Microbe Interactions

7/29/2019 Microbe Interactions

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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

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Microbe Interactions