Gilmour (Spring - Microbial Ecology) Flashcards
What do MOs recycle, where and why?
- organic material in aquatic and terrestrial ecosystems
- to provide resources for higher organisms
- MOs throughout biosphere recycle C, N, S and other elements essential for all life
What are the 2 key principles of microbial ecology formulated by Van Niel?
1) every molecule in nature can be used as C source and energy by MO somewhere on Earth, if energy yielding reaction exists, some MO will evolve to use it
2) MOs found in every env on Earth, largest part of biosphere (below Earth’s surface) inhabited solely by MOs
Total vol of anaerobic MO communities far exceeds what?
- total vol of oxygenated biosphere
Where is MO life found on Earth?
- every env down to 3km below surface
What is an ecosystem?
- pops of species (community) plus their habitat or env
What is a niche?
- set of conditions enabling organism to grow and reproduce
What carries out assimilation?
- 1º producers
What is dissimilation?
- breaking down of organic nutrients to inorganic minerals, eg. CO2 and NO2-
What is biomass?
- bodies of living organisms
What do food webs consist of?
- 1º producers
- grazers
- predators
- 2º predators
- decomposers
What are the main 1º producers in oceans?
- phytoplankton
What are the main 1º producers in forests?
- plants
What is parasitism?
- MO benefits at expense of another MO
- specific
What is amensalism?
- MO benefits (hard to demonstrate) at expense of another MO
- non-specific
What is commensalism?
- MO benefits but has no discernible impact on other MO
What is synergism?
- both species benefit
- easily separated
- can grow independently
What is mutualism?
- both species benefit
- may not grow independently
Why are many MOs unculturable?
- need v specific nutrients, physical conditions or other MOs to be present
What % of MOs can be grown in pure cultures in lab and how can this problem be overcome?
- less than 1%
- use DNA seq of env samples
What is the metagenome?
- used to represent all genomes in particular community
How can the species diversity be estimated?
- ecosystem sampled
- filter and break open cells (w/o breaking DNA strands) to isolate DNA
- clone DNA fragments or amplify by PCR
- read DNA seq
- assemble genome or look at specific genes (housekeeping genes)
What gene seq is used to estimate species diversity?
- 16S rRNA gene seq for proks
- or 18S rRNA gene seq for euks
What term is often used instead of species when analysing genome to estimate species diversity?
- operational taxonomic units (OTUs)
How can community diversity be estimated?
- plotting OTUs identified against no. samples analysed
Which envs have the lowest and highest diversity?
- greatest in soil
- then water
- lowest in air
Why are extreme envs often used in metagenomic studies?
- species diversity low
What other technique can be used to find specific MOs of interest?
- culture-dependent isolation
- can use v specific media/growth conditions to find MOs of interest –> enrichment cultures
What role do MOs play in marine ecosystems?
- 1º producers and CO2 fixers
In the open ocean, what is the water column (pelagic zone) subdivided into?
- neuston (approx 10μm) –> air-water interface
- euphotic zone –> receives light, phototrophs present
- aphotic zone –> heterotrophs and lithotrophs
- benthos –> ocean floor and sediment
What does oligotrophic mean, and what part of the ocean is?
- low in nutrients
- the open ocean
How deep can the photic zone be?
- 200m
What are plankton?
- free-floating organisms in water column
- include members of all 3 domains
What are the 3 types of plankton?
- microplankton (20-200μm) –> large ciliated protists and algae
- nanoplankton (2-20μm) –> smaller algae and flagellated protists plus filamentous cyanobacteria
- picoplankton (0.3-2μm) –> bacterial phototrophs, heterotrophs and lithotrophs
Where are the highest concs of nutrients in the ocean and what does this mean?
- coastal regions (coastal shelf)
- so highest conc of organisms
What levels of light penetration are there in coastal regions?
- low compared to open ocean
- lots of sediment, esp in certain weather conditions
How can fluorescence microscopy be used to culture marine MOs in lab?
- using DNA binding dyes
- can visualise planktonic MOs
- diff taxonomic classes detected
What is metatranscriptomics?
- study of RNA transcripts obtained from env community
- provides “snapshot” of gene expression at given point in time
How was the metatranscriptome used to give measure of expressed genes?
- metatranscriptome of mRNAs reverse transcribed to cDNA
- amplified and sequenced
- metagenomic DNA amplified from same marine Mo community and level of gene expression calc
Most highly expressed genes v rare in metagenome, what does this suggest?
- approx 40% expressed genes had no match in genomic DNA
- strongly suggests many organisms not detected by current metagenomic techniques and still unknown to science
What samples were taken and what method was used on the Sorcerer II expedition?
- every 200 miles from E coast USA through Panama Canal and along S America coast
- most taken at 1-5m depth
- some coastal at 10-100m depth
- some open ocean at depths up to 4500m
- total of 44 samples collected on filters of different pore sizes from 20 to 0.1 µm
- stored at -20°C and returned to the lab for DNA extraction
- most of seq data from smallest organisms (mainly bacteria and archaea)
- used whole genome shotgun seq
What were the conclusions from the Sorcerer II expedition?
- only 30% seq DNA matched known bacterial genome
- Pelagibacter (which uses proteorhodopsin) 1 of most abundant strains identified, showing it has important adaption to growth in oligotrophic pelagic zone
- cyanobacteria , Prochlorococcus and Synechococcus also highly abundant
What is Prochlorococcus and where is it found?
- dominant photoautotroph in ocean surface waters from 40ºS to 40ºN
- smallest known oxygenic phototroph (0.5 - 0.7μm diameter)
- contains unique divinyl chlorophyll (=CH2 replaces
- CH3)
- no phycobilisomes
What is Prochlorococcus used as a model organism for and why?
- in cross scale bio
- small genome (approx 2000 genes)
- easily isolated
- grown on simple media
- measure pop dynamics on global scale
What is a piezophile?
- thrive at high pressure
- eg. benthic MOs in deep ocean
How much does hydrostatic pressure increase in ocean?
- increases by 1 atm for every 10m depth
What is the average depth and pressure of the ocean floor and where is the deepest part?
- av = 3800m –> 380 atm
- deepest = Mariana trench, 1100 atm
What happened when samples from 1000m brought to surface and how was this overcome?
- underwent decompression
- so cells lost that were adapted to high ATM
- pressurised chambers constructed to bring samples to surface and act as growth chambers on research vessel
- enabled isolation of piezophiles
What extremophiles are found in bulk of deep ocean and why?
- psychrophiles
- oligotrophic and low temps (2-3ºC)
What extremophiles are found in deep hydrothermal vents and why?
- thermophiles
- rich in nutrients and high temp (350ºC)
What is the highest temp poss for growth and what would happen above this?
- 120ºC
- at over 150ºC DNA would have to be x2 every few secs
What 2 sections can the deep subsurface ecosystem be split into?
- deep terrestrial biosphere (below land)
- deep marine biosphere (below sea/ocean)
What is the deep marine biosphere defined as?
- life existing 1m below seafloor in shallow seas or deep oceans
Which biosphere are hydrothermal vents part of?
- deep marine biosphere
- “windows” to subsurface ecosystems
Why is metabolic activity of individual cells v low in deep marine biosphere and fall between dormant and active?
- extreme conditions –> dark, anoxic, oligotrophic, saline, high pressure, high temp
How is access gained to marine ecosystem?
- drilling boreholes
How is access gained to terrestrial ecosystem and what is the problem w/ this method?
- deep mines and cave system
- problems of contamination
Why is Fe (and other metals) an important factor in the deep subsurface?
- Fe2+ e- source for Fe ox bacteria in deep mines
- Fe redox reactions key to many deep subsurface ecosystems
- heavy metal tolerance also key to many MOs growing in deep subsurface
- MO Fe ox shown to pot corrode steel used to enclose nuclear waste, problem as LT storage of waste from nuclear power plants planned for underground repositories
What is the main limiting factor of MO growth in deep subsurface?
- high temp
- also some nutrients in short supply, eg. NO3- and NH3
What are the problems in accurately measuring MO diversity and how can they be overcome?
- contamination, esp w/ boreholes
- can use lipid biomarkers to determine relative abundance of euks, bacteria and archaea
- don’t know how representative sample collected are
- need to preserve samples as removed from subsurface habitat
What levels of nutrients/MOs do large undisturbed lakes usually have?
- oligotrophic
- dilute concs of nutrients and MOs
What are eutrophic lakes and why are they not healthy?
- rich nutrients
- fish can only live at v top
- usually due to pollution
What can happen to lakes at certain times of year (normally spring/summer)?
- can become stratified into 2 layers separated by thermocline
- upper layer is epilimnion –> oxygenic phototrophs
- lower layer is hypolimnion –> anoxic
What happens to a lake that receives large concs of nutrients, and how can this happen?
- eg- runoff from agricultural fertiliser or septic systems
- becomes eutrophic
- causes algal blooms and heterotrophic bacteria feed on algae
- vertebrates die due to lack of O, which heterotrophic bacteria have consumed
- anoxic hypolimnion dominates
What chemicals are the major cause of eutrophication and why?
- increase in phosphates and N sources
- as P and N are nutrients which most often limit algal growth
How can organic compounds in sewage lead to anoxic conditions?
- directly feed heterotrophic bacteria in lake
- same end result, but no algal blooms
What happens to thermocline in lake in autumn and why?
- breaks down
- due to lower temps in epilimnion and stronger winds disturbing surface
What happens during “turnover” of lake?
- mixes epilimnion and hypolimnion
- distribute nutrients and O levels throughout lake
- no longer stratified
- only deepest parts and sediments remain anoxic
What is the hierarchy of e- acceptors in benthic sediments?
- a hierarchy of e- acceptors are used by diff groups of MOs, starting w / most energy yielding to least
What happens if lake completely turned over?
- CH4 can be released to surface which can cause fire hazard
What can gases from anoxic sediments cause?
- eg. H2S
- v toxic if released to atmosphere
- can kill nearby animals and v rarely humans
How complex are soil ecosystems?
- extremely complex
What similarity do soil ecosystems have w/ marine and freshwater?
- surface layers aerobic and deeper layers anaerobic
How do diff soil types vary?
- vary greatly in depth of diff soil layers
What is an individual soil particle made up of?
- complex mix of diff types of MOs, bound together by biofilms and interacting w/ plant roots
Where are decomposers found in soil?
- top aerated horizons
What does the lower water saturated anoxic horizon in soil contain?
- mainly lithotrophic bacteria and anaerobic heterotrophic bacteria
Where is bedrock found in soil?
- at start of deep subsurface
What is lignin? (structure, function, abundancy)
- key component of plant cell walls
- 1 of most difficult natural substances to break down
- 2nd most abundant plant polymer after cellulose
- polymer of phenolic group
How is lignin broken down and what is it broken down into?
- by white rot fungi using peroxidases to smaller units containing only a few or single phenol group
- products known as humic material and further degradation v slow, leading to slow release of nutrients into soil
What structure is lignin a part of in cell wall?
- interlinked w/ cellulose and hemi-cellulose to form strong barrier = lignocellulose
How could cellulose and hemi-cellulose be used as biofuels?
- breaking them down polymers to sugars that can be fermented into ethanol
Are 2nd gen biofuels better than 1st gen?
- 2nd more env friendly as no food vs fuel issue
- but harder to prod
What are 3rd gen biofuels?
- from algae
