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Microbial Ecology > Microbial Community Studies > Flashcards

Microbial Community Studies Flashcards

(75 cards)

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1
Q

are research projects that explore various aspects of communities, including their structures, dynamics, and interactions among members.

A

community studies

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2
Q

control microbial growth

A

abiotic parameters

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3
Q

when utilizng microscopy, this is used to know the appearance

A

morphology

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4
Q

are all organisms culturable

A

no

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5
Q

refers to the variety of life on Earth, encompassing all living organisms, from microscopic bacteria to large mammals, and the ecosystems they inhabit.

A

biodiversity

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6
Q

Microbial habitats tend to be
___in nature

A

heterogeneous

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7
Q

Selection of appropriate
sampling methods for
obtaining a ____
sample of this heterogeneity
must be considered.

A

representative

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8
Q

is the technique of preserving
the cells as close to their actual
distribution as possible

A

fixing

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9
Q

physical fixing can be thru

A

freezing

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10
Q

chemical fixing cn be thru

A

additives to arrest function

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11
Q

– most also preserve the
material you are after until you get to
the lab

A

preservation

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12
Q

a reagent for RNA
extraction

A

RNA later

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13
Q

Dry ice-ethanol, liquid nitrogen, refrigerator

what kind of fixing?

A

physical

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14
Q

ethanol, Glutaraldehyde,
Parafomaldehyde

what kind of fixing

A

chemical

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15
Q

When should we be MOST concerned with maintaining sterile technique

A

SEM samples
PCR samples
FISH samples
MPN samples
culture samples
shotgun samples

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16
Q

allows microbial ecologists to count the number of organisms present in
an environment, determine how many are metabolically active, visualize
morphologies associated with environmental features, and determine
the interactions between microorganisms and mineral surfaces

A

microscopy

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17
Q

A simple-to-use fluorescent stain, 4’,6-diamidino-2-phenylindole (DAPI), visualizes
nuclear DNA in both living and fixed cells.

A

microbialcell stain

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18
Q

flourescent stain to visualize nuclear DNA in both living and fixed cells

A

4’, 6-diamidino-2phenylindole (DAPI)

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19
Q

was used to determine the number of nuclei and to assess gross cell
morphology

A

DAPI staining

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20
Q

other types of mcirobial cell stain

A

methylene blue
iodine
acid fast staining

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21
Q

other DAPI, binds to nucleic acids or other constituents of the
cell, are used – fluorescence microscopy

A

acridine orange

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22
Q

Culturing microbes from environment and
count cfu.

A

direct count procedure

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23
Q

problems for direct count procedure?

A

unculturable
slow growing
extremely small

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24
Q

FISH meaning

A

fluorescene in situ hybridization

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25
probe is in contact with DNA
FISH
26
in situ means
within cell
27
A molecular cytogenetic technique that allows the localization of a specific DNA sequence or an entire chromosome in a cell.
FISH
28
It is utilized to diagnose genetic diseases, gene mapping, and identification of chromosomal abnormalities, and may also be used to study comparisons among the chromosomes' arrangements of genes of related species.
FISH
29
FISH involves unwinding of the double helix structure and binding of the DNA of all ___attached to a fluorescent molecule with a specific sequence of sample DNA, which can be visualized under the fluorescent microscope.
probes
30
FISH involves unwinding of the double helix structure and binding of the DNA of all probes attached to a fluorescent molecule with a specific sequence of sample DNA, which can be visualized under the ___microscope.
fluorescent
31
sequence of DNA with fluorescent dye, complementary with target DNA
probe
32
when probe binds to the gene of interest, this occurs
hybridization
33
when the probe does not bind to gene of interest, this means that
no hybridization (might have mutation)
34
in this sample, FISH can be used to see genes undergoing mutation/chromosomal aberrations
human sample
35
in this sample, FISH can be used to detect their presence
bacterial sample
36
Several studies in the 1990s proclaimed that less than __% of environmental organisms were culturable using standard media and conditions
1
37
use of media and conditions that incorporate nutrients and abiotic factors from an organism’s environment greatly enhances the success of the cultivation efforts
microorganism cultivation
38
Successful culturing efforts of environmental organisms rely on addressing two major challenges
❑supplying nutrient sources and abiotic conditions of the natural environment in which the desired organisms are growing and ❑preventing the fast-growing organisms from this environment from outperforming the slower-growing organisms from the same environment.
39
It is the science of using molecular data (DNA and protein sequences) to infer the phylogenetic relationships among species.
molecular phylogenetics
40
The objective of most phylogenetic studies is to
o reconstruct the treelike pattern that describes the evolutionary relationships between the organisms being studied
41
Obtaining copies of specific gene sequences i.e. 16s rRNA gene from organisms through amplification using ___– through specific primers
PCR
42
when the specific gene sequence were obtained, what happens next?
* Send for sequencing - as a result we get rDNA sequence data
43
sequencing results
rDNA
44
- Important step in the analysis of novel 16S rRNA sequences in processing the sequence data using computers (comparative analysis)
sequence alignment
45
If the obtained sequence is similar to sequences existing in database - the conclusion would be that the organism (or it’s close relative) is ___in the sample.
present
46
Sequences, that are dissimilar from those already known indicate ___ microbe group
novel
47
is conserved in bacteria, and contain hypervariable regions that can provide species-specific signature sequences
16s rRNA
48
is widely used in identification of bacteria and phylogenetic studies.
16S rRNA sequencing
49
important bacterial gene in their 30s ribosomal subunit
16s rRNA
50
is a section of DNA or protein sequence that exhibits a high degree of variation or polymorphism compared to other regions. These regions are often associated with important biological functions, particularly in interactions with other organisms or substances, such as antigens.
hypervariable region
51
Is the genomic analysis of microbial communities by extraction and sequencing or cloning of their DNA, that allows studying community of organisms directly from their natural environment.
metagenomics
52
Consists of the genomes of many individual microorganisms present in an environment sample
metagenome
53
Why do we study the metagenome?
Because most microorganisms cannot grow in a pure culture and culturing can never capture the full spectrum of microbial diversity Provides culture independent information about environmental microorganism. Offers a powerful lens for observing microbial communities on a broader scale and addressing fundamental questions of microbial diversity, evolution and ecology
54
The resulting metagenomic DNA can be then analyzed by two distinct approaches;
functional metagenomics metagenomic dna sequencing
55
– to search for specific enzymatic activity for proteins
functional metagenomics
56
– to study microbial and functional diversity
metagenomic DNA sequencing
57
* Starts with the construction of a metagenomic library. what kind of metagenomics
functional metagenomics
58
DNA fragments are generated by
restriction enzymes digestion
59
* DNA fragments are generated by restriction enzymes digestion or mechanical methods and then ligated to a ___, resulting in a library of recombinant vectors
vector
60
* This library is used to transform a bacterial host that can be manipulated in a laboratory
functional metagenomics
61
The resulting metagenomic library can be later screened in order to find genes that are expressing a particular function such as
UV radiation resistance
62
Provides insights into the microbial diversity as well as the functional potential of microorganisms of a sample
metagenomics sequencing
63
* Sequencing of the highly conserved 16s rRNA gene amplified i
metagenomic DNA
64
* The sequences can be aligned to generate a ___ tree in which the diversity of microorganisms present in the sample is revealed.
phylogenetic tree
65
ragments that overlaps are reassembled into a longer sequence, or continuous sequence (CONTIG).
smaller DNA
66
16s rRNA sequence are commonly used for molecular identification of bacterial species true or false
true
67
Functional metagenomics is used for analysis of relationship of microbes from a given environmental sample true or false
false
68
The utilization of microscope in analyzing their morphological structures
microscopy
69
A technique that analyze the entire genomic sequence of microbes in a given sample coming from an environmental source
metagenomics
70
The addition of a staining agent to visualize microbial specimen under the microscope
staining methods
71
Counting microbial population in-situ or in culture media
direct counting
72
A technique that hybridize molecular probes to target DNA sequence in a sample, use for the detection of the presence of a specific DNA sequence in a sample
FISH
73
A technique that is used to construct a hypothetical diagram that shows the relationship of microbes to each other using their 16s rRNA sequences
molecular phylogenetics
74
Metagenomics DNA sequencing is used for the analysis of relationship of microbes from a given environmental sample t/f
true
75
The 16s rRNA sequence contains a hypervariable region (V1-V9) useful for molecular identification of different species of bacteria t/f
true

Microbial Ecology (18 decks)

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