Beiko biogeography

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Biogeography of microorganisms No borders. No limits. No fear. hanggliding.org Rob Beiko Faculty of Computer Science Dalhousie University

Transcript of Beiko biogeography

Biogeography of microorganisms

No borders. No limits. No fear.

hanggliding.org

Rob BeikoFaculty of Computer Science

Dalhousie University

http://www.merrittcartographic.co.uk/earth_structure.html

‘‘the lower the organization of the body is, the more generally it is distributed.”

Augustin Pyramus de Candolle (1821)tr. Kurt Sprengel

‘‘everything is everywhere: but the environment selects”Lourens Baas-Becking (1934)

‘‘He [Martinus Beijernick] proposed that most ‘germs’ were cosmopolitan, and that their presence or absence could be predicted and practically produced by creating specific environmental conditions, rather than being subject to the historical contingency of simply being in a particular place at a particular time.”

Maureen O’Malley (2007) Nat Rev Micro

Intertwined questions

DIVERSITY GEOGRAPHY EVOLUTION FUNCTION / ROLE

(1)(2)

(3)

Do microbial “species” show spatial structure?

van Gremberghe et al. (2011) PLoS ONE

Microcystis (freshwater) – no!

Parsimony network oftrimmed ITS sequences

EuropeAsiaOceaniaAfricaSouth AmericaNorth America

Mantel r = 0.131

Burkholderia pseudomallei(soil transmission)– yes!

Pearson et al. (2009) BMC Biol

Do microbial communities show spatial structure?

Qualitative β-diversity= presence / absence of different groups

Quantitative β-diversity= relative abundance of different groups

Phylogenetic β-diversity= either of the above, but related groups contribute less to diversity

Pairwise β-diversity

Outcome: 0 = identical1 = maximally different

Arctic soil microbes – no!

Data from Chu et al. (2010) Environ MicrobiolRetrieved from Earth Microbiome ProjectVisualization / Analysis in GenGIS

Bray

-Cur

tis d

istan

ce

Longitude difference between sites

R2 = 0.001p = 0.25

Mantel test of Bray-Curtis dissimilaritybetween pairs of sites (genus level), vs. difference in longitude between sites

Bray-Curtis clustering of Arctic samples (http://www.ncbi.nlm.nih.gov/pubmed/20561020), colored by pH

Data from Chu et al. (2010) Environ MicrobiolRetrieved from Earth Microbiome ProjectVisualization / Analysis in GenGIS

The environment selects

Martiny et al. (2008) Env Micro

“Due to the large population size and relatively short generation time, cells may evolve faster than ocean currents can mix themand this may maintain local microdiversity.”

Prochlorococcus (marine) – slightly!

Relationship between community similarity and dispersal time wasonly significant at a very fine taxonomic threshold e.g. “sub-sub-sub-subspecies”

Hypersaline communities – maybe?

Martiny et al. (2011) PNAS

Community similarity variedwith distance only WITHIN marshes,not regionally or continentally

(1) Local, spatially structured environmental variable?(2) Restricted movement within marshes / colonizationeffects?

Relating phylogeny to function

PICRUSt

(Morgan) Langille et al. (2013) Nat Biotechnol

Sequenced genomes(known function)

Reference phylogeny(known function +unknown function)

- AND -Taxonomic samples

= FUNCTIONALPREDICTIONS

It workssurprisingly well!

Langille et al. (2013) Nat Biotechnol

but…

Larsbrink et al. (2014) Nature

Growth on xyloglucans

Red: YESBlue: NOGreen: MAYBE

Larsbrink et al. (2014) NatureDysgonomonas (termites!)

P. aeruginosaP. fluorescensP. putidaP. syringaeP. entomophilaP. stutzeriP. mendocina

Holloway and Beiko, 2010

Function *mostly* correlates with phylogeny

(but maybe not for the functions and roles you care about!)

Rethinking beta diversity

Boon, Meehan et al. (2013) FEMS Microbiol Rev

(a) Marker-gene phylogeny(b) Functional gene distribution

(PICRUSt!)

(c) Co-occurrence patterns (d) Functional gene phylogeny

Questions

• Do bacteria have biogeography? It depends on the dispersal mechanism

• Is phylogeny predictive of function? Yes and no• LGT and other modes of convergence can drastically diminish the

predictive value of phylogeny• Strain-level information can be critical!

• Do *genes* have biogeography, or do they follow Baas-Becking as well?• Interactions between dispersal-limited species?• Limiting factors on LGT including co-localization of donor and

recipient

Acknowledgments

Community evolution / LGT• Morgan Langille• Conor Meehan• Dennis Wong• Donovan Parks• Eva Boon• Catherine Holloway

PICRUSt• Jesse Zaneveld• Rob Knight• Curtis Huttenhower• Greg Caporaso• Dan Knights• Daniel MacDonald• Josh Reyes• Jose Clemente

Fin