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Introductory Microbiology > Soil > Flashcards

Soil Flashcards

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1
Q

What is the ecosystem

A

The sum of all organisms and abiotic factors in a particular environment. An ecosystem is a dynamic complex of plants, animals, microbial communities and the non-living surroundings, which interact as a functional unit

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2
Q

What is a habitat

A

Portion of an ecosystem where a community could reside. An ecosystem contains many different habitats

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3
Q

Microbes account for ___ of all biomass on Earth

A

50%

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4
Q

What is the population

A

A group of microorganisms of the same species residing in the same place at the same time

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5
Q

What is a community

A

A group of populations

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6
Q

Two ways how microbial diversity is expressed in a ecosystem

A
  • Species richness

- Species abundance

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7
Q

What is species richness

A

The total number of different species present

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8
Q

What is species abundance

A

The proportion of each species in an ecosystem

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9
Q

Microbial species richness and abundance depend on

A

Kinds and amounts of nutrients available in a given habitat

As well as temperature, salinity, pH, water availability, etc.

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10
Q

What are guilds

A

Metabolically related microbial populations. Sets of guilds form microbial communities that interact with mcroorganisms and abiotic factors in the ecosystem

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11
Q

What is the niche

A

Habitat shared by a guild. Supplies nutrients as well as conditions for growth.
They way in which an organism fits into an ecological community

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12
Q

kinds of energy inputs

A

Sunlight, organic carbon, reduced inorganic substances

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13
Q

If we consider a lake as one ecosystem what kind of bacteria we can find there

A

Community one, where photic zone is:
Oxygenic phototrophs
Community 2: Oxic zone. Aerobes and faculatative aerobes
Community 3: a bunch of different bacteria->denitrifying, sulfate-reducing,fermentative, methanogens,acetogens

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14
Q

The deeper into the ground the bacteria goes, ___ (energy yield)

A

Less energy yield the bacteria has

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15
Q

What is determining the niche for each microbe

A

Difference in the type and quantity of resources and the physiochemical conditions of a habitat

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16
Q

What is the prime niche

A

A niche ( at least one for each organism) in which that organism is most successful

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17
Q

What is the microenvironment

A

-The immediate environmental surroundings of a microbial cell or group of cells

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18
Q

Soil particle contain different ___

A

Microenvironments

Inside there is no oxygen , comparing to the outside

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19
Q

What are the top 3 important things affecting microbial growth in the soil and the least important

A

Top 3: soil pH,organic carbon quality and quantity, soil(o2) and redox status
Least: predation and viral lysis

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20
Q

What conditions change rapidly with time and place in the soil

A

physiochemical

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21
Q

The difference between growth rates in the lab and in the nature

A

Growth rates of microbes in nature are usually well below maximum growth rates defined in the lab

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22
Q

What is happening between microbes in natural systems and between microbes and higher organisms

A

Competition and cooperation

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23
Q

What is parasitism

A

One member in the relationship is harmed and the other benefits

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24
Q

What is mutualism

A

Both species benefit (symbiosis)

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25
Q

What is commensalism

A

One species benefits and the other is neither harmed nor helped

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26
Q

What is biogeochemistry

A

The study of biologically mediated chemical transformations

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27
Q

What does biogeochemistry define

A

the transformations of a key elements by biological and chemical agents

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28
Q

Biogeochemistry agents usually proceed through

A

Oxidation-reduction reactions

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29
Q

How do microbes play critical role in energy transformation and biogeochemical processes

A

-Carbon cycle
Nitrogen cycle
Sulfur cycle
Through oxidation-reduction reactions

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30
Q

What is the soil

A

The loose outer material of Earth’s surface, distinct from bedrock (solid rock)

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31
Q

What two groups soil can be divided into

A

Mineral soils

Organic soils

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32
Q

What is the mineral soil

A

Derived from rock weathering (breaking down of rocks) and other inorganic materials

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33
Q

What are organic soils

A

Derived from sedimentation in bogs and marshes

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34
Q

Soils are composed of

A
  • Inorganic mineral matter (40% by volume)
  • Organic matter (5)
  • Air and water (50)
  • Living organisms
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35
Q

What is humus

A

Dead plant material that is resistant to decomposition.

Keep water and nutrients in the soil. Good for soil fertility

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36
Q

Different soil horizons and its characterization

A
  • O horizon.Very top. Layer of undecomposed plant material
  • A horizon. Dark color, high in organic matter; a lot of nutrients in this environment; plants and large numbers of microorganims grow here; high microbial activity
-B horizon.Subsoil (minerals, humus,
and so on, leached from
soil surface accumulate
here; little organic matter;
microbial activity
detectable but lower than
at A horizon)

C horizon. Soil base (develops
directly from underlying
bedrock; microbial activity
generally very low)

37
Q

How do you figure out what microorganisms live in the soil

A
  • Extract soil microbial community DNA

- Isolate, sequence and analyze 16s rRNA genes

38
Q

What organisms dominate soil environements

A

Bacteria, in specific proteobacteria

39
Q

Where does the most of microbial growth takes place

A

On the surfaces of soil particles

40
Q

What is the most important factor influencing microbial activity in surface soils

A

Availability of water

41
Q

What is the most important component in subsurface environments

A

Nutrient availability

42
Q

Different soil particles and what is their size

A

Sand( the largest 0.1-2mm)
Silt(0,002-0.1mm)
Clay( very small)

43
Q

What is the best particle in the soil and why

A

Sand particles are too big and water drains quickly
Silt retains water to the right extent
Clay: water retained too well, soil becomes anoxic

44
Q

What are rhizosphere

A

Soil that surrounds plant roots and receive plant secretions

45
Q

What are mycorrhizae

A

Association of fungi with plant roots

46
Q

Microorganisms in the top few centimeters of soil in the rank of their abundance

A
  • Bacteria
  • fungi
  • Protozoa
  • Algae
47
Q

Explain carbon cycle

A

CO2 is fixed by photosynthetic land plants and marine microbes.
CO2 is returned to the atmosphere by respiration as well as anthropogenic activities ( the use of fossil fuels)

48
Q

What is the largest producer of CO2 released to the atmosphere

A

Microbial decomposition

49
Q

What is the other major end product of decomposition (besides CO2)

A

CH4

50
Q

What is the most important reservoir of carbon in earth

A

Rocks and sediments

CO2

51
Q

Why only certain prokaryotes can fix nitrogen N2

A

A lot of energy is required to break the bond because of the triple bond

52
Q

What in general bacteria do with nitrogen

A

It is converting it to the sources that plants can use

53
Q

Nitrogen fixation is ___ the process

A

the most important process on earth

54
Q

In the absence of fertilizers, other organisms need

A

Nitrogen fixers

55
Q

Two types of nitrogen fixers and their examples

A

Free-living (cyanobacteria)

Symbiotic (rhizobium)

56
Q

The reaction of nitrogen fixation is catalyzed by

A

Nitrogenase complex (metal cofactors)

57
Q

Nitrogenase complex requires

A

8 electrons from pyruvate , 2 are lost as H2 in the process and input of energy

58
Q

What is the final product of nitrogen fixation

A

NH3

59
Q

denitrogenase reductase is inhibited by

A

The presence of oxygen

60
Q

How the electrons flow in nitrogen fixation reaction

A

The sequence of electron transfer in nitrogenase is as follows:
electron donor(flavodoxin) -> dinitrogenase reductase -> dinitrogenase ->
N2

61
Q

Example of free-living nitrogen fixers

A

Azotobacter
Beijerinckia
Clostridium

62
Q

Where do free-living nitrogen fixers live

A

Widespread in soil because require a soil rich in organic matter to provide energy for nitrogen fixation

63
Q

Clostridium is ___ ( metabolism)

A

Strict anaerobe

64
Q

Azotobacter is ___ ( metabolism)

A

Strict aerobe

65
Q

How plants can use ammonia produced bu nitrogen fixers

A

NH3 dissolves in water to produce ammonium NH4

66
Q

As denitrogenase reductase is inhibited by oxygen, how azotobacter keeps nitrogen fixing

A

They have a very rapid O2 consumption, which keeps the intracellular environment anaerobic

67
Q

Why only some cyanobacteria are able of nitrogen fixation

A

Because they produce energy by oxygenic photosynthesis , oxygen is produced in the cell

68
Q

As denitrogenase reductase is inhibited by oxygen, how cyanobacteria keeps nitrogen fixing

A

Nitrogen fixation occurs in specialized anaerobic cells (heterocysts), which lack photosystem II (does not produce O2)

69
Q

How do heterocysts have their pyruvate and its structure

A

Heterocysts have a thick cell wall that slow down the diffusion of O2
The regular cells provide the heterocysts with carbohydrate (pyruvate)

70
Q

What is the most important symbioses known

A

The mutualistic relationship between leguminous plants and nitrogen-fixing bacteria

71
Q

Examples of legumes

A

Soybeans, clover, alfalfa,beans, and peas

72
Q

What is the best-known bacteria, inolved in nitrogen -fixing bacteria engaged with soybeans

A

Rhizobium

73
Q

What is happening with bacteria and soybean plants

A

Colonization of legume roots by nitrogen-fixing bacteria leads to the formation of root nodules that fix nitrogen

74
Q

6 steps in nodule formation

A
  1. Recognition and attachment of bacterium to root hairs
  2. Excretion of nod factors by the bacterium
  3. bacterial invasion of the root hair
  4. Travel to the main root via infection thread( tube composed of cellulose)
  5. Formation of bacteriod state within plant cell (swollen and misshapen bacteria-fix N2). Surrounded by plant cytoplasm
  6. Continued plant and bacterial division, forming the mature root nodule
75
Q

Oxygen levels are important for nitrogen fixation. How are they controlled

A

The O2 binding protein leghemoglobin, produced by plant cells

76
Q

Do bacteriods go away with time?

A

No, they are terminal. The nodules contain regular Rhizobium cells that serve ti inoculate the environment

77
Q

Explain in general what happens at nodules

A

Plant give bacteria organic acids, with NH3 produced inside bacteria, giving off glutamine and asparagine

78
Q

Nitrogen fixation in aerial roots

A

through Mucilage-associated microbiota

79
Q

Plant acquire ___% of its nitrogen from the air.

A

29-82%. At least some of this N is fixed by bacteria in the mucilage

80
Q

What is mucilage

A

Viscous sugar-rich fluid secreted by some plants that includes diverse community of bacteria with N fixers

81
Q

Examples of N fixers bacteria in sierra

A

Rhizobiaceae

82
Q

What is amonification

A

Organic N->NH4

83
Q

Most plants will use nitrogen compounds produced by ___

A

Free-living nitrogen fixers or by other organisms during ammonification, which is good for farmers because they do not need to use as much fertilizers

84
Q

Nitrate is more ___ than ammonium and is more ____

A

Soluble and available to plasnts, though plasnts can use both ammonium and nitrate

85
Q

Sources of nitrate and what is required

A

Nitrifying bacteria: NH3-> NO2->NO3

Requires O2

86
Q

As both Nitrifying bacteria and plants need NH3, so there is

A

a competition for NH3

87
Q

What is bad for plants and farmers with the soil

A

If the soil is poorly drained and becomes waterlogged, the soil becomes anaerobic, which promotes denitrification: NO3->NO2->NO->N2O->N2

88
Q

Anaerobic conditions in the soil promote

A

Sulfur and sulfate reduction which produce H2S ( toxic for plants)

Introductory Microbiology (21 decks)

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