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Microbial Ecology > Midterm-Final > Flashcards

Midterm-Final Flashcards

1
Q

Astrobiology: What is the primary characteristic used to define life

A

That it necessitates having an energy source

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2
Q

____ or ____ is the process in which chemicals spontaneously become an organism

A

Biopoeisis, Abiogenesis

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3
Q

How does Mars compare to Earth in terms of habitat?

A

Low pressure, atmosphere mostly CO2, low gravity (1/3rd of earth)

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4
Q

What is the Gaia hypothesis?

A

The idea that, as life becomes more ubiquitous the metabolic wastes produced by said life must be released into the atmosphere and is then measurable

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5
Q

An ammonia-based biosolvent would likely have _____ as the primary molecule in life

A

Silicon

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6
Q

What is a “BIF”?

A

Banded iron formation - large deposits of iron found at the bottoms of lakes and oceans

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7
Q

Differentiate between pelagic, epipelagic and bathypelagic habitats

A

Pelagic - open ocean near surface
Epipelagic - 0-200m deep
Bathypelagic - below 200 m

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8
Q

What is the “Hadal” portion of the ocean?

A

Below 6000m

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9
Q

the _____ zone is the ocean zone running from the intertidal zone to the edge of the continental shelf

A

neritic

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10
Q

What is the Redfield ratio?

A

Ratio of C:N:P - usually 106:16:1

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11
Q

What do highly productive areas of the ocean look like”

A

Usually near the shore, shallow water with upwelling. Usually iron-limited

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12
Q

What is the primary limiting nutrient in aquatic environments?

A

Phosphorus

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13
Q

Why are nitrates usually higher in the ocean benthos than at the surface

A

Nitrates will be assimilated by organisms at the bottom of the ocean

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14
Q

Amount of nitrogen available in the ocean is almost entirely dependent on what type of organisms????

A

Cyanobacteria.

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15
Q

What is “marine snow”

A

The constant drift of POC toward the bottom of the ocean from microorganisms dying

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16
Q

What happens during ocean upwelling in south america/the united states

A

nitrogen (and P) upwells along the land to the top of the ocean, fertilizing the ocean. This results in algal blooms (not limiting nutrients), and as nutrients move up the food chain, large amounts of fish appear

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17
Q

Where is most of the sediment carbon found in the world?

A

Mostly coastal sediments

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18
Q

What compounds decrease in the sediments with ocean depth

A

O2, NO3, Fe3+

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19
Q

What compounds INCREASE in the sediments with ocean depth?

A

CO2, CH4, NO2/NH3, Fe2+

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20
Q

Sediment productivity is ~___% of surface productivity

A

1%

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21
Q

TEAS are what

A

Terminal electron acceptors

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22
Q

How does the TEA profile of soil differ from aquatic sediments?

A

Soil is more porous so Oxygen can be found all throughout (no anoxia). Aquatic usually goes O2 on top, NO2, Fe, then SO4

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23
Q

how does sediment methanogenesis affect climate change?

A

deep sediment methane must pass through every other sediment layer before going back into the water. It usually binds to things like O2 so it’s not dangerous. It can also be locked up in deep sediments

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24
Q

Is all organic Carbon recycled by sedimenntous microorganisms?

A

Nope, about 1% enters rock

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25
Q

How does carbon sequestration in rock affect global O2 concentrations?

A

more carbon locked in rocks, more O2 available

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26
Q

study elemental cycles

A

oh boy

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27
Q

What kind of primary productivity occurs in deep dea hydrothermal vents?

A

Based on oxidation of sulphur compounds (sulphides) - NOT CONNECTED TO PHOTOSYNTHESIS

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28
Q

How does the temperature gradient in hydrothermal vents influence the bacterial populations

A

hydrothermal vents shoot hot water straight out, and the temperature gradient exists in cones of temperature

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29
Q

What is a microbial mat?

A

A group of bacteria adhering to a substrate that is a mixed community

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30
Q

How does hydrothermal vent plume H2S influence microbial mats near the vent?

A

lots of sulphur bacteria live in mats beside hydrothermal vents (cannot live directly in vent or even in water directly around it)

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31
Q

What is thought to be the terminal electron acceptor for hydrogen oxidizing bacteria near thermal vents?>

A

SO4 (sulphate)

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32
Q

Can infrared radiation be used for a form of photosynthesis?

A

Though it has never been proven, it is thought to be possible. There is not a lot of energy in infrared radiation, so any organisms that use it would grow extremely slowly

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33
Q

Distinguish between first year ice and multi year ice

A

First year ice - has survived one spring

Multi year ice - has survived more than one spring

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34
Q

What conditions are necessary to have life on floating ice?

A

Ice must be thin enough to allow radiation through, with a temp. gradient from the surface to the warmer water below. Multi year ice may also have grooves/cracks inside it in which microorganisms can grow

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35
Q

How do crevices in floating ice provide space for microorganisms to grow in multi year ice

A

Crevices of hyper-saline water can develop (hyper saline because much of the water has frozen, leaving salt behind) with algae (usually eukaryotic) along the cracks.

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36
Q

How does fisheries and oceans canada scrape microorganisms off of sea ice?

A

SCUBA DIVING TEAMS!!!

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37
Q

What does it mean to say that eukaryotic algae “leak”?

A

They often release oxygen and other compounds that can be eaten by bacteria, which may grow in small colonies on the surface of the cell

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38
Q

What is “root exuding”?

A

Soil microbes living off of the substances secreted by root cells in plants

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39
Q

How are marine microbial samples collected?

A

Using nets with super small

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40
Q

What types of organisms are found in marine picoplankton?

A

Cyanobacteria (coccoid/filamentous), prochlorophytes, heterotrophs, archaea, eukaryotes (picoalgae, picoflagellates)

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41
Q

The Marine group called “picoplankton” is sometimes inaccurately called

A

bacterioplankton

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42
Q

The picoplankton exhibit an almost constant ratio of ___:1 primary productivity to secondary productivity

A

5:1

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43
Q

What are some predators of bacteria in the ocean?

A

Sponges, filter feeders (ex. mussels),

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44
Q

Most primary productivity in ocean waters above 30m deep is dominated by what organisms?

A

Macroalgae, seagrasses

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45
Q

TRUE OR FALSE: Most primary productivity in the ocean is performed by seaweed

A

FALSE, it’s bacteria (pelagic, planktonic)

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46
Q

_____ is the most abundant pelagic cyanobacterium

A

Synechococus

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47
Q

Do eukaryotes fix nitrogen?

A

No

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48
Q

What is the general colony formation used by most nitrogen-fixers?

A

Filaments

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49
Q

How do deep sea cyanobacteria essentially control the growth of every other organism in the ecosystem?

A

Nitrogen fixation rates determine overall productivity

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50
Q

What organisms are considered to be nanoplankton?

A

protists of all kinds - primarily eukaryotic.

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51
Q

_____ is a photosynthetic bacterium related to cyanobacteria. Why is it significant?

A

Prochlorococcus. IT is the most abundant photosynthetic organism in ocean water - can perform photosynthesis at very low light levels

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52
Q

What are some representative members of the microzooplankton

A

ciliates, euglenids, large dinoflagellates,

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53
Q

How are levels of cyanobacteria and prochlorophytes different in the ocean? Why is this thought to be the case?

A

In oligotrophic environments, prochlorophytes prefer cold water whereas cyanobacteria prefer warm water. This is likely because in low nutrient environments blooms float on the surface of the water and can block light from others .

54
Q

Prochlorophytes were discovered in the 1970s. how were they detected?

A

They are so small that they generally cannot be seen under a microscope, and in fact they were discovered by running deep sea water through a flow cytometer

55
Q

About ___% of total world primary productivity occurs in the ocean

A

50%

56
Q

About ___% of carbon produced by oceanic primary productivity is lost as DOC in the ocean

A

50%

57
Q

What is meant when one says that oceanic bacteria are “patchily” distributed?

A

bacteria cluster in areas of higher nutrients, for

58
Q

What are some forms of “patchy” distribution?

A
  1. heterotrophs cling to the outside of photosynthesizers so taking samples with no photosynthesizers may not yield results
  2. may be in marine snow
59
Q

What is the criterion for calling a bacterium “marine”?

A

Must need NaCl in some way to grow or proliferate - found in ocean

60
Q

Usually, culture-dependent techniques for analyzing marine water result in a few species of organisms. What can be said about these?

A

usually gram negatives

61
Q

What kind of fungi are found in open water? Where are fungi more common?

A

Very few filamentous fungi - more common in soil

62
Q

Why was 16SrRNA used moreso in marine microbiology than in soil?

A

it’s easier to extract pure bacteria from the ocean than from soil (too many tiny particles)

63
Q

TRUE OR FALSE: Within one genus, all members are either cultivatable or non cultivatable

A

FALSE, closely related species may or may not be cultivatable

64
Q

Proteobacteria are gram _____

A

negative

65
Q

Most gamma proteobacteria in the ocean serve what purpose?

A

Oxidize small molecular weight compounds

66
Q

What is the Roseobacter clade of marine microbes

A

Members of the alpha proteobacteria - extremely ubiquitous within water column as well as across the world. Obligate marine bacteria, aerobic phototrophs. Can perform sulphur metabolism.

67
Q

Why is it thought that the Roseobacter clade is very old?

A

Presence of sulphur metabolism as well as phototrophy

68
Q

What is unique about both Sphingomonas and Pseudomonas species in the ocean?

A

Both can metabolize a lot of different types of molecules (even hundreds)

69
Q

How do Sphingomonas and Pseudomonas species differ?

A

Sphingomonas clade are ultramicrobes (extremely small), and are oligotrophic. Pseudomonas species are copitrophic - grow well and quickly when there are lots of nutrients available

70
Q

Small size of bacteria appears to be an adaptation to what?

A

Oligtrophic environments - small cell, less maintenance

71
Q

Where in the water column do methane oxidizers usually reside? Why?

A

In the interface between aerobic and anaerobic layers. This is because methane oxidation requires oxygen, but many of the organisms that do it are anaerobic. Methane also bubbles up from the sea floor

72
Q

TRUE OR FALSE: methane oxidizers can only oxidize methane

A

False: some can oxidize anything with a methyl group

73
Q

Bacteria that are motile by gliding generally live in what area of the ocean? What properties do they have to make this life easier?

A

Live on marine snow or other hard environments (shells, macroalgae), glide around the substrate and release polymerases, breaking down nutrients in the water and providing food for bacteria nearby

74
Q

What is an example of a group of gliding marine bacteria?

A

CFB - Cytophaga/Flavobacterium/Bacterioides

75
Q

A group of bacteria residing on marine snow and consuming each other’s waste products is referred to as a ____

A

Consortium

76
Q

The Planctomycetales are a group of bacteria that have an adaptation allowing them to hold to a substrate using what? How do they remove themselves from the substrate?

A

A sticky stalk.

They can bud off, and new bacteria grow flagella and swim to a new substrate

77
Q

How do we obtain an idea of what kinds of bacteria may be found in the ocean, despite them being unculturable

A

Can perform 16SrRNA studies and look for DNA sequences that indicate the presence of say, alpha proteobacteria so you know there are lots of that group

78
Q

What is significant about the SAR11 bacterial group?

A

Most ubiquitous marine bacteria (about 25%). A branch of the alpha proteobacteria. Found in nearly all water samples as well as sediment and fresh water

79
Q

What interesting group of bacteria are SAR 86 related to?

A

The group that forms symbiotic associations with marine organisms

80
Q

Marine Actinobacteria are found where in the ocean?

A

Ubiquitous but not abundant, confined to the photic zone

81
Q

SAR202 bacteria are usually where?

A

Bottom of photosynthetic zone, basically only green non-sulphur bacteria (do not deposit sulphur)

82
Q

Distinguish between Marine bacteria groups A and B

A

Group A - related to sulphur bacteria, bottom photosynthetic zone
Group B - No cultured representative, deep water bacteria

83
Q

Where can marine Archaea be found?

A

Related to medophilic Archaea, ubiquitous. Group I - surface waters, associated with cyanobacteria. Group II - Deep water

84
Q

What are the different soil horizons?

A 
O1 - identifiable materials like leaves
O2 - broken down organic matter
A - mineral layer where leaching occurs
B horizon
C horizon - Layer of deposition, carbonates
Bedrock
85
Q

What are EPS?

A

Extracellular polysaccharides

86
Q

What is the most important part of an aggregate of microbes in soil?

A

The pore size - pores inside of the soil for bacteria to live.

87
Q

How do bacteria in soil pores obtain nutrients? What conditions must be the case?

A

Firstly, must be water-filled. There must be some form of nutrients (unless they are a chemo-lithotroph, they will need carbon, O2. The bigger the pore, the better (more O2/carbon diffusion)

88
Q

What is the ideal soil pore neck size for bacteria

A

0.8-3 micrometers

89
Q

What is the ideal soil pore neck size for fungi?

A

30 micrometers

90
Q

What is the minimum soil pore neck size for protozoa?

A

6 micrometers

91
Q

What kind of protozoa can easily obtain bacteria from small pores in the soil?

A

Amoebae, because they have no cell walls and very flexible membranes

92
Q

How do some bacteria predate each other?

A

Sometimes, they will aggregate around a large bacterial colony and degrade it

93
Q

Describe the predation strategies of Bdellovibrio

A

They enter under the peptidoglycan layer of the cell. It “Drinks” the cytoplasm of the prey, increasing its own body size. At the end, there is a long string of bdellovibrio under the cell walls, and it breaks up into multiple daughter cells, using the original cell’s outer walls+membranes to form those of the new cells

94
Q

How do bacteria and fungi kill each other without direct predation?

A

Producing antibiotics

95
Q

How do so many cells in a clonal colony die off?

A

Intraspecific competition

96
Q

How does the half life of materials related to the presence of certain materials in the soil? Which particular molecules will be most common?

A

Low MW molecules breakdown more quickly and will therefore be less common in the soil.
Most common, in descending order:
Lignin, cellulose, hemi-cellulose, starch

97
Q

What compounds come from the organic carbon found in plants?

A

polymers, starch, but primarily hemi-cellulose, cellulose, and lignin

98
Q

Which materials make up the soil organic material?

A

Hemi-cellulose, cellulose, lignin

99
Q

Humic acids are one thing that we do not see in the ocean. What is up with that???????

A

It’s a complex organic molecule of undefined, irregular structure/composition. A polymer of substituted aromatic compounds linked by ether, amino and carbon-carbon bonds. We’re not really sure what it is?

100
Q

What is the operational definition of humic acids?

A

Extractable with NaOH and soluble at pH 2. Whatever precipitates out is called humic acid. what didn’t precipitate is called fulvic acids

101
Q

Generally higher populations of soil bacteria/fungi is associated with increasing percentage of what?

A

Organic material, aeration, and moisture content

102
Q

Populations of bacteria/fungi generally _____ (increase/decrease) with soil depth

A

Decrease

103
Q

Populations of bacteria/fungi generally _____ (increase/decrease) with decreasing plant coverage/plant roots

A

decrease

104
Q

In viable plate counts of soil bacteria, there is generally ____ gram-negative than gram positive organisms

A

more

105
Q

How does one remove bacteria from soil particles?

A

Essentially shake up soil in water, soil particles will filter out and you can plate the remaining water

106
Q

What are some problems with removing bacteria from soil?

A

Soil contains inhibitors of PCR reactions (can co-purify with DNA - get no PCR product), DNA can bind clay and mineral particles.

107
Q

How can thermal denaturation curves be used to analyze soil?

A

Can give an idea of how many different species there are in a given volume of soil

108
Q

Members of the division Acidobacterium include what?

A

Very few cultured representatives, have 8 major subdivisions (similar to families). Found in all soils, peat bogs, acid mine drainage, aquifers, hot springs, freshwater lakes.

109
Q

OP11 is a group of bacteria with what traits?

A

Widespread in soil, freshwater sediment, hot springs. Very few cultivated representatives, with highly atypical 16SrRNA sequences (low homology to most bacteria).

110
Q

The bacterial group referred to as “Verrucomicrobia” has what traits?

A

Widespread, abundant, active. 1-10% of total bacteria, related closely to Chlamydia

111
Q

Why are Actinobacteria the most widely studied group of bacteria?

A

Because they produce antibiotics

112
Q

What are the Actinobacteria?

A

Includes many many bacteria, most well studied group (mostly over last 50 years)

113
Q

What is the rhizosphere?

A

The area of soil around a root - usually has much larger amounts of bacteria and higher diversity than surrounding soil

114
Q

The proportion of gram negatives is _____ in the rhizosphere vs surrounding soil

A

high

115
Q

Why are Pseudomonads important in the rhizosphere?

A

inhibit plant pathogens, breakdown a lot of low MW compounds

116
Q

How dobacteria interact with plants in the rhizosphere?

A

Bacteria produce auxins (plant hormones) to manipulate plants

117
Q

Do microorganisms in the rhizosphere compete?

A

Yes, they can produce antiboitics and sideophores to suppress some plant pathogenic fungi (plant protective organisms)

118
Q

What does Pseudomonas fluorescens do in the soil in the rhizosphere?

A

Produce many compounds toxic to plant pathogens, from large to small molecules. They may inhibit Pythium, Fusarium, and even nematodes. these defenses are secreted by the organism and diffuse into the water around the root

119
Q

What kind of bacteria grow in the phyllosphere (plant surfaces)?

A

Mostly gram negatives and pigmented bacteria, mostly phototrophs

120
Q

Why are fewer bacteria found on leaves than roots?

A

Less than 1% of photosynthate lost by plants onto leaf surfaces, so there’s not a lot of food

121
Q

Why is there typically more fungal plant disease in the phyllosphere than rhizosphere?

A

Spores are usually spread above ground, and can enter stomata in leaves

122
Q

What are the primary biogeochemical cycles?

A

Carbon, nitrogen

123
Q

What are we mostly concerned about when analyzing biogeochemical cycles?

A

Transformation: change in oxidative state, primarily

124
Q

What is meant by the term “global reservoir”?

A

The global scale of one form of an element (ex. CO2 in the atmosphere)

125
Q

Where has a lot of nitrogen come from recently in the N cycle?

A

Humans making synthetic fertilizers

126
Q

Where is a lot of the earth’s carbon?

A

Most is buried in sedimentary rock as organic compounds/carbonates

127
Q

What is the largest reservoir of C on the planet?

A

Inorganic C in the ocean

128
Q

What is the standard unit of C measurement?

A

Pg (petogram), aka 10^15g

129
Q

How is the carbon cycle going to change with climate change?

A

All sorts of carbon will be release from the soil and far less will be returned to the soil.

130
Q

IF carbon moves from the ocean to the atmosphere, it will likely be in what form?

A

Methane (CH4)

131
Q

Why is it that carbon has a very low residence time around bacterial cells?

A

There is a large influx of nutrients to bacterial cells bu t an equally large efflux. Bacteria have very high affinity for nutrients, taking them in as quickly as possible (so very little found in water around cells) and also processing and removing them as quickly as possible.

132
Q

Most of terrestrial carbon is found in what forms?

A

Found as polymers such as cellulose, etc.

Microbial Ecology (2 decks)

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