Gilmour - Microbial Ecology

Question 1

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

Answer 1

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

Question 2

define ecoystem

Answer 2

populations of species (community) plus their habitat/env

Question 3

define niche

Answer 3

set of conditions enabling an organism to grow and reproduce

Question 4

define assimilation

Answer 4

building of organic molecules from inorganic metabolites by primary producers

Question 5

define dissimilation

Answer 5

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

Question 6

define biomass

Answer 6

bodies of living organisms

Question 7

define parasitisum

Answer 7

microbe that benefits at the expense of another microbe

Question 8

define amensalism

Answer 8

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

Question 9

define commensalism

Answer 9

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

Question 10

define mutualism

Answer 10

both species benefit and may not grow independently

Question 11

define synergism

Answer 11

both species benefit from each other but can grow independently

Question 12

name the main issue with estimating species diversity via culturing

Answer 12

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

Question 13

define metagenome

Answer 13

all genomes present in a particular community

Question 14

how is a metagenome collected?

Answer 14

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

Question 15

name a method of estimating species diversity in prok and euk

Answer 15

16s/18s rRNA gene sequencing

Question 16

what is an OTU and why is it used?

Answer 16

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

Question 17

how can community diversity be estimated using otu’s?

Answer 17

plotting OTU against no of species analysed

Question 18

compare the microbe concentration in water air and soil

Answer 18

most in soil, then water then air (least)

Question 19

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

Answer 19

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

Question 20

define oligotrophic and eutrophic

Answer 20

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

Question 21

is the ocean oligotrophic or eutrophic

Answer 21

oligotrophic

Question 22

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

Answer 22

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

Question 23

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

Answer 23

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

Question 24

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

Answer 24

fluorescence microscopy using DNA binding dyes

different taxonomic classes visualised by fluorescence in situ hybridisation

Question 25

how are unculturable oceanic organisms characterised?

Answer 25

using metagenomics

Question 26

what is metatranscriptomics?

Answer 26

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

Question 27

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

Answer 27

very rare

Question 28

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

Answer 28

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

Question 29

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?

Answer 29

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

Question 30

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

Answer 30

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)

Question 31

what are piezophiles? where are they usually found?

Answer 31

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

Question 32

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

Answer 32

1 atm

Question 33

what is the depth of the ocean roughly?

Answer 33

3800m

Question 34

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

Answer 34

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

Question 35

what are psychrophiles and thermophiles?

Answer 35

psychrophiles: like the cold thermophiles: like the heat

Question 36

what organisms can be found in/on hydrothermal vents?

Answer 36

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

Question 37

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

Answer 37

2.9x10^29

Question 38

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

Answer 38

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

Question 39

how is the deep subsurface reached in terrestrial and marine biospheres

Answer 39

marine: boreholes terrestrial: mines and caves

Question 40

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

Answer 40

Fe2+ used as an e- source for MOs | therefore heavy metal tolerance is key in MOs

Question 41

what is a problem using steel in storing nuclear waste underground

Answer 41

steel contains iron which can be degraded by MOs

Question 42

which 3 properties limit subsurface growth of MOs

Answer 42

nitrate availability ammonia availability temperature

Question 43

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

Answer 43

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?

Question 44

are large, undisturbed lakes oligotrophic or eutrophic?

Answer 44

oligotrophic

Question 45

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

Answer 45

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

Question 46

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

Answer 46

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

Question 47

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

Answer 47

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

Question 48

what is an individual soil particle made up of?

Answer 48

MOs bound by biofilms which interact with plant roots

Question 49

describe the oxygen distribution in a soil environment

Answer 49

surface layers aerobic and deeper layers are anaerobic

Question 50

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

Answer 50

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

Question 51

what is lignin?

Answer 51

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

Question 52

which organism can break down lignin?

Answer 52

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

Question 53

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

Answer 53

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

Question 54

how is lignocellulose formed?

Answer 54

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

Question 55

how are biofuels produced from cellulose?

Answer 55

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

Question 56

what are the problems associated with biofuel production?

Answer 56

resistance of biomass to chemicals and enzymes | plants have evolved mechanisms to avoid breakdown by MOs and animals

Question 57

what does a lignocellulosic biorefinery comprise of?

Answer 57

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

Question 58

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?

Answer 58

by chemical pretreating using a high and an acid | enzyme has to withstand low pH and temperature

Question 59

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

Answer 59

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

Question 60

are cellulose and hemicellulose heter or homo polymers

Answer 60

cellulose: homopolymer (glucose) hemicellulose: heteropolymer

Question 61

what is the % composition of lignocellulose?

Answer 61

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