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BIO 207 > Biology 207 Exam #3 > Flashcards

Biology 207 Exam #3 Flashcards

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1
Q

Microorganisms rarely live as single free-floating cells

A

They form populations and communities

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2
Q

Populations

A

Derived from a single cells, all cells of the same genetic strain

Populations can grow up as microcolonies, interact to form communities

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3
Q

Communities

A

A unified assemblage of multiple populations that coexist and interact at a given location (habitat)

The combination of a community and habitat can form a functional supporting system (ecosystem)

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4
Q

Microbiota

A

The microorganisms of a particular site, habitat or geological period

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5
Q

Microbiome

A

The microorganisms of a particular environment

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6
Q

Surfaces are important microbial habitats for symbiotic communities and metabolic conversion of environmental compounds

A

Nutrients absorb to surfaces, microbial cells can attach to surfaces

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7
Q

Biofilms

A

Assemblages of cells adhered to a surface and enclosed in an adhesive matrix excreted by the cells

The matrix is typically a mixture of polysaccharides, proteins and nucleic acids; binds the cells together
*trap nutrients for microbial growth and help prevent detachment of cells in flowing systems

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8
Q

Bacteria form biofilms for several reasons

A

Allows bacterial cells to live in close association with one another
*facilitates cell-to-cell communication and increases chances for survival
*more opportunities for nutrient and genetic exchange

Biofilm formation appears to be the “default” mode of growth for bacteria in natural environments

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9
Q

Steps in Biofilm Formation

A

Initiated by attachment of a cell to a surface followed by expression of biofilm-specific genes

Biofilms typically contain multiple layers of cells embedded in the porous extracellular matrix that develops

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10
Q

Biofilms are inherently more tolerant to stressors

A

A given species growing in a biofilm can be up to 100 times more tolerant of an antimicrobial substance

Mechanisms of tolerance
*slower growth rates in biofilms
*reduce penetration of substance
*expression of genes that increase tolerance

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11
Q

Biofilms are functional and growing microbial communities

A

May contain only one or two species, biofilms can also contain many more species of bacteria or even fungi, algae

Bacteria do not need to be motile to form biofilms

Transcriptional profile of cells in a biofilm is significantly different from that of cells grown planktonically

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12
Q

Symbiosis

A

Close, prolonged physical or metabolic interactions between two or more populations

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13
Q

Positive interactions between biological populations enhance survival capacity of the interacting populations

A

Permits more efficient use of available resources than can be accomplished by an individual population growing alone

Sometimes populations co-exist in habitats where neither could live alone

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14
Q

Mutualism

A

Two-way relationships can occur between populations in which both populations benefit
*both additive or synergistic outcomes are possible

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15
Q

Mycorrhizae

A

Symbiotic association between plant roots and fungi
*endomycorrhiza penetrate deeper into the root layers and into root cells

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16
Q

Mycorrhizal Benefits to Fungi

A

Plants are a dependable source of carbohydrates due to photosynthesis

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17
Q

Mycorrhizal Benefits to Plants

A

Fungi improve a plant’s access to mineral nutrients
*by extending the volume of soil accessible to plants, acquiring nutrient forms, localization secretion of degradative enzymes

Fungi improve a plant’s access to water

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18
Q

Two-way relationships can occur between populations in which populations benefit

A

Two populations can supply each other’s nutritional needs (syntrophism or cross feeding)

This allows two microbial populations to:
*complete a metabolic pathway that neither organism is capable of carrying out alone
*mutually provide required growth factors for the other population

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19
Q

Amensalism

A

The first population gains a competitive edge as a result of its ability to inhibit the growth of competitive populations

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20
Q

Negative interactions between populations act as feedback mechanisms that limit population densities

A

May eliminate a population that is not well-adapted for continued existence within the community of a given habitat
*tend to prevent the invasion of an established community composed of indigenous populations by foreign populations

Negative interactions also act to maintain community stability in an ecosystem

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21
Q

Competition occurs when two populations are striving for the same resource

A

Often it is for a single nutrient present in limiting concentrations
*as a result, both populations achieve lower densities than would be achieved by individual populations in the absence of competition

Competitive interactions tend to result in exclusion of a closely related population

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22
Q

“Competitive Exclusion” can precent two populations from occupying the same ecological niche

A

Because they cannot play the same functional role in the same location
*when two populations compete for the same limiting resource, one succeeds and the other fails

The population with a higher growth rate under the given set of environmental conditions in the habitat will prevail over the population with the lower growth rate

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23
Q

Fluctuations in environmental conditions can lead to shifts in competitive balances

A

This can result in population oscillations within the microbial community
*spatial separation allows microbes to escape competitive pressures, permitting coexistence of competitive populations

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24
Q

The intensity of positive/negative interactions are greatest at high population densities with growth

A

Under these conditions, organisms living together within a community interact and compete for the available resources

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25
Q

Neutralism

A

Microorganisms coexist without competing for the same available resources in the habitat
*low rates of metabolic activity favor lack of interactions
*more likely at low population densities

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26
Q

Commensalism

A

Often occurring when the unaffected population chemically or physically modifies a habitat in such a way that a second population benefits

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27
Q

Predator-Prey Interactions

A

Short duration
*predatory populations derive nutrition from prey
*exerts a negative influence on the prey population

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28
Q

Parasitism

A

One populations benefits, other is harmed
*long period of contact, parasite is smaller than the host

Parasite derives its nutritional requirement from the host cells or organisms, and in the process, the host is damaged

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29
Q

Resources typically enter an ecosystem intermittently

A

A large pulse of nutrients may be followed by a period of nutrient deprivation

Microorganisms in nature often face a “feast or famine”
*produce intracellular storage polymers when resources are abundant, draw upon later during starvation

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30
Q

Resources typically enter an ecosystem intermittently Cont.

A

Extended periods of exponential microbial growth are rare
*typically grow in spurts, linked to availability of resources

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31
Q

A given species has an effect on a small number of other species but not entire community

A

Extinction of a single species usually does not affect the long term viability of a community/ecosystem
*other species provide the missing elements

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32
Q

Keystone Species

A

Species that plays a role in its community that is far more important than its relative abundance may suggest

The most abundant species are not usually keystone species
*keystone species typically exist in low numbers

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33
Q

Indicator Species

A

May be used as a proxy to indicate a change in the ecosystem
*may also reflect the presence or absence of a unique set of environmental qualities or characteristics found in a place

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34
Q

Viewing the mammalian host as a symbiotic partner with the bacterial microbiota

A

Mammalian host is the mutualistic partner, amensalistic organism and predator for the microbiota and pathogens
*host is a multi-cellular organism
*differentiation

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35
Q

Host Microbiome

A

Conservation of bacterial genes despite taxonomic variation
*firmicutes and bacteriodetes most common in distal gut
*functional characteristics of the microbiome isn conserved

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36
Q

Host Microbiome Cont.

A

Across various body sites, bacterial colonization varies between healthy individuals while metabolic pathways remains stable for each environment

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37
Q

Guilds

A

Distinct collections of microbial populations that cooperate toe exploit the same resources
*requires a habitat that supplies a specific collection of resources and conditions for growth

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38
Q

Every species has a optimal environment in which it performs particularly well

A

The combination of abiotic factors in a particular environment fundamentally determines whether a species can persist there
*all species have limits to the abiotic conditions they tolerate

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39
Q

Fundamental Niche

A

The range of environmental conditions under which an organism can survive, metabolize and grow/reproduce

40
Q

Realized Niche

A

Where a microbe is the most successful
*in other niches, microbe is less ecologically successful but still may be able to metabolize and reproduce

Metabolism/nutrients, environmental, ecologic/symbiotic factors combine to determine realized niche

41
Q

Realized Niche Cont.

A

If a microbe can persist in an environment that is not its realized niche, then that microbe can be the source of a bloom, when the biotic/abiotic factors of an environment are disturbed in favor of a microbe

42
Q

Genome Size and Environmental Adaptability

A

The more environmentally adaptable a bacterial cell is, the larger its genome

Bacteria that can grow in multiple environmental niches tend to have larger genomes

43
Q

Nice vs. Genome Size

A

For a bacterial strain, the larger its genome, the broader its fundamental niche is predicted to be

For a bacterial species, the larger its pan genome, the greater the number of niches in which it likely to be found

44
Q

Core Genome

A

Genes in common with all cells of a species
*genes shared by all strains of all the species

45
Q

Accessory Genome

A

The non-core genes in a cell’s genome

46
Q

Pan Genome

A

All the possible genes that may be present in a strain from a species
= core + accessory

47
Q

Ecosystems

A

The TYPES of microbial activities possible in an ecosystem are a function of:
*species present, population sizes, physiological state

The RATES of microbial activities in an ecosystem are controlled by the nutrients and growth conditions that prevail

48
Q

The activites of microbes have a major influence on the environment

A

Relationships between microorganism and their biotic/abiotic environments
*dynamic

49
Q

van Niel Hypothesis

A

Every molecule existing in nature can be used as a source of carbon or energy by a microorganism somewhere

Microbes are found in every environment on Earth

50
Q

van Niel Hypothesis Cont.

A

Imply that a limitless variety of species carry out different energy-yield reactions, depending on what their environment has to offer

51
Q

Ecological Succession

A

Changes in species composition of communities over time
*environmental that are devoid of pre-existing communities
*environments with community disturbance

52
Q

Ecological Succession Cont.

A

The initial colonizers alter the physical and chemical environment, thereby allowing subsequent colonization
*each additional colonizer continues to alter the abiotic and biotic factors
*continues under a dynamic equilibrium

53
Q

Problem in Studying Microbial Communities from ANY Site

A

The Great Plate Count Anomaly

54
Q

DNA Sequencing

A

Sanger dideoxy method
*uses dNTPs, ddNTPS (to prevent further extensions) and radioactive phosphate

55
Q

Metagenomics

A

Total DNA from a microbial community is isolated and sequenced without culture or enrichment

DNA can be directly sequenced or specific genes can be amplified by PCR
*tool for assessing the genetic/metabolic diversity

56
Q

Great Plate Count Anomaly

A

Only a minority of bacterial species have been cultured from all environments

57
Q

Bacterial Culture

A

Culture media: nutrient solutions used to grow microbes in the laboratory

Defined media: precise chemical composition is known

Complex media: composed of digests of chemically undefined substances

58
Q

Bacterial Culture Cont.

A

Nutrient-rich media: contains plentiful nutrients for a variety of microbes

Selective media: contains compounds that selectively inhibit growth of some microbes but not others

Differential media: contains an indicator that detects particular reactions during growth, which allows for selection of a bacterial colony

59
Q

Enrichment Cultures

A

Can prove the presence of an organism in a habitat
*cannot prove that an organisms does not inhabit an environment

The ability to isolate and organism from an environment says nothing about its ecological significance

60
Q

Enrichment Bias

A

Microorganisms cultured in lab are frequently only minor components of the microbial ecosystem

61
Q

Molecular Phylogeny

A

Using rRNA sequences, established the presence of three domains of life
*unified phylogenetic framework

62
Q

Molecular Phylogeny Cont.

A

The most widely used rRNA are the small subunit ribosomal RNA genes
*found in all domains of life, 16S rRNA in prokaryotes
*functionally constant, sufficiently conserved, sufficient gene length

63
Q

16S rRNA

A

Differences in loops, lengths of stems, etc. between species

Some areas areas are slow change (stems) while others change quickly (loops)

64
Q

Molecular Phylogeny Cont.

A

Comparative rRNA sequencing is a routine procedure that involves:
*amplification of the gene encoding SSU rRNA
*sequencing of the amplified gene
*analysis of sequence in reference to other sequences

65
Q

How do you identify bacteria by sequencing only?

A

Exploit the combination of the highly conserved and highly variable regions in the 16S rRNA sequence when thousands of bacterial species are compared

Perform PCR using primers from highly conserved regions that flank highly variable regions

66
Q

PCR

A

Add DNA, primer, DNA polymerase, heat and cool

67
Q

How do you identify bacteria by sequencing only? Cont.

A

Sequence each amplicon individually, group them and add them up

68
Q

“Next Generation” DNA sequencing

A

Uses increased computer power, miniaturization and optical detection
*illumina sequencing

69
Q

Beyond “Next Generation” DNA sequencing

A

Optical detection no longer used -> nanopore technologies
*passes DNA through nanoscale sized protein pores embedded in membrane
*detector measures change in electric current
*generates long reads of DNA sequence
*extremely fast

70
Q

BLAST

A

Compares sequences

71
Q

The Species Concept in Microbiology

A

Not meaningful because bacteria are haploid and do not undergo sexual reproduction

72
Q

Bacterial Species

A

A group of strains that, based upon DNA sequences of multiple genes, cluster closely with others phylogenetically and are distinct from other groups

73
Q

The Species Concept in Microbiology Cont.

A

Current definition of prokaryotic species: collection of strains sharing a high degree of similarity in several independent traits
*GC content, Average Nucleotide Identity, 16S rRNA

74
Q

Phylogenetic Analysis

A

There is relatively little divergence of the 16S rRNA gene between bacterial species in the same genus

There are multiple copies of the 16S rRNA gene in bacterial cells of most species
*limits the effectiveness of the 16S rRNA gene in discriminating between bacteria at the species and strain level

75
Q

Operational Taxonomic Units

A

Thing beings studied

76
Q

E. Coli

A

Gram-negative, facultative, rod-shaped, does not form endospores
*majority are nonpathogenic, found in gut microbiome (minor member)

Few strains are foodborne pathogens, few protect against pathogen colonization

77
Q

E. Coli Cont.

A

One strain is a probiotic

All pathogenic strains are intestinal parasites, a few produce potent enterotoxins

78
Q

E. Coli Cont.

A

One strain is a probiotic

All pathogenic strains are intestinal parasites, a few produce potent enterotoxins

79
Q

E. Coli Pathogenesis

A

Produces two important virulence mechanisms
*production of enterotoxin
*adherence to cells of small intestine, causing “pedastal” formation and attaching and effacing lesion

80
Q

E. Coli 0157:H7

A

Responsible for several large food poisoning outbreaks
*contaminated food/water are sources

81
Q

Microbial Exotoxins

A

Microbial toxins kill or inhibit host cells
Exotoxins: toxic proteins released from pathogenic microbes as they grown, which can cause tissue damage locally or distantly
*can be classified according to their mechanism of activity

82
Q

Enterotoxins

A

Exotoxins whose activity affects the gastrointestinal tract
*generally cause massive secretion of fluid into the lumen

83
Q

Type III Secretion

A

Use a molecular syringe to inject proteins from the bacterial cytoplasm directly into a host cells
*flagellar genes were evolutionarily reengineered to encode proteins to act like molecular syringes
*usually located on pathogenicity island

84
Q

Some pathogens use Type III Secretion alter the host cells

A

Some microbes do not rely solely on the natural array of host receptors for attachment
*these bacterial pathogens use T3SS to insert their own receptors into target cells

85
Q

Intestinal Effacing

A

At sites of bacterial attachment, surface microvilli are effaced and bacteria immediately adhere to the host cell surface

86
Q

Intestinal Effacing Cont.

A

Locus of enterocyte effacement is pathogenicity island
*genes for lesions, characteristic lesion for adherence of bacteria to enterocytes, signaling cascade leading to disruption and loss of ions

87
Q

Pedestal Formation

A

Adherence to cells of intestine, causing “pedestal” formation and attaching and effacing

88
Q

Mucus Layer

A

Naturally protects the gut epithelium form bacterial adherence, colonization and damage

89
Q

Mucus Layer Cont.

A

Epithelial surface: extreme low level of colonization
Diffuse mucin layer: low level bacterial colonization
Gut lumen (liquid): diverse bacterial community
Gut lumen (substrate): specialized digestive bacteria

90
Q

EHEC/STEC Mechanisms to Invade Through the Mucus
Layer

A

Secrete a serine protease that cleave the mucus proteins mucin-2 and protocadherin-24, leading to bacterial attachment to the epithelium and microvillar effacement.

Also secrete a metalloprotease that reduces the inner mucus layer, leading to EHEC access and binding to the epithelium

91
Q

UTI

A

Causative Agent: Uropathogenic E. Coli

92
Q

Probiotic E. coli

A

Protects against diarrhea due to rotavirus and some enteropathogenic bacteria
*lacks defined virulence factors

Essentially a deconstructed pathogen, an avirulence E. coli derived from a UPEC strain

93
Q

Horizontal Gene Transfer and Genome Stability

A

Presence of genes typically found only in distantly related species

Presence of a DNA with GC content or codon bias that differs significantly from the remainder of genome
*HGT genes typically do not encode metabolic function

94
Q

Genomic/Chromosomal Islands

A

Have foreign origin based on several observations
*extra regions often flanked by inverted repeats
*GC content and codon usage differ from rest of genome
*often found in some strains of a species but not others

95
Q

Genomic/Chromosomal Islands Cont.

A

Chromosomal islands contribute specialized function essential to growth
*virulence, biodegradation, symbiosis, survival in ecological niche

96
Q

Bacterial Genomes

A

Have plenty of opportunity to adapt and evolve to a changing environment

Antibiotic resistance: overuse leading to selective pressures in microbes to evolve
Bioremediation: identification of new degradative pathways

BIO 207 (2 decks)

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