Gilmour - Microbial Ecology Flashcards
name the 2 key principles of microbial ecology proposed by van Niel
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
define ecoystem
populations of species (community) plus their habitat/env
define niche
set of conditions enabling an organism to grow and reproduce
define assimilation
building of organic molecules from inorganic metabolites by primary producers
define dissimilation
breaking down of organic molecules forming inorganic minerals eg CO2/NO2-
define biomass
bodies of living organisms
define parasitisum
microbe that benefits at the expense of another microbe
define amensalism
a microbe benefits at the expense of another microbe (non-specific)
define commensalism
a microbe benefits but has no discernible impact on the other microbe
define mutualism
both species benefit and may not grow independently
define synergism
both species benefit from each other but can grow independently
name the main issue with estimating species diversity via culturing
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
define metagenome
all genomes present in a particular community
how is a metagenome collected?
sample ecosystem, concentrate and break open cells, amplify by PCR, read sequence or assemble whole genome
name a method of estimating species diversity in prok and euk
16s/18s rRNA gene sequencing
what is an OTU and why is it used?
operation taxonomic units - can’t distinguish between species at this point
how can community diversity be estimated using otu’s?
plotting OTU against no of species analysed
compare the microbe concentration in water air and soil
most in soil, then water then air (least)
define pelagic zone. state the divisions of this region and what is found in each zone
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
define oligotrophic and eutrophic
oligotrophic: body of water low in nutrient concentration
eutrophic: body of water high in nutrient concentration
is the ocean oligotrophic or eutrophic
oligotrophic
what is plankton? state and describe the 3 domains that make up plankton
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
why does nutrient concentration increase as you get closer to the coastal shelf?
reach a phototrophic zone - photosynthesis occurs and there is a stable food source
name 2 ways in which different microbes and taxonomic classes can be visualised
fluorescence microscopy using DNA binding dyes
different taxonomic classes visualised by fluorescence in situ hybridisation
how are unculturable oceanic organisms characterised?
using metagenomics
what is metatranscriptomics?
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
in a graph comparing metatranscriptomics and metagenomics; are highly expressed genes very common or very rare in the metagenome?
very rare
~40% expressed genes had no match in the genomic data, what does this show?
strongly suggests that many organisms are not detected by current metagenomic techniques and are still unknown to science
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?
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
how does Prochlorococcus get its energy and carbon? where is it found? name 2 distinctive features it has.
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)
what are piezophiles? where are they usually found?
organisms that can withstand v high pressures, usually found on the seafloor
how much does atmospheric pressure increase by for every 10m depth?
1 atm
what is the depth of the ocean roughly?
3800m
what property of a microorganism at 1000m means that it easy to collect?
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
what are psychrophiles and thermophiles?
psychrophiles: like the cold
thermophiles: like the heat
what organisms can be found in/on hydrothermal vents?
sulphur-oxidising/sulphur-reducing bacteria/methanogens/methanotrophic bacteria
bacteria that oxidise H2S and methane feed symbiotic animals eg tube worms
how many cells are estimated to live in deep subsurface ecosystems?
2.9x10^29
describe the metabolic activity of deep subsurface microorganisms and state why this is the case
v low activity due to dark, anoxic, oligotrophic, saline, pressurised and hot environment
how is the deep subsurface reached in terrestrial and marine biospheres
marine: boreholes
terrestrial: mines and caves
iron is one of the most common metals found in deep subsurface environments, whats the significance of this?
Fe2+ used as an e- source for MOs
therefore heavy metal tolerance is key in MOs
what is a problem using steel in storing nuclear waste underground
steel contains iron which can be degraded by MOs
which 3 properties limit subsurface growth of MOs
nitrate availability
ammonia availability
temperature
name a method of directly MO diversity and the 3 problems with collecting subsurface MOs
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?
are large, undisturbed lakes oligotrophic or eutrophic?
oligotrophic
what happens to a lake in summer/spring in relation to its oxygen content?
lake becomes stratified with the boundary being callled the thermocline
upper layer is epilimnion - oxygenic phototrophs
lower layer is hypolimnion - anoxic
what happens to the ratio of hypolimnion and epilimnion in a eutrophic lake in spring/summer?
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
what happens to the thermocline in autumn? what are the effects and problems associated with this?
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
what is an individual soil particle made up of?
MOs bound by biofilms which interact with plant roots
describe the oxygen distribution in a soil environment
surface layers aerobic and deeper layers are anaerobic
describe the organisms/MOs found in the aerated and anoxic regions of soil
aerated: fungi and actinomycetes
anoxic: lithotrophic and anaerobic heterotrophic bacteria
what is lignin?
plant cell wall component, 2nd most abundant plant polymer (after cellulose) - phenolic compound polymer
which organism can break down lignin?
white rot fungi (breaks it down into smaller units with few/single phenol groups
what is the product of lignin breakdown? what happens when this is broken down further?
humic material - further breakdown is v slow - slow release of nutrients into the soil
how is lignocellulose formed?
the interlinking of lignin with cellulose and hemi-cellulose
forms v strong barrier
how are biofuels produced from cellulose?
breakdown of lignin then the hydrolysis of (hemi-)cellulose to sugars that can be fermented to ethanol
what are the problems associated with biofuel production?
resistance of biomass to chemicals and enzymes
plants have evolved mechanisms to avoid breakdown by MOs and animals
what does a lignocellulosic biorefinery comprise of?
feedstock harvest and storage
chemical pretreatment at a high temperature
enzymatic hydrolysis to produce sugars
fermentation of sugars to ethanol
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?
by chemical pretreating using a high and an acid
enzyme has to withstand low pH and temperature
name the 6C and 5C sugars hemicellulose is made up of
6C: glucose, mannose, galactose
5C: arabinose, xylose
are cellulose and hemicellulose heter or homo polymers
cellulose: homopolymer (glucose)
hemicellulose: heteropolymer
what is the % composition of lignocellulose?
40-50% cellulose
17-19% hemicellulose
rest is lignin
