microbe interactions
TRANSCRIPT
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Microbial Ecology
(with thanks to Ariane Peralta)
1. What is the global distribution of microorganisms?Why are they so challenging to study?
2. What are some examples of microbial interactions?3. How can microbial diversity be assessed? What are
major challenges?
4.
Is there evidence for macro scale ecologicalprocesses occurring at the micro scale?
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Tree
ofLife
Pace 1997
Universal phylogenetic tree based
on SSU rRNA sequences
Fungi
AnimalsPlants
*Microbial world(sometimes + fungi)
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Microbes rule the biosphere Ecosystem functions = biogeochemical Massive numbers: ~ 1030 cells Biomass: ~ 1017 g of carbon Diversity: ~ 105-107 species
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NH4+
NO3-
N2
O2
H2
Meox
Mered
C2H3O2-
CO2
Acyl-HSL
HPO42-
C6H12O6
SO42-
HS-
Me2+
MeS
N2
Microbial communities carry out many
functions related to biogeochemical cycling
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Species InteractionsCompetition
A B-
- Predation
A B
-
+
Mutualism
A B+
+
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CompetitionWhat are some challenges to studying microbial competition?
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Competition -
exampleQuestion: Do species coexist if dispersal, movement,
and interaction occur over small spatial scales?
Hypothesis: Local interaction and dispersal aresufficient to ensure coexistence of species.
To test this hypothesis, a non-transitive modelcommunity composed of 3 toxin (colicin) producing E.colistrains were used (Kerr et al. 2002).
a b c
a b c
transitive
non-transitive
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Competition -
example
3 bacterial types:
Colicinogenicbacteria (C) produce colicin (toxin) andproducing this toxin is costly
Resistantbacteria (R) avoid the competitive cost of
carrying col plasmid but suffer because colicinreceptor is involved in nutrient metabolism
Colicin-sensitive (S) bacteria are killed by colicin
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Competition
Strains grown in three environments:
(1) flask (well-mixed environment where dispersal
and interaction not local)
(2) static plate (environment in which dispersal andinteraction are primarily local; and
(3) mixed plate (intermediate environment).
What would you predict the outcome will be?
S R
S wins=
R C
R wins=
C S
C wins=
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Competition
Kerr et al. 2002
Coexistence occurs whenlocal structure is maintained(Fig. 2a)
With no spatial structure (inflask or mixed plate), Rstrain wins (Fig. 2b-2c)
Results support hypothesis:
local interaction anddispersal in this non-hierarchical competitiveinteractions promotedspecies coexistence
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Protection from predation:
Bacterial response to grazing pressures
Perthaler 2005
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How does bacterial community composition
change in response to predation?
Composition changes, not just abundance
In response to phenotypic properties thatallow bacteria to defend themselves frompredation Deplete populations within the edible size range Cause a shift in population sizes
Predation can increase abundance ofgrazing-resistant populations
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Mutualism Between aphid and bacteria
(Buchnera aphidicola)
Bacteria synthesizes necessaryamino acids for aphid
Aphid provides shelter Ex. Obligate mutualism: Phylogeny
ofBuchnera completely concordant
with aphids cannot exist without
each other; mutualism began 150 -250 MYA
Vertical transmission*Remember to past microbial mutualism
example: leaf-cutter ants/fungi
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From species to communities
What are some challenges associated
when studying ecology from a microbial
perspective?
vs.
Think about the scaling issue
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Challenges associated with
microbial assessmentClassification based on morphology
is of limited help.
Ability to only culture
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Microbial ecology is a
methodology driven disciplinePhylogenetic resolution capability of a method to distinguish between
community members; choosing a method depends on questions asked
Range of methods allows for sampling a range of resolutions from broad
scale physiological patterns (PFLA) to community level analysis(DGGE, ARISA) to individual sequence analysis (16S + ITS,
pyrosequencing)
Coarse(low resolution)
Finehigh resolution
ARISA
16S + ITS sequencing
PFLA
DGGE
pyrosequencing
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Defining diversity is trickyAre these 2 bacteria the same operational taxonomic unit
(OTU)?
*Term OTU is used more often than species b/c it is
specifically defined by user, whereas species is a moreelusive term
100% similarity 85% similarity 50% similarity
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Counting the uncountable?
When have you sampledenough?
Never! (especially for soilmicrobes)
Use accumulation curvesto describe how well you
sampled
Proportion of individuals*sampled versus proportion
of OTUs (operational
taxonomic unit observed)
Hughes et al. 2001, AEM
*Data are standardized as fraction of species and OTUs to facilitate
comparisons across studies.
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Counting the uncountable
DOTUR = computer program,which can be used forcomparing differentspecies level definitions(used for definingecological unit)
Calculate sampling curves atdifferent taxonomic scales -you decide which scale
100% similarity results inincomplete sampling - eachtime the community issampled, a new OTU isobserved
Schloss and Handelsman 2005, AEM
Number of sequences sampled
N
umberofOTUsO
bserved
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Rank abundance curves
(2A) Rank abundance for
tropical moths
(2B) Rank abundance for
soil bacteria
Microbial communitiesmore realistically followpower law curve: a fewdominant, many rare
Hughes et al. 2001
What to do?Focus on common?Simplify to functional groups of microbes?
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Species-Area relationship
Remember from lecture 12 (and exam!):
At large spatial scales species richness
increases with the area sampled as a log-logrelationship (power law)
Log S = log c+ zlogA
-Where A = Area, cis intercept and zis slope-Values ofzare often reported to be around0.2 - 0.3 (on islands - where species richnessdata are best described)
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Species-Area Relationship
At large spatial scales
species richness
increases with thearea sampled as a
log-log relationship
(power law)
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Species-area relationships observed
in microbial communities
(A) Bacterial genetic diversity
increases with increasing
island size (water-filled tree
holes)
(B) Relationship betweenmicrobial diversity and area
(z-value) similar for animals
and plants
Bell et al. 2005
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Geographic patterns in mammalian biodiversity
Davies T J et al. PNAS 2008;105:11556-11563
Latitudinal diversity gradient: species diversity
increases from the poles to the tropics.
Give examples of habitats with high and low complexity from a
microbial perspective.
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Latitudinal diversity gradient
Latitudinal gradient - lower latitudes have morespecies than higher latitudes Strength of pattern decreases as organism size
decreases (Hillenbrand 2004,Am. Nat)
Supporting evidence: Bacterial latitudinal richness gradient in marine
bacterioplankton; richness correlated most withtemperature and latitude but not productivity (Fuhrman etal. 2008, PNAS)
Refuting evidence No discernible latitudinal gradient; instead, bacterial
richness patterns best explained by pH gradient (Fiererand Jackson 2006, PNAS)
Soil environment is more spatially heterogeneous than marine/aquatic ecosystems
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Biogeography
Biogeography is the study of the distribution ofbiodiversity through space and time
Would you expect differences on a micro-scale?
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Baas-Becking Hypothesis:
Everything is everywhere, butthe environment selects
Microbes are promiscuous Microbes are considered cosmopolitan (widely
dispersed globally distributed) at higher taxonomiclevels
Microbial genes are mobile Horizontal gene flow is common (e.g. bacteria share
genes with other bacteria (and can be totally withunrelated species) or eukaryotes
Microbes are everywherewhy?
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Do microorganisms have
biogeography?
Evidence against phylogenetic clusteringby geography:Not considered dispersal limitedExtinction may be rare because of large
populations sizes, high growth rates
Ability to be dormant for extended periodsto protect from inhospitable conditions (e.g.spore-forming)
Diversified early?? (3.8 billion years ago!)
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But microorganisms can have a
non-cosmopolitan distributionLocally distributed due to barriers to dispersal:
-physical barriers (e.g. topography)
-physiological requirements (e.g. narrowtemperature, salinity, pH range)-ecological constraints (higher competition)-limited resource availability
**Important to think about what level of taxonomicresolution to use to evaluate biogeographicpatterns
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Example of microbial biogeography
Sulfulobus -Archaea,inhabits hyperthermal pools
Compared genetically;isolated populations were
adapted over time to localenvironment (little gene flowbetween populations)
Sulfolobus likely do notdisperse across geographic
barriers or disperserscannot establish in foreign
hyperthermal habitats
Whitaker et al. 2003
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Summary
Microorganisms are globally distributed and are vital toecosystem function.
Species interactions can be evaluated underlaboratory conditions. Microbial systems in culture canbe easy to experimentally manipulate.
Microbial ecology has made incredible advances dueto culture-independent molecular analyses butsampling is always in issue.
Keeping taxonomic resolution in mind is important foraddressing questions from the individual strain topopulation to community.
Ecological patterns and processes studied at themacro-scale have been applied at the micro-scale.Evidence for and against particular patterns exist: Microorganisms have biogeography or NOT Latitudinal bacterial diversity gradient supported and not