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ETT > microbial ecology 1 > Flashcards

microbial ecology 1 Flashcards

1
Q

Competition

A

a conflict of resources, affecting the growth of both organisms

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2
Q

Commensalism

A

one member benefits from another member, which itself is unaffected

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3
Q

Mutualism

A

both organism benefit from each other
- Interspecies hydrogen transfer
- Holobiont concept

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4
Q

Amensalism

A

one population adversely affects the growth of another populations, while itself is being unaffected by the other population

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5
Q

Parasitism

A

one organism, the parasite, consumes another organism, the host, often in a subtle way

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6
Q

Predation

A

one organism, the predator, engulfs and digest another organism, the prey

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7
Q

16S rRNA sequencing

A

This method targets a specific region of the 16S ribosomal RNA (rRNA) gene, which is present in the genetic material of these microorganisms

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8
Q

Syntrophy

A

process in which two or more organisms cooperate in the anaerobic degradation of organic compounds

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9
Q

Methanogenesis

A

the biological production of CH4: carried out by strictly anaerobic Archaea
- methane is produced in anoxic environments by methanogens from the reduction of Co2 with hydrogen H2 or from the splitting of acetate into CH4 and CO2

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10
Q

Complete nitrification by Nitrospira

A

comammox

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11
Q

Symbioses

A

mutualistic relationship where one species lives on or within another species

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12
Q

Phycosphere

A

a region surrounding phytoplankton calles that results from the basic physics of the diffusive boundary layer and has a higher concentrations of organic matter (produced by the eukaryote) than local waters

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13
Q

Mixotrophic predation

A

a combination of phototrophic and heterotrophic metabolism.

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14
Q

Kleptoplasty

A

a symbiotic phenomenon whereby plastids, notably chloroplast from algae, are sequestered by host organisms

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15
Q

Intermezzo

A

What can be the reason that only a minute fraction of bacteria in Natura can be isolated in pure culture?  only a few can live separately from the colony, they depend on each other. Some don’t like to grow on a medium. we can’t mimic the natural environment on a Petry dish

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16
Q

Redox cascade

A

microbial processes in marine sediments: Pathways of organic carbon degradation (mineralization) in marine sediments and their relation to the geochemical zonation and consumption of oxidants.

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17
Q

Advective-driven sediments

A

mostly permeable (sandy), where bottom water currents
produce deep oxygen penetration and high aerobic mineralization. (water diffusive trough by force)  aerobic respiration  nitrification

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18
Q

Bioturbated sediments

A

where particle reworking and ventilation of burrow structures by
fauna alter the reoxidation zones in the sediment.

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19
Q

Diffusive sediments

A

with overlapping O2 and H2S, with no bioturbation and small grain
size. Chemical gradients are driven by diffusion

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20
Q

CO2

A

carbon dioxide

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21
Q

CH4

A

methane

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22
Q

NO3

A

nitrate

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23
Q

NO2

A

nitrite

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24
Q

N2O

A

nitrogen oxide

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25
Q

NH3

A

ammonia

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26
Q

NH4

A

ammonium

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27
Q

SO4

A

sulfate

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28
Q

SO3

A

sulfite

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29
Q

S

A

Sulfide

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30
Q

nitrification

A

conversion of ammonia into easily absorbable form of nitrogen

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31
Q

denitrification

A

nitrate to nitrogen gas

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32
Q

hydrolysis

A

molecule broken down in >2 smaller molecules through addition of water

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33
Q

oxidation

A

electron-donating reaction

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34
Q

reduction

A

electron accepting reaction

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35
Q

colourless sulfur bacteria (CSB)

A

use reduced sulfur compounds as energy source -> H2S

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36
Q

sulfate reduction

A

production of hydrogen sulfide (H2S)

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37
Q

phototrophs

A

use light as E-source and produce ATP

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38
Q

protist

A

those eukaryotes that are not plants, animals, for fungi

39
Q

Why are SSU rRNA genes so widely used in biodiversity studies?

A
  • Ubiquitous occurrence among all living things  easy for comparison
  • Functional uniformity  gene that doesn’t change during evolution
  • Absence of lateral gene transfer  you don’t what the gene to be shared of crossed with different functionary line
  • Possession of conserved and variable regions that allow for nucleotide base pair alignments between closely and distantly related organisms
  • Large database
40
Q

Monophyletic group

A

groups contain all of the descendants of a common ancestor  a group of organisms that share a common ancestor

41
Q

Principle of FISH

A
  1. probe design
  2. sample preperation
  3. hybridization
  4. washing
  5. detection
  6. analysis
    –> keep cells, but it makes holes in them
42
Q

stable isotope probing (SIP)

A

similar to FISH but with radioactive substrates

43
Q

Principle of metagenomic analysis

A

-extract all DNA from the environmental sample
- Perform shot gun sequencing
- Use powerful software programs an d computers to assemble the genomes of individual community members (MAGs
= metagenome assembled genomes)

44
Q

Principles of metatranscriptomics

A
  1. total RNA exrtaction
  2. mRNA enrichment
  3. cDNA synthesis
  4. amplification
  5. preparation for high throughput sequencing
45
Q

Principles of multiple displacement amplification (MDA)

A
  • With amplification, you can increase the amount of DNA
46
Q

Convergent evolution

A

structurally the same, but very different species

47
Q

Divergent evolution

A

very close related, but have very different life strategies and morphological traits

48
Q

Saprobic (saprotrophic) nutrition

A

a process of chemoheterotrophic extra-cellular digestion involved in the processing of dead or decayed organic matter that occurs in saprobes and is most often associated with fungi

49
Q

Chytridiomycota

A

often considered ‘lower’ or ‘simple’ fungi due to the presence of primitive features such as zoospores (obliged to reproduce in water)

50
Q

Yeast

A

are fungi that are normally unicellular and reproduce by budding, although some will, under appropriate conditions, produce hyphae, just as some normally hyphal fungi may produce a yeast phase

51
Q

Arbuscular mycorrhizae

A

a symbiosis between plants and members of an ancient phylum of fungi (kleine balletjes in de hyphae)

52
Q

Ericoid mycorrhizae

A

heathlands. Are common in nutrient-poor environments  Unlike arbuscular mycorrhizal fungi, ericoid mycorrhizal fungus is facultative symbiont and can grow without the plant

53
Q

Ectomycorrhizae

A

mainly with trees and shrubs. A symbiotic association of fungi with the feeder roots of higher plants in which both the partners are mutually benefited

54
Q

Orchid mycorrhizae

A

symbiosis with fungus and an orchid  The plant partner is lacking chlorophyl (they are ‘mycoheterotrophic’) – and could not often even germinate without infection of the right fungus

55
Q

Endophytes

A

Some fungal inhabitants of plants do not cause disease or form any close contact
with the plant cells, but inhabit the apoplastic spaces of their plant hosts.
They can be specific to particular plant species.

56
Q

Lichens

A

are intimate symbiotic associations of a fungus, nearly always an Ascomycete, with an algal or a cyanobacterial species  the fungal partner uses its extracellular enzymes to gain inorganic nutrients from i.e. rock while the algal or bacterial partner provides the carbon

57
Q

Fungi causing mycoses

A

an infection caused by any fungus that invades the tissues, causing superficial, subcutaneous, or systemic disease

58
Q

Different kind of plant-parasitic fungi: Biotrophic

A

feeding on living tissue

59
Q

Different kind of plant-parasitic fungi: Necrotrophic

A

first killing the tissue, then living on it

60
Q

Generalist pathogens

A

capable of infecting a wide range of host species

61
Q

Opportunistic pathogens

A

are microorganisms that are usually harmless in healthy, immunocompetent persons but may become virulent in compromised hosts such as the immunocompromised, or people with underlying disease

62
Q

Cellulose

A

the process by which cellulose, a complex carbohydrate and a major structural component of plant cell walls, is broken down into simpler sugars or monosaccharides

63
Q

Hemicellulose

A

is a complex carbohydrate that, like cellulose, is found in plant cell walls + has a structural role in plants, providing strength to the cell wall, and it also serves as a source of energy and nutrients when broken down and metabolized by various microorganisms.

64
Q

Lignin

A

Lignin degradation is essential for the recycling of plant biomass and plays a crucial role in carbon cycling and nutrient recycling in natural ecosystems.

65
Q

Methods to study (soil) fungi

A
  • Quantifying specific fungal biomarkers; chitin, ergosterol
  • Marker selection for PCR based analysis
  • Databases
66
Q

Biofilms

A

are defined as matrix-enclosed bacterial populations adherent to each other and/or to surfaces or interfaces. This definition embraces microbial aggregates and floccules and also adherent populations within the pore spaces of porous media

67
Q

Phycosphere

A

a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell

68
Q

Plastisphere

A

consists of ecosystems that have evolved to live in human-made plastic environments

69
Q

adhesion

A

Adhesion occurs when adhesive molecules expressed on the bacterial surface bind to host surface receptors. Adhesins are cell-surface components or appendages of bacteria that facilitate adhesion or adherence to other cells or to surfaces, usually in the host they are infecting or living in

70
Q

Ecological impacts of plastic marine debris

A
  1. Entanglement  marine mammals become entanglement
  2. Ingestion  fish and birds die because of choking
  3. Adsorption/release of Persistent Organic Pollutants (POPs)
  4. Invasive species and pathogen transport  disease-causing bacteria, displacement of “native” species; located at another location because of fishing gear, nets.
  5. Unknown ecosystem effects
71
Q

How do you study plastics?

A
  • Raman/ FT-IR spectroscopy; provides signatures of what type of plastic it is
  • Illumina Next-Gen sequencing; visualize the structure of the communities that live on the microplastic
  • Scanning electron microscopy; provides signatures of large abundances of different microbes that live in the plastisphere
  • Culture isolation
72
Q

Biodegradability

A

only if all fragmented residues consumed by microorganisms as a food & energy source as measured by evolved CO2 in a defined time and disposal environment

73
Q

Great plate count anomaly

A

only 1% in cultivatable (an observation in microbiology that highlights the discrepancy between the number of microbial cells detected by microscopic examination and the number of microbial cells that can be grown and counted on agar plates.)

74
Q

18S sequencing used for

A

fungi

75
Q

±50% of applied N makes it to the crop, the rest?

A

1) leaching 2) volatilization 3) denitrification

76
Q

Killing-the-winner principle

A

mechanism where selective loss processes like host-specific viral lysis prevent the best competitors form sequenstering all the available resources

77
Q

The highest density of microbes in the column (large intestine) of the gut. Why?

A

o Food source is our own food + dead cells
o Body temperature
o The body learned to not “attack” these microbes
o Fibbers are very important for microbes to keep alive and to get a higher diversity of gut microbes

78
Q

Microbiota

A

the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space

79
Q

Metagenome

A

the collection of genes that are encoded by the members of a microbiota

80
Q

Microbiome

A

the entire habitat, including the microorganisms, their genomes (I.e. genes) and the surrounding environmental conditions (based on “biome”)

81
Q

Koch’s postulates

A
  1. Micro-organisms must be found in abundance in all organisms suffering from disease, but should not be found in healthy organisms
  2. Micro-organisms must be isolated from a diseased organism and grown in pure culture
  3. Cultured micro-organisms should cause disease when introduced in a healthy organism
  4. Micro-organism must be reisolated from the inoculated, diseased (experimental) host and identified as being identical to the original specific causative agent
82
Q

Dysbioses

A

Dysbiosis is often defined as an “imbalance” in the gut microbial community that is associated with disease. This imbalance could be due to the gain or loss of community members or changes in relative abundance of microbes.

83
Q

To analyze the spatial diversity

A

V6 – 454 sequencing; sequence a particular region of the 16S ribosomal RNA (rRNA) gene in microbial communities. This approach is a variation of the more general 16S rRNA sequencing technique, and it specifically focuses on the V6 region of the 16S rRNA gene for characterizing microbial communities.

84
Q

what happens with all the produced methane?

A

anaerobic methane oxidation (AOM); reversal of methanogenesis pathway (use of methane as electron doner, using sulfate as electron acceptor)
- Mediated by anaerobic methane oxidizing Euryachaeota (ANME)

85
Q

Where do ANME occur?

A

sulfate methane transition zone (SMTZ)

86
Q

Extremotolerant

A

can tolerate extremes but prefers less extreme for optimal growth
- Broader growth range

87
Q

Extremophile

A

adapted and require extreme environments
- Small growth range

88
Q

Halophiles

A

is an extremophile that thrives in high salt concentrations

89
Q

Water activity (Aw)

A

measure for the availability of free water molecules for biological processes

90
Q

Low salt inside cell, low salt outside

A

osmotic equilibrium

91
Q

Low salt inside cell, high salt outside

A

cell shrinks

92
Q

Low salt inside cell but with compatible solutes, high salt

A

osmotic equilibrium

93
Q
A

ETT (2 decks)

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