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MICR 2420 > Microbial Ecology and Microbial Association > Flashcards

Microbial Ecology and Microbial Association Flashcards

1
Q

how do lithoautotrophs get energy?

A
  • acidophilic and thermophilic sulfur oxidizers
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2
Q

example of how symbiotic microbial community can provide essential components for its host

A
  • bacteria can encode enzymes to synthesize nutrients that are limited in the hosts diet
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3
Q

define a population

A

group of individuals of one species living in a common location

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4
Q

define an ecosystem

A

collection/populations of specie plus their habitat or environment

*we need tos tudy the interactions of organisms within the ecosystem

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5
Q

what is a community

A
  • the sum of all populations of different spcies constitute a community
  • microbial communities critically impact other organisms in all habitats from oceans and forests to the interstices of rock
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6
Q

what is a microbiome

A
  • the microbes associated with ahost animal or plant

*biome = refers to genetic composition, all these microbes carry genes with different properties

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7
Q
A
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8
Q

main things in molecular evolution

A

** until recently microbial world was largely unknown bc relied on cultures

  • 1977 Carl Woese pioneered use of rRNA in phylogeny
  • 1991 Normal Pace sequenced ‘unfractionated’ samples from pacific ocean (without subculture)

^took samples from env and sequenced them

  • 1988-2004: Rita Colwell studied microbial populations in ocean environment
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9
Q

how is a meta genome

A

metagenome = sum total of ALL DNA sequenced directly from an environmental sample (not subcultuing or isolating first

  • sequencing the small subunit rRNA but also seq and assemble entire genomes directly from ecosystem
  • take a sample from env, do a total breakdown of cell walls (isolate DNA), fractionate DNA into smaller fragments and label then sequence
  • using computational tools they assemble these peices into genomes

* does not inform on organisms morphology, viability or interactsions

* relies on having a alrge database of genes to match, figure out metabolic traits

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10
Q

what is phylogenomics

A

profiling ecosystems composition by taxonomic reference genes

  • looking at presence of specific genes that identify one species from another
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11
Q

what is metatranscriptomics

A
  • sequencing entire collections of mRNA from an ecosystem andmapping back to genomes to identify them

*info on genes actively transcribed at a given time (just bc mRNA is being made does not mean it is being translated)

-living cells make mRNA to then make protetins - seeing what genes are active and what organisms have these genes

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12
Q

what is proteomics

A
  • comparative protein sequence analysis
  • information of protein components of a cell at a given time
  • looks at total protein components- are you looking at cell actively growing or in stationary phase (will have diff protein components)
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13
Q

what is lipidomics

A
  • looks at the lipid composition of a cell
  • ex: comparison of cell wall lipids
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14
Q

what is the most powerful took to identfy the microbed that inhabit an ecosystem

A
  • metagenomics
  • limited bc can miss community members, may represent organisms of the ‘rare biosphere’ in low abundance in the env
  • thigns like copiotrophs or weed organisms prevail when nutrients suddenly apear
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15
Q

what has marine metagenomics found

A
  • where are the microbes
  • even if not cultures marine microbial communies are now emerging through metagenomes
  • in one study examined microbial communities associated with great pacific garbage patch
  • revealed surprisongly consistent presence of cyanobacteria and alphaproteobacteria across ocean in env without these contaminants
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16
Q

How do marine ecosystems coonect with human medicine

A
  • human cholera pathogen, vibrio cholerae is a mutualist of marine copeods
  • the bacterium gets a free ride in global oceans currents contrinuting to rapid dispersal to far-flyng areas & cholera outbreaks especially in the southern hemispheres
  • cholera was seen in diff coutnries bc it rode ocena currents by associating with copepods, association was of mutual benefit
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17
Q

what is functional ecology

A
  • all organisms in an ecosystem/community depend directly or indirectly on presence of other organisms
  • within a community each organism fills a specific niche

*a set of conditions, includign habitat (chemical, physical) resources and relations with other species of the ecosystem that enable an organism to grow and reproduce

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18
Q

how do organisms perform nich contruction

A

by shaping the biochemical dimensions of the habitat

  • metabolism has consequences on the envrionments, may take complex organic matter digest it and release either simpler, more oxidized comp. these could have diff pH (change thenichie)
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19
Q

how do unique microbial metabolisms provide roles for microbes in ecosystems

A
  • metabolic biproducts of one organism can be beenficial or harmful to toher organisms in the ecosystem
20
Q

why do all ecosystems require microbed

A
  • Van Niel Hypothesis: limitless variety of species carries out different energy yeilding reactions depending on what their environment has to offer
  • evolution may generate microbes that can digest ‘xenobiotic’ molecules that dont naturally exist in nature
  • ex: ideonella sakaiensis soil bacterium can breakdown polyethylene terephthalate (PET) found in plastic
21
Q

describe carbon assilimation and dissimilation

A
  • interactions between micrboes and their ecosystems include:

Assimilation: processes by which organisms acquire an element to build into cells (anabolism)

  • Dissimilartion: Process of breaking down organic nutrients to inorganic minerals (cataboism)
22
Q

what is biomass

A
  • bodies of living organisms
  • to obtain energy and materials for biomass all organisms particpate in the food web
  • levels of consumption are called trophic levels
23
Q

key features of food webs

A
  • produces: make organic material available, build biomass
  • phototrophs: bring in energy from sun to build biomass
  • Lithotrophs: prokaryotes that use energy from inorganic minerals to build biomass
  • grassers that are preys upon by predators
  • decomposers (fungi, bacteria)
  • also big role for viruses in killing and recycling of biomass
24
Q

what are the priamry producers in marine ecosystems vs land/forest ecosystems?

A

Marine: bacteria, archaea and algae

land: trees, main decomposers = fungi and bacteria

25
Q

what are the types of factors affecting microbial growth

A
  1. Biotic factors
  2. Abiotic factors
    - oxygen and other electron aceptors (availability of an electron acceptor is the most important factor for nutreint assimilarion and dissimilartion, growth slower in anoxic environemnts)

- availability of other nutrients (nitrogen, phosphotous, sulfur and minerals)

  • temp, salinity, pH
26
Q

what is symbiosis

A
  • biotic factor
  • how organaism adapt to each others presence - they do not live alone
  • mostly live in assocaitions or symbiosis

*symbiosis associations are the most intimate association between organisms of different species

  • range of pos and neg relationships- both partners respond to each other
  • each organism in the association is a symbiont- udually involves 2
27
Q

what is mutualism

A
  • each partner gains benefits from the other and may not grow independently
28
Q

whaat in syntrophy

A

•A beneficial metabolic association requiring both partners to complete

29
Q

what is synergism

A

•An optional cooperation where both species benefit, but can grow independently

30
Q

what is commensalism

A

•One partner benefits, while the other is unaffected e.g. the majority of normal gut microbiota.

31
Q

what is amensalism

A

•One partner is harmed, without an intimate association.

–E.g. Actinomycetes naturally produce antimicrobial products that hurt surrounding bacteria (that just happen to be there!)

32
Q

what is parasitism

A

An intimate association where one partner benefits, while harming a specific host

33
Q

describe the details of mutualism

A
  • partner species that require each other to survive
  • in mutualism, each partner benefits from the other and may fail to grow independently
  • can involve 2 or more partners or one or more partners with a plant or animal host
  • removal of microbial partner leads to death or decreased growth of host
  • the microbial genome shows extensive degeneration (reduction) of normally essential genes for metabolism and protective structures
    ex: lichens, zooxanthellae, gut microbiome of plant/wood digesting animals/insects
34
Q
A
35
Q

what are lichens

A
  • example of mutalism
  • ancience highly evolved mutualistic associations between a fungi and one or two microbial phototrophs
    ex: fungi and an algae or a cyanobacterium
  • fungus and BOTH an algae and a cyanobacterium
  • algae provides organic material and cyanobacteria is nitrogen fixers, algae also absorbs minerals to feed partner
  • the fungi has intense cell walls and is resistant- protect the partner and anchor them
36
Q

examples of photosynthetic endosymbionts of animals

A
  • many invertebrate animals acquire endosymbiotic algae, most commonly dinoflagellates (microbial eukaryotes)
  • these endosymbionts are called zooxanthellae
  • the algae receive rpotection from predators while the animal recieves phtosythetic products
37
Q

describe the termite wood-degesting microbiome

A
  • termites feed on wood and are completely dependent on its cymbiotic microbed to breakdown the plant lignins and cellulose to provide nutrients and growth factors
  • gut has large protzoa with large flagella- source is bacteria that is fed by protists and then they provide motility
  • the endosymbiotic bacteria have formed highly complex associations with protists such as micotricha paradoxa

*use flagellated spirochetes for propulsion/motility, has cellulose digesting endosymbiotic bacteris

  • termite ut microbiome include cellulolytic bacteria and fermenting bacteria
38
Q

describe the gut microbiome

A
  • highly complex and nutritionally important communities of microbes found within the gut of certebrate animals
  • include: bacteria, fungi, protists and phages
  • most extensively studied digestive communities are ruminants (cown and sheep)
  • microbiome carry a multitude of digestive enzymes not present in the host so it can digest the plant material
  • Bovine system has 4 charmers - rumen is the largest

*its microbial community allows the herbivore to acquire nutrition from complex plant fibers that it cannot otherwise digest, microbial fermentation gneerates short fatty acids that are abs by the host

39
Q

describe the human colon

A
  • gut microbiome contributes to digestion
  • colonic fermentation favours bacteria capable of digesting complex plant materials that pass through the small intestine

*anerobic environment

  • anaerobes release acetate and short chain fatty acids that provide up to 15% of our caloric intake
  • commensal/normal microbiota members of the gut microbiome normally outcompete pathogens (release antimicrobal product, colonize surface of epithelium so pathogens have no where to attach)
  • human gut microbes communicate with their host - send chemical systems to our immune tissues and to brain
40
Q
A
41
Q

describe microbes associated with plant roots

A
  • microbes are located in two zones around the root
  • rhizoplane - direct contact with the plant root surface

- Risosphere - away from root surface but influenced by plant secreted factors

  • mibcrobed in these zoens help to protect plant frmo pathogens mircobes and in return they feed off nutrients and provide by the plant
42
Q

what is Mycorrhizae

A

“fungal internet”

  • ectomycorrhizae: colonize the root surface
  • endomycorrhizae: more intimate associations, hyphae penetrate the root and root cells
  • mycorrhizae vastly increase the absorptive surface area of the plant roots
  • promote plant health: secrete antibicrobial compounds, absorb nutrients/minerals and protect root surfaces
  • plant internet: plant root to root contact - distribution fo substances between plants
43
Q

what are endophytes

A
  • grow within plant cells
  • can be bacterial or fungal, symbionts or pathogens
  • specialist symbiotic endophytes of plants include nitrogen-fixing bacteria: rhizobium, frankia species
  • form an elaborate partnership -bacterium enters and adapts to life within plant tissues, plant forms nodules (a nitrogen fixing organ for the plant)
  • endophyte bactera are fed by the host plant
44
Q

describe parasitic associations of plant pathogens

A
  • when a pathogen does colonize a plant its growth has effects ranging from minimal to devastating
  • most common plant pathogen = fungi

*viruses and bacteria can also cause plant infections

ex: Phytoplasma (tenericute family bacteria) infections interefere with gene regulation causing phyllody (flowers are replaced by leaves

45
Q

what are rhizobia

A
  • bacteria that fix nitrogen for legumes
46
Q

where do nitrogen fixing bacteroids gain energy from?

A
  • gain energy from plant cell respiration but must remain anaerobic

MICR 2420 (29 decks)

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