

A

They tend to have fewer microbes per unit volume, but increased diversity

282
Q

What is humic material?

A

The incomplete breakdown of plant biomass

283
Q

What is the importance of humic material?

A

It aids in the aggregation of soil

284
Q

How are microbes arranged in the soil?

A

Non-uniformly, in a biofilm near soil pores

285
Q

What is a major component of humic material?

A

Lignin

286
Q

How come lignin is a major component of humic material?

A

It is resistant to degradation

287
Q

How does diversity correlate to soil pH?

A

A neutral soil has more diversity than acidic or alkaline soil

288
Q

What is brown rot?

A

The degradation of cellulose and hemicellulose, but not lignin

289
Q

What is white rot?

A

The degradation of cellulose and hemicellulose, and the mineralization of lignin

290
Q

What is the role of fungi in the soil ecosystem?

A

The degradation of plant matter

291
Q

What is the importance of actinomycetes?

A

They help break down substances in terrestrial ecosystems by releasing enzymes

292
Q

What is an example of cometabolism?

A

The methane or toluene pathways can degrade TCE

293
Q

True or false: bioremediation can only occur in terrestrial ecosystems

A

False: they can also occur in marine ecosystems

BIO 315 (12 decks)

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