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microbial ecology 1 Flashcards

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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
NH3
ammonia
26
NH4
ammonium
27
SO4
sulfate
28
SO3
sulfite
29
S
Sulfide
30
nitrification
conversion of ammonia into easily absorbable form of nitrogen
31
denitrification
nitrate to nitrogen gas
32
hydrolysis
molecule broken down in >2 smaller molecules through addition of water
33
oxidation
electron-donating reaction
34
reduction
electron accepting reaction
35
colourless sulfur bacteria (CSB)
use reduced sulfur compounds as energy source -> H2S
36
sulfate reduction
production of hydrogen sulfide (H2S)
37
phototrophs
use light as E-source and produce ATP
38
protist
those eukaryotes that are not plants, animals, for fungi
39
Why are SSU rRNA genes so widely used in biodiversity studies?
- 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
Monophyletic group
groups contain all of the descendants of a common ancestor  a group of organisms that share a common ancestor
41
Principle of FISH
1. probe design 2. sample preperation 3. hybridization 4. washing 5. detection 6. analysis --> keep cells, but it makes holes in them
42
stable isotope probing (SIP)
similar to FISH but with radioactive substrates
43
Principle of metagenomic analysis
-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
Principles of metatranscriptomics
1. total RNA exrtaction 2. mRNA enrichment 3. cDNA synthesis 4. amplification 5. preparation for high throughput sequencing
45
Principles of multiple displacement amplification (MDA)
- With amplification, you can increase the amount of DNA
46
Convergent evolution
structurally the same, but very different species
47
Divergent evolution
very close related, but have very different life strategies and morphological traits
48
Saprobic (saprotrophic) nutrition
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
Chytridiomycota
often considered ‘lower’ or ‘simple’ fungi due to the presence of primitive features such as zoospores (obliged to reproduce in water)
50
Yeast
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
Arbuscular mycorrhizae
a symbiosis between plants and members of an ancient phylum of fungi (kleine balletjes in de hyphae)
52
Ericoid mycorrhizae
heathlands. Are common in nutrient-poor environments  Unlike arbuscular mycorrhizal fungi, ericoid mycorrhizal fungus is facultative symbiont and can grow without the plant
53
Ectomycorrhizae
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
Orchid mycorrhizae
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
Endophytes
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
Lichens
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
Fungi causing mycoses
an infection caused by any fungus that invades the tissues, causing superficial, subcutaneous, or systemic disease
58
Different kind of plant-parasitic fungi: Biotrophic
feeding on living tissue
59
Different kind of plant-parasitic fungi: Necrotrophic
first killing the tissue, then living on it
60
Generalist pathogens
capable of infecting a wide range of host species
61
Opportunistic pathogens
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
Cellulose
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
Hemicellulose
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
Lignin
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
Methods to study (soil) fungi
- Quantifying specific fungal biomarkers; chitin, ergosterol - Marker selection for PCR based analysis - Databases
66
Biofilms
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
Phycosphere
a microscale mucus region that is rich in organic matter surrounding a phytoplankton cell
68
Plastisphere
consists of ecosystems that have evolved to live in human-made plastic environments
69
adhesion
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
Ecological impacts of plastic marine debris
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
How do you study plastics?
- 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
Biodegradability
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
Great plate count anomaly
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
18S sequencing used for
fungi
75
±50% of applied N makes it to the crop, the rest?
1) leaching 2) volatilization 3) denitrification
76
Killing-the-winner principle
mechanism where selective loss processes like host-specific viral lysis prevent the best competitors form sequenstering all the available resources
77
The highest density of microbes in the column (large intestine) of the gut. Why?
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
Microbiota
the ecological community of commensal, symbiotic, and pathogenic microorganisms that share our body space
79
Metagenome
the collection of genes that are encoded by the members of a microbiota
80
Microbiome
the entire habitat, including the microorganisms, their genomes (I.e. genes) and the surrounding environmental conditions (based on “biome”)
81
Koch’s postulates
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
Dysbioses
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
To analyze the spatial diversity
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
what happens with all the produced methane?
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
Where do ANME occur?
sulfate methane transition zone (SMTZ)
86
Extremotolerant
can tolerate extremes but prefers less extreme for optimal growth - Broader growth range
87
Extremophile
adapted and require extreme environments - Small growth range
88
Halophiles
is an extremophile that thrives in high salt concentrations
89
Water activity (Aw)
measure for the availability of free water molecules for biological processes
90
Low salt inside cell, low salt outside
osmotic equilibrium
91
Low salt inside cell, high salt outside
cell shrinks
92
Low salt inside cell but with compatible solutes, high salt
osmotic equilibrium
93

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