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 ecological processes occurring at the micro scale?

Tree of Life
*Microbial world (sometimes + fungi) Fungi Animals Plants Universal phylogenetic tree based on SSU rRNA sequences

Pace 1997

Microbes rule the biosphere

Ecosystem functions = biogeochemical Massive numbers: ~ 1030 cells Biomass: ~ 1017 g of carbon Diversity: ~ 105-107 species

Microbial communities carry out many functions related to biogeochemical cycling

C6H12O6 CO2 N2 O2 NH4+ H2 NO3N2 SO42MeS C2H3O2HPO42Meox Mered
Acyl-HSL

HSMe2+

Species Interactions
Competition Mutualism

A B A

+
B

Predation

A B

Competition
What are some challenges to studying microbial competition?

Competition example
Question: Do species coexist if dispersal, movement, and interaction occur over small spatial scales? Hypothesis: Local interaction and dispersal are sufficient to ensure coexistence of species. To test this hypothesis, a non-transitive model community composed of 3 toxin (colicin) producing E. coli strains were used (Kerr et al. 2002). transitive non-transitive a a b b c c

Competition example
3 bacterial types: Colicinogenic bacteria (C) produce colicin (toxin) and producing this toxin is costly Resistant bacteria (R) avoid the competitive cost of carrying col plasmid but suffer because colicin receptor is involved in nutrient metabolism Colicin-sensitive (S) bacteria are killed by colicin

Competition
Strains grown in three environments: (1) flask (well-mixed environment where dispersal and interaction not local) (2) static plate (environment in which dispersal and interaction are primarily local; and (3) mixed plate (intermediate environment). What would you predict the outcome will be?

R = S wins

C = R wins

S = C wins

Competition
Coexistence occurs when local structure is maintained (Fig. 2a) With no spatial structure (in flask or mixed plate), R strain wins (Fig. 2b-2c) Results support hypothesis: local interaction and dispersal in this nonhierarchical competitive interactions promoted species coexistence
Kerr et al. 2002

Protection from predation: Bacterial response to grazing pressures

Perthaler 2005

How does bacterial community composition change in response to predation? Composition changes, not just abundance
In response to phenotypic properties that allow bacteria to defend themselves from predation
Deplete populations within the edible size range Cause a shift in population sizes

Predation can increase abundance of grazing-resistant populations

Mutualism
Between aphid and bacteria (Buchnera aphidicola) Bacteria synthesizes necessary amino acids for aphid Aphid provides shelter Ex. Obligate mutualism: Phylogeny of Buchnera 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

From species to communities

What are some challenges associated when studying ecology from a microbial perspective?

vs.

Think about the scaling issue

Challenges associated with microbial assessment

Classification based on morphology is of limited help. Ability to only culture <1%? of microorganisms using standard culturing techniques

Microbial ecology is a methodology driven discipline

Phylogenetic 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)

DGGE

16S + ITS sequencing

Coarse (low resolution)

PFLA

ARISA

pyrosequencing

Fine high resolution

Defining diversity is tricky

Are 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 more elusive term

100% similarity

85% similarity

50% similarity

Counting the uncountable?

When have you sampled enough?
Never! (especially for soil microbes) Use accumulation curves to 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.

Counting the uncountable

DOTUR = computer program, which can be used for comparing different species level definitions (used for defining ecological unit) Calculate sampling curves at different taxonomic scales you decide which scale 100% similarity results in incomplete sampling - each time the community is sampled, a new OTU is observed
Schloss and Handelsman 2005, AEM

Number of OTUs Observed Number of sequences sampled

Rank abundance curves

(2A) Rank abundance for tropical moths (2B) Rank abundance for soil bacteria Microbial communities more realistically follow power law curve: a few dominant, many rare
Hughes et al. 2001

What to do? Focus on common? Simplify to functional groups of microbes?

Species-Area relationship
Remember from lecture 12 (and exam!): At large spatial scales species richness increases with the area sampled as a log-log relationship (power law) Log S = log c + z log A -Where A = Area, c is intercept and z is slope -Values of z are often reported to be around 0.2 - 0.3 (on islands - where species richness data are best described)

Species-Area Relationship
At large spatial scales species richness increases with the area sampled as a log-log relationship (power law)

Species-area relationships observed in microbial communities

(A) Bacterial genetic diversity increases with increasing island size (water-filled tree holes) (B) Relationship between microbial diversity and area (z-value) similar for animals and plants

Bell et al. 2005

Latitudinal diversity gradient: species diversity increases from the poles to the tropics.
Geographic patterns in mammalian biodiversity

Give examples of habitats with high and low complexity from a microbial perspective.
Davies T J et al. PNAS 2008;105:11556-11563

Latitudinal diversity gradient

Latitudinal gradient - lower latitudes have more species 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 with temperature and latitude but not productivity (Fuhrman et
al. 2008, PNAS)

Refuting evidence
No discernible latitudinal gradient; instead, bacterial richness patterns best explained by pH gradient (Fierer
and Jackson 2006, PNAS)

Soil environment is more spatially heterogeneous than marine/aquatic ecosystems

Biogeography
Biogeography is the study of the distribution of biodiversity through space and time Would you expect differences on a micro-scale?

Baas-Becking Hypothesis: Everything is everywhere, but the environment selects

Microbes are everywherewhy? Microbes are promiscuous
Microbes are considered cosmopolitan (widely dispersed globally distributed) at higher taxonomic levels Microbial genes are mobile Horizontal gene flow is common (e.g. bacteria share genes with other bacteria (and can be totally with unrelated species) or eukaryotes

Do microorganisms have biogeography?

Evidence against phylogenetic clustering by geography:
Not considered dispersal limited Extinction may be rare because of large populations sizes, high growth rates Ability to be dormant for extended periods to protect from inhospitable conditions (e.g. spore-forming) Diversified early?? (3.8 billion years ago!)

But microorganisms can have a non-cosmopolitan distribution

Locally distributed due to barriers to dispersal: -physical barriers (e.g. topography) -physiological requirements (e.g. narrow temperature, salinity, pH range) -ecological constraints (higher competition) -limited resource availability **Important to think about what level of taxonomic resolution to use to evaluate biogeographic patterns

Example of microbial biogeography

Sulfulobus - Archaea,
inhabits hyperthermal pools Compared genetically; isolated populations were adapted over time to local environment (little gene flow between populations) Sulfolobus likely do not disperse across geographic barriers or dispersers cannot establish in foreign hyperthermal habitats

Whitaker et al. 2003

Summary
Microorganisms are globally distributed and are vital to ecosystem function. Species interactions can be evaluated under laboratory conditions. Microbial systems in culture can be easy to experimentally manipulate. Microbial ecology has made incredible advances due to culture-independent molecular analyses but sampling is always in issue. Keeping taxonomic resolution in mind is important for addressing questions from the individual strain to population to community. Ecological patterns and processes studied at the macro-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