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MBB163 > Gilmour - Microbial Ecology > Flashcards

Gilmour - Microbial Ecology Flashcards

1
Q

name the 2 key principles of microbial ecology proposed by van Niel

A

1) every molecule existing in nature can be used as a C-source and energy by a microbe
2) MOs are found in every env on earth, the largest part of the biosphere (under earth’s surface) solely inhabited by microbes

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2
Q

define ecoystem

A

populations of species (community) plus their habitat/env

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3
Q

define niche

A

set of conditions enabling an organism to grow and reproduce

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4
Q

define assimilation

A

building of organic molecules from inorganic metabolites by primary producers

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5
Q

define dissimilation

A

breaking down of organic molecules forming inorganic minerals eg CO2/NO2-

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6
Q

define biomass

A

bodies of living organisms

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7
Q

define parasitisum

A

microbe that benefits at the expense of another microbe

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8
Q

define amensalism

A

a microbe benefits at the expense of another microbe (non-specific)

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9
Q

define commensalism

A

a microbe benefits but has no discernible impact on the other microbe

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10
Q

define mutualism

A

both species benefit and may not grow independently

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11
Q

define synergism

A

both species benefit from each other but can grow independently

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12
Q

name the main issue with estimating species diversity via culturing

A

many MOs are unculturable - need v specific conditions nutrients and possible other MOs
best estimate is that <1% of MOs can be cultured
overcome this via DNA sequencing

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13
Q

define metagenome

A

all genomes present in a particular community

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14
Q

how is a metagenome collected?

A

sample ecosystem, concentrate and break open cells, amplify by PCR, read sequence or assemble whole genome

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15
Q

name a method of estimating species diversity in prok and euk

A

16s/18s rRNA gene sequencing

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16
Q

what is an OTU and why is it used?

A

operation taxonomic units - can’t distinguish between species at this point

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17
Q

how can community diversity be estimated using otu’s?

A

plotting OTU against no of species analysed

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18
Q

compare the microbe concentration in water air and soil

A

most in soil, then water then air (least)

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19
Q

define pelagic zone. state the divisions of this region and what is found in each zone

A

pelagic zone: open ocean water column
regions:
neuston: (10micrometers) air-water interface
euphoric zone: receives light - phototrophs
aphotic zone: heterotrophs & lithotrophs
benthos: ocean floor plus sediment

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20
Q

define oligotrophic and eutrophic

A

oligotrophic: body of water low in nutrient concentration
eutrophic: body of water high in nutrient concentration

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21
Q

is the ocean oligotrophic or eutrophic

A

oligotrophic

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22
Q

what is plankton? state and describe the 3 domains that make up plankton

A

free-floating organisms in the H2O column

1) microplankton: large ciliated protists and algae
2) nanoplankton: smaller algae and flagellated protists and filamentous cyanobacteria
3) picoplankton: bacterial phototrophs/lithotrophs/heterotrophs

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23
Q

why does nutrient concentration increase as you get closer to the coastal shelf?

A

reach a phototrophic zone - photosynthesis occurs and there is a stable food source

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24
Q

name 2 ways in which different microbes and taxonomic classes can be visualised

A

fluorescence microscopy using DNA binding dyes

different taxonomic classes visualised by fluorescence in situ hybridisation

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25
Q

how are unculturable oceanic organisms characterised?

A

using metagenomics

26
Q

what is metatranscriptomics?

A

the study of RNA transcripts obtained from an environmental community - provides snapshot of gene expression at a given time. the mRNA is reverse transcribed to cDNA and then amplified and sequenced

27
Q

in a graph comparing metatranscriptomics and metagenomics; are highly expressed genes very common or very rare in the metagenome?

A

very rare

28
Q

~40% expressed genes had no match in the genomic data, what does this show?

A

strongly suggests that many organisms are not detected by current metagenomic techniques and are still unknown to science

29
Q

the sorcerer II mission carried out by craig venter involved sailed down the USA coast to the Galapagos whilst taking samples. what 3 things were concluded from this mission?

A

1) only 30% sequenced DNA matched known bacteria genera
2) Pelagibacter uses proteorhodopsin (retinal-type H+ pump)
3) cyanobacteria Prochlorococcus and Synechococcus were also highly abundant

30
Q

how does Prochlorococcus get its energy and carbon? where is it found? name 2 distinctive features it has.

A

photoautotroph - energy from sunlight and carbon from fixed CO2
found 40 degrees north and south of the equator
1 of most abundant organisms on earth
smallest known oxygenic photoautoroph
contains divinyl chlorophyll (unique)
has no phycobilisomes (light harvesting antenna)

31
Q

what are piezophiles? where are they usually found?

A

organisms that can withstand v high pressures, usually found on the seafloor

32
Q

how much does atmospheric pressure increase by for every 10m depth?

A

1 atm

33
Q

what is the depth of the ocean roughly?

A

3800m

34
Q

what property of a microorganism at 1000m means that it easy to collect?

A

MOs at 1000m are piezotolerant (ie their optimum growth is at 1atm but they can tolerate high pressures) not piezophilic and therefore dont require high pressures to survive

35
Q

what are psychrophiles and thermophiles?

A

psychrophiles: like the cold
thermophiles: like the heat

36
Q

what organisms can be found in/on hydrothermal vents?

A

sulphur-oxidising/sulphur-reducing bacteria/methanogens/methanotrophic bacteria
bacteria that oxidise H2S and methane feed symbiotic animals eg tube worms

37
Q

how many cells are estimated to live in deep subsurface ecosystems?

A

2.9x10^29

38
Q

describe the metabolic activity of deep subsurface microorganisms and state why this is the case

A

v low activity due to dark, anoxic, oligotrophic, saline, pressurised and hot environment

39
Q

how is the deep subsurface reached in terrestrial and marine biospheres

A

marine: boreholes
terrestrial: mines and caves

40
Q

iron is one of the most common metals found in deep subsurface environments, whats the significance of this?

A

Fe2+ used as an e- source for MOs

therefore heavy metal tolerance is key in MOs

41
Q

what is a problem using steel in storing nuclear waste underground

A

steel contains iron which can be degraded by MOs

42
Q

which 3 properties limit subsurface growth of MOs

A

nitrate availability
ammonia availability
temperature

43
Q

name a method of directly MO diversity and the 3 problems with collecting subsurface MOs

A

use lipid biomarkers to distinguish abundance of euks/bac/archaea
problems:
1) contamination of surface-organisms when drilling boreholes
2) don’t know if samples are representative
3) how can the MOs be preserved if their taken out of the environment they require to grow?

44
Q

are large, undisturbed lakes oligotrophic or eutrophic?

A

oligotrophic

45
Q

what happens to a lake in summer/spring in relation to its oxygen content?

A

lake becomes stratified with the boundary being callled the thermocline
upper layer is epilimnion - oxygenic phototrophs
lower layer is hypolimnion - anoxic

46
Q

what happens to the ratio of hypolimnion and epilimnion in a eutrophic lake in spring/summer?

A

lake stratifies into epilimnion and hypolimnion
anoxic hypolimnion dominates due to the heterotrophic bacteria eating the algae, causing the death of vertebrates due to the lack of O2

47
Q

what happens to the thermocline in autumn? what are the effects and problems associated with this?

A

thermocline breaks down due to wind mixing the epilimnion and hypolimnion
distributes nutrients and O2
if the lake completely turns over methane can be brought to the surface - fire hazard. also gases of anoxic sediments are v toxic

48
Q

what is an individual soil particle made up of?

A

MOs bound by biofilms which interact with plant roots

49
Q

describe the oxygen distribution in a soil environment

A

surface layers aerobic and deeper layers are anaerobic

50
Q

describe the organisms/MOs found in the aerated and anoxic regions of soil

A

aerated: fungi and actinomycetes
anoxic: lithotrophic and anaerobic heterotrophic bacteria

51
Q

what is lignin?

A

plant cell wall component, 2nd most abundant plant polymer (after cellulose) - phenolic compound polymer

52
Q

which organism can break down lignin?

A

white rot fungi (breaks it down into smaller units with few/single phenol groups

53
Q

what is the product of lignin breakdown? what happens when this is broken down further?

A

humic material - further breakdown is v slow - slow release of nutrients into the soil

54
Q

how is lignocellulose formed?

A

the interlinking of lignin with cellulose and hemi-cellulose
forms v strong barrier

55
Q

how are biofuels produced from cellulose?

A

breakdown of lignin then the hydrolysis of (hemi-)cellulose to sugars that can be fermented to ethanol

56
Q

what are the problems associated with biofuel production?

A

resistance of biomass to chemicals and enzymes

plants have evolved mechanisms to avoid breakdown by MOs and animals

57
Q

what does a lignocellulosic biorefinery comprise of?

A

feedstock harvest and storage
chemical pretreatment at a high temperature
enzymatic hydrolysis to produce sugars
fermentation of sugars to ethanol

58
Q

how is (hemi)cellulose released from lignocellulose? what properties do the hydrolytic enzymes have to possess in order for them to be functional during this stage?

A

by chemical pretreating using a high and an acid

enzyme has to withstand low pH and temperature

59
Q

name the 6C and 5C sugars hemicellulose is made up of

A

6C: glucose, mannose, galactose
5C: arabinose, xylose

60
Q

are cellulose and hemicellulose heter or homo polymers

A

cellulose: homopolymer (glucose)
hemicellulose: heteropolymer

61
Q

what is the % composition of lignocellulose?

A

40-50% cellulose
17-19% hemicellulose
rest is lignin

MBB163 (12 decks)

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